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Implications of climate change for terrestrial microbiomes and global cycles

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Implications of climate change for terrestrial microbiomes and global cycles
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Soil microbiomes are highly diverse ecosystems that play a central role in ecosystem functioning and regulating global biogeochemical cycles. Through these processes, soil microbes make major contributions to the production and consumption of greenhouse gases. They also regulate the availability of essential nutrients, such as nitrogen and phosphorous, thereby influencing plant growth and global primary productivity. As such, soil microbial communities are intimately involved in climate feedback processes.

Predicting the contribution and response of soil microbiomes to future climate change represents a major research challenge. For example, uncertainties remain around the extent to which soils will act as a source or sink of carbon under future climate scenarios. A greater understanding of the microbial molecular pathways involved in biogeochemical cycling will be essential if we are to predict these outcomes. Similarly, further insight is needed into the response of soil microbial communities to climate extremes, such as drought, floods and increasing salinity, so that we can predict and mitigate changes to vital ecosystem services.

The special collection ‘Implications of climate change for terrestrial microbiomes and global cycles’ guest-edited by Drs Michael Macey (Open University), Sarah Worsley (UEA), and Geertje van Keulen (Swansea University), aims to highlight key research investigating the role of soil microbiomes in climate feedback processes, and their response to global change. It will also include articles on the characterisation of biogeochemical cycles and terrestrial microbiomes. We would also like to invite contributions on advances made in affordable and sustainable research methods, e.g. focussing on in situ activities where access to energy and/or data sources may be unreliable or unavailable.

This collection is open for submissions – please submit your article here, stating that your manuscript is part of the ‘Implications of climate change for terrestrial microbiomes and global cycles’ collection.  

Image credit: Guido Gerding - external homepage, CC BY-SA 3.0, via Wikimedia Commons

Collection Contents

4 results

    • Spatial variation in microbial communities associated with sea-ice algae in Commonwealth Bay, East Antarctica

      Antarctic sea-ice forms a complex and dynamic system that drives many ecological processes in the Southern Ocean. Sea-ice microalgae and their associated microbial communities are understood to influence nutrient flow and allocation in marine polar environments. Sea-ice microalgae and their microbiota can have high seasonal and regional (>1000 km) compositional and abundance variation, driven by factors modulating their growth, symbiotic interactions and function. In contrast, our knowledge of small-scale variation in these communities is limited. Understanding variation across multiple scales and its potential drivers is critical for informing on how multiple stressors impact sea-ice communities and the functions they provide. Here, we characterized bacterial communities associated with sea-ice microalgae and the potential drivers that influence their variation across a range of spatial scales (metres to >10 kms) in a previously understudied area in Commonwealth Bay, East Antarctica where anomalous events have substantially and rapidly expanded local sea-ice coverage. We found a higher abundance and different composition of bacterial communities living in sea-ice microalgae closer to the shore compared to those further from the coast. Variation in community structure increased linearly with distance between samples. Ice thickness and depth to the seabed were found to be poor predictors of these communities. Further research on the small-scale environmental drivers influencing these communities is needed to fully understand how large-scale regional events can affect local function and ecosystem processes.

    • Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)

      The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil–climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.

    • Specific inhibitors of respiratory sulfate reduction: towards a mechanistic understanding

      Microbial sulfate reduction (SR) by sulfate-reducing micro-organisms (SRM) is a primary environmental mechanism of anaerobic organic matter mineralization, and as such influences carbon and sulfur cycling in many natural and engineered environments. In industrial systems, SR results in the generation of hydrogen sulfide, a toxic, corrosive gas with adverse human health effects and significant economic and environmental consequences. Therefore, there has been considerable interest in developing strategies for mitigating hydrogen sulfide production, and several specific inhibitors of SRM have been identified and characterized. Specific inhibitors are compounds that disrupt the metabolism of one group of organisms, with little or no effect on the rest of the community. Putative specific inhibitors of SRM have been used to control sulfidogenesis in industrial and engineered systems. Despite the value of these inhibitors, mechanistic and quantitative studies into the molecular mechanisms of their inhibition have been sparse and unsystematic. The insight garnered by such studies is essential if we are to have a more complete understanding of SR, including the past and current selective pressures acting upon it. Furthermore, the ability to reliably control sulfidogenesis – and potentially assimilatory sulfate pathways – relies on a thorough molecular understanding of inhibition. The scope of this review is to summarize the current state of the field: how we measure and understand inhibition, the targets of specific SR inhibitors and how SRM acclimatize and/or adapt to these stressors.

    • The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO enrichment

      The soil bacterial community at the Giessen free-air CO enrichment (Gi-FACE) experiment was analysed by tag sequencing of the 16S rRNA gene. No substantial effects of CO levels on bacterial community composition were detected. However, the soil moisture gradient at Gi-FACE had a significant effect on bacterial community composition. Different groups within the Acidobacteria and Verrucomicrobia phyla were affected differently by soil moisture content. These results suggest that modest increases in atmospheric CO may cause only minor changes in soil bacterial community composition and indicate that the functional responses of the soil community to COenrichment previously reported at Gi-FACE are due to factors other than changes in bacterial community composition. The effects of the moisture gradient revealed new information about the relationships between poorly known Acidobacteria and Verrucomicrobia and soil moisture content. This study contrasts with the relatively small number of other temperate grassland free-air CO enrichment microbiome studies in the use of moderate CO enrichment and the resulting minor changes in the soil microbiome. Thus, it will facilitate the development of further climate change mitigation studies. In addition, the moisture gradient found at Gi-FACE contributes new knowledge in soil microbial ecology, particularly regarding the abundance and moisture relationships of the soil Verrucomicrobia.

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