The microbiome of cryospheric ecosystems

The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires. The melting of the cryosphere is among the most conspicuous consequences of climate change, with impacts on microbial life and related biogeochemistry. However, we are missing a systematic understanding of microbiome structure and function across cryospheric ecosystems. Here, we present a global inventory of the microbiome from snow, ice, permafrost soils, and both coastal and freshwater ecosystems under glacier influence. Combining phylogenetic and taxonomic approaches, we find that these cryospheric ecosystems, despite their particularities, share a microbiome with representatives across the bacterial tree of life and apparent signatures of early and constrained radiation. In addition, we use metagenomic analyses to define the genetic repertoire of cryospheric bacteria. Our work provides a reference resource for future studies on climate change microbiology.

Benthic Biofilms in Glacier-Fed Streams from Scandinavia to the Himalayas Host Distinct Bacterial Communities Compared with the Streamwater

Tom Ian Battin, Massimo Bourquin, Jade Brandani, Susheel Bhanu Busi, Vincent Henri De Staercke, Leïla Ezzat, Stylianos Fodelianakis, Tyler Joe Kohler, Grégoire Marie Octave Edouard Michoud, Emmy Marie Oppliger, Hannes Markus Peter, Paraskevi Pramateftaki, Martina Andrea Schön, Michail Styllas, Virginia Tadei, Matteo Tolosano

Microbial life in glacier-fed streams (GFSs) is dominated by benthic biofilms which fulfill critical ecosystem processes. However, it remains unclear how the bacterial communities of these biofilms assemble in stream ecosystems characterized by rapid turnover of benthic habitats and high suspended sediment loads. Using16S rRNA gene amplicon sequence data collected from 54 GFSs across the Himalayas, European Alps, and Scandinavian Mountains, we found that benthic biofilms harbor bacterial communities that are distinct from the bacterial assemblages suspended in the streamwater. Our data showed a decrease in species richness in the benthic biofilms compared to the bacterial cells putatively free-living in the water. The benthic biofilms also differed from the suspended water fractions in terms of community composition. Differential abundance analyses highlighted bacterial families that were specific to the benthic biofilms and the suspended assemblages. Notably, source-sink models suggested that the benthic biofilm communities are not simply a subset of the suspended assemblages. Rather, we found evidence that deterministic processes (e.g., species sorting) shape the benthic biofilm communities. This is unexpected given the high vertical mixing of water and contained bacterial cells in GFSs and further highlights the benthic biofilm mode of life as one that is determined through niche-related processes. Our findings therefore reveal a "native" benthic biofilm community in an ecosystem that is currently threatened by climate-induced glacier shrinkage. IMPORTANCE Benthic biofilms represent the dominant form of life in glacier-fed streams. However, it remains unclear how bacterial communities within these biofilms assemble. Our findings from glacier-fed streams from three major mountain ranges across the Himalayas, the European Alps and the Scandinavian Mountains reveal a bacterial community associated with benthic biofilms that is distinct from the assemblage in the overlying streamwater. Our analyses suggest that selection is the underlying process to this differentiation. This is unexpected given that bacterial cells that are freely living or attached to the abundant sediment particles suspended in the water continuously mix with the benthic biofilms. The latter colonize loose sediments that are subject to high turnover owing to the forces of the water flow. Our research unravels the existence of a microbiome specific to benthic biofilms in glacier-fed streams, now under major threats due to global warming. Benthic biofilms represent the dominant form of life in glacier-fed streams. However, it remains unclear how bacterial communities within these biofilms assemble.

AMER SOC MICROBIOLOGY2022

Snow cover manipulation effects on microbial community structure and soil chemistry in a mountain bog

Luca Bragazza, Alexandre Buttler, Vincent Eric Jules Jassey, Bjorn Jozef Maria Robroek

Alterations in snow cover driven by climate change may impact ecosystem functioning, including biogeochemistry and soil (microbial) processes. We elucidated the effects of snow cover manipulation (SCM) on above-and belowground processes in a temperate peatland. In a Swiss mountain-peatland we manipulated snow cover (addition, removal and control), and assessed the effects on Andromeda polifolia root enzyme activity, soil microbial community structure, and leaf tissue and soil biogeochemistry. Reduced snow cover produced warmer soils in our experiment while increased snow cover kept soil temperatures close-to-freezing. SCM had a major influence on the microbial community, and prolonged 'close-to-freezing' temperatures caused a shift in microbial communities toward fungal dominance. Soil temperature largely explained soil microbial structure, while other descriptors such as root enzyme activity and pore-water chemistry interacted less with the soil microbial communities. We envisage that SCM-driven changes in the microbial community composition could lead to substantial changes in trophic fluxes and associated ecosystem processes. Hence, we need to improve our understanding on the impact of frost and freeze-thaw cycles on the microbial food web and its implications for peatland ecosystem processes in a changing climate; in particular for the fate of the sequestered carbon.

Springer Netherlands2013

Ecohydrological and Metacommunity Studies of Proliferative Kidney Disease Spread in Freshwater Salmonid Fish

Luca Carraro

Proliferative kidney disease (PKD) is a high-mortality pathology affecting freshwater salmonid populations in Europe and North America. Its causative agent, the myxozoan Tetracapsuloides bryosalmonae, has a complex life-cycle exploiting freshwater bryozoans (mainly Fredericella sultana) and salmonids as hosts. PKD has recently increased in incidence and severity, causing remarkable declines in fish catches. In addition, environmental change is feared to cause PKD outbreaks in regions at higher latitude and altitude, as warmer water temperatures exacerbate disease development and fish mortality. In this perspective, this Thesis develops an integrated approach, involving field and modelling work, for the prediction of the incidence of PKD in river basins. In particular, the Thesis develops a novel spatially-explicit model of PKD epidemiology in riverine host metacommunities. The model, summarizing the current knowledge on disease transmission modes and parasite's life-cycle, accounts for both local population and disease dynamics of bryozoans and fish, as well as hydrodynamic dispersion of parasite spores and hosts along the river network. Model validation was attained through an integrated study of PKD in a prealpine Swiss river, where data on fish abundance, disease prevalence, concentration of primary hosts' and parasite's DNA in environmental samples (eDNA) and water temperatures were gathered at multiple locations within the catchment. In this context, a new method for predicting the spatial distribution of bryozoan density based on eDNA samples was developed. As water temperature is crucial to PKD severity, a deterministic, spatially-explicit water temperature model was formulated and tested on the case-study basin. The model, based on water and energy budgets at the reach scale, considers the effects of the spatial heterogeneity in environmental drivers, allowing the evaluation of gradients of daily mean water temperature along the river network. Stability and sensitivity analyses performed on the local epidemiological model proved that the introduction of T. bryosalmonae in a disease-free community is very likely to trigger a PKD outbreak. Simulation experiments conducted on synthetic river network replicas showed that network connectivity engenders high PKD prevalence at downstream sites, while the speed of invasion fronts in disease-free environments is amplified by climate change. Moreover, patchily located bryozoan hotspots proved able to sustain the infection at the whole river scale. Validation on the case study confirmed the reliability of the epidemiological model, and identified the prediction of bryozoan distribution as a key direction for future research. In this regard, the developed eDNA transport model possibly opens avenues for the modeling of species distributions in freshwater ecosystems, also beyond the case of PKD. The spatially-explicit temperature model was shown to outperform traditional models based on local heat budgets. Such a tool is instrumental to several ecohydrological applications, from the identification of river reaches at highest PKD-related risk, to the assessment of habitat suitability of fish or other freshwater species. Overall, this Thesis bridges the fields of ecology, epidemiology, hydrology and mathematical modelling in order to produce an integrated study of PKD, in the perspective of grasping the factors allowing disease persistence and devising mitigation strategies.

EPFL2018

Benthic Biofilms in Glacier-Fed Streams from Scandinavia to the Himalayas Host Distinct Bacterial Communities Compared with the Streamwater

AMER SOC MICROBIOLOGY2022

Ecohydrological and Metacommunity Studies of Proliferative Kidney Disease Spread in Freshwater Salmonid Fish

Luca Carraro

EPFL2018