Composition and functioning of the soil microbiome in the highest altitudes of the Italian Alps and potential effects of climate change

Abstract

As the European Alps are experiencing a strong climate warming; this study analyzed the soil microbiome at different altitudes and among different vegetation types at the Stelvio Pass (Italian Alps), aiming to i) characterize the composition and functional potential of the microbiome of soils and their gene expression during the peak vegetative stage; ii) explore the potential short-term (using open top chambers) and long-term (space-for-time substitutions) effects of increasing temperature on the alpine soil microbiome. We found that the functional potential of the soil microbiome and its expression differed among vegetation types. Microbial α-diversity increased along the altitudinal gradient. At lower altitude, shrubland had the highest proportion of fungi, which was correlated with higher amounts of CAZymes, specific for degrading fungal biomass and recalcitrant plant biopolymers. Subalpine upward vegetation shift could lead a possible loss of species of alpine soils. Shrub encroachment may accelerate higher recalcitrant C decomposition and reduce total ecosystem C storage, increasing the efflux of CO2 to the atmosphere with a positive feedback to warming. Five years of warming had no effect on the composition and functioning of microbial communities, indicating that longer-term warming experiments are needed to investigate the effects of temperature increases on the soil microbiome.

Fungal communities in European alpine soils are not affected by short‐term in situ simulated warming than bacterial communities

“…Proteobacteria was the most abundant bacterial phylum found in soils under study. They are typically the most abundant bacteria in all soil libraries (D'Alò et al ., 2022; Janssen, 2006). Moreover, Proteobacteria were also the most abundant bacterial phyla found in high alpine environment reaching values of 24.3% of total phyla found in Swiss alpine mountain summits and around 50% of the total phyla in the Damma glacier (Adamczyk et al ., 2019; Rime et al ., 2015).…”

“…Similarly, Ascomycota represented the dominant filamentous fungal phylum found in studied soils. This phylum dominates the fungal communities of worldwide soils characterized by filamentous forms, thanks to the high number of genes related to stress tolerance, competitive abilities and resource uptake (Egidi et al ., 2019; Baldrian et al ., 2021, D'Alò et al ., 2022). In contrast, Basidiomycota dominated within yeast communities of studied soils, in agreement with current literature (Buzzini et al ., 2017 and references therein) even though the unexpected dominance of amplicon sequence variants assigned to the ascomycetous genus Meyerozyma in the permafrost sampled at Stelvio pass was recently described (Sannino et al ., 2021).…”

“…The effect of short‐ and long‐term simulated warming was also monitored in an alpine meadow on the Qinghai‐Tibet Plateau of China: both types of experimental warming affected soil nutrients, microbial biomass and enzyme activities (Wang et al ., 2014). On the other hand, a direct effect of short‐term warming was observed both on microbial community structure (Li et al ., 2017) and on the enzymatic activities expressed by microbial communities (D'Alò et al ., 2021, 2022). In addition, metagenomics and metatranscriptomics studies reported that long‐term warming experiments significantly affected the structure of both fungal (Rinnan et al ., 2007) and bacterial (Klarenberg et al ., 2020, 2021) communities, and gene expression of microorganisms, especially those genes involved in the degradation of recalcitrant carbon compounds, which were stimulated by warming (Xue et al ., 2016).…”

Untangling the Effects of Plant Genotype and Soil Conditions on the Assembly of Bacterial and Fungal Communities in the Rhizosphere of the Wild Andean Blueberry (Vaccinium floribundum Kunth)

“…This result is related to the findings of Vega et al (2019) on the V. floribundum genetic diversity and genetic distribution, which showed that the expected plant heterozygosity decreases while the elevation increased and that Cluster 4 is restricted to higher altitudes, making the individuals of this cluster part of a “sky island” with a reduced genetic flow to other locations [ 18 ]. Although altitude has been reported to be a significant factor that affects the fungal composition in the soil and the rhizosphere, its effect is mainly indirect by driving the distribution of plant species [ 65 , 66 , 67 ]. Altogether, our results indicate that bacterial and fungal communities in the rhizosphere respond differently to the plant genetics in the wild, which is consistent with earlier work suggesting a link between plant community composition and fungal diversity [ 68 , 69 ].…”

Effects of 5‐year experimental warming in the Alpine belt on soil Archaea: Multi‐omics approaches and prospects

“…To study the effect of short-term warming, a manipulative experiment was conducted in situ (D'Alò et al, 2021(D'Alò et al, , 2022Sannino et al, 2022). In 2014, small hexagonal OTCs (2.08 m in diameter) were installed in both Alpine grassland and Alpine snowbed.…”