Differential sensitivity of total and active soil microbial communities to drought and forest management

Abstract

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change.

Drought and its legacy modulate the post‐fire recovery of soil functionality and microbial community structure in a Mediterranean shrubland

“…The soil microbial community plays an important role in the recovery of post‐fire ecosystem functioning, but how reduced rainfall due to climate change might affect the post‐fire community is poorly understood. In unburned soils, it has been reported that an increase in the intensity and frequency of droughts can lead to a decrease in microbial growth as well as to changes in microbial community structure (e.g., Iovieno & Bååth, ; Barnard et al, ; Evans, Wallenstein, & Burke, ; Bastida et al, ). In the burned soils of this experiment, microbial biomass was significantly reduced because of drought, while its effects persisted over the 4 years under drought treatments.…”

“…In unburned soils, it has been reported that an increase in the intensity and frequency of droughts can lead to a decrease in microbial growth as well as to changes in microbial community year the entire rainfall manipulation system was dismantled and all plots received a natural rainfall pattern. For each sampling time, significant differences among the studied treatments are noted with different letters (p-values ≤ 0.05) structure (e.g., Iovieno & Bååth, 2008;Barnard et al, 2013;Evans, Wallenstein, & Burke, 2014;Bastida et al, 2017). In the burned soils of this experiment, microbial biomass was significantly reduced because of drought, while its effects persisted over the 4 years under drought treatments.…”

“…Consequently, drought can lead to reduced decomposition rates and microbial growth, as well as to changes in the microbial community structure (Barnard, Osborne, & Firestone, 2013;Iovieno & Bååth, 2008;Maestre et al, 2015). While research supporting the direct effects of drought on microbial communities is common (e.g., Toberman, Freeman, Evans, Fenner, & Artz, 2008;Rousk, Smith, & Jones, 2013;Bastida et al, 2017), there is also evidence that some microbial groups are resistant to drought (Bouskill et al, 2013;Griffiths & Philippot, 2013;Pailler, Vennetier, Torre, Ripert, & Guiral, 2014). In addition, changes in the soil biota, due to drought, are associated with changes in soil biogeochemistry (Nielsen & Ball, 2015).…”

Gene copy normalization of the 16S rRNA gene cannot outweigh the methodological biases of sequencing

“…Logically we suggest that GCN in communities of low Shannon diversity (≪2.7) could be beneficial. However, the Shannon diversity of bacterial communities typically range between 3 and 6 in both terrestrial 16–19 and aquatic ecosystems 20,21 , which are likely too diverse for GCN to have an impact as shown for Mock-2 and Mock-20.…”

Incomplete cell disruption of resistant microbes

“…Noteworthy, ultra-sonication in a bath for 10 min revealed a strong resistance of the fungal and the gram-positive bacterial enrichment culture, both remained almost intact, whereas no intact cells could be found in the gram-negative bacterial enrichment culture after identical treatment, suggesting complete cell disruption beyond recognition (Figs 2 and S2-4). In fact, this could be the reason for the underrepresentation of resistant microbes, particularly fungi, in ecological studies [15][16][17] that might skew microbiomes of various nature towards easy-to-lyse microbes. Even though we specifically searched for single cells, the gram-positive bacterial and the fungal enrichment cultures showed higher amounts of cell aggregation compared to the gram-negative bacterial enrichment culture.…”