Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities

Abstract

The growing demand for renewable, carbon-neutral materials and energy is leading to intensified forest land-use. The long-term ecological challenges associated with maintaining soil fertility in managed forests are not yet known, in part due to the complexity of soil microbial communities and the heterogeneity of forest soils. This study determined the long-term effects of timber harvesting, accompanied by varied organic matter (OM) removal, on bacterial and fungal soil populations in 11- to 17-year-old reforested coniferous plantations at 18 sites across North America. Analysis of highly replicated 16 S rRNA gene and ITS region pyrotag libraries and shotgun metagenomes demonstrated consistent changes in microbial communities in harvested plots that included the expansion of desiccation- and heat-tolerant organisms and decline in diversity of ectomycorrhizal fungi. However, the majority of taxa, including the most abundant and cosmopolitan groups, were unaffected by harvesting. Shifts in microbial populations that corresponded to increased temperature and soil dryness were moderated by OM retention, which also selected for sub-populations of fungal decomposers. Biogeographical differences in the distribution of taxa as well as local edaphic and environmental conditions produced substantial variation in the effects of harvesting. This extensive molecular-based investigation of forest soil advances our understanding of forest disturbance and lays the foundation for monitoring long-term impacts of timber harvesting.

Following the terrestrial tracks of Caulobacter - redefining the ecology of a reputed aquatic oligotroph

“…Yet, in general, the ecology and function of Caulobacter from non-aquatic or nutrient-rich environments has received little attention. With the rise of metagenomics, one can find a patchwork of cultivation-independent evidence for the presence of Caulobacter in soils and their role in decomposition, including the degradation of cellulose [24][25][26], lignin [27,28], and polyaromatic hydrocarbons [29,30]. Their role in decomposition is supported by the capacity of C. crescentus CB15 to grow on lignocellulosedegradation by-products, like xylose and vanillin [31][32][33][34], and the capacity of other species to grow on cellulose [35].…”

Restoration of belowground fungal communities in reclaimed landscapes of the Canadian boreal forest

“…Only when whole trees were removed and the upper organic layer of forest floor scraped away were fungal communities differentiated from those of reference forests. However, most of the variation in fungal community composition in this broad‐scale, long‐term study was explained by geography (Wilhelm et al ). Considering the scale and range of treatments applied in our study, our findings are aligned with those above.…”

“…The primary conclusion from a review of the impacts of clearcut logging on EcM fungi was that it changes the species composition of the fungal community (Jones et al ; Jones ). However, geographic and edaphic factors can outweigh the effects of harvesting on microbial communities (Kranabetter et al ; Wilhelm et al ). For instance, 11–17 years following harvest, the majority of microbial taxa were unaffected by timber harvesting across 18 reforested long‐term soil productivity study sites (Wilhelm et al ).…”

“…However, geographic and edaphic factors can outweigh the effects of harvesting on microbial communities (Kranabetter et al ; Wilhelm et al ). For instance, 11–17 years following harvest, the majority of microbial taxa were unaffected by timber harvesting across 18 reforested long‐term soil productivity study sites (Wilhelm et al ). Only when whole trees were removed and the upper organic layer of forest floor scraped away were fungal communities differentiated from those of reference forests.…”

Bacterial and fungal contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

“…Samples were collected from mature coniferous forest corresponding to ‘reference’ plots in the Long-Term Soil Productivity Study in northern Ontario (BS ON and JP ON ), British Columbia (IDF BC ), California (PP CA ) and Texas (LP TX ). Detailed descriptions of geographical locations, soil properties and sampling methods can be found in Wilhelm b et al (2017) as well as in Table S1. Samples were collected from three sites in each geographical region, except IDF BC where three plots were samples from a single site.…”