Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration

Abstract

Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, ␤-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping ␤-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial ␤-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities. IMPORTANCE Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages.KEYWORDS bacteria, chronosequence, cooccurrence networks, disturbance, fungi, reclaimed mine soils, soil microbiota E cologists have been studying the succession dynamics of plant communities for more than a century (1, 2), and the patterns of changes in plant community composition are used as indicators for the restoration of ecosystems (3-5). However,

Linking diversity, synchrony and stability in soil microbial communities

“…In contrast to bacteria, fungi have been known to be strongly reduced in abundance and richness following the physical destruction of the soil structure and hyphal networks that may require a longer time to re‐establish and recover in abundance (Hartmann et al., ; Lauber et al., ; Oehl et al., ; Rousk & Bååth, ; Sun, Li, Avera, Strahm, & Badgley, ; van der Wal et al., ; Verbruggen et al., ). Furthermore, soil tilling is well known to alter the abiotic properties of the soil and in our system it was observed that tilling increased soil pH and reduced soil silt content.…”

“…This result is in line with the many past studies that have observed that soil tilling reduces soil fungal abundance and richness (Hartmann et al., ; Oehl et al., ; van der Wal et al., ; Verbruggen et al., ). Considering the physical destruction of fungal hyphae by tilling, the instability in the fungal abundance likely results from fungi requiring longer periods of time to re‐establish hyphal networks post disturbance (Rousk & Bååth, ; Sun et al., ). The slow development in fungal abundance post disturbance is also evidenced in our system where the tilling reduced fungal abundance throughout the growing season that only seemed to recover towards the end of the year, 6–7 months post tilling.…”

Amphibian skin fungal communities vary across host species and do not correlate with infection by a pathogenic fungus

“…Sequencing reads associated with the skin fungal communities were processed as in Sun et al (2017). Sequences were quality filtered and processed using the USEARCH pipeline (Edgar, 2010).…”

Effect of forest fire prevention treatments on bacterial communities associated with productive Boletus edulis sites

“…The phyla Proteobacteria, Actinobacteria and Acidobacteria were the most abundant, which support the findings reported in previous studies of forest soils (Deveau et al ., ; Sun et al ., ). These phyla seem to be abundant in most soils (Lauber et al ., ), which appears to indicate their functional importance (Lladó et al ., ).…”