A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies

Abstract

Deadwood is an important biodiversity hotspot in forest ecosystems. While saproxylic insects and wood-inhabiting fungi have been studied extensively, little is known about deadwood-inhabiting bacteria. The study we present is among the first to compare bacterial diversity and community structure of deadwood under field conditions. We therefore compared deadwood logs of two temperate forest tree species Fagus sylvatica and Picea abies using 16S rDNA pyrosequencing to identify changes in bacterial diversity and community structure at different stages of decay in forest plots under different management regimes. Alphaproteobacteria, Acidobacteria and Actinobacteria were the dominant taxonomic groups in both tree species. There were no differences in bacterial OTU richness between deadwood of Fagus sylvatica and Picea abies. Bacteria from the order Rhizobiales became more abundant during the intermediate and advanced stages of decay, accounting for up to 25% of the entire bacterial community in such logs. The most dominant OTU was taxonomically assigned to the genus Methylovirgula, which was recently described in a woodblock experiment of Fagus sylvatica. Besides tree species we were able to demonstrate that deadwood physico-chemical properties, in particular remaining mass, relative wood moisture, pH, and C/N ratio serve as drivers of community composition of deadwood-inhabiting bacteria.

Figure 1. Relative abundances of phylogenetic groups (bacterial phyla including proteobacterial classes) in deadwood from two species (Fagus sylvatica = FASY, Picea abies = PIAB) in different stages of decay (decay classes 1–4).

OTUs that could not be taxonomically assigned at the phylum/subphylum level are reported as “Others” and comprise ≤ 0.006% of all sequences. The category “other” also includes all OTUs with <1.5% relative sequence abundance.

Figure 2. Relative abundances of the three dominant phylogenetic groups (bacterial orders) in deadwood of the two studied tree species (Fagus sylvatica = FASY, Picea abies = PIAB) in different stages of decay (decay classes 1–4).

Differences between decay classes and tree species were analyzed by employing one-way analysis of variance and Fisher's Least Significant Difference (LSD) post hoc test (ns = not significant, * P < 0.05, ** P < 0.01, *** P < 0.001).

Figure 3. Two-dimensional non-metric multidimensional scaling (NMDS) ordination plots of bacterial community structure across the different tree species at each stage of decay (FASY1-4, PIAB1–4).

Plots show centroids within a single decay stage, bars represent one SD along both NMDS axes. Statistical significances (R² and P-values) are based on Goodness-of-fit statistics for environmental variables and bacterial order abundances per sample.