First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes.

Nematodes represent a diverse and ubiquitous group of metazoans in terrestrial environments. They feed on bacteria, fungi, plants, other nematodes or parasitize a variety of animals and hence may be considered as active members of many food webs. Deadwood is a structural component of forest ecosystems which harbors many niches for diverse biota. As fungi and bacteria are among the most prominent decomposing colonizers of deadwood, we anticipated frequent and diverse nematode populations to co-occur in such ecosystems. However, knowledge about their ability to colonize this habitat is still limited. We applied DNA-based amplicon sequencing (metabarcoding) of the 18S rRNA gene to analyze nematode communities in sapwood and heartwood of decaying logs from 13 different tree species. We identified 247 nematode ASVs (amplicon sequence variants) from 27 families. Most of these identified families represent bacterial and fungal feeders. Their composition strongly depended on tree species identity in both wood compartments. While pH and water content were the only wood properties that contributed to nematodes' distribution, co-occurring fungal and prokaryotic (bacteria and archaea) α- and ß-diversities were significantly related to nematode communities. By exploring thirteen different tree species, which exhibit a broad range of wood characteristics, this study provides first and comprehensive insights into nematode diversity in deadwood of temperate forests and indicates connectivity to other wood-inhabiting organisms.

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs.

In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.

Divergence of 3' ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae.

Short interspersed nuclear elements (SINEs) are small, non-autonomous and heterogeneous retrotransposons that are widespread in plants. To explore the amplification dynamics and evolutionary history of SINE populations in representative deciduous tree species, we analyzed the genomes of the six following Salicaceae species: Populus deltoides, Populus euphratica, Populus tremula, Populus tremuloides, Populus trichocarpa, and Salix purpurea. We identified 11 Salicaceae SINE families (SaliS-I to SaliS-XI), comprising 27 077 full-length copies. Most of these families harbor segmental similarities, providing evidence for SINE emergence by reshuffling or heterodimerization. We observed two SINE groups, differing in phylogenetic distribution pattern, similarity and 3' end structure. These groups probably emerged during the 'salicoid duplication' (~65 million years ago) in the Salix-Populus progenitor and during the separation of the genus Salix (45-65 million years ago), respectively. In contrast to conserved 5' start motifs across species and SINE families, the 3' ends are highly variable in sequence and length. This extraordinary 3'-end variability results from mutations in the poly(A) tail, which were fixed by subsequent amplificational bursts. We show that the dissemination of newly evolved 3' ends is accomplished by a displacement of older motifs, leading to various 3'-end subpopulations within the SaliS families.

Genetic diversity and bark physiology of the European beech (Fagus sylvatica): a coevolutionary relationship with the beech scale (Cryptococcus fagisuga).

In 1994 and 1995, the degree of infestation by the beech scale (Cryptococcus fagisuga Lind.) was recorded on 120 beech trees (Fagus sylvatica L.) in the Pless Forest near Göttingen, Germany. Simultaneously, the trees were characterized genetically and compounds of primary and secondary metabolism of beech bark were analyzed. A correlation was established between beech scale infestation and the genotype of the host trees, based on gene locus A of isocitrate dehydrogenase (IDH-A). The fraction of infested beech trees was higher in the heterozygous genotype A2A3 group than in the homozygous genotype A2A2 and A3A3 groups, whereas the fraction of beech trees with decreasing infestation from one year to the next was lower in the heterozygous genotype A2A3 group than in the homozygous genotype A2A2 and A3A3 groups. Concentrations of soluble carbohydrates, protein amino acids and proanthocyanidins were determined in the inner and outer bark of trees with differing degrees of infestation. The results indicate that the defense reaction of beech against infestation by beech scale comprises multiple processes in which nutrient availability to the beech scale is reduced by concentration shifts and by the formation of inhibiting compounds.