Changes of Scots Pine Phyllosphere and Soil Fungal Communities during Outbreaks of Defoliating Insects

Weather and leaf age separately contribute to temporal shifts in phyllosphere community structure and composition

Microbial communities living on plant leaves can positively or negatively influence plant health and, by extension, can impact whole ecosystems. Most research into the leaf microbiome consists of snapshots, and little is known about how microbial communities change over time. Weather and host physiological characteristics change over time and are often collinear with other time-varying factors, such as substrate availability, making it difficult to separate the factors driving microbial community change. We leveraged repeated measures over the course of an entire year to isolate the relative importance of environmental, host physiological, and substrate age-related factors on the assembly, structure, and composition of leaf-associated fungal communities. We applied both culturing and sequencing approaches to investigate these communities, focusing on a foundational, widely-distributed plant of conservation concern: basin big sagebrush ( Artemisia tridentata subsp. tridentata ). We found that changes in alpha diversity were independently affected by the age of a community and the air temperature. Surprisingly, total fungal abundance and species richness were not positively correlated and responded differently, sometimes oppositely, to weather. With regard to beta diversity, communities were more similar to each other across similar leaf ages, air temperatures, leaf types, and δ 13 C stable isotope ratios. Nine different genera were differentially abundant with air temperature, δ 13 C, leaf type, and leaf age, and a set of 20 genera were continuously present across the year. Our findings highlight the necessity for longer-term, repeated sampling to parse drivers of temporal change in leaf microbial communities.

Open Research Statement

All ITS DNA amplicon sequence raw data are deposited in the NCBI Sequence Read Archive (SRA), BioProject number PRJNA1107252, data will be released upon publication. All community data, metadata, taxonomic data, and R code necessary to reproduce these results are deposited in the GitHub repository archived on Zenodo: 10.5281/zenodo.11106439.

Variations of Phyllosphere and Rhizosphere Microbial Communities of Pinus koraiensis Infected by Bursaphelenchus xylophilus

Pine wood nematode, Bursaphelenchus xylophilus, as one of the greatest threats to pine trees, is spreading all over the world. Plant microorganisms play an important role in the pathogenesis of nematodes. The phyllosphere and rhizosphere bacterial and fungal communities associated with healthy Pinus koraiensis (PKa) and P. koraiensis infected by B. xylophilus at the early (PKb) and last (PKc) stages were analyzed. Our results demonstrated that pine wood nematode (PWD) could increase the phyllosphere bacterial Pielou_e, Shannon, and Simpson index; phyllosphere fungal Chao 1 index, as well as rhizosphere bacterial Pielou_e, Shannon, and Simpson index; and rhizosphere fungal Pielou_e, Shannon, and Simpson index. What's more, slight shifts of the microbial diversity were observed at the early stage of infection, and the microbial diversity increased significantly as the symptoms of infection worsened. With the infection of B. xylophilus in P. koraiensis, Bradyrhizobium (rhizosphere bacteria), Massilia (phyllosphere bacteria), and Phaeosphaeriaceae (phyllosphere fungi) were the major contributors to the differences in community compositions among different treatments. With the infection of PWD, most of the bacterial groups tended to be co-excluding rather than co-occurring. These changes would correlate with microbial ability to suppress plant pathogen, enhancing the understanding of disease development and providing guidelines to pave the way for its possible management.

High-resolution melting (HRM) curve analysis as a potential tool for the identification of earthworm species and haplotypes

Background

Earthworm communities are an important component of soil biodiversity and contribute to a number of ecosystem functions such as soil-nutrient cycling. Taxonomic identification is an essential requirement to assess earthworm biodiversity and functionality. Although morphological identification of species is labour-intensive, it is the most commonly used method due to a lack of cost-efficient alternatives. Molecular approaches to identify earthworms at species and haplotype level such as DNA barcoding are gaining popularity in science but are rarely applied in practice. In contrast to barcoding, the differentiation of PCR products based on their thermal denaturation properties using high-resolution melting (HRM) curve analysis is a fast and cost-efficient molecular closed-tube, post-PCR tool that allows identification of taxa.

Methods

We developed a HRM curve assay to identify eight earthworm species common to agricultural soils in Central Europe (Allolobophora chlorotica, Aporrectodea caliginosa, Apo. limicola, Apo. longa, Apo. rosea, Lumbricus castaneus, L. rubellus, and L. terrestris). For this, a new primer pair targeting a 158-bp long subregion of the cytochrome c oxidase I (COI) gene was designed. Our HRM assay was further tested for the differentiation of COI haplotypes using 28 individuals of the earthworm species Allo. chlorotica. Furthermore, we developed a novel extraction method for DNA from earthworm tissue that is fast and requires minimal consumables and laboratory equipment.

Results

The developed HRM curve assay allowed identifying all eight earthworm species. Performing the assay on 28 individuals of the earthworm species Allo. chlorotica enabled the distinction among different COI haplotypes. Furthermore, we successfully developed a rapid, robust, scalable, and inexpensive method for the extraction of earthworm DNA from fresh or frozen tissue.

Conclusions

HRM curve analysis of COI genes has the potential to identify earthworm species and haplotypes and could complement morphological identification, especially for juvenile or damaged individuals. Our rapid and inexpensive DNA extraction method from earthworm tissue helps to reduce the costs of molecular analyses and thereby promote their application in practice.

Early response of soil fungal communities to the conversion of monoculture cropland to a temperate agroforestry system

Background

Alley-cropping systems in the temperate zone are a type of agroforestry in which rows of fast-growing trees are alternated with rows of annual crops. With numerous environmental benefits, temperate agroforestry is considered a promising alternative to conventional agriculture and soil fungi may play a key in maintaining productivity of these systems. Agroforestry systems that are established for more than 10 years have shown to increase the fungal biomass and impact the composition of soil fungal communities. Investigations of soil fungi in younger temperate agroforestry systems are scarce and the temporal dynamic of these changes is not understood.

Methods

Our study was conducted in a young poplar-based alley cropping and adjacent monoculture cropland system in an Arenosol soil in north-west Germany. We investigated the temporal dynamics of fungal populations after the establishment of agroforestry by collecting soil samples half, one, and one and a half years after conversion of cropland to agroforestry. Samples were collected within the agroforestry tree row, at 1, 7, and 24 m distance from the tree row within the crop row, and in an adjacent conventional monoculture cropland. The biomass of soil fungi, Asco-, and Basidiomycota was determined by real-time PCR. Soil fungal community composition and diversity were obtained from amplicon sequencing.

Results

Differences in the community composition of soil fungi in the tree row and arable land were detected as early as half a year following the conversion of monoculture cropland to agroforestry. In the tree row, soil fungal communities in the plots strongly diverged with the age of the system. The presence of young trees did not affect the biomass of soil fungi.

Conclusions

The composition of soil fungal communities responded rapidly to the integration of trees into arable land through agroforestry, whereas the fungal biomass was not affected during the first one and a half years after planting the trees. Fungal communities under the trees gradually diversified. Adaptation to spatially heterogeneous belowground biomass of the trees and understory vegetation or stochastic phenomena due to limited exchange among fungal populations may account for this effect; long-term monitoring might help unravelling the cause.

Ectomycorrhizal Community on Norway Spruce Seedlings Following Bark Beetle Infestation

Ectomycorrhizal (ECM) fungi importantly influence seedling growth, nutrition, and survival and create an extensive mycelial network interconnecting tree species and enabling resource redistribution. Due to their symbiotic relationship with trees, they are impacted by forest disturbances, which are of increasing relevance due to climate change. The effect of disturbance on seedling colonization and their morphology is still largely unknown. Seedling growth parameters and the ECM fungal assemblage on the roots of Norway spruce (Picea abies (L.) H. Karst.) seedlings were assessed in mature spruce forests attacked and destroyed by bark beetle and in a mature non-attacked forest as a reference. We did not detect significant differences in number of ECM species on seedling roots among forest types, but ECM species composition changed; Tylospora fibrillosa (Burt) Donk, Meliniomyces variabilis Hambl. & Sigler, and Phialocephala fortinii C.J.K. Wang & H.E. Wilcox were characteristic species in the forest destroyed by bark beetle, whereas Lactarius, Cortinarius, and Russula were in the mature forest. Forest type further significantly influenced the height, root length, and root collar thickness of seedlings and the proportion of exploration types of mycorrhizae.

Conversion of monoculture cropland and open grassland to agroforestry alters the abundance of soil bacteria, fungi and soil-N-cycling genes

Integration of trees in agroforestry systems can increase the system sustainability compared to monocultures. The resulting increase in system complexity is likely to affect soil-N cycling by altering soil microbial community structure and functions. Our study aimed to assess the abundance of genes encoding enzymes involved in soil-N cycling in paired monoculture and agroforestry cropland in a Phaeozem soil, and paired open grassland and agroforestry grassland in Histosol and Anthrosol soils. The soil fungi-to-bacteria ratio was greater in the tree row than in the crop or grass rows of the monoculture cropland and open grassland in all soil types, possibly due to increased input of tree residues and the absence of tillage in the Phaeozem (cropland) soil. In the Phaeozem (cropland) soil, gene abundances of amoA indicated a niche differentiation between archaeal and bacterial ammonia oxidizers that distinctly separated the influence of the tree row from the crop row and monoculture system. Abundances of nitrate (napA and narG), nitrite (nirK and nirS) and nitrous oxide reductase genes (nosZ clade I) were largely influenced by soil type rather than management system. The soil types’ effects were associated with their differences in soil organic C, total N and pH. Our findings show that in temperate regions, conversion of monoculture cropland and open grassland to agroforestry systems can alter the abundance of soil bacteria and fungi and soil-N-cycling genes, particularly genes involved in ammonium oxidation.

Increased Forest Soil CO2 and N2O Emissions During Insect Infestation

Forest soils are major sinks of terrestrial carbon, but this function may be threatened by mass outbreak events of forest pests. Here, we measured soil CO2-C and N2O-N fluxes from a Scots pine (Pinus sylvestris L.) forest that was heavily infested by the nun moth (Lymantria monacha L.) and an adjacent noninfested (control) forest site during one year. In the infested forest, net emissions of CO2-C were higher during main defoliation, summer and autumn, while indications of increased N2O-N emissions were found at one sampling date. On basis of this, a microcosm incubation experiment with different organic matter treatments was conducted. Soil treatments with needle litter, insect feces plus needle litter, and insect feces showed 3.7-, 10.6-, and 13.5-fold higher CO2-C emissions while N2O-N of the insect feces plus needle litter, and insect feces treatment was 8.9-, and 10.4-fold higher compared with soil treatments without added organic matter (control). Hence, the defoliation in combination with high inputs of organic matter during insect outbreaks distinctly accelerate decomposition processes in pine forest soils, which in turn alters forests nutrient cycling and the functioning of forests as carbon sinks.

The Abundance of Fungi, Bacteria and Denitrification Genes during Insect Outbreaks in Scots Pine Forests

Outbreaks of defoliating insects may affect microbial populations in forests and thereby mass balances and ecosystem functioning. Here, we investigated the microbial dynamics in Scots pine (Pinus sylvestris L.) forests during outbreaks of the nun moth (Lymantria monacha L.) and the pine-tree lappet (Dendrolimus pini L.). We used real-time PCR (polymerase chain reaction) to quantify genes that characterize bacterial and fungal abundance and the denitrification processes (nirK, nirS, nosZ clades I and II) in different forest compartments and we analyzed the C and N content of pine needles, insect feces, larvae, vegetation layers, organic layers, and mineral soil horizons. The infestation of the nun moth increased the bacterial abundance on pine needles, in the vegetation layer, and in the upper organic layer, while fungal populations were increased in the vegetation layer and upper organic layer during both outbreaks. In soil, the abundance of nirK increased after insect defoliation, while the C/N ratios decreased. nosZ clades I and II showed variable responses in different soil layers and to different defoliating insects. Our results illustrate changes in the microbial populations in pine forests that were infested by defoliating insects and changes in the chemical soil properties that foster these populations, indicating a genetic potential for increased soil N2O emissions during the defoliation peak of insect outbreak events.