|dc.description.abstracteng||Tropical rain forests are representing biodiversity hotspots, but their species richness is threatened by human driven land use changes. Between 1990 and 2015 most of the global deforestation of about 129 million hectares occurred in tropical regions, especially in south-east Asian countries. Among those countries, Indonesia reached the highest deforestation rate with a massive conversion of rain forests into agroforestry or agricultural plantations of oil palm (Elaies guineesis) and rubber (Hevea brasiliensis) as major tree crops. The effects of rain forest transformation into tree-species poor systems are currently intensely being studied. The majority of research conducted in the tropical regions has focused on aboveground biodiversity in relation to ecosystem functioning, whereas the immense biodiversity found belowground and its impact on ecosystem functions and services such as tree health or carbon storage have rarely been addressed. Roots and root-associated fungi play an important role in this regard because they supply nutrients and water to the aboveground parts of the plant and anchor the trees in soil. The roots are characterized by different traits. One highly important trait is their fungal assemblage, which can influence root health and decrease productivity (pathogenic fungi) or enhance nutrient supply and increase productivity (mycorrhizal fungi). Furthermore, mycorrhizal fungi can protect their host plants against herbivores and pathogens and act as main pathway of carbon to the soil The influence of land-use intensification in tropical ecosystems on root traits, fungal diversity and community structure is not well understood. The overarching goal of this thesis was to investigate the influence of tropical low land rain forest transformation into agricultural plantations on root community traits and root-associated fungal communities.
The study was conducted in the Jambi Province on Sumatra Island, Indonesia. Sumatra has lost, on average, 550.000 hectares of forest per year over the last 30 years with the majority of land use changes occurring in the low land regions. The sampling sites were therefore chosen in two different low land landscapes, i.e. the Harapan and the Bukit Duabelas (Bukit12) landscapes. In each landscape, the sampling sites were located along a land use gradient representing unmanaged rain forests, less-managed jungle rubber agroforests, and intensely managed monoculture rubber and oil palm plantations.
This sampling design was used to investigate (i) root community traits such as colonization by mycorrhizal fungi and root vitality (performance traits) as well as nutrient concentrations (chemical traits). These traits can indicate the impact of land use change on root functions at the community level. (ii) Root-associated fungal communities in terms of diversity and structural and functional composition. The root-associated fungal community compositions were analyzed by Illumina sequencing, which is a next generation sequencing technique that generates relatively short sequences. This technique has not often been applied for analyzing fungal communities. Therefore, a subset of the samples was additionally analyzed by 454 Pyrosequencing, which generates longer sequences and is the most common next generation sequencing technique applied in fungal research so far.
The present thesis is, therefore, organized in two main chapters in which ecological questions on root communities and root-associated fungal communities were addressed and one technical chapter (iii), in which the results on root-associated fungal communities obtained by Illumina sequencing and 454 Pyrosequencing were compared.
(i) Characterization of root community traits along a transformation gradient
from low land rain forests into plantations with tree crops
We hypothesized that root community traits vary with land use system indicating increasing transformation intensity and loss of ecosystem functions.
In tropical rain forests most trees, including the introduced rubber trees and oil palms, are associated with arbuscular mycorrhizal (AM) fungi, but some tree species-rich families, e.g. Dipterocarpaceae, are associated with ectomycorrhizal (EM) fungi. The ability of tree roots to form mutualistic AM or EM associations is a typical species-related trait that can mediate differences in plant nutrition, especially of phosphorus and nitrogen. In species-rich tropical rain forests traits of distinct tree taxa are difficult to measure, but instead root traits can be gathered at a community level of the co-occurring species and can then be defined as “root community-weighted traits”.
To analyze root community-weighted traits, mixed root samples were collected in different land use systems. The chemical traits (carbon, nitrogen, mineral nutrients, potentially toxic elements (aluminum, iron)), and the performance traits (root mass, vitality, mycorrhizal colonization) of root communities were analyzed. Chemical traits were analyzed by applying a combustion method using an organic element analyzer (carbon and nitrogen) and by inductively coupled plasma optical emission spectrometry (mineral nutrients and potentially toxic elements). Performance traits were analyzed by measuring root biomass, determining root vitality (counting of distorted and vital root tips), and colonization by EM and AM. The influence of land use on root community traits was tested by applying multivariate statistics. Variation of root community traits related to land systems were analyzed by principle component analysis (PCA) and dissimilarities were visualized by non-metric multidimensional scaling (NMDS).
Roots of oil palm and rubber plantations showed a decrease in nutrient concentrations (carbon, nitrogen, sulfur, manganese, and base cations) compared with those from rain forests. However, the mycorrhizal colonization by AM fungi was stable across land use systems and EM colonization was rare and only found in rain forest and jungle rubber. Furthermore, a degradation of root health in monoculture plantations was evident which was related to an accumulation of plant toxic elements. Concentrations of aluminum and iron were higher in roots from oil palm plantations than those of rain forests, whereas the amount of distorted root tips was, on average, nearly doubled in oil palm plantations in comparison to the other systems. Additionally, root community traits were linked to important ecosystem properties (i.e. soil nitrogen concentrations, soil pH, and litter nitrogen concentrations.
These findings supported the initial hypothesis that root community traits declined with increasing transformation intensity. It was demonstrated that the degradation of root community traits was an indicator for tropical low land rain forest transformation into monoculture plantations. The study revealed a relationship between deteriorating root community traits and a loss of ecosystem functionality and showed that increasing transformation intensity resulted in decreasing root nutrition and health. These findings suggest that land management practices that improve root vitality may enhance the ecological functions of intense tropical production systems.
(ii) Characterization of richness, diversity, and community structure of root-associated fungal communities along a tropical land use gradient
We hypothesized that the fungal diversity of root-associated communities is higher in plant species-rich rain forests than in monoculture plantations because higher plant diversity creates more different habitats for root-colonizing fungi. Consequently, an impact of land use change on the community composition of root-associated fungi was expected. Based on the finding that the roots in oil palm plantations had a distorted appearance, a shift from beneficial functional fungal groups towards pathogens was expected in the highly managed systems compared to natural rain forests.
To examine the impact of rain forest transformation into rubber and oil palm plantations on root-associated fungal communities, mixed root samples were taken in the different land use systems. The composition of root-associated fungal communities was determined by Illumina sequencing. Fungal operational taxonomic units (OTUs) were characterized by amplifying the internal transcribed spacer (ITS) region 1 of the environmental DNA samples by using fungal-specific primers. The resulting fungal OTUs were assigned to functional groups: arbuscular mycorrhizal fungi, ectomycorrhizal fungi, plant pathogenic fungi, and saprotrophic fungi. In addition, land use intensity indices were calculated based on data for fertilizer, animal manure, and herbicide applications as well as by soil amendment by liming. Land use intensity indices, data on root community traits, and soil and litter properties were included as explanatory variables for analyses of the community structure. The impact of land use on the community composition was tested with permutational multivariate analysis of variance (PERMANOVA) using distance matrices. The influence of land use on richness and abundances of fungal OTUs was tested by applying generalized linear mixed effects models.
OTU richness and diversity of root-associated fungi did not support the hypothesis that transformation from tree species-rich forests into species-poor plantations led to species reduction. Fungal diversity in the plant species-rich rain forests was not higher than in monoculture plantations but the root-associated fungal community composition was clearly influenced by land use. The fungal communities in oil palm roots showed an increase in the abundance in Ascomycota and a decrease in Basidiomycota compared to those in rain forests. Glomeromycota, on the other hand, were most abundant in fungal communities of rain forests. These findings underpin the expectation that land use changes have massive impact on the fungal community structure in roots. The differences among root-associated fungal communities were mainly explained by chemical root community traits and land use intensity. The results obtained on relative abundances of different fungal functional groups showed an increase of plant pathogenic fungi and a decrease of beneficial EM and AM fungi in oil palm plantations compared to natural forests. This supported the hypothesis that a shift from beneficial toward pathogenic fungi in monoculture plantation compared to natural forests existed.
To conclude, it was demonstrated that rain forest transformation into highly managed plantations impacts the community composition but not the diversity of root-associated fungi. The alterations caused by land use changes led to an accumulation of pathogenic fungi in highly managed monoculture plantations and were mainly explained by land use intensification and root chemical traits. Based on these findings we speculate that land use management at a lower intensity and management practices, which improve root nutrition, may create environmental conditions favorable to beneficial mycorrhizal fungi and unfavorable for plant pathogenic fungi and, thereby, sustain productivity at lower environmental destruction.
(iii) Comparison of 454 Pyrosequencing and Illumina sequencing for root-associated fungal communities
The application of different next generation sequencing techniques may influence the result obtained for microbial communities because of methodology-dependent advantages and disadvantages, e.g., limitations of species annotation due to different sequence lengths obtained by different methods or different numbers of sequence reads that can be generated. To test whether Illumina sequencing and 454 Ppyrosequencing methods yielded strongly diverging results or not, the same root samples were analyzed by both methods.
As expected root community samples analyzed by 454 Pyrosequencing recovered a lower sequence and fungal OTU richness than by Illumina sequencing. The taxonomic composition of root-associated fungal communities obtained by both techniques was similar regarding the relative abundance of Ascomycota present. The relative abundance of Basidiomycota was decreased and the one of unidentified fungi was increased in samples analyzed by Illumina sequencing. However, both techniques sampled the same fraction of diversity because the Shannon and Simpson indices for diversity showed no significant differences.
In conclusion, this comparison revealed that both applied next generation sequencing techniques provided comparable results in terms of the recovered diversity of root-associated fungal communities. This finding matters because it indicates that results from differing studies using either 454 Pyrosequencing or Illumina sequencing can be used to compare diversity indices but should be used with caution when comparing the taxonomic composition of samples.
In summary, this thesis demonstrated that the transformation of tropical low land rain forest into agricultural plantations affects root community traits and root-associated fungal communities. The degradation of root community traits can be considered as indicator for rain forest transformation into rubber and oil palm plantations. The diversity of root-associated fungi was not influenced by rain forest transformation. However, root-associated fungal community composition was impacted by land use changes. The dissimilarities of fungal communities were mainly explained by the degradation of chemical root community traits and the intensification of land management practices. The degradation of root traits and the increase of land use intensity led to an increase of pathogenic fungi and a decrease of mycorrhizal fungi in monoculture plantations compared to unmanaged rain forests.||de