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Large tropical trees are rightly perceived as supporting a plethora of organisms. However, baseline data about the variety of taxa coexisting on single large tropical trees are lacking and prevent a full understanding of both the magnitude of biodiversity and the complexity of interactions among organisms in tropical rainforests. The two main aims of the research program “Life on Trees” (LOT) are (1) to establish baseline knowledge on the number of eukaryote species supported/hosted by the above-ground part of a single tropical tree and (2) to understand how these communities of organisms are assembled and distributed on or inside the tree. To achieve the first goal, we integrated a set of 36 methods for comprehensively sampling eukaryotes (plants, fungi, animals, protists) present on a tropical tree. The resulting LOT protocol was conceived and implemented during projects in the Andean Amazon region and is proposed here as a guideline for future projects of a similar nature. To address the second objective, we evaluated the microclimatic differences between tree zones and tested state-of-the-art terrestrial laser scanning (TLS) and positioning technologies incorporating satellite and fixed base station signals (dGNSS). A marked variation in temperature and relative humidity was detected along a 6-zones Johansson scheme, a tree structure subdivision system commonly used to study the stratification of epiphytic plants. Samples were collected from these six zones, including three along the trunk and three in the canopy. To better understand how different tree components (e.g., bark, leaves, fruits, flowers, dead wood) contribute to overall tree biodiversity, we categorized observations into communities based on Johansson zones and microhabitats. TLS was an essential aid in understanding the complex tree architecture. By contrast, the accuracy of positioning samples in the tree with dGNSS was low. Comprehensively sampling the biota of individual trees offers an alternative to assessing the biodiversity of fewer groups of organisms at the forest scale. Large old tropical trees provide a wealth of microhabitats that encompass a wide range of ecological conditions, thereby capturing a broad spectrum of biodiversity.

IntroductionHigh-throughput sequencing (HTS) provides an efficient and cost-effective way to generate large amounts of sequence data, providing a very powerful tool to analyze biodiversity of soil organisms. However, marker-based methods and the resulting datasets come with a range of challenges and disputes, including incomplete reference databases, controversial sequence similarity thresholds for delimitating taxa, and downstream compositional data analysis. MethodsHere, we use HTS data from a soil nematode biodiversity experiment to explore standardized HTS data processing procedures. We compared the taxonomic assignment performance of two main rDNA reference databases (SILVA and PR2). We tested whether the same ecological patterns are detected with Amplicon Sequence Variants (ASV; 100% similarity) versus classical Operational Taxonomic Units (OTU; 97% similarity). Further, we tested how different HTS data normalization methods affect the recovery of beta diversity patterns and the identification of differentially abundant taxa.ResultsAt this time, the SILVA 138 eukaryotic database performed better than the PR2 4.12 database, assigning more reads to family level and providing higher phylogenetic resolution. ASV- and OTU-based alpha and beta diversity of nematodes correlated closely, indicating that OTU-based studies represent useful reference points. For downstream data analyses, our results indicate that loss of data during subsampling under rarefaction-based methods might reduce the sensitivity of the method, e.g. underestimate the differences between nematode communities under different treatments, while the clr-transformation-based methods may overestimate effects. The Analysis of Compositions of Microbiome with Bias Correction approach (ANCOM-BC) retains all data and accounts for uneven sampling fractions for each sample, suggesting that this is currently the optimal method to analyze compositional data.DiscussionOverall, our study highlights the importance of comparing and selecting taxonomic reference databases before data analyses, and provides solid evidence for the similarity and comparability between OTU- and ASV-based nematode studies. Further, the results highlight the potential weakness of rarefaction-based and clr-transformation-based methods. We recommend future studies use ASV and that both the taxonomic reference databases and normalization strategies are carefully tested and selected before analyzing the data.

Land-use change is threatening biodiversity worldwide and is predicted to increase in the next decades, especially in tropical regions. Most studies focused on the response of single or few species to land-use change, only few investigated the response of entire communities. In particular the response of belowground communities to changes in land use received little attention. Oribatid mites (Oribatida, Acari) are among the most abundant soil animals, involved in decomposition processes and nutrient cycling. Oribatid mite species span a wide range of trophic niches and are known to sensitively respond to changes in land use. Here, we investigated shifts in the community-level trophic niche of oribatid mites with the conversion of rainforest into rubber and oil palm plantations. Due to a wider range of resources in more natural ecosystems, we expected the community-level trophic niche to shrink with conversion of rainforest into plantations. As the conversion of rainforest into plantations is associated with reduced availability of litter resources, we expected the average trophic level (indicated by the 15N/14N ratio) to be higher and basal resources (indicated by the 13C/12C ratio) to shift toward living plant material in rubber and oil palm plantations. Our analysis showed that community-level trophic niches in rainforest and rubber agroforest (“jungle rubber”) were separated from those in monoculture plantation systems, indicating a trophic niche shift with land-use intensification. As hypothesized, oribatid mites shifted their diet toward predation and/or scavenging and toward the plant-based energy channel with transformation of rainforest into plantations. Exceptionally low minimum 13C/12C ratios in rubber plantations suggest that certain oribatid mite species in this land-use system use resources not available in the other studied ecosystems. We detected high isotopic uniqueness in oil palm plantations suggesting a low trophic redundancy and thus high vulnerability of trophic functioning in this system in comparison to rainforest. Overall, the results suggest that the conversion of rainforest into plantations is associated with pronounced shifts in community-level trophic niches of mesofauna detritivores with potential major consequences for the functioning of the decomposer system.

Forest soil food webs have been assumed to be fueled substantially by root-derived resources. However, until today the flux of root-derived resources into soil animals has been investigated virtually exclusively using isotope labeling experiments, whereas studies on the consequences of disrupting the flux of root-derived resources into the soil animal food web are scarce. We here investigated the importance of root-derived resources for a wide range of soil animals by interrupting the resource flux into the soil of different forest types in Central Europe using a trenching experiment. We recorded the abundance of soil animal taxa varying in body size (micro-, meso-, and macrofauna) 1 and 3 years after root trenching, and quantified changes in biomass, species composition, and trophic shift using stable isotopes and NLFA analysis. Among the microfauna groups studied (trophic groups of Nematoda) only the abundance of plant feeding nematodes showed a trend in being decreased by -58% due to root trenching. Major soil mesofauna groups, including Collembola and Oribatida, suffered to a similar extent from root trenching with their abundance and biomass being reduced by about 30–40%. The soil macrofauna groups studied (Diplopoda, Isopoda, Chilopoda, Araneae, Coleoptera) generally were only little affected by root trenching suggesting that they rely less on root-derived resources than micro- and in particular mesofauna. Notably, the community structure of micro-, meso-, and macrofauna was not affected by root trenching. Further, we observed trophic shifts only in 2 out of 10 investigated species with the shifts generally being only minor. The results indicate that soil animal communities are markedly resilient to deprivation of root-derived resources suggesting that links to root-derived resources are non-specific. However, this resilience appears to vary with body size, with mesofauna including both decomposers as well as predators being more sensitive to the deprivation of root-derived resources than microfauna (except for root feeders) and macrofauna. Overall, this suggests that body size constrains the channeling of energy through soil food webs, with root-derived resources in temperate forests being channeled predominantly via soil taxa of intermediate size, i.e., mesofauna.

Tidal coasts are characterized by natural disturbances, forming a broad variety of habitats, which provide different niches and varying food resources for benthic foraminifera. Foraminifera occupy different trophic levels and fill key trophic positions in benthic food webs, but detailed studies on their nutrition spectrum in inter- to supratidal environments are lacking. Further, it is unknown to what extent foraminifera can switch between different feeding modes depending on resource availability in different Wadden Sea habitats. In order to shed light on these questions, we investigated potential food resources in sediments as well as the food spectrum of two dominant benthic foraminifera, Trochammina inflata and Ammonia tepida, in four characteristic habitats of the Wadden Sea: salt marsh, mixed flat, oyster reef and mud flat, using fatty acid (FA) analysis. The sediments of the four habitats provide a broad range of food sources including green algae, brown algae, diatoms and bacteria for benthic foraminifera. The FA profile of T. inflata from the salt marsh and mixed flat was dominated by green algae and bacteria, whereas the brown algae biomarker was only found in specimens from the salt marsh. In comparison, FA profiles of A. tepida suggested dominant algae feeding (green algae and diatoms), whereas brown algae and bacterial FAs were only found in specimens from the oyster reef. The results suggest that foraminifera mainly feed at low trophic levels with selective food intake closely depending on their habitat. The diverse nutritional strategies may allow efficient exploitation of resources in dynamic tidal habitats. Presumably, foraminifera serve as an important link between lower and higher trophic levels and thus fill key trophic positions in the benthic food web of the Wadden Sea.

Focusing on nematodes and their well-developed indices of community, ecosystem structure and function, we investigated the effects of the conversion of rainforest into rubber and oil palm plantations in Sumatra, Indonesia. Land use did not affect the total abundance of litter- and soil-dwelling nematodes, neither in riparian nor in well-drained sites. However, the rainforest nematode community differed from communities in plantations, with differences in litter being more pronounced compared to soil. In litter, fungivores and nematodes with short generation time (c-p2) increased in monoculture plantations, while that of bacterivores, herbivores, and nematodes with longer generation time and higher sensitivity to disturbances (c-p3) decreased. This indicates higher environmental pressure on nematodes in monoculture plantations than in rainforest. In soil of monoculture plantations, bacterivores, and c-p3 nematodes decreased while herbivores increased. This suggests that the damage of plants by nematodes in oil palm plantations exceeds that in rainforest. Overall, nematode functional diversity indices suggest that the stability of the decomposer community is higher in rainforest compared to monoculture plantations. Importantly, functional diversity indices were much more meaningful than nematode abundance. Further, changes with land use manifested more in litter than in soil, reflecting that nematode communities in soil are buffered against changes in land use and associated environmental conditions. Therefore, to fully assess changes in the structure and functioning of decomposer systems with changes in land use, the litter layer, which often receives little attention, requires more careful consideration.

Oil palm plantations are intensively managed agricultural systems that increasingly dominate certain tropical regions. Oil palm monocultures have been criticized because of their reduced biodiversity compared to the forests they historically replaced, and because of their negative impact on soils, water, and climate. We experimentally test whether less intensive management schemes may enhance biodiversity and lessen detrimental effects on the environment while maintaining high yields. We compare reduced vs. conventional fertilization, as well as mechanical vs. chemical weed control (with herbicides) in a long-term, full-factorial, multidisciplinary experiment. We conducted the experiment in an oil palm company estate in Sumatra, Indonesia, and report the results of the first 2 years. We measured soil nutrients and functions, surveyed above- and below-ground organisms, tracked oil palm condition and productivity, and calculated plantation gross margins. Plants, aboveground arthropods, and belowground animals were positively affected by mechanical vs. chemical weed control, but we could not detect effects on birds and bats. There were no detectable negative effects of reduced fertilization or mechanical weeding on oil palm yields, fine roots, or leaf area index. Also, we could not detect detrimental effects of the reduced fertilization and mechanical weeding on soil nutrients and functions (mineral nitrogen, bulk density, and litter decomposition), but water infiltration and base saturation tended to be higher under mechanical weeding, while soil moisture, and microbial biomass varied with treatment. Economic performance, measured as gross margins, was higher under reduced fertilization. There might be a delayed response of oil palm to the different management schemes applied, so results of future years may confirm whether this is a sustainable management strategy. Nevertheless, the initial effects of the experiment are encouraging to consider less intensive management practices as economically and ecologically viable options for oil palm plantations.

Protists, abundant but enigmatic single-celled eukaryotes, are important soil microbiota providing numerous ecosystem functions. We employed high-throughput sequencing of environmental DNA, targeting the V4 region of the 18S rRNA gene, to characterize changes in their abundance, species richness, and community structure with conversion of lowland rainforest into rubber agroforest (jungle rubber), and rubber and oil palm plantations; typical agricultural systems in Sumatra, Indonesia. We identified 5,204 operational taxonomic units (OTUs) at 97% identity threshold of protists from 32 sites. Protists species richness was similar in rainforest, jungle rubber and oil palm plantations but significantly lower in rubber plantations. After standardization, 4,219 OTUs were assigned to five trophic groups, and inspected for effects of land-use change, and potential biotic and abiotic driving factors. The most abundant trophic group was phagotrophs (52%), followed by animal parasites (29%), photoautotrophs (12%), plant parasites (1%), and symbionts (

Arbuscular mycorrhizal fungi (AMF) are important symbionts for plant nutrient uptake, but their exact role in plant nitrogen (N) nutrition is unclear. Protists on the other hand play an acknowledged role in plant N acquisition, and there is increasing evidence for a close interaction with AMF. In a split root set up, we investigated the distinct roles of mycorrhiza (Rhizophagus irregularis), protists (Acanthamoeba castellanii), and their interaction on plant N uptake, within-root system allocation patterns, and shoot-to-root ratio of winter wheat. In addition, we applied a quantitative metabolomics approach to characterize associated changes in soil microbial communities by microbial phospholipid fatty acid (PLFA) analysis from rhizosphere soil. AMF markedly altered plant shoot-to-root allometry by reducing root biomass of wheat, and mycorrhiza partly took over root system functioning. Protists promoted shoot and root growth, and improved plant N uptake by the release of N from consumed bacterial biomass, a mechanism known as microbial loop. The shoot system however responded little to these alterations of the root system and of the rhizosphere community composition, indicating that the plants optimized shoot growth despite varying investment into roots. Mycorrhiza reduced root biomass and plant N, especially in the combined treatments with protists by changing within root system allocation of N and root biomass. These systemic effects on root allocation pattern suggest that mycorrhiza also gained control over N provided by protist grazers. Protists and mycorrhiza altered rhizosphere bacterial communities in contrasting but consistent ways as shown by quantitative shifts in microbial PLFA profiles. Remarkably, the changes in bacterial community composition were systemically conveyed within the root system to the split-root chamber where the symbionts were lacking. Accordingly the synergistic effects of protists and mycorrhiza indicated systemic effects on nutrient- and on root-allocation within root systems as an emergent property that could not be predicted from single treatments with mycorrhiza or protists alone. The tight plant and microbial feed backs uncovered in this study have far reaching implications for understanding the assembly of plant microbiomes, and testify central roles of both protists and mycorrhizas in the assembly process.

Climate change models predict reduced summer precipitations for most European countries, including more frequent and extreme summer droughts. Rainout-shelters which intercept part of the natural precipitation provide an effective tool to investigate effects of different precipitation levels on biodiversity and ecosystem functioning. In this study, we evaluate and describe in detail a fixed-location rainout-shelter (2.5 × 2.5 m) with partial interception of natural rainfall. We provide a complete parts list, a construction manual and detailed CAD drawings allowing to rebuild and use these shelters for rainfall manipulation studies. In addition, we describe a rainout-shelter control treatment giving the possibility to quantify and account for potential shelter artifacts. To test the rainout-shelters, we established the following three treatments each in eight winter wheat plots of the agricultural long-term farming system comparison trial DOK in Therwil (Switzerland): (1) A rainout-shelter with 65% interception of rainfall, (2) a rainout-shelter control without interception of rainfall, and (3) an ambient control. The rainout-shelter effectively excluded 64.9% of the ambient rainfall, which is very close to the a priori calculated exclusion of 65.1%. In comparison to the ambient control plots, gravimetric soil moisture decreased under the rainout-shelter by a maximum of 11.1 percentage points. Air temperature under the rainout-shelter differed little from the ambient control (−0.55°C in 1.2 m height and +0.19°C in 0.1 m height), whereas soil temperatures were slightly higher in periods of high ambient temperature (+1.02°C), but remained basically unaffected in periods of low ambient temperature (+0.14°C). A maximum edge effect of 0.75 m defined a sampling area of 1 × 1 m under the rainout-shelter. The rainout-shelters presented here, proved to sustain under heavy weather and they were well-suited to be used in agricultural fields where management operations require the removal of the rainout-shelters for management operations. Overall, the results confirmed the good performance of the presented rainout-shelters regarding rainout-shelter artifacts, predictable rain exclusion, and feasibility for experimental studies in agricultural fields.

Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio, and extractable P content. Archaeal community composition and diversity were correlated to pH value, exchangeable Fe content, water content, and total N. The distribution of bacterial and archaeal taxa involved in biological N cycle indicated functional shifts of the cycle during conversion of rainforest to plantations.