Identification and functional roles of amoeboid protozoa in soil

Protozoa are the major consumers of bacterial production in soil, forming the base of the heterotrophic eukaryotic food web that channels the energy flow via bacteria to higher trophic levels in soil (i.e. the bacterial energy channel). Among them, amoebae and amoeboid flagellates are of major importance due to their small size, high abundance, fast turnover and ability to penetrate even the smallest pores with their flexible pseudopodia, making them key regulators of bacterial biomass and nutrient cycling. Despite these important functions for soils we have only a vague idea on the identity of the dominant taxa of amoeboid organisms in soils. Major reasons for the general ignorance in environmental studies of these key eukaryotes are methodological difficulties in cultivation and quantification in the opaque soil environment as well as a lack of taxonomic expertise. However, recent developments in molecular techniques now allow closing the methodological gap on this functionally important trophic link in the soil food web. Within my PhD project as part of the EU-project EcoFINDERS we aim at designing DNA-based barcodes for dominant taxa of amoeboid organisms, eventually to determine their diversity across soils throughout Europe and China using high-throughput sequencing. Cultivation of amoeboid organisms from several soils already indicated an enormous hidden diversity. Morphological and molecular information retrieved from these cultures indicates deep phylogenetic relationships among many amoeboid organisms and the existence of high numbers of new taxa and even genera. This information is crucial to develop effective genetic barcodes targeting broader protozoan taxa for pyrosequencing. First ecological studies investigating grazing of amoebae have confirmed strong impacts on total bacterial biomass and community composition. Further we found grazing differences even between closely related taxa suggesting niche specialisation, making it difficult to treat protozoa as a single functional black box in soil food webs

Soil Protists Diversity, Distribution and Ecological Functioning

Soil protists occupy key nodes in soil food webs due to their high abundance, fast turnover and functional importance as bacterial grazers. However, methodological drawbacks obscure the knowledge of soil protists, so that many taxa remain unknown. The structure of natural protist communities and taxa-specific ecological functions are also largely unknown. This thesis aims to increase the knowledge on soil protists using a variety of approaches. In the first part, naked amoebae being presumably the most neglected protist morphogroup were cultivated from several distinct geographical locations across Europe and from high altitude sites in Tibet. During the course of this study, 16 new species and seven new genera were discovered, representing two eukaryotic supergroups (Amoebozoa and Excavata), three classes (Discosea, Variosea and Heterolobosea), and 12 genera (Cochliopodium, Stenamoeba, Acanthamoeba, Ischnamoeba n.g., Darbyshirella n.g., Heliamoeba n.g., Arboramoeba n.g., Angulamoeba n.g., Telaepolella, Schizoplasmodiopsis, Allovahlkampfia and Pagea n.g.). This vast number of taxonomic descriptions unveils the tremendous lack of knowledge especially on soil naked amoebae. The second part aims at deciphering the diversity and community structure of soil protists using four different techniques. First, a modified cultivation technique enabled the quantification of individual morphogroups, allowing determination often up to genus level. It was shown that soil moisture not only impacts the total abundance, but also affects the community composition of soil protists. Second, established cultures of morphologically indistinguishable Acanthamoeba spp. were sequenced, enabling differentiation to strain level. Highly diverse Acanthamoeba communities were detected that differed between geographically remote soils. Third, a high-throughput amplicon sequencing approach targeting the protist phylum Cercozoa illustrated that cercozoan communities strongly differed between geographically distant soils and that community composition depended on the type of land management. Finally, a metatranscriptomic approach unveiled the entire active protist community in different soil and litter samples, uncovering a previously unknown diversity. Each of these methods confirmed that soils harbour an enormous diversity of protists and all methods detected differences in soil protist communities depending on geographic origin or treatment. Therefore it is important to understand the respective advantages and disadvantages associated with each of those methods. Further, available skills, equipment and financial resources need to be considered before applying a method to study soil protists. The third part of this thesis aims to elucidate rarely considered ecological functions performed by soil protists. Generally, soil protists are considered as bacterivores, but diverse protists facultatively consumed fungi. The small amoeba Cryptodifflugia operculata revealed another feeding mode – trapping and consuming nematodes. Metatranscriptomic data revealed high relative abundances of both functional groups in all terrestrial soil samples indicating wider ecological functions carried out by soil protists as has been suggested before

Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth

Schenk J, Geisen S, Kleinbölting N, Traunspurger W. Metabarcoding data allow for reliable biomass estimates in the most abundant animals on earth. Metabarcoding and Metagenomics. 2019;3: e46704.Microscopic organisms are the dominant and most diverse organisms on Earth. Nematodes, as part of this microscopic diversity, are by far the most abundant animals and their diversity is equally high. Molecular metabarcoding is often applied to study the diversity of microorganisms, but has yet to become the standard to determine nematode communities. As such, the information metabarcoding provides, such as in terms of species coverage, taxonomic resolution and especially if sequence reads can be linked to the abundance or biomass of nematodes in a sample, has yet to be determined. Here, we applied metabarcoding using three primer sets located within ribosomal rRNA gene regions to target assembled mock-communities consisting of 18 different nematode species that we established in 9 different compositions. We determined abundances and biomass of all species added to examine if relative sequence abundance or biomass can be linked to relative sequence reads. We found that nematode communities are not equally represented by the three different primer sets and we found that relative read abundances almost perfectly correlated positively with relative species biomass for two of the primer sets. This strong biomass-read number correlation suggests that metabarcoding reads can reveal biomass information even amongst more complex nematode communities as present in the environment and possibly can be transferred to better study other groups of organisms. This biomass-read link is of particular importance for more reliably assessing nutrient flow through food-webs, as well as adjusting biogeochemical models through user-friendly and easily obtainable metabarcoding data.</jats:p

Resilience of rhizosphere microbial predators and their prey communities after an extreme heat event

Climate change is known to disrupt above‐ground food chains when the various trophic layers respond differently to warming. However, little is known about below‐ground food chains involving microbial preys and their predators. Here, we study how climate warming‐induced heat shocks influence resistance (change immediately after a disturbance) and resilience (ability to recover back to pre‐disturbance levels) in rhizosphere microbial communities. We used three species of rhizosphere protists as microbial predators and six different rhizosphere bacterial communities as their prey. Protist species and bacterial communities were extracted from Centaurea stoebe—a range‐expanding plant species in the Northern Europe. We then examined the temporal dynamics of protists and bacterial communities after an extreme heat event for several generations with sufficient recovery periods. We hypothesized that bacterial community resistance and resilience after the extreme heat event would be higher particularly when extreme heat effects would negatively affect their predators. Our results show that prey community biomass was strongly reduced after the extreme heat event and persisted with lower biomass throughout the recovery period. Opposite to what was expected, predators showed negligible changes in their active density after the same heat event. However, abundances of the three predators varied markedly in their temporal dynamics independent of the extreme heat event. Extreme heat event further increased the inactive density of predators, whereas one of the predators showed a decline in its body size owing to extreme heat event. Bacterial community resistance and resilience after the extreme heat event were independent of predator presence, although species‐specific effects of predators on bacterial community resilience were different in the last week of recovery. Predator resilience (based on active predator density) also varied among the three predators but converged over time. Our results highlight that extreme heat events can be more detrimental to microbial prey communities than microbial predators when microbial predators can exhibit thermal acclimation (e.g. change in body size or become inactive) to overcome heat stress. Such thermal acclimation may promote predator resilience after extreme heat events

A global database of soil nematode abundance and functional group composition

As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns

Metagenomic assessment of the global distribution of bacteria and fungi

Bacteria and fungi are of uttermost importance in determining environmental and host functioning. Despite close interactions between animals, plants, their associated microbiomes, and the environment they inhabit, the distribution and role of bacteria and especially fungi across host and environments as well as the cross‐habitat determinants of their community compositions remain little investigated. Using a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and function of 25 host‐associated and environmental habitats, focusing on potential interactions between bacteria and fungi. We found that the metagenomic relative abundance ratio of bacteria‐to‐fungi is a distinctive microbial feature of habitats. Compared with fungi, the cross‐habitat distribution pattern of bacteria was more strongly driven by habitat type. Fungal diversity was depleted in host‐associated communities compared with those in the environment, particularly terrestrial habitats, whereas this diversity pattern was less pronounced for bacteria. The relative gene functional potential of bacteria or fungi reflected their diversity patterns and appeared to depend on a balance between substrate availability and biotic interactions. Alongside helping to identify hotspots and sources of microbial diversity, our study provides support for differences in assembly patterns and processes between bacterial and fungal communities across different habitats

Five Groups in the Genus Allovahlkampfia and the Description of the New Species Vahlkampfia bulbosis n.sp.

Heterolobosea is one of the major protist groups in soils. While an increasing number of soil heterolobosean species has been described, we have likely only scratched the surface of heterolobosean diversity in soils. Here, we expand this knowledge by morphologically and molecularly classifying four novel strains. One was identified as Naegleria clarki, while the remaining three strains had no identical Blast hit against GenBank and could only be reliably identified to the genus level: two strains as Allovahlkampfia spp. and one strain as Vahlkampfia sp. One Allovahlkampfia strain was most closely affiliated with Allovahlkampfia sp. Nl64 and the other strain was affiliated with ‘Solumitrus’ palustris, which is now named Allovahlkampfia palustris comb.nov. As there are only two valid species described within Allovahlkampfia, we combined all published sequences related to Allovahlkampfia and propose five new groups within this genus. The last strain was most closely related, but clearly distinct from, Vahlkampfia orchilla, based on DNA barcoding. As such, we propose this amoeba as a new species named Vahlkampfia bulbosis n.sp. Together, our study extends the described diversity of soil heteroloboseans through the description of a new Vahlkampfia species and by revising the morphologically and phylogenetically diverse genus Allovahlkampfia

Including food systems, biodiversity, nutrition and health in the Post-2020 Global Biodiversity Framework: a submission from the Alliance of Bioversity International and the International Center for Tropical Agriculture.

Tice_etal.2016.SupplementalText.pdf. Supplementary text that includes: an extended materials and methods section, details of light microscope observations, and a discussion on the justification for taxonomic reassignment of Stereomyxa ramosa ATCC® 50982™. (PDF 524 kb

Essays in Applied Economics

Essay 1 studies physician agency problems, which arise whenever physicians fail to maximize their patients\u27 preferences, given available information. These agency problems are well documented, but the magnitude of their welfare consequences for patients---the losses from suboptimal treatment choice induced by agency---are unclear. I infer patient drug preference from their compliance decisions. I begin by showing that initial prescriptions respond to physician financial incentives to control costs and to pharmaceutical detailing, but compliance does not, pointing to agency problems. I then develop and estimate a model of physician-patient interactions where physician write initial prescriptions, but patients choose whether to comply. Fully eliminating agency problems increases compliance by 6.5 percentage points, and raises patient welfare by 22\% of drug spending. Contracts that better align doctor and patient preferences can improve patient welfare, but attain only half the gains from eliminating agency completely. Although physician agency problems reduce patient welfare, eliminating them is thus likely difficult. Essay 2, co-authored with Alexander M. Gelber and Damon Jones, studies frictions in adjusting earnings to changes in the Social Security Annual Earnings Test (AET) using a panel of Social Security Administration microdata on one percent of the U.S. population from 1961 to 2006. Individuals continue to bunch at the convex kink the AET creates even when they are no longer subject to the AET, consistent with the existence of earnings adjustment frictions in the U.S. We develop a novel estimation framework and estimate in a baseline case that the earnings elasticity with respect to the implicit net-of-tax share is 0.23, and the fixed cost of adjustment is \$152.08. Essay 3 studies the impact of health expenditure risk on annuitization. Theoretical research suggests that such risk can have an ambiguous influence on the annuitization decisions of the elderly. I provide empirical evidence on this linkage, by estimating the impact of supplemental Medicare insurance (Medigap) coverage on the annuity demand of older Americans. Medigap coverage has a strong impact on annuitization: the extensive margin elasticity is 0.39, the overall elasticity of private annuity income with respect to Medigap coverage is 0.56. These results are robust to controls for health, wealth, and preferences, as well as other robustness tests. They suggest that medical expenditure risk has a large impact on underannuitization