Microbes and nutrients
We study the processes affecting microbial biomass and the feedback on nutrient content and availability in soils
Organic P mineralization is an enzymatic process mediated by phosphatases that contribute to P recycling in soil. Phosphatases are secreted by soil microorganisms such as bacteria. However, little is known about the prevalence, the identity and diversity of organic P-mineralizing bacteria in soil.
In this project, we designed genetic tools that target three phosphatase-encoding genes, phoD, phoX, acpA. These allow us to study the composition of the bacterial community carrying and expressing these genes using 454- and Illumina sequencing technologies. In particular, we aim to evaluate the effect of environment, soil types and properties, climates and fertilization managements on the genes. We also quantify phoD gene and gene expression response to a substrate addition using qPCR.
Supervisors: Emmanuel Frossard (ETH Zurich), Else Bünemann (ETH Zurich)
Collaboration with: Michael Kertesz (Univ. of Sidney, Australia); Klaus Jarosch (ETH Zurich)
Funding source: Swiss National Foundation (SNF)
Full Project title: Community assembly of arbuscular mycorrhizal fungal root symbionts of a uniform population of bioassay plants after reciprocal topsoil mixing at eight grassland sites
Background: Community assembly can happen in response to stochastic (dispersal) and deterministic (niche/trait-based) processes, and in the later case it can be restricted by either community-extrinsic abiotic and biotic environmental filtering, or community-intrinsic factors, such as lacking functional differences and hence competitive exclusion or pathogen pressure. Knowing the basic ecological drivers of community assembly in arbuscular mycorrhizal fungi (AMF) is important to rationalize the management of resident assemblages as well as choosing foreign fungal inoculants. Arbuscuar mycorrhizal fungi are promoted for agriculture and restoration ecology, because these ubiquitous and abundant root symbionts have abilities to assist plants in mineral nutrient uptake from soil and/or to alleviate abiotic and biotic stress in plants. Further, identifying the main drivers of AMF community assembly will enable predictions on how the accelerated and much increased propagule dispersal and environmental change by modern human activities will influence future functioning of natural and agro-ecosystems.
Objectives and approach: To determine the relative importance of origin (pre-adaptation to soil pH), dispersal limitation (biogeography), and competition by resident AMF (functional similarity) as limiting factors in successful establishment of foreign AMF. To do so, we adopted a crude whole-community, instead of only single-inoculant approach, which offers a greater chance to observe putative immigration events and alterations to the structuring of naturally occurring AMF assemblages. Transferring soil samples and thus entire communities of soil biota reflects, moreover, human-mediated accidental, or natural dispersal of AMF propagules much closer – something that may happen during soil works, agricultural activities, or by global trade, soil and wind erosion, or animal migration. We transferred topsoil samples reciprocally among eight different sites, four in the north and four in the south of the Swiss Alps and two each on either slightly acidic or alkaline grassland soils in each of those biogeographic regions (--> in total 56 experimental and 8 control plots; seven and one at each site, respectively). The symbiotically established AMF in the roots of a genetically uniform population of bioassay plants were analyzed on phylogenetic patterns of community assembly (phylogenetic clustering or overdispersion) and community composition and structure, using long, phylogenetically highly resolving nuclear ribosomal DNA sequences and a polymorphic protein-encoding gene marker.
Collaboration with: Manuela Krüger (Institute of Botany, Academy of the Czech Republic), Emilia Pelc (MSc, ETH Zurich).
Funding Source: Swiss National Science Foundation (SNSF), project nr 127522
Full title: Zinc biofortification of wheat through organic matter management in sustainable agriculture (ZOMM)
Background: Zinc deficiency in human populations is recognized as a global nutritional problem. To address this issue, biofortification strategies aim at increasing the bioavailable micronutrient density of the edible parts of plants. Apart from plant breeding, biofortification research has focused mainly on mineral fertilizer application. Recent studies have highlighted the potential of organic matter inputs to biofortify cereal grains with zinc.
Objectives and approach: The ZOMM project aims at developing agronomic measures to increase the zinc concentration of wheat grains. The effects of organic fertilizers on soil zinc phytoavailability and wheat zinc uptake are studied under field trial conditions in Switzerland and in India. Moreover, we are looking at bacterial processes controlling soil zinc solubilization, and how much these processes are affected by organic matter inputs.
Supervisors: Emmanuel Frossard (ETH Zurich), Cécile Thonar (Research Institute of Organic Agriculture: FiBL, Frick)
Collaboration with: Rainer Schulin (Institute of Terrestrial Ecosystems, Soil Protection, ETH Zurich)
Funding source: Mercator Research Program of ETH’s World Food System Center.
Cowpea (Vigna unguiculata L. Walp) is the third most important grain legume in Kenya. In the drier parts of Coast (Kilifi) and Eastern (Mbeere) Kenya it is the most important legume. Challenges to production in both regions include drought, pests and diseases and more abundantly low soil fertility (mainly N and P deficiency). Biological nitrogen fixation (BNF) is among the technologies that can enable increases in cowpea grain yield and improve soil fertility.
This project aims to improve cowpea yield for small holder farmers in two different agro-ecologies (Kilifi and Mbeere), through inoculation with Bradyrhizobia.
- To isolate and characterize indigenous Bradyrhizobia forming symbiosis with cowpea from two different agro-ecologies in Kenya.
- To identify competitive and effective rhizobial strains capable of providing sufficient nitrogen derived from BNF for cowpea cultivated in the 2 different agro-ecologies in Kenya.
- To evaluate under farmers fields competitive and symbiotically effective rhizobia strains capable of being used as inoculants for cowpea.
This project via the use of advanced technologies in microbiology and molecular biology to study the cowpea-rhizobia symbiosis and trials on BNF optimization will give insight on how to increase yields to small holder cowpea farmers through use of effective rhizobia inoculants.
Supervisors: Emmanuel Frossard (ETHZ), Cécile Thonar (FiBL), Monika Messmer (FiBL), Bernard Vanlauwe (IITA)
Collaborations: Research Institute for Organic Agriculture (FiBL), International Institute of Tropical Agriculture (IITA)
Funded by: ETHZ North-South Centre through the Sawiris scholarship programme
Institut für Agrarwissenschaften
Samuel Mathu Ndungu
Background: Anthropogenic environmental change and species dispersal are rampant. Arbuscular mycorrhizal fungi (AMF) are omnipresent in soils and assist the majority of plants in phosphorus (P) uptake and by alleviating a multitude of abiotic and biotic stresses. Therefore, future primary production of most natural ecosystems and agro-ecosystems is thought to be closely linked to mycorrhizal functioning, which will depend on how well AMF deal with new abiotic and biotic habitat conditions after perturbation and how they react to immigrating AMF.
Objectives and approach: To determine how the fluxes of carbon (C) from, and nitrogen (N), and P transfers to a plant shift when AMF of different sites intermingle and natural AMF communities are challenged by altered soil physicochemical conditions. Radio- (33P) and stable isotope (15N) tracing will be used to estimate fungal hypha-mediated N and P acquisition from a small root-exclusion and soil nutrient-labeling compartment. 13C-CO2 pulse-labeling and tracing to AMF-specific phospho- and neutral lipid fatty acids will serve together with microscopic measurements on AMF root colonization as indicators of fungal abundance and C drain. Community sequencing will show how different all the re-assembled symbiotic AMF assemblages are and reveal the identities of the AMF, which may have been involved in 33P acquisition, translocation and transfer to the plant.
Supervisor: Hannes Gamper (ETH Zurich)
Collaboration with: Jan Jansa (Laboratory of Fungal Biology, Academy of the Czech Republic)
Funding source: Scientific Exchange Program Between the New Member States and Switzerland, Sciex-NMS-ch, project nr 14.057