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Manuel Kleiner

Assistant Professor

Microbiomes and Complex Microbial Communities Cluster

Thomas Hall 4510B


Microbial communities are ubiquitous in all environments on Earth that support life, and they play crucial roles in global biogeochemical cycles, plant and animal health, and biotechnological processes. However, most microbial species from a given habitat cannot be cultured and thus cannot be experimentally characterized in the laboratory. Therefore, to study environmental microbes we rely on so-called cultivation-independent methods that allow us to study microorganisms directly in their environment.

We study the metabolism, physiology, and evolutionary ecology of microbial symbioses and uncultured microorganisms. To this end we develop and use cultivation-independent approaches such as metagenomics, metaproteomics, and metabolomics, as well as more targeted approaches such as enzyme assays, single-cell imaging methods, and stable isotope-based experiments. We combine the study of uncultured microorganisms with genetic, molecular, and biochemical studies on cultivable microorganisms to gain an in-depth understanding of specific metabolic pathways and physiological strategies.

The current projects focus on:

  • Factors governing energy efficiency of metabolism in free-living and symbiotic bacteria, looking specifically at a novel CO2 fixation pathway
  • The role of horizontal gene transfer in the metabolic evolution of bacterial symbionts
  • Development of cutting-edge methods for microbial community analyses focusing on metagenomics and high-end mass spectrometry based metaproteomics

For a more detailed description of our projects, visit the Kleiner Lab website.

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Ph.D. Marine Microbiology Max Planck Institute for Marine Microbiology, Germany 2012

Diploma Biology University of Greifswald, Germany 2008

Area(s) of Expertise

Microbial physiology and metabolism, bacteria-animal symbiosis , metagenomics and metaproteomics, environmental microbiology, marine microbiology, and renewable resources


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Date: 10/01/19 - 12/31/25
Amount: $1,862,709.00
Funding Agencies: Novo Nordisk Foundation

Our Vision is to provide a science-based platform for new agricultural practices enabling plant producers to manage their production ecosystems in a resource-efficient way with limited environmental footprint based on an in-depth understanding of key ecological functions in the soilplant interphase (rhizosphere). Our Motivation is to address the major research gaps in deciphering the complexity of microbemicrobe and microbe-plant interactions in the rhizosphere, and thereby provide new conceptual understanding on how these interactions influence plant performance. This motivation is timely due to recent developments in methodology and will enable us to provide the knowledge-base for unlocking the potential of the soil rhizobiota (microbes living on in the rhizosphere) as the key to development of sustainable and resilient plant production systems. Our Focus is to identify and quantify main determinants of microbial interactions and networks in the rhizosphere leading toward a resilient ecological unit, and thus reveal the importance and potential of microbial interactions and functions in the rhizosphere. The proposed research will take advantage of a multi-faceted, integrative and cross-disciplinary approach, which is fundamental for 1) achieving a deep understanding of the chemical and biological factors that control microbe-microbe and plantmicrobe interactions and functions under natural soil conditions, 2) establishing improved predictive models for microbial interactions in soil and 3) exploiting the microbial potential in plant-soil production systems for the benefit of plant growth and resilience. INTERACT will decode these important, yet often transient, microbial interactions in the complex soil matrix, in relation to soil biogeochemical status, water stress as well as pathogen attack, and the impact of these interactions on plant performance. We will challenge the currently accepted view among scientists that plants are the primary drivers for rhizobiome assembly. Hence, we will determine whether in fact soil microbes, largely through chemical communication and signaling, play a greater role in rhizobiome development and function than has been previously appreciated. INTERACT will provide critical insight into the rhizosphere ecology, as a basis for actively influencing the assembly of effective rhizosphere communities to support plant health and productivity, either through biotechnological or agronomic approaches.

Date: 10/01/19 - 9/30/25
Amount: $837,933.00
Funding Agencies: Novo Nordisk Foundation

One of the grand challenges facing humanity is to secure sufficient and healthy food for the increasing world population. This requires maintaining sustainable cultivation of crop plants under changing climate conditions. Plant roots and soil microbes have been associated since the emergence of plants on land. Nevertheless, the mechanisms that coevolved to control and regulate microbiota associations with healthy plants are largely unexplored. The photosynthetically active green leaf tissues supply assimilated carbon to roots for development and also to feed its associated microbes. To maintain balanced growth, plants have to integrate this underground demand and regulate the rate of photosynthetic CO2 fixation, and sugar allocation needs to be coordinated between root and shoot. Research on plants and their naturally associated microorganisms is therefore in a prime position to provide new perspectives and concepts for understanding plant function, plant performance and plant growth under limited input conditions with a reduced environmental footprint and could also define breeding targets and develop microbial interventions. InRoot aims to: 1. Disentangle the effects of climate and soil type from the impact of root-microbe interactions through transplantation experiments and exploit natural variation to identify the plant genetic components responsible for adaptation to the local microbiota. 2. Identify key bacterial taxa governing the establishment of host-driven microbial networks in the rhizosphere by analysing the microbe-microbe and microbe-host interactions established in tailored synthetic communities (SynComs) with direct consequences on host performance. 3. Define the plant genetic components that control infection of plant roots by ubiquitous and host-specific endophytes using advanced genetic screens and new methods for quantifying root cellular responses to microbes 4. Understand molecular mechanisms integrating root-microbe interactions into whole-plant physiology by investigating systemic physiological responses induced by SynComs using whole plant phenotyping. 5. Predict plant performance as a function of plant and microbiota genotypes by building multiscale models based on genotype, phenotype, and mechanistic data thereby providing knowledge for application. InRoot perspective: Provide knowledge and tools for science-based development of new crop varieties and associated microbial interventions that will improve productivity, reduce the need for fertilizers and pesticides, and alleviate negative environmental impact.

Date: 01/01/22 - 12/31/24
Amount: $849,000.00
Funding Agencies: US Dept. of Agriculture - National Institute of Food and Agriculture (USDA NIFA)

Our Overall Goal is to identify genes and proteins that are causal to functional interactions within the microbiome and between the microbiome and the plant that impact drought tolerance in maize. We propose to develop new experimental resources and metaproteomics methods for studying plant microbiome function, and use them to identify molecular mechanisms underlying plant-microbiome interactions that confer improved drought resilience in maize. First, we will isolate and sequence a collection of root-associated bacteria from across a natural precipitation gradient in Kansas, and screen them for beneficial effects on drought-stressed maize. Second, we will develop and optimize metaproteomics methods for the study of plant-associated microbiomes. Finally, we will deploy these new resources in a tractable, fully controlled, simplified maize-microbiome experimental system to investigate causal relationships between plant and microbial genes, proteins, and enhanced drought resistance in maize. The resulting research tools and mechanistic knowledge would bring us closer to the goal of using beneficial microbes to protect maize yields under water-limited conditions without further depleting our natural freshwater resources. This project thus specifically addresses the Program Area Priority “Agricultural Microbiomes in Plant Systems and Natural Resources”, A1402.

Date: 10/01/19 - 9/30/24
Amount: $638,751.00
Funding Agencies: National Science Foundation (NSF)

When seeking solutions to today's elevated atmospheric CO2 levels, it is critical that we include data from the past, because atmospheric CO2 concentrations have fluctuated throughout Earth history. In fact, CO2 levels have been consistently higher in the past—often significantly higher, at times perhaps as much as 6x pre-industrial values. The biological response of life on Earth to these global conditions, from their onset to their cessation, is recorded in the rock record. Intriguingly, Konservat Lagerstätte (e.g., sedimentary deposits that preserve fossils in extraordinary detail) occur more frequently in the distant past (i.e., deep time) than in more recent depositional environments. Could these be linked? We hypothesize that ancient microorganisms responded to pre-Cenozoic high atmospheric CO2 by sequestering carbon through very rapid precipitation of carbonate minerals in terrestrial, as well as marine settings. This increase in microbial precipitation of carbonates, sometimes as concretions, created conditions favorable to the stabilization of normally labile tissues and the exclusion of exogenous, degradative influences. These factors very likely contributed to exceptional preservation of fossil remains, including persistence of non-biomineralized (i.e., “soft”) tissues. Although microbes have been invoked as agents of preservation as well as destruction, because they act to “seal” sediments surrounding bone to form a relatively closed system, to date, the effect of contemporaneous atmospheric CO2 levels on microbial carbonate precipitation, and its implications for preservation, have not been explored. The convergence research we propose would enable us to design and implement empirical studies that directly test this idea, and characterize the microbial influence in depositional environments producing exceptionally preserved fossils. Thus, we ask the following: 1) Did the elevated CO2 in Mesozoic atmospheres play a role in microbially mediated exceptional preservation? 2) If this can be demonstrated through actualistic experiments and fossil studies, could this mechanism of fossil preservation also shed light on microbial sequestration of atmospheric CO2 in terrestrial environments? 3) Furthermore, can this understanding of microbially mediated CO2 sequestration be harnessed for development of robust, scalable carbon-capture systems? To test these hypotheses, we propose a two-pronged approach. We will conduct empirical tests that involve growing known microbially induced carbonate precipitation (MCIP) strains, as well as microbial communities from relevant environments, under conditions of Mesozoic proxy atmospheres. We will compare the rate and degree of precipitation in organisms grown in enriched CO2 with those of the same strains grown in ambient atmospheres, to characterize the effects of elevated CO2 on precipitation rates. Then, we will examine: 1) the sediments surrounding exceptionally preserved fossils, 2) the composition of concretions that contain fossil material, 3) the morphological and molecular preservation of the fossils themselves, and 4) biomarkers associated with microbes in these fossil materials, using a combination of chemical and molecular techniques. Our interdisciplinary team will work synergistically to examine the role of microbes in both fostering and impeding exceptional preservation, the relationship of exceptional preservation to elevated atmospheric CO2, and potential microbial pathways that can be exploited to accomplish terrestrial carbon sequestration. Such pathways are rarely considered in the dialogue regarding potential solutions to anthropogenic carbon release, but may present a viable, cost-effective mitigation measure

Date: 05/15/21 - 5/14/24
Amount: $570,602.00
Funding Agencies: US Dept. of Agriculture - National Institute of Food and Agriculture (USDA NIFA)

Research has shown that microbial communities substantively impact plant health and resilience to both abiotic and biotic environmental stresses. To address rising global food security concerns, it is critical to gain a more comprehensive and integrated understanding of plant-microbe systems. Current technologies generate large quantities of data, but there is an urgent need to develop a more comprehensive systems understanding of the metabolic pathways that lead to observed results. Our central hypothesis is that microbial interactions and metabolite exchanges with key microbial species drive plant health (maize) and maintain robustness in the face of stress. Our goal in addressing this hypothesis is to elucidate the interactions and metabolite exchanges taking place by integrating theoretical modeling with experimental data to build a comprehensive metabolic model of the maize rhizosphere. We will employ a systems approach to guide our inquiries into plant-microbe interactions. Genome-scale metabolic models will be constructed, and metabolic pathways will be analyzed with elementary flux mode analysis, a pathway analysis technique which allows a comprehensive, unbiased examination of all possible metabolic pathways in a network. Multiple layers of experimental data will be incorporated as constraints to restrict the community model to a physiologically relevant solution space. Expected outcomes from the proposed project include the development of an experimentally validated community-level metabolic model to describe plant-microbe interactions and the effect of nutrient limitation. This will improve our understanding of maize response to nutrient stress conditions and the role that microbial communities play. Moreover, this project will provide new knowledge about the interplay between different levels of cellular expression by collecting extensive corresponding data sets on a single system to better understand the patterns between different levels of cellular expression and activity. Ultimately, the methods and concepts will be translatable to other crop systems and will contribute to development of microbial strategies for improving growth and managing susceptibility to pests and pathogens.

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