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Manuel Kleiner

Associate 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: 06/01/22 - 5/31/27
Amount: $200,000.00
Funding Agencies: USDA - Agriculture Research Service (ARS)

In maize and many other plants, F1 hybrids perform better than their inbred parent lines - a phenomenon known as heterosis or hybrid vigor. The causes of heterosis have been investigated for over a century but are still poorly understood. Our preliminary data suggest a novel mechanism in which growth in sterile conditions reduces or eliminates heterosis for root size- a pattern that we term Microbe-Dependent Heterosis (MDH). Potential explanations for MDH include (1) superior resistance of hybrids to weakly pathogenic soil biota, or (2) immune over-reactions by inbred maize in response to innocuous soil biota. The proposed experiments will help to distinguish between these possibilities by exploring the genetic, ecological, and molecular causes of MDH. First, we will test a wide range of individual microbial strainsas well as naturally-occurring soil biota for the ability to induce MDH. Second, we will map the genetic architecture of MDH to identify genomic loci whose effect on heterosis is dependent on the microbial environment, and test for a genetic correlation with loci underlying resistance to a variety of pathogenic microbes in the field. Third, we will investigate the molecular mechanisms of MDH by measuring gene and protein expression of both hybrid and inbred plants as well as the microbes inside their roots. The results of these experiments will clarify the microbial features and patterns of plant immune activity that result in MDH. This work will be led by Drs. Maggie Wagner (U. Kansas), Peter Balint-Kurti (USDA-ARS), and Manuel Kleiner (North Carolina State U.)

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: 09/01/22 - 8/31/25
Amount: $454,934.00
Funding Agencies: US Dept. of Energy (DOE)

Some soil carbon persists, sometimes for a long time, but we don???t know why. An important precursor to soil organic matter (SOM) is microbial necromass, composed of biomolecules that vary in nutrient (N, P) content. We hypothesize that nutrient demand, driven by community structure and bioavailability, explains why some microbial communities are associated with more persistent SOM. We will study microbiome effects on necromass decomposition across nutrient and mineral gradients using sequencing, metaproteomics, and stable isotope analysis. By applying our results to a CNP process model, we will develop a predictive understanding of necromass decomposition and persistence in upland soils.

Date: 08/01/20 - 5/31/25
Amount: $1,944,834.00
Funding Agencies: National Institutes of Health (NIH)

In this research I will use cutting-edge, high-resolution mass spectrometry methods to investigate interactions between diet, the host and the microbiota.

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