Plant-associated microbial communities in indoor environments

Funding organisation, Project no.: FWF and federal state government of Styria, P-29285-BBL

Project leader: Gabriele Berg; Coworker: Alexander Mahnert; Wisnu Wicaksono

Duration: 2016 – 2019 (3 years)

Abstract: Despite the fact that the majority of our lifetime is spent in indoor environments, our knowledge of the factors that shape the diversity of their microbial communities is limited. Indoor plants have been linked to health benefits but little is known about their associated microbiome and its impact. The objective of our project is to analyze the phyllosphere microbiome of house plants to understand their structure and function for both, the host plant and for the whole indoor microbiome. To study the microbial diversity, we will take advantage of a well-controlled and -maintained environment at the Graz Botanical Garden greenhouse. Here, the impact of biotic and abiotic factors on the plant microbiome and their internal interaction can be simultaneously investigated. The microbiome of selected plant species grown under these controlled as well as under more typical conditions will be compared via 16S rRNA/ITS amplicon libraries, correlation and network analysis and complementary microscopy (FISH-CLSM). To study the function of phyllosphere communities, we will analyze model metagenomes from three plants in detail. In parallel, isolates, their properties and interactions with model organisms will be studied. Our hypothesis that plant-associated microorganisms can improve plant health and quality of indoor microbiomes will be proven by a targeted selection of microbes and their transfer to sterilized plants and cleaned indoor environments. In addition, selected microbes will be labeled and investigated with fluorescence dyes to reveal their physiological properties and interaction with other microbes and the host organism. Results obtained by all methods will be comparatively evaluated. Stable transfer (structural and functional) of selected microbes onto plants and indoor environments in different setups will be assessed additionally on gene expression level (metatranscriptomics). This study should provide new insights into the phyllosphere as a hypothetically diverse and beneficial source for the indoor microbiome.

Partners: Thomas Rattei, Christine Moissl-Eichinger, Kevin Francesconi, Christian Berg, Martin Grube, Robert Krause, Christoph Högenauer, Kasthuri J. Venkateswaran, Parag A. Vaishampayan, Martin Täubel, Miia Pitkäranta

Publications/Highlights:  Berg G, Mahnert A, Moissl-Eichinger C. (2014). Front Microbiol 5:1–5;

Mahnert A, Moissl-Eichinger C, Berg G. (2015). Front Microbiol 6:1–11;
Ortega, R. A., Mahnert, A., Berg, C., Müller, H. & Berg, G. (2016). FEMS Microbiol. Ecol. 92.

Mahnert A, Ortega R A, Berg C, Grube M, Berg G (2018). Front. Microbiol 9:2343
Mahnert A, Haratani M, Schmuck M, Berg G (2018). Front. Microbiol 9:2985

Mahnert A, Moissl-Eichinger C, Zojer M, Bogumil D, Mizrahi I, Rattei T, Martinez JL, Berg G (2019). Nature Communications 10:968.


Bridging metabolome and microbiome diversification

Funding organization, project no.: Austrian Science Fund FWF, T 847 (Hertha Firnberg Programme)

Project leader: Martina Köberl

Duration: 2016/10/01 – 2019/09/30 (3 years)

Abstract: The plant microbiome has been extensively studied in recent years, whereby a variety of plant-microbe interactions that are essential for growth and health of the host plant were discovered. However, the majority of these interactions and functions, such as the impact of the microbiome on the metabolome, are poorly understood. Plants use metabolites to shape and direct their associated microbial communities; however, there is some evidence that, vice versa, the plant-associated microorganisms influence the metabolic fingerprint of their host plant, leading to different metabolic phenotypes. The overall objective of the project is to experimentally investigate the possibility to direct the plant’s chemical profile via plant-associated microorganisms. Studies concerning correlations between microbial communities and plant metabolites will be conducted on two Asteraceae medicinal plants, the German chamomile (Matricaria chamomilla L.) and the pot marigold (Calendula officinalis L.). These plant species were selected as suitable model plants for these studies because of their rich secondary metabolism with particularly high levels of flavonoids, sesquiterpenes, and triterpenes, their known diversification in chemical profiles, and their cultivation and medicinal utilization all over the world. An interconnected experimental design enables (i) to analyze the effect of the soil microbiome on the plant metabolome, (ii) the development of a model for predicting metabolite production, (iii) targeted inoculation experiments to verify correlations, and (iv) to elucidate the functional linkage of the rhizosphere microbiome by a metagenomic study. A multi-phasic approach exploiting novel “meta-omics” technologies will be used to deeply analyze plants grown in natural ecosystems as well as in specifically developed in vitro systems. Promising correlations will be evaluated in detail under strictly controlled conditions. We aim to elucidate the linkage of the plant microbiome and metabolome in order to improve the plants’ usability as bioresource for compounds with therapeutic and biotechnological relevancy.

Partners: Pacific Northwest National Laboratory (PNNL), Environmental Molecular Sciences Laboratory (EMSL), Richland, WA, USA

Publications/Highlights: TU Graz News: Firnberg scholarships for scientists at TU Graz


The algae microbiome for sustainable success in the biotechnological perspective

Funding organisation: FFG-ACIB

Duration: 01.10.16 - 31.03.18

Project leader: Gabriele Berg; Tomislav Cernava Coworker: Lisa Krug

Partners: Company Partner: BDI - BioLife Science GmbH
                     Scientific Partner:  Technische Universität Graz


Abstract: This project aims to characterize the microbiome associated with the green algae H. pluvialis used in the biotechnological production of astaxanthin. Microbiome composition and structure is of significance for bioproduction performance and as such, identification of optimal microbiome composition and subsequent development of stable optimal microbial inocula with desired characteristics can be used to maximize microalgal bioprocesses.

The apple microbiome: research and complex analysis of health benefits

Funding organisation: Sparkling Science - bmwfw

Duration: 01.08.2017 - 31.07.2019

Project leader: Gabriele Berg Coworker: Birgit Wassermann

Partners: Biotenzz Gesellschaft für Biotechnology mbH, Roombiotic GmbH, Sekem Energy GmbH

Partner schools: Akademisches Gymnasium Graz, Modellschule Graz, Sacré Coeur Graz





The investigation of foodstuff microbiomes has been designated as number one research focus in international microbiome research. This was supported by current research achievements, demonstrating an impact of fresh produce-associated microbiota on human health. However, not only human health but also the plant itself benefits and suffers from intimate relationships to its inherent microbiome. In cooperation with Sparkling Science1, a bmwfw2-sponsored program introducing engaged adolescents to academic research, the present project aims to uncover the microbiome of the apple, which has not been researched so far. Together with students from three Graz schools, microorganism community diversity amongst healthy, diseased, organically and commercially grown apples will be investigated and compared with one another, to draw conclusion on potential health benefits of the apple consumption. Due to the lack of biological alternatives to chemical pesticides, organic farming facilities are suffering from repercussions of plant pathogens like apple scarp and storage rot. The project focuses on modeling sustainable und ecologically sound methods to combat those apple diseases und develop products to optimize the apple storage systems of industrial project partners.


Neueste Forschungsergebnisse konnten aufzeigen, dass Mikroorganismen die mit roh verzehrtem Gemüse und Früchten assoziiert sind, einen Einfluss auf die menschliche Gesundheit haben. Die Erforschung der Mikrobiome von Nahrungsmitteln wurde diesbezüglich als Forschungsschwerpunkt Nummer eins in der internationalen Mikrobiomforschung klassifiziert. Nicht nur der Mensch als Konsument, sondern auch die Vitalität der Pflanze wird grundlegend durch ihr inhärentes Mikrobiom beeinflusst. In Zusammenarbeit mit Sparkling Science1, einem bmwfw2-geförderten Programm das Jugendlichen einen Einblick in universitäre Forschung gewährt, wird das Mikrobiom des Apfels untersucht, über dessen Zusammensetzung bisher noch wenig bekannt ist. Gemeinsam mit Schülern aus drei Grazer Schulen, werden die Mikrobiome von gesunden und kranken, sowie biologisch und konventionell gezüchteten Äpfeln miteinander verglichen. Welchen potentiellen Einfluss der Apfel dabei auf die menschliche Gesundheit haben kann, soll aufgezeigt werden. Die Bekämpfung von Apfelpathogenen wie Apfelschorf und Lagerfäule ist bislang nur durch den Einsatz von Pestiziden möglich, was massive ökonomische Probleme für die biologische Landwirtschaft mit sich bringt. Ein weiterer Forschungsschwerpunkt des Projekts ist es daher, nachhaltige und ökologisch sinnvolle Möglichkeiten zu modellieren, um diese Apfelkrankheiten einzudämmen sowie gemeinsam mit industriellen Projektpartnern Apfellagerungsbedingungen zu optimieren.

1 Sparkling Science:
2 Bundesministerium für Wissenschaft, Forschung und Wirtschaft:








Main Project Leader
Univ.-Prof Dr.rer.nat. Gabriele Berg


Plant-associated microbial communities in indoor environments
Dr. techn. Alexander Mahnert


Bridging metabolome and microbiome diversification
Dr.rer.nat. Martina Köberl


The algae microbiome for sustainable success in the biotechnological perspective
Dr.techn. Tomislav Cernava


The apple microbiome: research and complex analysis of health benefits
Birgit Wassermann, M.Sc.