Plant – microbe and microbe – microbe interactions (Eric Kemen)
The plant phyllosphere faces a broad range of harsh abiotic fluctuations such as strong radiation by sunlight, severe dryness alternating with raindrops hitting the leaves, wind and temperature fluctuations. Nevertheless, numerous microbes colonize this challenging habitat either to benefit the plant in case of symbionts, to harm the plant in case of pathogens or just as neutral residents, randomly spread by wind, water, insects or any other vector.
Numerous studies on plant-, animal- or insect-associated microorganisms have revealed a critical affect on host physiology and performance suggesting that evolution and ecology of plants, animals and insects, or any other organism, can only be understood in the context of its natural interactions with associate organisms, in particular microbes (Kemen et al. 2015). Host-associated microbial community structures are strongly affected by abiotic factors causing stochasticity, host factors, however, have drawn more and more attentions due to their stability over a range of conditions and their potential to influence the microbiome in a way that might reduce or prevent pathogen attack and manifestation (Kemen 2014).
Within the research group, we aim to answer the following questions:
- Which factors structure the leaf microbiome and how are microbial communities established and stabilized?
- How do microbes interact with their host and how are host signals transmitted to the microbial community?
- How do microbial communities evolve and which consequences does communal evolution have on gene flow?
1) Signals mediating symbioses in host-associated microbial communities (Matthew Agler)
Plant-, insect- and animal- associated microorganisms have been shown to critically affect host physiology and performance suggesting that evolution and ecology of plants, insects and animals can only be understood in a holobiont (host + associated organisms) context.
To dissect host microbe interactions, we are focusing on phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi, and oomycetes) using a systems biology approach. We have therefore evaluated multiple potential factors of microbial community control: we sampled wild A. thaliana populations (location and sampling time), performed field plantings (host genotype) and implemented successive host colonization experiments under lab conditions (both abiotic and host genotype control of pathogen colonization and direct fungal-bacteria interactions) (Agler et al. 2016).
Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe-microbe interactions, however, uncovered a network of inter-kingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial 'hubs', are strongly interconnected and have a severe effect on communities. By documenting these microbe-microbe interactions, we were able to uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on 'hub' microbes, which via microbe-microbe interactions transmit the effects to the microbial community.
The revelation that effects can cascade through communities via 'hub' microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome “keystone” pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes.
We are currently investigating microbe-microbe and microbe-host signaling mechanisms which promote the development of microbial dependencies and how these in turn affect the host.
2a) How ‘hub microbes’ control and organize their ecological niche (Jonas Ruhe)
Albugo sp., the microbial ‘hubs’ and causal agents of white rust on Brassicacea (Agler et al. 2016), have been shown under lab conditions to suppress non-host resistance and therefore enable pathogens to grow that are otherwise not able to grow. We asked how pathogens such as obligate biotroph Albugo sp. that are vitally dependent on a living host can compete in nature for limited niche space while paradoxically enabling colonization of its host plant for competitors?
Our current findings reveal that Albugo sp. are able to hide themselves from plant immune recognition or suppress recognition and therefore do not induce any defense responses. Plants showing activated immunity levels, however, are still colonize by Albugo sp. but already activated defense is not suppressed. Looking into field samples we could show that plants growing in the wild show constitutive active immune responses. We could further show that a common competitor of Albugo on A. thaliana shows reduced infection rates on plants with pre-induced immune responses (Ruhe et al. submitted).
We therefore hypothesize that the microbial ‘hub’ Albugo sp., restricts growth of competitors using the plant immune system. How specificity for certain bacteria and fungi is implemented by a microbial ‘hub’ and why and how Albugo sp. promote growth of certain microbes is subject of our current research.
2b) Hidden ‘hubs’: Endophytic fungi and their role as potential ‘hubs’ (Ronny Kellner)
Non-infected and infected seed pods of Arabis ciliata (A). The smut fungus Thecaphora thlaspeos produces thick-walled teliospores (B) that replace the seeds of its hosts.[less]
Non-infected and infected seed pods of Arabis ciliata (A). The smut fungus Thecaphora thlaspeos produces thick-walled teliospores (B) that replace the seeds of its hosts.
A natural plant microbiome is highly diverse creating a complex evolutionary landscape of plant-microbe and microbe-microbe interactions. In this CEPLAS funded project in collaboration with the group of Michael Feldbrügge, we aim to understand how the plant pathogenic fungus Thecaphora thlaspeos interacts with the microbiome of Arabidopsis thaliana and how this interaction impacts plant fitness.
T. thlaspeos is a basidiomycete that has adapted to Brassicaceae host plants. It establishes a systemic infection that lasts over months without causing macroscopic symptoms. The infection cycle finishes with the production of sexual teliospores that develop inside seed pods by replacing the seeds with spores. This particular life cycle requires balanced virulence and a high degree of adaptation to the host, and might also depend on specific interactions with the plant microbiome. We hypothesise that host adaptation also requires adaptation to the plant microbiome and that T. thlaspeos therefore acquired high connectivity within the host microbiome, becoming a microbial hub which actively shapes the community structure of Brassicaceae-associated microbes. To challenge this hypothesis, we use the model plant A. thaliana. Using deep microbial profiling, we monitor how the structure of microbial communities, isolated from wild A. thaliana populations, change in the presence/absence of T. thlaspeos over time. In addition, we co-infect A. thaliana with T. thlaspeos and the plant-biotrophic oomycete Albugo laibachii to characterise microbiome formation in the presence of the two competing plant pathogens.
This project will contribute to our understanding of how plant pathogens interfere with holobiont plant-microbe and microbe-microbe interactions, and how this interference creates niche differences between infected and non-infected plants.
3) Control of signal output in the coenocytic microbial ‘hub’ organism Albugo (Ariane Kemen)
The microbial ‘hub’ Albugo, is a coenocytic oomycete, meaning the whole organism consist of a cytoplasmic continuum containing multiple nuclei. In most cases, haustoria, the feeding and communication structures of this obligate biotroph pathogen (Kemen and Jones 2012), do not contain nuclei. It is therefore a key question, how such a coenocytic microbe differentially targets proteins to distinct compartments.
Considering three different possibilities of targeting protein deposition, namely on a transcriptional, translational or posttranslational level, we could exclude transcriptional regulations and most likely translational regulations. We are therefore looking into posttranslational signals, including compartment specific short linear motifs.
4) ‘Dark Matter’ in the phylosphere microbiome: Eukaryotic components of foliar biofilms (Alfredo Mari)
Protists, due to their ability in re-shaping the bacterial community composition by selectively grazing, are likely to hold a top-level role within biotic factors that structure the core microbiome. In this context, significant knowledge has been acquired regarding the rhizosphere, while evidences for an importance of protists in the phyllosphere are lacking in several aspects.
Protists in general are taxonomically difficult to intereprete and cover all known branches of eukaryotic life and might even form distinct branches just being discovered. We are currently analysing how protist communities can impact the plant microbiome through having an impact on microbial ‘hubs’ (Agler et al. 2015) or if protists functions as hubs on their own.
We are pursuing this goal, via 18s amplicon Illumina sequencing in order to cover as many eukaryotic branches as posiible. Our goal is to re-construct and model complex microbial communities computationally and via gnotobiotic systems experimentally in the lab.
5) Dynamics in microbial networks (Samuel Kroll)
Plants and their associated microbes face a constant change of biotic and abiotic perturbations. These are short term abiotic fluctuations such as humidity, light intensity or temperature or long term changes such as day length, seasonal influences, drought or flooding. Microbes either from soil or air are a constant inoculum that may contain pathogenic microbes or beneficial microbes that cause change to the existing plant microbiome. While static microbial networks have been under intense investigation, there is hardly any knowledge on dynamics of host associated microbial communities. This is in particular due to the broad variability in factors different microbial communities are facing and requires a broad support by metadata. Monitoring plant factors and environmental factors in combination with a deep profiling of eukaryotic and prokaryotic microbes over time in field experiments and wild sampling will give us new insights into host-microbe and microbe-microbe dynamics.
References and further reading:
Agler MT, Ruhe J, Kroll S, Morhenn C, Kim S, Weigel D, Kemen E (2016) Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biology DOI:10.1371/journal.pbio.1002352
Kemen A, Agler MT, Kemen E (2015) Host-microbe and microbe-microbe interactions in the evolution of obligate plant parasitism. New Phytologist DOI: 10.1111/nph.13284
Kemen E (2014) Microbe-microbe interactions determine oomycete and fungal host colonization. Curr Opin Plant Biol 20:75-81