1. You Are What You Can Find to Eat: Bacterial Metabolism in the Rhizosphere

Nicola Holden

Metabolism is the underpinning force that sustains life. Within the rhizosphere it is a cyclic process, with substrates flowing between different compartments of the complete soil-plant-microbe system. The physiochemical and structural environment of the rhizosphere is shaped by a combination of plant genotype and soil type, both of which strongly impact the microbial community structure. External influences such as seasonality, the degree of water saturation and anthropomorphic inputs also play a role. Together these factors influence the flux of metabolites through the rhizosphere community, which in turn impacts on plant growth, development and disease. In this review, the focus is on metabolism within the bacterial population of the rhizosphere, since this group covers every type of plant-microbe interaction: from obligately symbiotic to destructively pathogenic, and includes those have little or no direct impact on plant hosts. The focus of the review is on metabolic functions that occur in the rhizosphere either during bacteria-plant interactions or bacteria-bacteria interactions and mainly covers heterotrophic metabolism of organic substrates. As such, many of the autotrophic (and phototrophic) reactions of inorganic compounds are not included.

2. Role of Plasmids in Plant-Bacteria Interactions

Jasper Schierstaedt, Nina Bziuk, Nemanja Kuzmanović, Khald Blau, Kornelia Smalla and Sven Jechalke

Plants are colonized by diverse microorganisms, which may positively or negatively influence the plant fitness. The positive impact includes nutrient acquisition, enhancement of resistance to biotic and abiotic stresses, both important factors for plant growth and survival, while plant pathogenic bacteria can cause diseases. Plant pathogens are adapted to negate or evade plant defense mechanisms, e.g. by the injection of effector proteins into the host cells or by avoiding the recognition by the host. Plasmids play an important role in the rapid bacterial adaptation to stresses and changing environmental conditions. In the plant environment, plasmids can further provide a selective advantage for the host bacteria, e.g. by carrying genes encoding metabolic pathways, metal and antibiotic resistances, or pathogenicity-related genes. However, we are only beginning to understand the role of mobile genetic elements and horizontal gene transfer for plant-associated bacteria. In this review, we aim to provide a short update on what is known about plasmids and horizontal gene transfer of plant associated bacteria and their role in plant-bacteria interactions. Furthermore, we discuss tools available to study the plant-associated mobilome, its transferability, and its bacterial hosts.

3. Plant Immunity: The MTI-ETI Model and Beyond

Hanna Alhoraibi, Jean Bigeard, Naganand Rayapuram, Jean Colcombet and Heribert Hirt

In plant-microbe interactions, a pathogenic microbe initially has to overcome preformed and subsequently induced plant defenses. One of the initial host-induced defense responses is microbe-associated molecular pattern (MAMP)-triggered immunity (MTI). Successful pathogens attenuate MTI by delivering various effectors that result in effector-triggered susceptibility and disease. However, some host plants developed mechanisms to detect effectors and can trigger effector-triggered immunity (ETI), thereby abrogating pathogen infection and propagation. Despite the wide acceptance of the above concepts, more and more accumulating evidence suggests that the distinction between MAMPs and effectors and MTI and ETI is often not given. This review discusses the complexity of MTI and ETI signaling networks and elaborates the current state of the art of defining MAMPs versus effectors and MTI versus ETI, but also discusses new findings that challenge the current dichotomy of these concepts.

4. Endofungal Bacteria Increase Fitness of their Host Fungi and Impact their Association with Crop Plants

Ibrahim Alabid, Stefanie P. Glaeser and Karl-Heinz Kogel

Endofungal bacteria are bacterial symbionts of fungi that exist within fungal hyphae and spores. There is increasing evidence that these bacteria, alone or in combination with their fungal hosts play a critical role in tripartite symbioses with plants, where they may contribute to plant growth and disease resistance to microbial pathogens. As the frequency of bacteria in fungi is commonly very low, breakthroughs in technology such as molecular taxonomy and laser scanning microscopy were required to establish the functional contribution of these bacteria in complex symbioses. Yet, the overall biological significance of endofungal bacteria is largely unknown and further progress in understanding is hampered by a very few biological systems where endofungal bacteria have been described mechanistically. We review here the current knowledge on endobacteria (EB) and their role in different types of fungal symbioses with plants. We show that various attempts to cure fungal cells from endobacteria failed, further suggesting that they play a crucial role in the symbiosis. Moreover, isolation of some of the endobacteria from their fungal hosts allowed confirming their autonomous beneficial activity such as plant growth promotion and resistance-inducing activity. The review addresses the potential agricultural significance of endofungal bacteria and their role in supporting sustainable agriculture by promoting plant growth, improving plant resistance, and decreasing yield loss caused by many microbial pathogens.

5. Plant-Nematode Interactions Assisted by Microbes in the Rhizosphere

Olivera Topalović and Holger Heuer

Plant health is strongly influenced by the interactions between parasites/pathogens and beneficial microorganisms. In this chapter we will summarize the up-to date knowledge on soil suppressiveness as a biological tool against phytonematodes and explore the nature of monoculture versus crop rotation in this regard. Since nematodes are successfully antagonized by different microbiological agents, we highlighted this phenomenon with respect to the most important antagonists, and a nature of these interactions. The focus is on the hyperparasitic microbes of phytonematodes such as Pasteuria sp. and egg parasites. Furthermore, we comprised the studies on the defence system expressions in plants triggered by nematode-associated microbes. The attachment of bacteria and fungi to phytonematodes and putative effects of the attachment on the induced systemic resistance in plants are discussed. Finally, our chapter is rounded up with the importance of incorporating the knowledge on plant-nematode-microbe interactions in the integrated pest management.

6. Apple Replant Disease: Causes and Mitigation Strategies   Free download

Traud Winkelmann, Kornelia Smalla, Wulf Amelung, Gerhard Baab, Gisela Grunewaldt-Stöcker, Xorla Kanfra, Rainer Meyhöfer, Stefanie Reim, Michaela Schmitz, Doris Vetterlein, Andreas Wrede, Sebastian Zühlke, Jürgen Grunewaldt, Stefan Weiß and Michael Schloter

After replanting apple (Malus domestica Borkh.) on the same site severe growth suppressions, and a decline in yield and fruit quality are observed in all apple producing areas worldwide. The causes of this complex phenomenon, called apple replant disease (ARD), are only poorly understood up to now which is in part due to inconsistencies in terms and methodologies. Therefore we suggest the following definition for ARD: ARD describes a harmfully disturbed physiological and morphological reaction of apple plants to soils that faced alterations in their (micro-) biome due to the previous apple cultures. The underlying interactions likely have multiple causes that extend beyond common analytical tools in microbial ecology. They are influenced by soil properties, faunal vectors, and trophic cascades, with genotype-specific effects on plant secondary metabolism, particularly phytoalexin biosynthesis. Yet, emerging tools allow to unravel the soil and rhizosphere (micro-) biome, to characterize alterations of habitat quality, and to decipher the plant reactions. Thereby, deep insights into the reactions taking place at the root rhizosphere interface will be gained. Counteractions are suggested, taking into account that culture management should emphasize on improving soil microbial and faunal diversity as well as habitat quality rather than focus on soil disinfection.