Birgit Mitter

Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis.

Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.

Endophytes of Grapevine Flowers, Berries, and Seeds: Identification of Cultivable Bacteria, Comparison with Other Plant Parts, and Visualization of Niches of Colonization

Endophytic bacteria can colonize various plants and organs. However, endophytes colonizing plant reproductive organs have been rarely analyzed. In this study, endophytes colonizing flowers as well as berries and seeds of grapevine plants grown under natural conditions were investigated by cultivation as well as by fluorescence in situ hybridization. For comparison, bacteria were additionally isolated from other plant parts and the rhizosphere and characterized. Flowers, fruits, and seeds hosted various endophytic bacteria. Some taxa were specifically isolated from plant reproductive organs, whereas others were also detected in the rhizosphere, endorhiza or grape inflo/infructescence stalk at the flowering or berry harvest stage. Microscopic analysis by fluorescence in situ hybridization of resin-embedded samples confirmed the presence of the isolated taxa in plant reproductive organs and enabled us to localize them within the plant. Gammaproteobacteria (including Pseudomonas spp.) and Firmicutes (including Bacillus spp.) were visualized inside the epidermis and xylem of ovary and/or inside flower ovules. Firmicutes, mainly Bacillus spp. were additionally visualized inside berries, in the intercellular spaces of pulp cells and/or xylem of pulp, but also along some cell walls inside parts of seeds. Analysis of cultivable bacteria as well as microscopic results indicated that certain endophytic bacteria can colonize flowers, berries, or seeds. Our results also indicated that some specific taxa may not only derive from the root environment but also from other sources such as the anthosphere.

Metabolic potential of endophytic bacteria

Graphical abstract

Nitrifiers and denitrifiers respond rapidly to changed moisture and increasing temperature in a pristine forest soil

Complete cycling of mineral nitrogen (N) in soil requires the interplay of microorganisms performing nitrification and denitrification, whose activity is increasingly affected by extreme rainfall or heat brought about by climate change. In a pristine forest soil, a gradual increase in soil temperature from 5 to 25 degrees C in a range of water contents stimulated N turnover rates, and N gas emissions were determined by the soil water-filled pore space (WFPS). NO and N(2)O emissions dominated at 30% WFPS and 55% WFPS, respectively, and the step-wise temperature increase resulted in a threefold increase in the NO(3)(-) concentrations and a decrease in the NH(4)(+) concentration. At 70% WFPS, NH(4)(+) accumulated while NO(3)(-) pools declined, indicating gaseous N loss. AmoA- and nirK-gene-based analysis revealed increasing abundance of bacterial ammonia oxidizers (AOB) with increasing soil temperature and a decrease in the abundance of archaeal ammonia oxidizers (AOA) in wet soil at 25 degrees C, suggesting the sensitivity of the latter to anaerobic conditions. Denitrifier (nirK) community structure was most affected by the water content and nirK gene abundance rapidly increased in response to wet conditions until the substrate (NO(3)(-)) became limiting. Shifts in the community structure were most pronounced for nirK and most rapid for AOA, indicating dynamic populations, whereas distinct adaptation of the AOB communities required 5 weeks, suggesting higher stability.

Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants

Burkholderia phytofirmans PsJN is a naturally occurring plant-associated bacterial endophyte that effectively colonizes a wide range of plants and stimulates their growth and vitality. Here we analyze whole genomes, of PsJN and of eight other endophytic bacteria. This study illustrates that a wide spectrum of endophytic life styles exists. Although we postulate the existence of typical endophytic traits, no unique gene cluster could be exclusively linked to the endophytic lifestyle. Furthermore, our study revealed a high genetic diversity among bacterial endophytes as reflected in their genotypic and phenotypic features. B. phytofirmans PsJN is in many aspects outstanding among the selected endophytes. It has the biggest genome consisting of two chromosomes and one plasmid, well-equipped with genes for the degradation of complex organic compounds and detoxification, e.g., 24 glutathione-S-transferase (GST) genes. Furthermore, strain PsJN has a high number of cell surface signaling and secretion systems and harbors the 3-OH-PAME quorum-sensing system that coordinates the switch of free-living to the symbiotic lifestyle in the plant-pathogen R. solanacearum. The ability of B. phytofirmans PsJN to successfully colonize such a wide variety of plant species might be based on its large genome harboring a broad range of physiological functions.

COMPLETE GENOME SEQUENCE OF THE PLANT GROWTH-PROMOTING ENDOPHYTE BURKHOLDERIA PHYTOFIRMANS STRAIN PsJN

Burkholderia phytofirmans PsJN(T) is able to efficiently colonize the rhizosphere, root, and above-ground plant tissues of a wide variety of genetically unrelated plants, such as potatoes, canola, maize, and grapevines. Strain PsJN shows strong plant growth-promoting effects and was reported to enhance plant vigor and resistance to biotic and abiotic stresses. Here, we report the genome sequence of this strain, which indicates the presence of multiple traits relevant for endophytic colonization and plant growth promotion.

Advances in Elucidating Beneficial Interactions Between Plants, Soil, and Bacteria

Abstract Survival of every organism on earth depends on its interactions with other organisms. For example, animals form associations with the intestinal microflora, while plants develop symbiotic associations with neighboring plants, microflora, and microfauna. Most of the associations between plants and microorganisms are mediated by organic compounds released by the plant. The plant root system acts as a factory and exudes enormous amount of chemicals to effectively communicate with the surrounding soil organisms. Bacteria on roots and in the rhizosphere can also utilize these organic compounds as a source of nutrients and enhance their population size and metabolic activities. In return, plant-associated bacteria improve plant growth and development by different mechanisms including nitrogen fixation, provision of nutrients, and mediating resistance against pathogens. Although plant–bacterial partnerships have been found effective to enhance biomass production, their importance and relevance in agricultural systems are still underestimated. A better understanding of beneficial interactions between plant, soil, and bacteria could be exploited to improve growth and health of food and feed crops. Plant growth-promoting mechanisms of bacteria might enhance biomass production in a more sustainable manner, even on marginal land. Furthermore, plant growth-promoting and/or pollutant-degrading activities of bacteria could be exploited to improve the efficiency of phytoremediation of organic and inorganic pollutants from the soil and water or to protect the food chain by decreasing the concentrations of pollutants in food crops.

Community profiling and gene expression of fungal assimilatory nitrate reductases in agricultural soil

Although fungi contribute significantly to the microbial biomass in terrestrial ecosystems, little is known about their contribution to biogeochemical nitrogen cycles. Agricultural soils usually contain comparably high amounts of inorganic nitrogen, mainly in the form of nitrate. Many studies focused on bacterial and archaeal turnover of nitrate by nitrification, denitrification and assimilation, whereas the fungal role remained largely neglected. To enable research on the fungal contribution to the biogeochemical nitrogen cycle tools for monitoring the presence and expression of fungal assimilatory nitrate reductase genes were developed. To the ∼100 currently available fungal full-length gene sequences, another 109 partial sequences were added by amplification from individual culture isolates, representing all major orders occurring in agricultural soils. The extended database led to the discovery of new horizontal gene transfer events within the fungal kingdom. The newly developed PCR primers were used to study gene pools and gene expression of fungal nitrate reductases in agricultural soils. The availability of the extended database allowed affiliation of many sequences to known species, genera or families. Energy supply by a carbon source seems to be the major regulator of nitrate reductase gene expression for fungi in agricultural soils, which is in good agreement with the high energy demand of complete reduction of nitrate to ammonium.

Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development

&NA; The rhizosphere hosts a rich microflora supporting plant nutrition and health. We examined bacterial rhizosphere microbiota of Solanum tuberosum grown in its center of origin, the Central Andean Highlands, at different vegetation stages and sites at altitudes ranging from 3245 to 4070 m.a.s.l., differing in soil characteristics, climate and the agricultural practices by 454 sequence analysis of 16S rRNA genes. We observed that the taxonomic composition of bacteria repeatedly occurring at particular stages of plant development was almost unaffected by highly diverse environmental conditions. A detailed statistical analysis on the operational taxonomic unit (OTU) level, representing bacterial species, revealed a complex community structure of the rhizosphere. We identified an opportunistic microbiome which comprises OTUs that occur randomly or under specific environmental conditions. In contrast, core microbiome members were found at all sites. The ‘stable’ component of the core microbiome consisted of few ubiquitous OTUs that were continuously abundant in all samples and vegetation stages, whereas the ‘dynamic’ component comprised OTUs that were enriched at specific vegetation stages.

Editorial special issue: soil, plants and endophytes

Despite the inception of the endophyte research dates back to the nineteenth century, studies on this topic have only recently bloomed, producing a fast-growing body of literature (Compant et al. 2012; Hardoim et al. 2015; Saikkonen et al. 2016). Several definitions of endophyte have been furthermore proposed; while some have been criticized, others have been suggested to better define this particular lifestyle. We currently describe endophytes as any microbe that can be isolated from asymptomatic plant tissue (Chanway 1995; Wilson 1995; Hardoim et al. 2015). This definition includes neutral, commensal and/or beneficial microorganisms as well as dormant saprobes and pathogens during their latent phase of their life cycle. These microorganisms engage an intimate association within their host plants, establishing a microbial community in the plant endosphere and could be found in various plant parts (Hardoim et al. 2015). Although endophytes have been previously extensively studied, the interplay between different endophytes and their hosts is however yet poorly understood. The mechanisms underlying these interactions, the driving forces determining specific microbial community assemblages found in different plant organs, the influence that a range of factors (e.g. environmental, genetic, phenological, etc.) have on shaping the endophytic microbiomes, or how to exploit/harness the benefits these inner microbial consortia provide to their hosts are just a few exciting matters currently under study. Nevertheless, novel and powerful methodological approaches already available must be implemented to obtain a better picture of this complex and fascinating ecological niche (i.e. the host plant and its inner microbiome). Despite descriptive and comprehensive research is done, important gaps in our knowledge are evident, and thorough insights are still needed to fully understand these particular plant-microbe interactions. We need, for instance, to move beyond cataloguing microorganism identities in different plant organs/tissues, or from plants growing in different soils and/or under diverse environmental conditions. Indeed, providing more hypothesis-driven studies will help answering Plant Soil (2016) 405:1–11 DOI 10.1007/s11104-016-2927-9