Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly

Background: Plants have evolved intimate interactions with soil microbes for a range of beneficial functions including nutrient acquisition, pathogen resistance and stress tolerance. Further understanding of this system is a promising way to advance sustainable agriculture by exploiting the versatile benefits offered by the plant microbiome. The rhizosphere is the interface between plant and soil, and functions as the first step of plant defense and root microbiome recruitment. It features a specialized microbial community, intensive microbe-plant and microbe-microbe interactions, and complex signal communication. To decipher the rhizosphere microbiome assembly of soybean (Glycine max), we comprehensively characterized the soybean rhizosphere microbial community using 16S rRNA gene sequencing and evaluated the structuring influence from both host genotype and soil source. Results: Comparison of the soybean rhizosphere to bulk soil revealed significantly different microbiome composition, microbe-microbe interactions and metabolic capacity. Soil type and soybean genotype cooperatively modulated microbiome assembly with soil type predominantly shaping rhizosphere microbiome assembly while host genotype slightly tuned this recruitment process. The undomesticated progenitor species, Glycine soja, had higher rhizosphere diversity in both soil types tested in comparison to the domesticated soybean genotypes. Rhizobium, Novosphingobium, Phenylobacterium, Streptomyces, Nocardioides, etc. were robustly enriched in soybean rhizosphere irrespective of the soil tested. Co-occurrence network analysis revealed dominant soil type effects and genotype specific preferences for key microbe-microbe interactions. Functional prediction results demonstrated converged metabolic capacity in the soybean rhizosphere between soil types and among genotypes, with pathways related to xenobiotic degradation, plant-microbe interactions and nutrient transport being greatly enriched in the rhizosphere. Conclusion: This comprehensive comparison of the soybean microbiome between soil types and genotypes expands our understanding of rhizosphere microbe assembly in general and provides foundational information for soybean as a legume crop for this assembly process. The cooperative modulating role of the soil type and host genotype emphasizes the importance of integrated consideration of soil condition and plant genetic variability for future development and application of synthetic microbiomes. Additionally, the detection of the tuning role by soybean genotype in rhizosphere microbiome assembly provides a promising way for future breeding programs to integrate host traits participating in beneficial microbiota assembly

Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly

Background Plants have evolved intimate interactions with soil microbes for a range of beneficial functions including nutrient acquisition, pathogen resistance and stress tolerance. Further understanding of this system is a promising way to advance sustainable agriculture by exploiting the versatile benefits offered by the plant microbiome. The rhizosphere is the interface between plant and soil, and functions as the first step of plant defense and root microbiome recruitment. It features a specialized microbial community, intensive microbe-plant and microbe-microbe interactions, and complex signal communication. To decipher the rhizosphere microbiome assembly of soybean (Glycine max), we comprehensively characterized the soybean rhizosphere microbial community using 16S rRNA gene sequencing and evaluated the structuring influence from both host genotype and soil source. Results Comparison of the soybean rhizosphere to bulk soil revealed significantly different microbiome composition, microbe-microbe interactions and metabolic capacity. Soil type and soybean genotype cooperatively modulated microbiome assembly with soil type predominantly shaping rhizosphere microbiome assembly while host genotype slightly tuned this recruitment process. The undomesticated progenitor species, Glycine soja, had higher rhizosphere diversity in both soil types tested in comparison to the domesticated soybean genotypes. Rhizobium, Novosphingobium, Phenylobacterium, Streptomyces, Nocardioides,etc. were robustly enriched in soybean rhizosphere irrespective of the soil tested. Co-occurrence network analysis revealed dominant soil type effects and genotype specific preferences for key microbe-microbe interactions. Functional prediction results demonstrated converged metabolic capacity in the soybean rhizosphere between soil types and among genotypes, with pathways related to xenobiotic degradation, plant-microbe interactions and nutrient transport being greatly enriched in the rhizosphere. Conclusion This comprehensive comparison of the soybean microbiome between soil types and genotypes expands our understanding of rhizosphere microbe assembly in general and provides foundational information for soybean as a legume crop for this assembly process. The cooperative modulating role of the soil type and host genotype emphasizes the importance of integrated consideration of soil condition and plant genetic variability for future development and application of synthetic microbiomes. Additionally, the detection of the tuning role by soybean genotype in rhizosphere microbiome assembly provides a promising way for future breeding programs to integrate host traits participating in beneficial microbiota assembly

Bacterial Production of Indole Related Compounds Reveals Their Role in Association Between Duckweeds and Endophytes

Duckweed farming can be a sustainable practice for biofuel production, animal feed supplement, and wastewater treatment, although large scale production remains a challenge. Plant growth promoting bacteria (PGPB) have been shown to improve plant health by producing phytohormones such as auxin. While some of the mechanisms for plant growth promotion have been characterized in soil epiphytes, more work is necessary to understand how plants may select for bacterial endophytes that have the ability to provide an exogenous source of phytohormones such as auxin. We have isolated and characterized forty-seven potentially endophytic bacteria from surface-sterilized duckweed tissues and screened these bacterial strains for production of indole related compounds using the Salkowski colorimetric assay. Indole-3-acetic acid (IAA), indole-3-lactic acid (ILA), and indole produced by various bacterial isolates were verified by mass spectrometry. Using the Salkowski reagent, we found that 79% of the isolated bacterial strains from our collection may be capable of producing indole related compounds to various extents during in vitro growth. Of these bacteria that are producing indole related compounds, 19% are additionally producing indole. There is an apparent correlation between the type of indole related compound produced by a particular bacteria and the duckweed genus from which the bacterial strain is derived. These results suggest the possible association between different duckweed genera and endophytes that are producing distinct types of secondary metabolites. Understanding the role of indole related compounds during interaction between endophytes and the plant host may be useful to help design synthetic bacterial communities that could target specific or multiple species of duckweed in the future to sustainably enhance plant growth

Root-Associated Streptomyces Isolates Harboring melC Genes Demonstrate Enhanced Plant Colonization

Streptomycetaceae assemble into the internal, root endophytic compartment of a wide variety of plants grown in soils worldwide, suggesting their ability to survive during root microbiome assembly. A previous study found that among four nonpathogenic, root-isolated Streptomyces strains (303, 299, CL18, and 136), only 303 and 299 colonized endophytic root tissue of the majority of Arabidopsis thaliana roots when inoculated with 34 other bacterial isolates. Here we demonstrate that 303 and 299 also colonize significantly more in singly inoculated A. thaliana seedlings. The genomes of melanin-producing 303 and 299 each contain two copies of the gene encoding tyrosinase (melC2 and melD2), an enzyme necessary for melanin biosynthesis in Streptomyces. These genes were not found in the genomes of 136 or CL18. Tyrosinase activity was detected in 303 and 299 whole cell and supernatant protein extracts, suggesting functional intracellular and extracellular enzymes.. Because tyrosinase oxidizes phenolic compounds and Streptomyces colonization of A. thaliana appears to be influenced by the phenolic compound salicylic acid (SA), we measured direct sensitivity of Streptomyces isolates to the phenolic compounds catechol, ferulic acid (FA), and SA in vitro. While both 303 and 299 showed higher numbers of surviving colonies than CL18 and 136 in the presence of catechol, only 303 demonstrated a higher number of surviving colonies when isolates were challenges with FA and SA. Finally, when seedlings were singly inoculated with a collection of related plant-associated Streptomyces isolates, colonization was significantly higher in isolates possessing two tyrosinase gene copies than isolates with zero or one gene copy. Overall, we describe a connection between microbial tyrosinase activity and increased seedling colonization of nonpathogenic Streptomyces isolates in A. thaliana. We propose tyrosinase activity in Streptomyces partially protects against harmful plant-produced phenolic compounds as they transition into an endophytic lifestyle

Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol.

Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities

Overexpression of Strigolactone-Associated Genes Exerts Fine-Tuning Selection on Soybean Rhizosphere Bacterial and Fungal Microbiome

Strigolactones are a recently discovered class of carotenoid-derived plant hormones with a wide variety of functions, including acting as signaling molecules in the rhizosphere to promote arbuscular mycorrhizal fungi colonization and parasitic seed germination. To determine whether strigolactones influence the recruitment of microbes to the rhizosphere, we characterized both bacterial and fungal communities in response to the overexpression of genes involved in strigolactone biosynthesis (MAX1d) and signaling perception (D14 and MAX2a) in soybean (Glycine max). The amplicon sequencing-based results suggest that strigolactone overexpression lines had altered soybean rhizosphere bacteria composition at both the community level and individual taxa level with genera including Shinella and Bdellovibrio consistently more abundant across all three overexpression constructs. In addition, the responses of the soybean rhizosphere bacteria community differed significantly across the genes, with lines overexpressing genes involved in strigolactone biosynthesis (MAX1d) yielding a divergent bacterial community in comparison with those with altered expression of strigolactone perception genes (D14 and MAX2a). The overexpressed genes did not significantly impact the overall fungal community distribution; however, some individual taxa were altered in abundance. MAX1d and D14 overexpression lines had significantly enriched abundance of Fusarium solani. The mediating role of strigolactone biosynthesis and signaling genes on soybean rhizosphere bacterial and fungal communities confirmed strigolactone’s importance in the rhizosphere host–microbe communication and microbial community structure

Microbiota and Host Nutrition across Plant and Animal Kingdoms

Plants and animals each have evolved specialized organs dedicated to nutrient acquisition, and these harbor specific bacterial communities that extend the host's metabolic repertoire. Similar forces driving microbial community establishment in the gut and plant roots include diet/soil-type, host genotype, and immune system as well as microbe-microbe interactions. Here we show that there is no overlap of abundant bacterial taxa between the microbiotas of the mammalian gut and plant roots, whereas taxa overlap does exist between fish gut and plant root communities. A comparison of root and gut microbiota composition in multiple host species belonging to the same evolutionary lineage reveals host phylogenetic signals in both eukaryotic kingdoms. The reasons underlying striking differences in microbiota composition in independently evolved, yet functionally related, organs in plants and animals remain unclear but might include differences in start inoculum and niche-specific factors such as oxygen levels, temperature, pH, and organic carbon availability

Genomic features of bacterial adaptation to plants

Author(s): Levy, A; Salas Gonzalez, I; Mittelviefhaus, M; Clingenpeel, S; Herrera Paredes, S; Miao, J; Wang, K; Devescovi, G; Stillman, K; Monteiro, F; Rangel Alvarez, B; Lundberg, DS; Lu, TY; Lebeis, S; Jin, Z; McDonald, M; Klein, AP; Feltcher, ME; Rio, TG; Grant, SR; Doty, SL; Ley, RE; Zhao, B; Venturi, V; Pelletier, DA; Vorholt, JA; Tringe, SG; Woyke, T; Dangl, JL | Abstract: © 2017 The Author(s). Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

We report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. The approach has been applied to the genome of Mycobacterium tuberculosis (M.tb), the causative agent of one of today's most widely spread infectious diseases. The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’. The TB-drugome reveals that approximately one-third of the drugs examined have the potential to be repositioned to treat tuberculosis and that many currently unexploited M.tb receptors may be chemically druggable and could serve as novel anti-tubercular targets. Furthermore, a detailed analysis of the TB-drugome has shed new light on the controversial issues surrounding drug-target networks [1]–[3]. Indeed, our results support the idea that drug-target networks are inherently modular, and further that any observed randomness is mainly caused by biased target coverage. The TB-drugome (http://funsite.sdsc.edu/drugome/TB) has the potential to be a valuable resource in the development of safe and efficient anti-tubercular drugs. More generally the methodology may be applied to other pathogens of interest with results improving as more of their structural proteomes are determined through the continued efforts of structural biology/genomics

The potential for give and take in plant-microbiome relationships

Mutualistic microbes present in plant-associate microbial communities provide a variety of benefits for their host, including reciprocal exchange of nutrients and/or protection from biotic and abiotic environmental stresses. Plant microbiomes have remarkably robust composition in comparison to the complex and dynamic microbial environments from which they form, suggesting finely-tuned discrimination by the plant host. Here the intersection between the plant immune system and microbiomes will be explored, both as a possible means of shaping community membership and as a consequence elicited by certain colonizing microbes. Notably, the advent of massive parallel sequencing technologies allows the investigation of these beneficial microbial functions within whole community settings, so we can now ask how engagement of the immune response influences subsequent microbial interactions. Thus, we are currently poised for future work defining how the plant immune system impacts microbiomes and consequently host health, allowing us to better understand the potential of plant productivity optimization within complex microbial surroundings