Endophytic bacteria in toxic South African plants: identification, phylogeny and possible involvement in gousiekte

Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes

BACKGROUND

Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in the African plant genera Empogona and Tricalysia and, if present, to establish their identity.

METHODS

Total DNA was extracted from the leaves of four species of the Coffeeae tribe (Empogona congesta, Tricalysia hensii, T. lasiodelphys, and T. semidecidua) and sequenced. Bacterial reads were filtered out and assembled. Phylogenetic analysis of the endophytes was used to reveal their identity and their relationship with known symbionts.

RESULTS

All four species have non-nodulated leaf endophytes, which are identified as Caballeronia. The endophytes are distinct from each other but related to other nodulated and non-nodulated endophytes. An apparent phylogenetic or geographic pattern appears to be absent in endophytes or host plants. Caballeronia endophytes are present in the leaves of Empogona and Tricalysia, two genera not previously implicated in leaf symbiosis. This interaction is likely to be more widespread, and future discoveries are inevitable.

Cyclitol metabolism is a central feature of Burkholderia leaf symbionts

The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.

Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctata

Root-microbe interaction and its specialized root nodule structures and functions are well studied. In contrast, leaf nodules harboring microbial endophytes in special glandular leaf structures have only recently gained increased interest as plant-microbe phyllosphere interactions. Here, we applied a comprehensive metabolomics platform in combination with natural product isolation and characterization to dissect leaf and leaf nodule metabolism and functions in Ardisia crenata (Primulaceae) and Psychotria punctata (Rubiaceae). The results indicate that abiotic stress resilience plays an important part within the leaf nodule symbiosis of both species. Both species showed metabolic signatures of enhanced nitrogen assimilation/dissimilation pattern and increased polyamine levels in nodules compared to leaf lamina tissue potentially involved in senescence processes and photosynthesis. Multiple links to cytokinin and REDOX-active pathways were found. Our results further demonstrate that secondary metabolite production by endophytes is a key feature of this symbiotic system. Multiple anhydromuropeptides (AhMP) and their derivatives were identified as highly characteristic biomarkers for nodulation within both species. A novel epicatechin derivative was structurally elucidated with NMR and shown to be enriched within the leaf nodules of A. crenata. This enrichment within nodulated tissues was also observed for catechin and other flavonoids indicating that flavonoid metabolism may play an important role for leaf nodule symbiosis of A. crenata. In contrast, pavettamine was only detected in P. punctata and showed no nodule specific enrichment but a developmental effect. Further natural products were detected, including three putative unknown depsipeptide structures in A. crenata leaf nodules. The analysis presents a first metabolomics reference data set for the intimate interaction of microbes and plants in leaf nodules, reveals novel metabolic processes of plant-microbe interaction as well as the potential of natural product discovery in these systems.

Deep learning approaches for natural product discovery from plant endophytic microbiomes

Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely hidden through regulatory silencing of biosynthetic genes. The recent explosion of powerful interdisciplinary approaches, including multi-omics methods to address multi-trophic interactions and artificial intelligence-based computational approaches to infer distribution of function, together present a paradigm shift in high-throughput approaches to natural product discovery from plant-associated microbes. Arguably, the key to characterizing and harnessing this biochemical capacity depends on a novel, systematic approach to characterize the triggers that turn on secondary metabolite biosynthesis through molecular or genetic signals from the host plant, members of the rich 'in planta' community, or from the environment. This review explores breakthrough approaches for natural product discovery from plant microbiomes, emphasizing the promise of deep learning as a tool for endophyte bioprospecting, endophyte biochemical novelty prediction, and endophyte regulatory control. It concludes with a proposed pipeline to harness global databases (genomic, metabolomic, regulomic, and chemical) to uncover and unsilence desirable natural products.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s40793-021-00375-0.

Detection of Burkholderia in the seeds of Psychotria punctata (Rubiaceae) - Microscopic evidence for vertical transmission in the leaf nodule symbiosis

Background and aims

The bacterial leaf nodule symbiosis is a close interaction between endophytes and their plant hosts, mainly within the coffee family. The interaction between Rubiaceae species and Burkholderia bacteria is unique due to its obligate nature, high specificity, and predominantly vertical transmission of the endophytes to the next generation of host plants. This vertical transmission is intriguing since it is the basis for the uniqueness of the symbiosis. However, unequivocal evidence of the location of the endophytes in the seeds is lacking. The aim of this paper is therefore to demonstrate the presence of the host specific endophyte in the seeds of Psychotria punctata and confirm its precise location. In addition, the suggested location of the endophyte in other parts of the host plant is investigated.

Methods

To identify and locate the endophyte in Psychotria punctata, a two-level approach was adopted using both a molecular screening method and fluorescent in situ hybridisation microscopy.

Key results

The endophytes, molecularly identified as Candidatus Burkholderia kirkii, were detected in the leaves, vegetative and flower buds, anthers, gynoecium, embryos, and young twigs. In addition, they were in situ localised in leaves, flowers and shoot apical meristems, and, for the first time, in between the cotyledons of the embryos.

Conclusions

Both independent techniques detected the host specific endophyte in close proximity to the shoot apical meristem of the embryo, which confirms for the first time the exact location of the endophytes in the seeds. This study provides reliable proof that the endophytes are maintained throughout the growth and development of the host plant and are transmitted vertically to the offspring.

Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae

Partial gyrB gene sequence analysis of 17 isolates from human and environmental sources revealed 13 clusters of strains and identified them as Burkholderia glathei clade (BGC) bacteria. The taxonomic status of these clusters was examined by whole-genome sequence analysis, determination of the G+C content, whole-cell fatty acid analysis and biochemical characterization. The whole-genome sequence-based phylogeny was assessed using the Genome Blast Distance Phylogeny (GBDP) method and an extended multilocus sequence analysis (MLSA) approach. The results demonstrated that these 17 BGC isolates represented 13 novel Burkholderia species that could be distinguished by both genotypic and phenotypic characteristics. BGC strains exhibited a broad metabolic versatility and developed beneficial, symbiotic, and pathogenic interactions with different hosts. Our data also confirmed that there is no phylogenetic subdivision in the genus Burkholderia that distinguishes beneficial from pathogenic strains. We therefore propose to formally classify the 13 novel BGC Burkholderia species as Burkholderia arvi sp. nov. (type strain LMG 29317^T = CCUG 68412^T), Burkholderia hypogeia sp. nov. (type strain LMG 29322^T = CCUG 68407^T), Burkholderia ptereochthonis sp. nov. (type strain LMG 29326^T = CCUG 68403^T), Burkholderia glebae sp. nov. (type strain LMG 29325^T = CCUG 68404^T), Burkholderia pedi sp. nov. (type strain LMG 29323^T = CCUG 68406^T), Burkholderia arationis sp. nov. (type strain LMG 29324^T = CCUG 68405^T), Burkholderia fortuita sp. nov. (type strain LMG 29320^T = CCUG 68409^T), Burkholderia temeraria sp. nov. (type strain LMG 29319^T = CCUG 68410^T), Burkholderia calidae sp. nov. (type strain LMG 29321^T = CCUG 68408^T), Burkholderia concitans sp. nov. (type strain LMG 29315^T = CCUG 68414^T), Burkholderia turbans sp. nov. (type strain LMG 29316^T = CCUG 68413^T), Burkholderia catudaia sp. nov. (type strain LMG 29318^T = CCUG 68411^T) and Burkholderia peredens sp. nov. (type strain LMG 29314^T = CCUG 68415^T). Furthermore, we present emended descriptions of the species Burkholderia sordidicola, Burkholderia zhejiangensis and Burkholderia grimmiae. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and gyrB gene sequences determined in this study are LT158612-LT158624 and LT158625-LT158641, respectively.

Burkholderia: an update on taxonomy and biotechnological potential as antibiotic producers

Burkholderia is an incredibly diverse and versatile Gram-negative genus, within which over 80 species have been formally named and multiple other genotypic groups likely represent new species. Phylogenetic analysis based on the 16S rRNA gene sequence and core genome ribosomal multilocus sequence typing analysis indicates the presence of at least three major clades within the genus. Biotechnologically, Burkholderia are well-known for their bioremediation and biopesticidal properties. Within this review, we explore the ability of Burkholderia to synthesise a wide range of antimicrobial compounds ranging from historically characterised antifungals to recently described antibacterial antibiotics with activity against multiresistant clinical pathogens. The production of multiple Burkholderia antibiotics is controlled by quorum sensing and examples of quorum sensing pathways found across the genus are discussed. The capacity for antibiotic biosynthesis and secondary metabolism encoded within Burkholderia genomes is also evaluated. Overall, Burkholderia demonstrate significant biotechnological potential as a source of novel antibiotics and bioactive secondary metabolites.

Insecticide applications to soil contribute to the development of Burkholderia mediating insecticide resistance in stinkbugs

Some soil Burkholderia strains are capable of degrading the organophosphorus insecticide, fenitrothion, and establish symbiosis with stinkbugs, making the host insects fenitrothion-resistant. However, the ecology of the symbiotic degrading Burkholderia adapting to fenitrothion in the free-living environment is unknown. We hypothesized that fenitrothion applications affect the dynamics of fenitrothion-degrading Burkholderia, thereby controlling the transmission of symbiotic degrading Burkholderia from the soil to stinkbugs. We investigated changes in the density and diversity of culturable Burkholderia (i.e. symbiotic and nonsymbiotic fenitrothion degraders and nondegraders) in fenitrothion-treated soil using microcosms. During the incubation with five applications of pesticide, the density of the degraders increased from less than the detection limit to around 10(6)/g of soil. The number of dominant species among the degraders declined with the increasing density of degraders; eventually, one species predominated. This process can be explained according to the competitive exclusion principle using V(max) and K(m) values for fenitrothion metabolism by the degraders. We performed a phylogenetic analysis of representative strains isolated from the microcosms and evaluated their ability to establish symbiosis with the stinkbug Riptortus pedestris. The strains that established symbiosis with R. pedestris were assigned to a cluster including symbionts commonly isolated from stinkbugs. The strains outside the cluster could not necessarily associate with the host. The degraders in the cluster predominated during the initial phase of degrader dynamics in the soil. Therefore, only a few applications of fenitrothion could allow symbiotic degraders to associate with their hosts and may cause the emergence of symbiont-mediated insecticide resistance.

Metabolic potential of endophytic bacteria

The bacterial endophytic microbiome promotes plant growth and health and beneficial effects are in many cases mediated and characterized by metabolic interactions. Recent advances have been made in regard to metabolite production by plant microsymbionts showing that they may produce a range of different types of metabolites. These substances play a role in defense and competition, but may also be needed for specific interaction and communication with the plant host. Furthermore, few examples of bilateral metabolite production are known and endophytes may modulate plant metabolite synthesis as well. We have just started to understand such metabolic interactions between plants and endophytes, however, further research is needed to more efficiently make use of beneficial plant-microbe interactions and to reduce pathogen infestation as well as to reveal novel bioactive substances of commercial interest.

Distribution of endophytic bacteria in Alopecurus aequalis Sobol and Oxalis corniculata L. from soils contaminated by polycyclic aromatic hydrocarbons

The distributions of endophytic bacteria in Alopecurus aequalis Sobol and Oxalis corniculata L. grown in soils contaminated with different levels of polycyclic aromatic hydrocarbons (PAHs) were investigated with polymerase chain reaction followed by denaturing gradient gel electrophoresis technology (PCR-DGGE) and cultivation methods. Twelve types of PAHs, at concentrations varying from 0.16 to 180 mg·kg⁻¹, were observed in the roots and shoots of the two plants. The total PAH concentrations in Alopecurus aequalis Sobol obtained from three different PAH-contaminated stations were 184, 197, and 304 mg·kg⁻¹, and the total PAH concentrations in Oxalis corniculata L. were 251, 346, and 600 mg·kg⁻¹, respectively. The PCR-DGGE results showed that the endophytic bacterial communities in the roots and shoots of the two plants were quite different, although most bacteria belonged to Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. A total of 68 endophytic bacterial strains were isolated from different tissues of the two plants and classified into three phyla: Firmicutes, Proteobacteria and Bacteroidetes. In both plants, Bacillus spp. and Pseudomonas spp. were the dominant cultivable populations. With an increase in the PAH pollution level, the diversity and distribution of endophytic bacteria in the two plants changed correspondingly, and the number of cultivable endophytic bacterial strains decreased rapidly. Testing of the isolated endophytic bacteria for tolerance to each type of PAH showed that most isolates could grow well on Luria-Bertani media in the presence of different PAHs, and some isolates were able to grow rapidly on a mineral salt medium with a single PAH as the sole carbon and energy source, indicating that these strains may have the potential to degrade PAHs in plants. This research provides the first insight into the characteristics of endophytic bacterial populations under different PAH pollution levels and provides a species resource for the isolation of PAH-degrading endophytic bacteria.

Phylogenetic lineages in Vanguerieae (Rubiaceae) associated with Burkholderia bacteria in sub-Saharan Africa

PREMISE OF THE STUDY

It is well known that mutualistic bacteria can provide substantial benefits to their host plants. However, 'how,' 'why,' and the possible applications of such an interaction are only second to the questions 'who is involved?', and 'where does it occur?'. In the coffee family (Rubiaceae), certain species closely interact with endophytic leaf bacteria that are freely distributed among the mesophyll cells. This type of interaction was recently discovered in South Africa. Our aim is to document the bacterial diversity associated with Rubiaceae ('who') and to establish the geographic range of the interaction ('where').

METHODS

Representatives of the Vanguerieae tribe in Rubiaceae were investigated for the presence of endophytes with special emphasis on the distributional range of the plant-bacteria association by collecting specimens from different African regions.

KEY RESULTS

The interaction is found in five genera and is restricted to three major host lineages. The endophytic bacteria belong to the genus Burkholderia and are part of the plant-associated beneficial and environmental group. Some endophytes are similar to B. caledonica, B. graminis, B. phenoliruptrix or B. phytofirmans, while others are classified in OTUs that show no similarity with any previously described Burkholderia species of bacteria.

CONCLUSIONS

The association is not obligate from the bacterial point of view and is considered a loose and recent interaction, which is demonstrated by the fact that there is no evidence for coevolution. The geographical distribution of the association is restricted by the distributional range of the host plants covering the whole of sub-Saharan Africa.

Diversity of endophytic bacteria in medicinally important Nepenthes species

BACKGROUND

Nepenthes species are used in traditional medicines to treat various health ailments. However, we do not know which types of endophytic bacteria (EB) are associated with Nepenthes spp.

OBJECTIVE

The objective of this study was to isolate and to identify EB associated with Nepenthes spp.

MATERIALS AND METHODS

Surface-sterilized leaf and stem tissues from nine Nepenthes spp. collected from Peninsular Malaysia were used to isolate EB. Isolates were identified using the polymerase chain reaction-amplified 16S ribosomal DNA (rDNA) sequence similarity based method.

RESULTS

Cultivable, 96 isolates were analyzed; and the 16S rDNA sequences analysis suggest that diverse bacterial species are associated with Nepenthes spp. Majority (55.2%) of the isolates were from Bacillus genus, and Bacillus cereus was the most dominant (14.6%) among isolates.

CONCLUSION

Nepenthes spp. do harbor a wide array of cultivable endophytic bacteria.

Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil

Analysis of partial gyrB gene sequences revealed six taxa in a group of 17 Burkholderia glathei-like isolates which were further examined by (GTG)5-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA-DNA hybridizations, determination of the DNA G+C content, whole-cell fatty acid analysis and an analysis of cell and colony morphology and more than 180 biochemical characteristics. The results demonstrated that one taxon consisting of three human clinical isolates represented Burkholderia zhejiangensis, a recently described methyl-parathion-degrading bacterium isolated from a wastewater-treatment system in China. The remaining taxa represented five novel species isolated from soil or rhizosphere soil samples, and could be distinguished by both genotypic and phenotypic characteristics. We therefore propose to formally classify these bacteria as Burkholderia humi sp. nov. (type strain, LMG 22934(T) = CCUG 63059(T)), Burkholderia choica sp. nov. (type strain, LMG 22940(T) = CCUG 63063(T)), Burkholderia telluris sp. nov. (type strain, LMG 22936(T) = CCUG 63060(T)), Burkholderia udeis sp. nov. (type strain, LMG 27134(T) = CCUG 63061(T)) and Burkholderia terrestris sp. nov. (type strain, LMG 22937(T) = CCUG 63062(T)).

Toxin constraint explains diet choice, survival and population dynamics in a molluscivore shorebird

Recent insights suggest that predators should include (mildly) toxic prey when non-toxic food is scarce. However, the assumption that toxic prey is energetically as profitable as non-toxic prey misses the possibility that non-toxic prey have other ways to avoid being eaten, such as the formation of an indigestible armature. In that case, predators face a trade-off between avoiding toxins and minimizing indigestible ballast intake. Here, we report on the trophic interactions between a shorebird (red knot, Calidris canutus canutus) and its two main bivalve prey, one being mildly toxic but easily digestible, and the other being non-toxic but harder to digest. A novel toxin-based optimal diet model is developed and tested against an existing one that ignores toxin constraints on the basis of data on prey abundance, diet choice, local survival and numbers of red knots at Banc d'Arguin (Mauritania) over 8 years. Observed diet and annual survival rates closely fit the predictions of the toxin-based model, with survival and population size being highest in years when the non-toxic prey is abundant. In the 6 of 8 years when the non-toxic prey is not abundant enough to satisfy the energy requirements, red knots must rely on the toxic alternative.

Distribution of the cardiotoxin pavettamine in the coffee family (Rubiaceae) and its significance for gousiekte, a fatal poisoning of ruminants

Gousiekte, a cardiac syndrome of ruminants in southern Africa, is caused by the ingestion of plants containing the polyamine pavettamine. All the six known gousiekte-causing plants are members of the Rubiaceae or coffee family and house endosymbiotic Burkholderia bacteria in their leaves. It was therefore hypothesized that these bacteria could be involved in the production of the toxin. The pavettamine level in the leaves of 82 taxa from 14 genera was determined. Included in the analyses were various nodulated and non-nodulated members of the Rubiaceae. This led to the discovery of other pavettamine producing Rubiaceae, namely Psychotria kirkii and Psychotria viridiflora. Our analysis showed that many plant species containing bacterial nodules in their leaves do not produce pavettamine. It is consequently unlikely that the endosymbiont alone can be accredited for the synthesis of the toxin. Until now the inconsistent toxicity of the gousiekte-causing plants have hindered studies that aimed at a better understanding of the disease. In vitro dedifferentiated plant cell cultures are a useful tool for the study of molecular processes. Plant callus cultures were obtained from pavettamine-positive species. Mass spectrometric analysis shows that these calli do not produce pavettamine but can produce common plant polyamines.

Symbiotic ß-proteobacteria beyond legumes: Burkholderia in Rubiaceae

Symbiotic ß-proteobacteria not only occur in root nodules of legumes but are also found in leaves of certain Rubiaceae. The discovery of bacteria in plants formerly not implicated in endosymbiosis suggests a wider occurrence of plant-microbe interactions. Several ß-proteobacteria of the genus Burkholderia are detected in close association with tropical plants. This interaction has occurred three times independently, which suggest a recent and open plant-bacteria association. The presence or absence of Burkholderia endophytes is consistent on genus level and therefore implies a predictive value for the discovery of bacteria. Only a single Burkholderia species is found in association with a given plant species. However, the endophyte species are promiscuous and can be found in association with several plant species. Most of the endophytes are part of the plant-associated beneficial and environmental group, but others are closely related to B. glathei. This soil bacteria, together with related nodulating and non-nodulating endophytes, is therefore transferred to a newly defined and larger PBE group within the genus Burkholderia.

Isolation, characterization, and insecticidal activity of an endophyte of drunken horse grass, Achnatherum inebrians

Abstract Endophytic microorganisms reside within plant tissues and have often been found to promote plant growth. In this study, endophytic microorganisms were isolated from the roots, stems, leaves, and seeds of healthy drunken horse grass, Achnatherum inebrians (Hance) Keng (Poales: Poaceae), through the use of a grinding separation method and identified by a dual approach of morphological and physiological observation and 16S rRNA gene-based (for bacteria) and internal transcribed sequence-based (for fungi) molecular identification. The endophytes were then inoculated into liquid media for fermentation, and their crude extracts were employed for insecticidal activity tests using slide disc immersion and nebulization methods. A total of 89 bacteria species, which were classified into eight genera, Bacillus, Pseudomonas, Actinomyces, Corynebacterium, Acinetobacter, Sphingomonas, Paenibacillus, and Phyllobacterium, and two fungi, Claviceps and Chaetomium, were isolated. Of these species, isolates Streptomyces albus (Rossi-Doria) Waksman and Henrici (Actinomycetales: Streptomycetaceae) (GA) and Claviceps purpurea (Fr.) Tul. (Hypocreales: Clavicipitaceae) (PF-2) were shown to produce mortality rates of more than 90% in the cotton aphid, Aphis gossypii Glover (Hemiptera: Aphididae), after first and second screenings. The isolates PF-2 and GA associated with A. inebrians had significant insecticidal activities towards A. gossypii Glover (Hemiptera: Aphididae) and may provide a new biological resource for exploring a new microbial insecticide.

Production of toxic pavettamine and pavettamine conjugates in the gousiekte-causing Fadogia homblei plant and its relation to the bacterial endosymbiont

Plant poisoning of livestock is responsible for considerable economic losses in southern Africa. Six plant species of the Rubiaceae family are known to cause gousiekte, a cardiac syndrome of ruminants induced by ingestion of the toxic compound pavettamine. Progress in understanding the etiology of this disease is largely hampered by the variable toxicity of the plants and the absence of a quantification method for pavettamine. The pavettamine concentration in leaf samples of Fadogia homblei, a known gousiekte causing plant, was analyzed by mass-spectrometry. In the most apical leaf pair, the highest concentration of pavettamine was detected. Distal leaves contained progressively less pavettamine. Besides a significant amount of free pavettamine, most pavettamine was found to occur in a conjugated form. To which molecules the pavettamine is conjugated remains unknown as is the function of conjugated pavettamine in the development of gousiekte. All know gousiekte-causing plants contain symbiotic bacteria in their leaves; it was hypothesized that these bacteria might be involved in the production of pavettamine. However, analysis of in vitro cultures of the F. homblei endosymbiont revealed no production of pavettamine. Pavettamine is therefore not produced by the bacteria alone. It is either the product of the interaction with the plant or solely produced by the host.

Screening for leaf-associated endophytes in the genus Psychotria (Rubiaceae)

Burkholderia endophytes were identified within the leaves of non-nodulated members of the genus Psychotria. In contrast to leaf-nodulated Psychotria species, which are known to accommodate their endosymbionts into specialized endosymbiont-housing structures, non-nodulated species lack bacterial leaf nodules and harbor endosymbionts intercellularly between mesophyll cells. Based on molecular data (rps16, trnG, and trnLF), the phylogenetic reconstruction of the host plants revealed a separate origin of leaf-nodulated and non-nodulated Psychotria species. Despite a distinct phylogenetic position of the two host clades, the endophytes of the non-nodulated plants were not placed into a single monophyletic group but were found to be closely related to the leaf-nodulated endosymbionts. The observation of genetically similar endophytes in both nodulated and non-nodulated Psychotria lineages suggests that the host plant is playing a crucial role in the induction of leaf nodule formation. Moreover, the concentration of endosymbionts into specialized leaf nodules may be considered as a more derived evolutionary adaptation of the host plant, serving as an interface structure to facilitate metabolic exchange between plant and endosymbiont.