Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm

Chemical ecology of symbioses in cycads, an ancient plant lineage

Cycads are an ancient lineage of gymnosperms that maintain a plethora of symbiotic associations from across the tree of life. They have myriad morphological, structural, physiological, chemical, and behavioral adaptations that position them as a unique system to study the evolution, ecology, and mechanism of symbiosis. To this end, we have provided an overview of cycad symbiosis biology covering insects, bacteria, and fungi, and discuss the most recent advances in the underlying chemical ecology of these associations.

Leaf Endophytes Relationship with Host Metabolome Expression in Tropical Gymnosperms

Plant-microbe interactions play a pivotal role in shaping host fitness, especially concerning chemical defense mechanisms. In cycads, establishing direct correlations between specific endophytic microbes and the synthesis of highly toxic defensive phytochemicals has been challenging. Our research delves into the intricate relationship between plant-microbe associations and the variation of secondary metabolite production in two closely related Zamia species that grow in distinct habitats; terrestrial and epiphytic. Employing an integrated approach, we combined microbial metabarcoding, which characterize the leaf endophytic bacterial and fungal communities, with untargeted metabolomics to test if the relative abundances of specific microbial taxa in these two Zamia species were associated with different metabolome profiles. The two species studied shared approximately 90% of the metabolites spanning diverse biosynthetic pathways: alkaloids, amino acids, carbohydrates, fatty acids, polyketides, shikimates, phenylpropanoids, and terpenoids. Co-occurrence networks revealed positive associations among metabolites from different pathways, underscoring the complexity of their interactions. Our integrated analysis demonstrated to some degree that the intraspecific variation in metabolome profiles of the two host species was associated with the abundance of bacterial orders Acidobacteriales and Frankiales, as well as the fungal endophytes belonging to the orders Chaetothyriales, Glomerellales, Heliotiales, Hypocreales, and Sordariales. We further associate individual metabolic similarity with four specific fungal endophyte members of the core microbiota, but no specific bacterial taxa associations were identified. This study represents a pioneering investigation to characterize leaf endophytes and their association with metabolomes in tropical gymnosperms, laying the groundwork for deeper inquiries into this complex domain.

Insight into saffron associated microbiota from different origins and explore the endophytes for enhancement of bioactive compounds

Crocus sativus L. is a perennial crop for its valuable active compounds. Plant-associated microbes impact on the quality and efficacy of medicinal herbs by promoting bioactive components accumulation. However, how microbes influence the accumulation of bioactive components in saffron have not been well studied. Here, the microbiome in C. sativus derived from 3 core production areas were deciphered by 16S rDNA sequencing and the relationship between endophytes and bioactive ingredients were further investigated. The main results are as follows: (1) Both Comamonadaceae and Burkholderiaceae were positively correlated with the content of bioactive components in the stigmas. (2) The synthesis of crocin was positively correlated with Xanthomonadaceae, negatively correlated with Lachnospiraceae and Prevotellaceae. Therefore, further investigation is required to determine whether Xanthomonadaceae plays an unknown function in the synthesis of crocin. These findings provide guidelines for disentangling the function of endophytes in the production of bioactive ingredients and thus for microbe-mediated breeding.

Emerging nitrogen-fixing cyanobacteria for sustainable cotton cultivation

Amid growing environmental concerns and the imperative for sustainable agricultural practices, this study examines the potential of nitrogen-fixing cyanobacteria as biofertilizers, particularly in cotton cultivation. The reliance on synthetic nitrogen fertilizers (SNFs), prevalent in modern agriculture, poses significant environmental challenges, including greenhouse gas emissions and water system contamination. This research aims to shift this paradigm by exploring the capacity of cyanobacteria as a natural and sustainable alternative. Utilizing advanced metabarcoding methods to analyze the 16S rRNA gene, we conducted a comprehensive assessment of soil bacterial communities within cotton fields. This study focused on evaluating the diversity, structure, taxonomic composition, and potential functional characteristics of these communities. Emphasis was placed on the isolation of native N2-fixing cyanobacteria strains rom cotton soils, and their subsequent effects on cotton growth. Results from our study demonstrate significant plant growth-promoting (PGP) activities, measured as N2 fixation, production of Phytohormones, Fe solubilization and biofertilization potential of five isolated cyanobacterial strains, underscoring their efficacy in cotton. These findings suggest a viable pathway for replacing chemical-synthetic nitrogen fertilizers with natural, organic alternatives. The reintegration of these beneficial species into agricultural ecosystems can enhance crop growth while fostering a balanced microbial environment, thus contributing to the broader goals of global sustainable agriculture.

Dictyophora indusiata and Bacillus aryabhattai improve sugarcane yield by endogenously associating with the root and regulating flavonoid metabolism

Introduction

Endophytes play a significant role in regulating plant root development and facilitating nutrient solubilization and transportation. This association could improve plant growth. The present study has uncovered a distinct phenotype, which we refer to as "white root", arising from the intricate interactions between endophytic fungi and bacteria with the roots in a sugarcane and bamboo fungus (Dictyophora indusiata) intercropping system.

Methods

We investigated the mechanisms underlying the formation of this "white root" phenotype and its impact on sugarcane yield and metabolism by metabarcoding and metabolome analysis.

Results and Discussion

Initial analysis revealed that intercropping with D. indusiata increased sugarcane yield by enhancing the number of viable tillers compared with bagasse and no input control. Metabarcoding based on second-generation and third-generation sequencing indicated that D. indusiate and Bacillus aryabhattai dominates the fungal and bacterial composition in the "white root" phenotype of sugarcane root. The coexistence of D. indusiata and B. aryabhattai as endophytes induced plant growth-promoting metabolites in the sugarcane root system, such as lysoPC 18:1 and dihydrobenzofuran, probably contributing to increased sugarcane yield. Furthermore, the association also enhanced the metabolism of compounds, such as naringenin-7-O-glucoside (Prunin), naringenin-7-O-neohesperidoside (Naringin)*, hesperetin-7-O-neohesperidoside (Neohesperidin), epicatechin, and aromadendrin (Dihydrokaempferol), involved in flavonoid metabolism during the formation of the endophytic phenotype in the sugarcane root system. These observations suggest that the "white root" phenotype promotes sugarcane growth by activating flavonoid metabolism. This study reports an interesting phenomenon where D. indusiata, coordinate with the specific bacteria invade, forms a "white root" phenotype with sugarcane root. The study also provides new insights into using D. indusiata as a soil inoculant for promoting sugarcane growth and proposes a new approach for improve sugarcane cultivation.

Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals

Cycads are known to host symbiotic cyanobacteria, including Nostocales species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition to Nostoc spp., symbiotic cyanobacteria of the genus Aulosira were identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includes Aulosira spp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.

Cyanobacteria as a critical reservoir of the environmental antimicrobial resistome

Antimicrobial resistance (AMR) is predicted to cause a worldwide annual toll of 10 million deaths by 2050. This looming public health threat has been linked to antibiotic overuse and pollution, which places selective pressures on AMR maintenance and transfer in and between microbial populations. We examined the distribution, diversity and potential mobility of AMR genes in cyanobacteria. While cyanobacteria are not pathogenic, we hypothesised that they could be a major environmental reservoir for AMR genes. Genes encoding AMR to seven antimicrobial drug classes were found in 10% of cyanobacterial genomes. AMR genes were found in 13% of freshwater, 19% of terrestrial, 34% of symbiotic, 2% of thermal spring, and 3% of marine genomes. AMR genes were found in five cyanobacterial orders with 23% of Nostocales and 8% of Oscillatoriales strains containing AMR genes. The most frequently observed alleles were ansamycin resistance genes, which were present in 7% of strains. AMR genes responsible for resistance to broad-spectrum β-lactams, chloramphenicols, tetracyclines, macrolides, and aminoglycosides were associated with mobile genetic elements or plasmid replicons or both. These results suggest that cyanobacteria are an extensive reservoir, and potential vector, for AMR genes in diverse terrestrial and aquatic habitats.

Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae)

As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to the composition of the endophytic microorganisms in cycad coralloid roots. However, the roles of host and environment in shaping the composition of endophytic bacteria during the recruitment process remain unclear. Here, we determined the diversity, composition, and function prediction of endophytic bacteria from the coralloid roots of a widely cultivated cycad, Cycas revoluta Thunb. Using next-generation sequencing techniques, we comprehensively investigated the diversity and community structure of the bacteria in coralloid roots and bulk soils sampled from 11 sites in China, aiming to explore the variations in core endophytic bacteria and to predict their potential functions. We found a higher microbe diversity in bulk soils than in coralloid roots. Meanwhile, there was no significant difference in the diversity and composition of endophytic bacteria across different localities, and the same result was found after removing cyanobacteria. Desmonostoc was the most dominant in coralloid roots, followed by Nostoc, yet these two cyanobacteria were not shared by all samples. Rhodococcus, Edaphobacter, Niastella, Nordella, SH-PL14, and Virgisporangium were defined as the core microorganisms in coralloid roots. A function prediction analysis revealed that endophytic bacteria majorly participated in the plant uptake of phosphorus and metal ions and in disease resistance. These results indicate that the community composition of the bacteria in coralloid roots is affected by both the host and environment, in which the host is more decisive. Despite the very small proportion of core microbes, their interactions are significant and likely contribute to functions related to host survival. Our study contributes to an understanding of microbial diversity and composition in cycads, and it expands the knowledge on the association between hosts and symbiotic microbes.

Core Microbiome and Microbial Community Structure in Coralloid Roots of Cycas in Ex Situ Collection of Kunming Botanical Garden in China

Endophytes are essential in plant succession and evolution, and essential for stress resistance. Coralloid root is a unique root structure found in cycads that has played a role in resisting adverse environments, yet the core taxa and microbial community of different Cycas species have not been thoroughly investigated. Using amplicon sequencing, we successfully elucidated the microbiomes present in coralloid roots of 10 Cycas species, representing all four sections of Cycas in China. We found that the endophytic bacteria in coralloid roots, i.e., Cyanobacteria, were mainly composed of Desmonostoc_PCC-7422, Nostoc_PCC-73102 and unclassified_f__Nostocaceae. Additionally, the Ascomycota fungi of Exophiala, Paraboeremia, Leptobacillium, Fusarium, Alternaria, and Diaporthe were identified as the core fungi taxa. The Ascomycota fungi of Nectriaceae, Herpotrichiellaceae, Cordycipitaceae, Helotiaceae, Diaporthaceae, Didymellaceae, Clavicipitaceae and Pleosporaceae were identified as the core family taxa in coralloid roots of four sections. High abundance but low diversity of bacterial community was detected in the coralloid roots, but no significant difference among species. The fungal community exhibited much higher complexity compared to bacteria, and diversity was noted among different species or sections. These core taxa, which were a subset of the microbiome that frequently occurred in all, or most, individuals of Cycas species, represent targets for the development of Cycas conservation.

Effects of antibiotics on the endophyte and phyllosphere bacterial communities of lotus from above and below surface water in a typical shallow lake

Antibiotics are ubiquitous pollutants that are widely found in aquatic ecosystems, where the bacterial community of aquatic plants is influenced by antibiotics. However, differences between endophyte and phyllosphere bacteria of Lotus from above and below surface water remains unclear. Lotus samples from above and below the surface water were collected to investigate the differences in endophyte and phyllosphere bacteria and dominant environmental factors in regions with low (L-) and high (H-) total antibiotic levels. There were significant differences in Shannon diversity between endophyte and phyllosphere bacteria except between the below-surface water phyllosphere bacteria and below-surface water endophytes in both L-antibiotic and H-antibiotic regions, with higher values for phyllosphere bacteria. The dominant phylum in all phyllosphere samples was Proteobacteria (76.1%-92.5%), while Cyanobacteria (47.8%-81.1%) was dominant in all endophyte samples. The dominant source of above-surface water endophytes was below-surface water endophytes (83.68-91.25%), below-surface water phyllosphere bacteria (48.43-55.91%) for above-surface water phyllosphere bacteria, and above-surface water endophytes (53.83-61.80%) for below-surface water endophytes, while the dominant contributor to the below-surface water phyllosphere bacteria was also below-surface water endophytes (52.96-61.00%) in two regions, indicating that antibiotic stress changed the sink‒source relationship between endophytes and phyllosphere bacteria. The physical-chemical properties of surface water and sediments could be responsible for the variations in the above- and below-surface water endophytes and phyllosphere bacteria in both regions. It is suggested that antibiotics may have a substantial effect on endophyte and phyllosphere bacterial community.

Combined intensive management of fertilization, tillage, and organic material mulching regulate soil bacterial communities and functional capacities by altering soil potassium and pH in a Moso bamboo forest

Intensive management is a common practice in agricultural and forestry ecosystems to improve soil quality and crop yield by influencing nutrient supply and soil microbiota; however, the linkage between soil nutrients and bacterial community and functional capacities in intensively managed economic forests has not been well studied. In this study, we investigated the soil properties such as available potassium (AK), available nitrogen (AN), available phosphorus (AP), ammonium (NH4+), nitrate (NO3-), organic matter (OM), total nitrogen (TN), total phosphorus (TP), bacterial diversity and community composition, potential functions of rhizome roots, and soil microbiota across a chronosequence of intensively managed Moso bamboo (Phyllostachys edulis) forests. Our results demonstrated that the combined intensive management (deep tillage, fertilization, and organic material mulching) in this study caused a significant increase in the concentrations of AK, AN, AP, NH4+, NO3-, OM, TN, and TP (P < 0.05). However, they led to a remarkable decrease in pH (P < 0.05). Such changes lowered the Shannon diversity of the soil and rhizome root microbiota but did not significantly affect the community composition and functional capacity. Soil bacterial community variation was predominantly mediated by soil total potassium (TK) (15.02%), followed by pH (11.29%) and AK (11.13%). We further observed that Nitrospirae accounted for approximately 50% of the variation in soil pH, NO3-, NH4+, and AK, indicating its importance in soil nutrient cycling, especially nitrogen cycling. Accordingly, we propose that the management-induced changes in soil parameters reshaped the bacterial community structure and keystone bacterial assemblage, leading to the differentiation of microbial functions.

The complete chloroplast genome of Cycas bifida, an extremely small population protected species

Cycas bifida (Dyer) K.D.Hill (2004) is an extremely small population-protected species of China. In this study, we reported the first chloroplast genome sequence of C. bifida. The chloroplast genome of C. bifida included two single-copy regions (large single-copy (LSC) and small single-copy (SSC)) and a pair of inverted repeats (IRs) regions comprising 88,946 bp, 23,107 bp, and 25,053 bp, respectively. The complete chloroplast genome of C. bifida contains 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The overall GC content of the C. bifida chloroplast genome is 39.41%, and the LSC, SSC, and IR regions occupy 38.70%, 36.52%, and 42.02%, respectively. A phylogenetic analysis was performed based on complete chloroplast genomes from 15 species and found that C. bifida was closely related to Cycas szechuanensis W.C.Cheng & L.K.Fu.

The diversity and community structure of symbiotic cyanobacteria in hornworts inferred from long-read amplicon sequencing

PREMISE

Nitrogen-fixing endosymbioses with cyanobacteria have evolved independently in five very different plant lineages. Expanding knowledge of these symbioses promises to improve the understanding of symbiosis evolution and broaden the toolkit for agricultural engineering to reduce artificial fertilizer use. Here we focused on hornworts, a bryophyte lineage in which all members host cyanobacteria, and investigated factors shaping the diversity of their cyanobiont communities.

METHODS

We sampled hornworts and adjacent soils in upstate New York throughout the hornwort growing season. We included all three sympatric hornwort species in the area, allowing us to directly compare partner selectivity. To profile cyanobacteria communities, we established a metabarcoding protocol targeting rbcL-X with PacBio long reads.

RESULTS

The hornwort cyanobionts detected were phylogenetically diverse, including clades that do not contain other known plant symbionts. We found significant overlap between hornwort cyanobionts and soil cyanobacteria, a pattern not previously reported in other plant-cyanobacteria symbioses. Cyanobiont communities differed between host plants only centimeters apart, but we did not detect an effect of sampling time or host species on the cyanobacterial community structure.

CONCLUSIONS

This study expands the phylogenetic diversity of known symbiotic cyanobacteria. Our analyses suggest that hornwort cyanobionts have a tight connection to the soil background, and we found no evidence that time within growing season, host species, or distance at the scale of meters strongly govern cyanobacteria community assembly. This study provides a critical foundation for further study of the ecology, evolution, and interaction dynamics of plant-cyanobacteria symbiosis.

Differences in lipid homeostasis and membrane lipid unsaturation confer differential tolerance to low temperatures in two Cycas species

BACKGROUND

C. panzhihuaensis is more tolerant to freezing than C. bifida but the mechanisms underlying the different freezing tolerance are unclear. Photosynthesis is one of the most temperature-sensitive processes. Lipids play important roles in membrane structure, signal transduction and energy storage, which are closely related to the stress responses of plants. In this study, the chlorophyll fluorescence parameters and lipid profiles of the two species were characterized to explore the changes in photosynthetic activity and lipid metabolism following low-temperature exposure and subsequent recovery.

RESULTS

Photosynthetic activity significantly decreased in C. bifida with the decrease of temperatures and reached zero after recovery. Photosynthetic activity, however, was little affected in C. panzhihuaensis. The lipid composition of C. bifida was more affected by cold and freezing treatments than C. panzhihuaensis. Compared with the control, the proportions of all the lipid categories recovered to the original level in C. panzhihuaensis, but the proportions of most lipid categories changed significantly in C. bifida after 3 d of recovery. In particular, the glycerophospholipids and prenol lipids degraded severely during the recovery period of C. bifida. Changes in acyl chain length and double bond index (DBI) occurred in more lipid classes immediately after low-temperature exposure in C. panzhihuaensis compare with those in C. bifida. DBI of the total main membrane lipids of C. panzhihuaensis was significantly higher than that of C. bifida following all temperature treatments.

CONCLUSIONS

The results of chlorophyll fluorescence parameters confirmed that the freezing tolerance of C. panzhihuaensis was greater than that of C. bifida. The lipid metabolism of the two species had differential responses to low temperatures. The homeostasis and plastic adjustment of lipid metabolism and the higher level of DBI of the main membrane lipids may contribute to the greater tolerance of C. panzhihuaensis to low temperatures.

Diversity, Phylogeny and Antagonistic Activity of Fungal Endophytes Associated with Endemic Species of Cycas (Cycadales) in China

The culture-based approach was used to characterize the fungal endophytes associated with the coralloid roots of the endemic Cycas debaoensis and Cycas fairylakea from various population sites in China. We aim to determine if the assemblages of fungal endophytes inside these endemic plant hosts are distinct and could be explored for bioprospecting. The isolation method yielded a total of 284 culturable fungal strains. Identification based on the analysis of the internal transcribed spacer (ITS) rDNA showed that they belonged to two phyla, five classes, eight orders and 22 families. At least 33 known genera and 62 different species were confirmed based on >97% ITS sequence similarity. The most frequent and observed core taxa in the two host species regardless of their population origin were Talaromyces, Penicillium, Fusarium, Pochonia and Gliocladiopsis. Seventy percent was a rare component of the fungal communities with only one or two recorded isolates. Contrary to common notions, diversity and fungal richness were significantly higher in C. debaoensis and C. fairylakea collected from a botanical garden, while the lowest was observed in C. debaoensis from a natural habitat; this provides evidence that garden management, and to a minor extent, ex-situ conservation practice, could influence fungal endophyte communities. We further selected nineteen fungal isolates and screened for their antagonistic activities via a co-cultivation approach against the phytopathogens, Diaporthe sp. and Colletotrichum sp. Among these, five isolates with high ITS similarity matches with Hypoxylon vinosupulvinatum (GD019, 99.61%), Penicillium sp. (BD022, 100%), Penicillifer diparietisporus (GD008, 99.46%), Clonostachys rogersoniana (BF024, 99.46%) and C. rosea (BF011, 99.1%), which showed exceptional antagonistic activities against the phytopathogenic fungi with a significant inhibition rate of 70-80%. Taken together, our data presented the first and most comprehensive molecular work on culturable fungal endophytes associated with the coralloid roots of cycads. Our study also demonstrated that about 5% of fungal endophytes were not detected by the high-throughput sequencing approach, implying the equal importance of a culture-dependent approach to study fungal communities of cycads. We further highlighted the potential role of endemic and rare plants to discover and isolate unique plant-associated fungal taxa with excellent biocontrol properties.

Full-Length 16S rRNA and ITS Gene Sequencing Revealed Rich Microbial Flora in Roots of Cycas spp. in China

Cycads have developed a complex root system categorized either as normal or coralloid roots. Past literatures revealed that a great diversity of key microbes is associated with these roots. This recent study aims to comprehensively determine the diversity and community structure of bacteria and fungi associated with the roots of two Cycas spp. endemic to China, Cycas debaoensis Zhong & Chen and Cycas fairylakea D.Y. Wang using high-throughput amplicon sequencing of the full-length 16S rRNA (V1-V9 hypervariable) and short fragment ITS region. The total DNA from 12 root samples were extracted, amplified, sequenced, and analyzed. Resulting sequences were clustered into 61 bacteria and 2128 fungal OTUs. Analysis of community structure revealed that the coralloid roots were dominated mostly by the nitrogen-fixer Nostocaceae but also contain other non-diazotrophic bacteria. The sequencing of entire 16S rRNA gene identified four different strains of cyanobacteria under the heterocystous genera Nostoc and Desmonostoc. Meanwhile, the top bacterial families in normal roots were Xanthobacteraceae, Burkholderiaceae, and Bacillaceae. Moreover, a diverse fungal community was also found in the roots of cycads and the predominating families were Ophiocordycipitaceae, Nectriaceae, Bionectriaceae, and Trichocomaceae. Our results demonstrated that bacterial diversity in normal roots of C. fairylakea is higher in richness and abundance than C. debaoensis. On the other hand, a slight difference, albeit insignificant, was noted for the diversity of fungi among root types and host species as the number of shared taxa is relatively high (67%). Our results suggested that diverse microbes are present in roots of cycads which potentially interact together to support cycads survival. Our study provided additional knowledge on the microbial diversity and composition in cycads and thus expanding our current knowledge on cycad-microbe association. Our study also considered the possible impact of ex situ conservation on cyanobiont community of cycads.

Chemical Element Concentrations of Cycad Leaves: Do We Know Enough?

The literature containing which chemical elements are found in cycad leaves was reviewed to determine the range in values of concentrations reported for essential and beneficial elements. We found 46 of the 358 described cycad species had at least one element reported to date. The only genus that was missing from the data was Microcycas. Many of the species reports contained concentrations of one to several macronutrients and no other elements. The cycad leaves contained greater nitrogen and phosphorus concentrations than the reported means for plants throughout the world. Magnesium was identified as the macronutrient that has been least studied. Only 14 of the species were represented by data from in situ locations, with most of the data obtained from managed plants in botanic gardens. Leaf element concentrations were influenced by biotic factors such as plant size, leaf age, and leaflet position on the rachis. Leaf element concentrations were influenced by environmental factors such as incident light and soil nutrient concentrations within the root zone. These influential factors were missing from many of the reports, rendering the results ambiguous and comparisons among studies difficult. Future research should include the addition of more taxa, more in situ locations, the influence of season, and the influence of herbivory to more fully understand leaf nutrition for cycads.

Niche Specialization and Functional Overlap of Bamboo Leaf and Root Microbiota

Leaves and roots harbor taxonomically diverse bacterial assemblages which enhance plant growth and performance by increasing nutrient supply and resistance to stress. An extensive investigation of bacterial diversity and composition between leaf and root microbiota of 15 bamboo species differing in rhizome types, lifeforms and sampling sites were conducted by high-through sequencing. The alpha diversity between leaf and root microbiota was not significantly different, whereas, their beta diversity differed remarkably. Niche specialization mainly in species from Actinobacteria was detected which prefer to colonize in roots than leaves. Community structure of leaf microbiota was highly resembled, however, the phylogeny inferred by host's chloroplast data was incongruent with microbiota dendrogram, indicating that phylosymbiosis didn't occur in bamboos and their associated microbiota. Large overlap in functional profiling of leaf and root-associated microbiota was found. Accordingly, we proposed that environmental conditions, structural variation and physiological differences between leaves and roots worked collaboratively for divergence of bamboo microbiota. This study confers to a robust knowledge of bamboo-microbe interaction and provides a list of bacterial lineages for investigation into specific plant-microbe interaction information of which could be used to enhance agricultural and forest productivity.

Exploring cycad foliage as an archive of the isotopic composition of atmospheric nitrogen

Molecular nitrogen (N₂ ) constitutes the majority of Earth's modern atmosphere, contributing ~0.79 bar of partial pressure (pN₂ ). However, fluctuations in pN₂ may have occurred on 10⁷ -10⁹  year timescales in Earth's past, perhaps altering the isotopic composition of atmospheric nitrogen. Here, we explore an archive that may record the isotopic composition of atmospheric N₂ in deep time: the foliage of cycads. Cycads are ancient gymnosperms that host symbiotic N₂ -fixing cyanobacteria in modified root structures known as coralloid roots. All extant species of cycads are known to host symbionts, suggesting that this N₂ -fixing capacity is perhaps ancestral, reaching back to the early history of cycads in the late Paleozoic. Therefore, if the process of microbial N₂ fixation records the δ¹⁵ N value of atmospheric N₂ in cycad foliage, the fossil record of cycads may provide an archive of atmospheric δ¹⁵ N values. To explore this potential proxy, we conducted a survey of wild cycads growing in a range of modern environments to determine whether cycad foliage reliably records the isotopic composition of atmospheric N₂ . We find that neither biological nor environmental factors significantly influence the δ¹⁵ N values of cycad foliage, suggesting that they provide a reasonably robust record of the δ¹⁵ N of atmospheric N₂ . Application of this proxy to the record of carbonaceous cycad fossils may not only help to constrain changes in atmospheric nitrogen isotope ratios since the late Paleozoic, but also could shed light on the antiquity of the N₂ -fixing symbiosis between cycads and cyanobacteria.

Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis

BACKGROUND

Given their adaptation to nutrient-poor and drought environments, cycads are vital models for plant-microbiome interaction research because they are likely to host an important reservoir of beneficial microbes that may support cycad survival. However, a comprehensive understanding of the diversity and community composition of microbiome associated with different plant compartments as well as bulk soils of cycad species remains elusive.

METHOD

An extensive investigation of species diversity and community composition of bacterial and fungal microbiome in roots, seeds, unfertilized seeds, ovules, pollens, and soils of Cycas panzhihuaensis L. Zhou & S. Y. Yang has been conducted by high-through sequencing technology. Moreover, principal component analysis (PCA), hierarchical cluster analysis (HCA), and heatmap analysis were applied to test the niche-specific effect and biogeography factor among different sample types of this cycad species.

RESULTS

Highly diverse microbiota and significant variation of community structure were found among different compartments of C. panzhihuaensis. Soils exhibited a remarkable differentiation of bacterial community composition compared to the other five plant organs as revealed by PCA, HCA, and heatmap analyses. Different compartments possessed unique core microbial taxa with Pseudomonadaceae and Nectriaceae shared among them. According to the indicator species analysis, there was almost no differentiation of dominant microbiomes with regard to the geography of the host cycad. Two main transmission models existed in the C. panzhihuaensis.

CONCLUSIONS

Each sample type represented a unique niche and hosted a niche-specific core microbial taxa. Contrary to previous surveys, biogeography hardly exerted impact on microbial community variation in this study. The majority of the cycad-associated microbes were horizontally derived from soils and/or air environments with the rest vertically inherited from maternal plants via seeds. This study offers a robust knowledge of plant-microbiome interaction across various plant compartments and soils and lends guidelines to the investigation of adaptation mechanism of cycads in arid and nutrient-poor environments as well as their evolutionary conservation.

Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon

Cycads are among the few plants that have developed specialized roots to host nitrogen-fixing bacteria. We describe the bacterial diversity of the coralloid roots from seven Dioon species and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species of Dioon that we evaluated, suggesting a recent divergence of Dioon populations and/or similar plant-driven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched with Nostoc spp and Calothrix spp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.

Cycad Coralloid Roots Contain Bacterial Communities Including Cyanobacteria and Caulobacter spp. That Encode Niche-Specific Biosynthetic Gene Clusters

Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species from Dioon (Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, including Bradyrhizobium, Burkholderia, Mesorhizobium, Rhizobium, and Nostoc species, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities. These data were used for whole-genome inferences that suggest two Dioon-specific monophyletic groups, and a level of specialization characteristic of co-evolved symbiotic relationships. Furthermore, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with detection of pigment emissions using multiphoton excitation fluorescence microscopy, we also show that Caulobacter species co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.