The Rhizosphere Microbiome of Mikania micrantha Provides Insight Into Adaptation and Invasion

Rhizosphere microbial community construction during the latitudinal spread of the invader Chromolaena odorata

The colonization of alien plants in new habitats is typically facilitated by microorganisms present in the soil environment. However, the diversity and structure of the archaeal, bacterial, and fungal communities in the latitudinal spread of alien plants remain unclear. In this study, the rhizosphere and bulk soil of Chromolaena odorata were collected from five latitudes in Pu' er city, Yunnan Province, followed by amplicon sequencing of the soil archaeal, bacterial, and fungal communities. Alpha and beta diversity results revealed that the richness indices and the structures of the archaeal, bacterial, and fungal communities significantly differed along the latitudinal gradient. Additionally, significant differences were observed in the bacterial Shannon index, as well as in the structures of the bacterial and fungal communities between the rhizosphere and bulk soils. Due to the small spatial scale, trends of latitudinal variation in the archaeal, bacterial, and fungal communities were not pronounced. Total potassium, total phosphorus, available nitrogen, available potassium and total nitrogen were the important driving factors affecting the soil microbial community structure. Compared with those in bulk soil, co-occurrence networks in rhizosphere microbial networks presented lower complexity but greater modularity and positive connections. Among the main functional fungi, arbuscular mycorrhizae and soil saprotrophs were more abundant in the bulk soil. The significant differences in the soil microbes between rhizosphere and bulk soils further underscore the impact of C. odorata invasion on soil environments. The significant differences in the soil microbiota along latitudinal gradients, along with specific driving factors, demonstrate distinct nutrient preferences among archaea, bacteria, and fungi and indicate complex microbial responses to soil nutrient elements following the invasion of C. odorata.

Compositional profiling of the rhizosphere microbiome of Canada thistle reveals consistent patterns across the United States northern Great Plains

Canada thistle is a pervasive perennial weed, causing challenges to agricultural and natural ecosystems globally. Although research has focused on the phenology, genetics, and control of Canada thistle, little is known about the rhizosphere microbiome and the role plant-microbe interactions play in invasion success. This study investigated the rhizosphere microbiome of Canada thistle across diverse climates, soils, and crops in the U.S. northern Great Plains. Soil and rhizosphere samples were collected and bacterial 16S and fungal ITS2 sequencing were performed to characterize the core microbiome and identify potential factors contributing to invasion success. Amplicon sequencing revealed a stable core microbiome that was detected in the Canada thistle rhizosphere across all locations. The core microbiome was dominated by the bacterial phyla Actinobacteriota and Proteobacteria and fungal phyla Ascomycota and Basidiomycota. Differential abundance analysis showed rhizosphere fungal communities were enriched in pathogen-containing genera with a 1.7-fold greater abundance of Fusaria and a 2.6-fold greater abundance of Gibberella compared to bulk soil. Predictive functional profiling showed rhizosphere communities were enriched (p < 0.05, FDR corrected) in plant pathogen fungal guilds which represented 19% of the fungal community. The rhizosphere microbiome was similar in composition across environments, highlighting the stable association between Canada thistle and specific microbial taxa. This study characterized the core microbiome of Canada thistle, and the findings highlight plant-microbe interactions shaping invasive behavior. These findings are important for understanding the ecological impacts of plant invasion and soil-microbe ecological processes.

Exploring Phosphate Solubilizing Bacterial Communities in Rhizospheres of Native and Exotic Forage Grasses in Alkaline-Sodic Soils of the Flooding Pampa

The flooding pampa is one of the most important cattle-raising regions in Argentina. In this region, natural pastures are dominated by low-productivity native grass species, which are the main feed for livestock. In this context, previous studies in the region with the subtropical exotic grass Panicum coloratum highlight it as a promising species to improve pasture productivity. Cultivable phosphate solubilizing bacteria (PSB) communities associated to native (Sporobolus indicus) and exotic (Panicum coloratum) forage grasses adapted to alkaline-sodic soils of the flooding pampa were analyzed. PSB represented 2-14% of cultivable rhizobacteria and Box-PCR fingerprinting revealed a high genetic diversity in both rhizospheres. Taxonomic identification by MALDI-TOF showed that PSB populations of P. coloratum and S. indicus rhizospheres are dominated by the phylum Proteobacteria (92,51% and 96,60% respectively) and to a lesser extent (< 10%), by the phyla Actinobacteria and Firmicutes. At the genus level, both PSB populations were dominated by Enterobacter and Pseudomonas. Siderophore production, nitrogen fixation, and indoleacetic acid production were detected in a variety of PSB genera of both plant species. A higher proportion of siderophore and IAA producers were associated to P. coloratum than S. indicus, probably reflecting a greater dependence of the exotic species on rhizospheric microorganisms to satisfy its nutritional requirements in the soils of the flooding pampa. This work provides a novel knowledge about functional groups of bacteria associated to plants given that there are no previous reports dedicated to the characterization of PSB rhizosphere communities of S indicus and P coloratum. Finally, it should be noted that the collection obtained in this study can be useful for the development of bioinputs that allow reducing the use of chemical fertilizers, providing sustainability to pasture production systems for livestock.

Phenolic Acids and Flavonoids Play Important Roles in Flower Bud Differentiation in Mikania micrantha: Transcriptomics and Metabolomics

Mikania micrantha is a highly invasive vine, and its ability to sexually reproduce is a major obstacle to its eradication. The long-distance dissemination of M. micrantha depends on the distribution of seeds; therefore, inhibiting M. micrantha flowering and seed production is an effective control strategy. The number of blooms of M. micrantha differs at different altitudes (200, 900, and 1300 m). In this study, we used a combination of metabolomics and transcriptomics methods to study the patterns of metabolite accumulation in the flower buds of M. micrantha. Using LC-MS/MS, 658 metabolites were found in the flower buds of M. micrantha at three different altitudes (200, 900, and 1300 m). Flavonoids and phenolic acids were found to be the main differential metabolites, and their concentrations were lower at 900 m than at 200 m and 1300 m, with the concentrations of benzoic acid, ferulic acid, and caffeic acid being the lowest. The biosynthesis pathways for flavonoids and phenolic compounds were significantly enriched for differentially expressed genes (DEGs), according to the results of transcriptome analysis. The production of flavonoid and phenolic acids was strongly linked with the expressions of phenylalanine ammonia-lyase (PAL), caffeoyl-CoA O-methyltransferase (COMT), and 4-coumarate-CoA ligase (4CL), according to the results of the combined transcriptome and metabolome analysis. These genes' roles in the regulation of distinct phenolic acids and flavonoids during M. micrantha bud differentiation are still unknown. This study adds to our understanding of how phenolic acids and flavonoids are regulated in M. micrantha flower buds at various altitudes and identifies regulatory networks that may be involved in this phenomenon, offering a new approach for the prevention and management of M. micrantha.

Co-evolution within the plant holobiont drives host performance

Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.

Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome

BACKGROUND

Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.

RESULTS

Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.

CONCLUSION

Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.

Plant invasion shifts soil microbiome and physico-chemical attributes along an elevational gradient in Kashmir Himalaya

Soil microbial communities, being situated at the interface of aboveground plant and belowground soil systems, can play a pivotal role in determining ecosystem response to the drivers of global environmental change, including invasive species. In mountains, invasive plants occurring along elevational gradients offer a unique natural experimental system to investigate the impact of invasions in determining patterns and relationships of soil microbial diversity and nutrient pools at much shorter spatial distances. Here, we studied the impact of a global plant invader, Leucanthemum vulgare, on the diversity of soil microbiome and physico-chemical attributes along an elevational gradient (1760-2880 m) in Kashmir Himalaya. We used Illumina MiSeq platform to characterize the soil microbiome in pair-wise invaded and uninvaded plots at four different sites along the gradient. We found a total of 1959 bacterial operational taxonomic units (OTUs) belonging to 152 species, and a relatively higher number of 2475 fungal OTUs belonging to 589 species. The α-diversity of soil microbiome showed a gradual increase from low to high elevation and differed significantly (p < 0.05) between the invaded and uninvaded plots. The β-diversity revealed distinct microbiome clustering among the sampling sites. Plant invasion also altered soil physico-chemical attributes along the elevational gradient. Overall, our findings suggest that the L. vulgare-induced shifts in soil microbiome and nutrient pools may be a belowground self-reinforced mechanism to facilitate its successful invasion along the elevational gradient. Our study provides new insights into invasive plant-microbe relationships with wide implications for climate warming-driven elevational range shifts in mountains.

Invasive Plant Alternanthera philoxeroides Benefits More Competition Advantage from Rhizosphere Bacteria Regardless of the Host Source

The rhizosphere plays a vital role in the exchange of materials in the soil-plant ecosystem, and rhizosphere microorganisms are crucial for plant growth and development. In this study, we isolated two strains of Pantoea rhizosphere bacteria separately from invasive Alternanthera philoxeroides and native A. sessilis. We conducted a control experiment to test the effects of these bacteria on the growth and competition of the two plant species using sterile seedlings. Our findings showed that the rhizobacteria strain isolated from A. sessilis significantly promoted the growth of invasive A. philoxeroides in monoculture compared to native A. sessilis. Both strains significantly enhanced the growth and competitiveness of invasive A. philoxeroides under competition conditions, regardless of their host source. Our study suggests that rhizosphere bacteria, including those from different host sources, can contribute to the invasion of A. philoxeroides by significantly enhancing its competitiveness.

Omics Approaches in Invasion Biology: Understanding Mechanisms and Impacts on Ecological Health

Invasive species and rapid climate change are affecting the control of new plant diseases and epidemics. To effectively manage these diseases under changing environmental conditions, a better understanding of pathophysiology with holistic approach is needed. Multiomics approaches can help us to understand the relationship between plants and microbes and construct predictive models for how they respond to environmental stresses. The application of omics methods enables the simultaneous analysis of plant hosts, soil, and microbiota, providing insights into their intricate relationships and the mechanisms underlying plant-microbe interactions. This can help in the development of novel strategies for enhancing plant health and improving soil ecosystem functions. The review proposes the use of omics methods to study the relationship between plant hosts, soil, and microbiota, with the aim of developing a new technique to regulate soil health. This approach can provide a comprehensive understanding of the mechanisms underlying plant-microbe interactions and contribute to the development of effective strategies for managing plant diseases and improving soil ecosystem functions. In conclusion, omics technologies offer an innovative and holistic approach to understanding plant-microbe interactions and their response to changing environmental conditions.

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion

Introduction

Plant invasion can profoundly alter ecosystem processes driven by microorganisms. The fundamental mechanisms linking microbial communities, functional genes, and edaphic characteristics in invaded ecosystems are, nevertheless, poorly understood.

Methods

Here, soil microbial communities and functions were determined across 22 Amaranthus palmeri (A. palmeri) invaded patches by pairwise 22 native patches located in the Jing-Jin-Ji region of China using high-throughput amplicon sequencing and quantitative microbial element cycling technologies.

Results

As a result, the composition and structure of rhizosphere soil bacterial communities differed significantly between invasive and native plants according to principal coordinate analysis. A. palmeri soils exhibited higher abundance of Bacteroidetes and Nitrospirae, and lower abundance of Actinobacteria than native soils. Additionally, compared to native rhizosphere soils, A. palmeri harbored a much more complex functional gene network with higher edge numbers, average degree, and average clustering coefficient, as well as lower network distance and diameter. Furthermore, the five keystone taxa identified in A. palmeri rhizosphere soils belonged to the orders of Longimicrobiales, Kineosporiales, Armatimonadales, Rhizobiales and Myxococcales, whereas Sphingomonadales and Gemmatimonadales predominated in the native rhizosphere soils. Moreover, random forest model revealed that keystone taxa were more important indicators of soil functional attributes than edaphic variables in both A. palmeri and native rhizosphere soils. For edaphic variables, only ammonium nitrogen was a significant predictor of soil functional potentials in A. palmeri invaded ecosystems. We also found keystone taxa in A. palmeri rhizosphere soils had strong and positive correlations with functional genes compared to native soils.

Discussion

Our study highlighted the importance of keystone taxa as a driver of soil functioning in invaded ecosystem.

Significant changes in soil microbial community structure and metabolic function after Mikania micrantha invasion

Currently, Mikania micrantha (M. micrantha) has invaded Guangdong, Guangxi and other provinces in China, causing serious harm to the forests of southeastern China. Soil microorganisms play an important role in the establishment of M. micrantha invasion, affecting plant productivity, community dynamics, and ecosystem function. However, at present, how M. micrantha invasion affects soil carbon, nitrogen, and phosphorus phase functional genes and the environmental factors that cause gene expression changes remain unclear, especially in subtropical forest ecosystems. This study was conducted in Xiangtoushan National Forest Park in Guangdong Province to compare the changes in soil nutrients and microorganisms after M. micrantha invasion of a forest. The microbial community composition and metabolic function were explored by metagenome sequencing. Our results showed that after M. micrantha invasion, the soil was more suitable for the growth of gram-positive bacteria (Gemmatimonadetes). In addition, the soil microbial community structure and enzyme activity increased significantly after M. micrantha invasion. Correlation analysis and Mantel test results suggested that total phosphorus (TP), nitrate nitrogen (NO₃^--N), and soil dissolved organic matter (DOM; DOC and DON), were the strong correlates of soil microbial nitrogen functional genes, while soil organic matter (SOM), soil organic carbon (SOC), total nitrogen (TN), and available phosphorus (Soil-AP) were strongly correlated with the expression of soil microbial phosphorus functional gene. Mikania micrantha invasion alters soil nutrients, microbial community composition and metabolic function in subtropical forests, creates a more favorable growth environment, and may form a positive feedback process conducive to M. micrantha invasion.

Transcriptome analysis of critical genes related to flowering in Mikania micrantha at different altitudes provides insights for a potential control

BACKGROUND

Mikania micrantha is a vine with strong invasion ability, and its strong sexual reproduction ability is not only the main factor of harm, but also a serious obstacle to control. M. micrantha spreads mainly through seed production. Therefore, inhibiting the flowering and seed production of M. micrantha is an effective strategy to prevent from continuing to spread.

RESULT

The flowering number of M. micrantha is different at different altitudes. A total of 67.01 Gb of clean data were obtained from nine cDNA libraries, and more than 83.47% of the clean reads were mapped to the reference genome. In total, 5878 and 7686 significantly differentially expressed genes (DEGs) were found in E2 vs. E9 and E13 vs. E9, respectively. Based on the background annotation and gene expression, some candidate genes related to the flowering pathway were initially screened, and their expression levels in the three different altitudes in flower bud differentiation showed the same trend. That is, at an altitude of 1300 m, the flower integration gene and flower meristem gene were downregulated (such as SOC1 and AP1), and the flowering inhibition gene was upregulated (such as FRI and SVP). Additionally, the results showed that there were many DEGs involved in the hormone signal transduction pathway in the flower bud differentiation of M. micrantha at different altitudes.

CONCLUSIONS

Our results provide abundant sequence resources for clarifying the underlying mechanisms of flower bud differentiation and mining the key factors inhibiting the flowering and seed production of M. micrantha to provide technical support for the discovery of an efficient control method.

Epichloë endophyte interacts with saline-alkali stress to alter root phosphorus-solubilizing fungal and bacterial communities in tall fescue

Epichloë endophytes, present in aboveground tissues, modify belowground microbial community. This study was conducted to investigate endophyte (Epichloë coenophialum) associated with tall fescue (Lolium arundinaceum) interacted with an altered saline-alkali stress (0, 200 and 400 mmol/l) to affect the belowground phosphorus solubilizing microorganisms including phosphorus solubilizing fungi (PSF) and bacteria (PSB). We found that a significant interaction between E. coenophialum and saline-alkali stress occurred in the diversity and composition of PSF in tall fescue roots. Under saline-alkali stress conditions (200 and 400 mmol/l), E. coenophialum significantly increased the PSF diversity and altered its composition in the roots, decreasing the relative abundance of dominant Cladosporium and increasing the relative abundance of Fusarium. However, there was no significant interaction between E. coenophialum and saline-alkali stress on the PSB diversity in tall fescue roots. E. coenophialum significantly reduced the diversity of PSB in the roots, and E. coenophialum effects did not depend on the saline-alkali stress treatment. Structural equation modeling (SEM) showed that E. coenophialum presence increased soil available phosphorus concentration under saline-alkali stress primarily by affecting PSF diversity instead of the diversity and composition of PSB.

Invasion of Spartina alterniflora on Zostera japonica enhances the abundances of bacteria by absolute quantification sequencing analysis

Plant invasion can alter soil organic matter composition and indirectly impact estuary ecology; therefore, it is paramount to understand how plant invasion influences the bacterial community. Here, we present an absolute quantification 16S rRNA gene sequencing to investigate the bacterial communities that were collected from Zostera japonica and Spartina alterniflora covered areas and Z. japonica degradation areas in the Yellow River Estuary. Our data revealed that the absolute quantity of bacteria in the surface layer was significantly (p < .05) higher than that in the bottom and degradation areas. Following the invasion of S. alterniflora, the abundances of Bacteroidia, Acidimicrobiaceae, and Dehalococcoidaceaewere enriched in the S. alterniflora sediment. In addition, variations in the composition of sediment bacterial communities at the phylum level were the most intimately related to total organic carbon (TOC), and the content of heavy metals could reduce the abundance of bacteria. This study provided some information to understand the effects of S. alterniflora invasion on Z. japonica from the perspective of microbiome level.

Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus

Bursaphelenchus xylophilus, a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus.

Diversity of Rhizo-Bacteriome of Crocus sativus Grown at Various Geographical Locations and Cataloging of Putative PGPRs

Earlier plant growth promoting rhizo-bacteria (PGPRs) were isolated from the plants, by cultivation based techniques and the interaction was mostly thought to be bilateral. The routine bilateral study, with no information on the associated microbiome, could be one of the reasons for the limited success of PGPRs in the field conditions. Keeping in view the role of PGPRs in rhizo-bacteriome on the growth and production of plant, the present study was aimed at studying the diversity of the rhizo-bacteriome of saffron grown across three geographical locations namely Kashmir, Kishtwar and Bengaluru. Variation in the rhizo-bacteriome of saffron growing across 10 different sites from 3 geographical locations was studied using 16S rDNA amplicon metagenomic sequencing. 16 bacterial phyla, 261 genera and 73 bacterial species were cataloged from all the rhizosphere samples. Proteobacteria was a dominant phylum in all the rhizosphere samples. Rhizo-bacteriome of saffron grown in Kishtwar was found to be significantly different from the rhizo-bacteriome of saffron grown in Kashmir and Bengaluru. Interestingly, the rhizo-bacteriome of saffron grown in Bengaluru was very similar to the saffron grown in Kashmir, thereby indicating that the rhizo-bacteriome in saffron is “plant driven” as the corm sown in Bengaluru were from Kashmir. Despite variation in rhizo-bacteriome, core rhizo-bacteriome in saffron was identified that was represented by 53 genera and eight bacterial species belonging to 11 phyla irrespective of their geographical distribution. In addition, 21 PGPRs were reported for the first time from the saffron rhizosphere. The high yielding saffron field Wuyan was found to have the highest number of PGPRs; this indicates that the presence of PGPR is important for yield enhancement than diversity. The two PGPR Rhizobium leguminosarum and Luteibacter rhizovicinus were reported from all the locations except Kishtwar that had escaped isolation in our previous attempts using cultivation based techniques. It is being proposed instead of going for random isolation and screening for PGPRs from plant rhizosphere, an alternate strategy using metagenomic cataloging of the rhizo-bacteriome community and cultivation of the dominant PGPR should be undertaken. This strategy will help in the selection of dominant PGPRs, specific to the plant in question.

Formation, characterization and modeling of emergent synthetic microbial communities

Microbial communities colonize plant tissues and contribute to host function. How these communities form and how individual members contribute to shaping the microbial community are not well understood. Synthetic microbial communities, where defined individual isolates are combined, can serve as valuable model systems for uncovering the organizational principles of communities. Using genome-defined organisms, systematic analysis by computationally-based network reconstruction can lead to mechanistic insights and the metabolic interactions between species. In this study, 10 bacterial strains isolated from the Populus deltoides rhizosphere were combined and passaged in two different media environments to form stable microbial communities. The membership and relative abundances of the strains stabilized after around 5 growth cycles and resulted in just a few dominant strains that depended on the medium. To unravel the underlying metabolic interactions, flux balance analysis was used to model microbial growth and identify potential metabolic exchanges involved in shaping the microbial communities. These analyses were complemented by growth curves of the individual isolates, pairwise interaction screens, and metaproteomics of the community. A fast growth rate is identified as one factor that can provide an advantage for maintaining presence in the community. Final community selection can also depend on selective antagonistic relationships and metabolic exchanges. Revealing the mechanisms of interaction among plant-associated microorganisms provides insights into strategies for engineering microbial communities that can potentially increase plant growth and disease resistance. Further, deciphering the membership and metabolic potentials of a bacterial community will enable the design of synthetic communities with desired biological functions.

Genome Survey Sequencing of In Vivo Mother Plant and In Vitro Plantlets of Mikania cordata

Mikania cordata, the only native congener of the invasive weed Mikania micrantha in China, is an ideal species for comparative study to reveal the invasion mechanism. However, its genome resources are lagging far behind its congener, which limits the comparative genomic analysis. Our goal is to characterize the genome of M. cordata by next-generation sequencing and propose a scheme for long-read genome sequencing. Previous studies have shown that the genomic resources of the host plant would be affected by the endophytic microbial DNA. An aseptic sample of M. cordata will ensure the proper genome in downstream analysis. Because endophytes are ubiquitous in the greenhouse-grown M. cordata, the in vitro culture with cefotaxime or timentin treatment was undertaken to obtain the aseptic plantlets. The in vivo mother plant and in vitro plantlets were used to survey the genome. The microbial contamination in M. cordata was recognized by blast search and eliminated from the raw reads. The decontaminated sequencing reads were used to predict the genome size, heterozygosity, and repetitive rate. The in vivo plant was so contaminated that microbes occupied substantial sequencing resources and misled the scaffold assembly. Compared with cefotaxime, treatment with timentin performed better in cultivating robust in vitro plantlets. The survey result from the in vitro plantlets was more accurate due to low levels of contamination. The genome size was estimated to be 1.80 Gb with 0.50% heterozygosity and 78.35% repetitive rate. Additionally, 289,831 SSRs were identified in the genome. The genome is heavily contaminated and repetitive; therefore, the in vitro culture technique and long-read sequencing technology are recommended to generate a high-quality and highly contiguous genome.