The invader Carpobrotus edulis promotes a specific rhizosphere microbiome across globally distributed coastal ecosystems

Selective shifts in the rhizosphere microbiome during the drought season could explain the success of the invader Nicotiana glauca in semiarid ecosystems

The rhizosphere microbiome plays a crucial role in the ability of plants to colonize and thrive in stressful conditions such as drought, which could be decisive for the success of exotic plant invasion in the context of global climate change. The aim of this investigation was to examine differences in the composition, structure, and functional traits of the microbial community of the invader Nicotiana glauca R.C. Graham and native species growing at seven different Mediterranean semiarid locations under two distinct levels of water availability, corresponding to the wet and dry seasons. The results show that the phylum Actinobacteriota was an indicator phylum of the dry season as well as for the community of N. glauca. The dominant indicator bacterial families of the dry season were 67-14 (unclassified family), Pseudonocardiaceae, and Sphingomonadaceae, being relatively more abundant in the invasive rhizosphere. The relative abundances of the indicator fungal families Aspergillaceae (particularly the indicator genus Aspergillus), Glomeraceae, and Claroideoglomeraceae were higher in the invasive rhizosphere. The relative abundance of mycorrhizal fungi was higher in the invasive rhizosphere in the dry season (by about 40 % in comparison to that of native plants), without significant differences between invasive and native plants in the wet season. Bacterial potential functional traits related to energy and precursor metabolites production and also biosynthesis of cell wall, cofactors, vitamins, and amino acids as well as catabolic enzymes involved in the P cycle prevailed in the invasive rhizosphere under drought conditions. This study shows that the pronounced and beneficial shifts in the microbiome assembly and functions in the rhizosphere of N. glauca under conditions of low soil water availability can represent a clear advantage for its establishment.

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.

Unveiling the influence of salinity on bacterial microbiome assembly of halophytes and crops

BACKGROUND

Climate change and anthropogenic activities intensify salinity stress impacting significantly on plant productivity and biodiversity in agroecosystems. There are naturally salt-tolerant plants (halophytes) that can grow and withstand such harsh conditions. Halophytes have evolved along with their associated microbiota to adapt to hypersaline environments. Identifying shared microbial taxa between halophyte species has rarely been investigated. We performed a comprehensive meta-analysis using the published bacterial 16S rRNA gene sequence datasets to untangle the rhizosphere microbiota structure of two halophyte groups and non-halophytes. We aimed for the identification of marker taxa of plants being adapted to a high salinity using three independent approaches.

RESULTS

Fifteen studies met the selection criteria for downstream analysis, consisting of 40 plants representing diverse halophyte and non-halophyte species. Microbiome structural analysis revealed distinct compositions for halophytes that face high salt concentrations in their rhizosphere compared to halophytes grown at low salt concentrations or from non-halophytes. For halophytes grown at high salt concentrations, we discovered three bacterial genera that were independently detected through the analysis of the core microbiome, key hub taxa by network analysis and random forest analysis. These genera were Thalassospira, Erythrobacter, and Marinobacter.

CONCLUSIONS

Our meta-analysis revealed that salinity level is a critical factor in affecting the rhizosphere microbiome assembly of plants. Detecting marker taxa across high-halophytes may help to select Bacteria that might improve the salt tolerance of non-halophytic plants.

Seasonality and assembly of soil microbial communities in coastal salt marshes invaded by a perennial grass

Plant invasion profoundly changes the microbial-driven processes in the ecosystem; however, the seasonality of soil microbial communities and their assembly under plant invasion is poorly understood. In this study, coastal salt marshes with native Suaeda salsa (L.) Pall. and exotic Spartina alterniflora Loisel. in the Yellow River Estuary, North China, were selected, and soil bacterial and fungal communities and their seasonal variance were characterized by metabarcoding sequencing of the 16S rRNA gene and ITS2 regions, respectively. The importance of deterministic and stochastic processes in shaping bacterial and fungal seasonal assembly was explored by the null model. Results showed that soil microbes exhibited the lowest diversities in spring, while their diversity significantly improved in summer and autumn with the increase in organic carbon and nitrogen content in soils. Strong seasonal variances in microbial communities were observed, but plant invasion reduced the seasonal variation strength of soil bacteria. For the microbial assembly, the seasonal variability of soil bacterial community was mainly controlled by homogeneous selection, whereas soil fungal community was dominantly structured by stochastic processes. Among the selected variables, soil pH was the key abiotic factor driving the seasonal changes in bacteria and fungi. The microbial function annotation derived from taxonomy-based inference suggested that carbon metabolism was relatively stronger in spring, but nitrogen and sulfur metabolism increased evidently in summer and autumn, and the proportion of saprophytic fungi increased substantially after plant invasion. The seasonal turnover of bacterial and fungal groups were tightly associated with the seasonal variation in soil carbon and nitrogen contents. Collectively, these findings reveal the strong seasonal variability of different soil microbial constituents in plant-invaded coastal salt marshes and suggest the linkage between microbial community assembly and microbial-mediated functions in the context of plant invasions.

Bacillus benefits the competitive growth of Ambrosia artemisiifolia by increasing available nutrient levels

Bacillus can help plants to acquire nutrients either directly or indirectly. However, the role of Bacillus community on the competitive growth of invasive Ambrosia artemisiifolia is poorly understood. Native Setaria viridis is often found in areas that have been invaded by A. artemisiifolia. We sought to determine whether the quantitative and/or qualitative differences in the Bacillus community present on the invasive A. artemisiifolia and native S.viridis provide a competitive advantage to the invasive over native species. A field experiment was established to imitate the invasion of A. artemisiifolia. The 16S rRNA gene was commercially sequenced to identify the bacilli isolated from the rhizosphere soil of field-grown A. artemisiifolia and S. viridis. The Bacillus communities in their rhizosphere were compared, and their effects on the competitive growth of A. artemisiifolia and S. viridis were tested in the pot experiments. Bacillus in the rhizosphere soil of A. artemisiifolia significantly enhanced its intra-specific competitive ability. The relative abundance of B. megaterium in the rhizosphere soil of A. artemisiifolia was significantly higher than that of S. viridis. Inoculation with B. megaterium that was isolated from the rhizosphere soil of both A. artemisiifolia and S. viridis significantly enhanced the relative competitiveness of A. artemisiifolia and inhibited that of S. viridis. The higher abundance of B. megaterium in the rhizosphere of A. artemisiifolia creates higher levels of available nutrients than that in the native S. viridis, which enhance the competitive growth of A. artemisiifolia. The result helps to discover the mechanism of Bacillus community in the invasion of A. artemisiifolia.

Both Adaptability and Endophytic Bacteria Are Linked to the Functional Traits in the Invasive Clonal Plant Wedelia trilobata

The role of the interactions between endophytes and host plants is unclear in invasive plants from different geographical latitudes. In this study, we aimed to explore the relationship between endophytic microbes and the functional traits of the invasive plant Wedelia trilobata. We explored the relationship between endophytes and the clonal growth traits of the invasive clonal plant Wedelia trilobata from different geographical latitudes using high-throughput sequencing technology and a common garden-planting experiment. We found that: (1) Different W. trilobata populations had similar endophytic fungi but different endophytic bacteria. However, no latitudinal variation pattern of the overall microbial community was found; (2) plant clonal growth performance (i.e., spacer length) was significantly correlated with endophytic bacterial diversity but not fungal diversity; and (3) the latitudinal variation pattern of the plant clonal growth performance of W. trilobata populations was found in pre-cultivated (i.e., wild) individuals but disappeared in post-cultivated W. trilobata. Our results suggest both environmental adaptability and the endophytic bacterial community are linked to the functional traits of the invasive clonal plant W. trilobata, and these functional traits tend to increase its invasiveness, which may enhance its invasion success.

Invasive Grass Dominance over Native Forbs Is Linked to Shifts in the Bacterial Rhizosphere Microbiome

Rhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasion. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plants. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses grown in a shade-house both individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how differentially abundant microbial families correlate to plant biomass under competition. We find that bacterial diversity and structure differ between native forbs and invasive grasses, but fungal diversity and structure do not. Furthermore, bacterial community structures under competition are distinct from individual bacterial community structures. We also identified five bacterial families that varied in normalized abundance between treatments and that were correlated with plant biomass under competition. We speculate that invasive grass dominance over these natives may be partially due to effects on the rhizosphere community, with changes in specific bacterial families potentially benefiting invaders at the expense of natives.

Soil Mineral Composition and Salinity Are the Main Factors Regulating the Bacterial Community Associated with the Roots of Coastal Sand Dune Halophytes

Soil salinity and mineral deficiency are major problems in agriculture. Many studies have reported that plant-associated microbiota, particularly rhizosphere and root microbiota, play a crucial role in tolerance against salinity and mineral deficiency. Nevertheless, there are still many unknown parts of plant–microbe interaction, especially regarding their role in halophyte adaptation to coastal ecosystems. Here, we report the bacterial community associated with the roots of coastal sand dune halophytes Spinifex littoreus and Calotropis gigantea, and the soil properties that affect their composition. Strong correlations were observed between root bacterial diversity and soil mineral composition, especially with soil Calcium (Ca), Titanium (Ti), Cuprum (Cu), and Zinc (Zn) content. Soil Ti and Zn content showed a positive correlation with bacterial diversity, while soil Ca and Cu had a negative effect on bacterial diversity. A strong correlation was also found between the abundance of several bacterial species with soil salinity and mineral content, suggesting that some bacteria are responsive to changes in soil salinity and mineral content. Some of the identified bacteria, such as Bacillus idriensis and Kibdelosporangium aridum, are known to have growth-promoting effects on plants. Together, the findings of this work provided valuable information regarding bacterial communities associated with the roots of sand dune halophytes and their interactions with soil properties. Furthermore, we also identified several bacterial species that might be involved in tolerance against stresses. Further work will be focused on isolation and transplantation of these potential microbes, to validate their role in plant tolerance against stresses, not only in their native hosts but also in crops.

Elevated functional versatility of the soil microbial community associated with the invader Carpobrotus edulis across a broad geographical scale

Exotic invasive plants may shape their own rhizosphere microbial community during global invasions. Nevertheless, the impacts of such plant invasions on the functional capacities of soil microbial communities remain poorly explored. We used an approach at a broad geographical scale to estimate the composition and abundance of the fungal functional groups, as well as the bacterial metabolic functions, associated with the rhizospheres of Carpobrotus edulis (L.) L. Bolus and the predominant native plants in coastal ecosystems located in different geographical regions. We used the ASV method to infer the potential functions of the soil microbial community with the PICRUSt2 and FUNGuild tools. The predictive functional profiling of the bacterial communities differed between the rhizospheres of the invasive and native plants, regardless of the biogeographic location of the invaded soil. Some predicted pathways related to the biosynthesis of nucleotides such as ppGpp and pppGpp, lipids, carbohydrates and secondary metabolites and the degradation of organic matter were enriched in the C. edulis rhizosphere. Moreover, the invasive microbiota was characterised by a greater richness and diversity of catabolic enzymes involved in nutrients cycling and higher relative abundances of saprotrophs and pathotrophs. Invasion by C. edulis promoted a shift in the potential functional versatility of the soil microbial communities, which can cope with nutrient limitations and biotic stress, and can favour the establishment of the invasive plant, but also alter the functioning and stability of the invaded ecosystems.

Managing the invasive plant Carpobrotus edulis: is mechanical control or specialized natural enemy more effective?

Carpobrotus edulis is an invasive clonal plant with drastic effects on biodiversity and functioning of coastal ecosystems. In recent years, authorities and land managers have implemented diverse management strategies that usually focus on mechanical removal and chemical control. However, applying mechanical control to remove C. edulis may cause indirect adverse effects since it could increase the probability of spreading new propagules, which do not lose their physiological activity. Therefore, reducing the physiological activity of these plant fragments should be a priority to avoid their spread and re-rooting. Our goal was to assess the plant regeneration capacity after applying mechanical control (i) when placing the plant material on different types of ground surface (on sand, on stones and using rooted plants as control) and (ii) combined with the attack of specialized herbivores (the soft scale Pulvinariella mesembryanthemi). To achieve this, we evaluated how these two factors (ground surface and herbivory) affected the plant physiological activity, its survival and re-rooting, biometric measurements, shoot and root nutrient composition and biochemical parameters (total phenols and tannins). Regardless of the ground surface type, our results indicated that the specialist herbivore greatly affected the C. edulis parameters studied. The attack of P. mesembryanthemi stimulated the plant defence mechanisms, even in those individuals with less photosynthetic activity. Furthermore, P. mesembryanthemi severely reduced the biomass and volume of plant material. Decomposition of C. edulis was accelerated by the combination between the inoculation of P. mesembryanthemi and placing the plants on the stones ground surface. Overall, preventing plant re-rooting by avoiding connection to the soil is an effective method of reducing its viability after the eighth-tenth month. After applying mechanical control, we recommend placing C. edulis fragments over an inert ground surface to avoid re-rooting, which would favour its death. We conclude that the combination of mechanical control and P. mesembryanthemi or even direct inoculation with this specialist herbivore could help authorities and land managers to improve management strategies for C. edulis.