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1. Despite commonly used to unveil the complex structure of interactions within ecological communities and their value to assess their resilience against external disturbances, network analyses have seldom been applied in plant communities. We evaluated how plant-plant spatial association networks vary in global drylands and assessed whether network structure was related to plant diversity in these ecosystems. 2. We surveyed 185 dryland ecosystems from all continents except Antarctica and built networks using the local spatial association between all the perennial plants species present in the communities studied. Then, for each network, we calculated four descriptors of network structure (link density, link weight mean and heterogeneity, and structural balance) and evaluated their significance with null models. Finally, we used structural equation models to evaluate how abiotic factors (including geography, topography, climate and soil conditions) and network descriptors influenced plant species richness and evenness. 3. Plant networks were highly variable world-wide, but at most study sites (72%) presented common structures such as a higher link density than expected. We also find evidence of the presence of high structural balance in the networks studied. Moreover, all network descriptors considered had a positive and significant effect on plant diversity and on species richness in particular. 4. Synthesis. Our results constitute the first empirical evidence showing the existence of common network architectures structuring dryland plant communities at the global scale and suggest a relationship between the structure of spatial networks and plant diversity. They also highlight the importance of system-level approaches to explain the diversity and structure of interactions in plant communities, two major drivers of terrestrial ecosystem functioning.

Microbial ecosystems are almost always dominated by only a few species, but their diversity resides in the rare biosphere. These rare members are usually considered passive passengers with little influence, yet our work reveals that they can collectively determine which species to become the most abundant taxon. We describe this process as a “nomination–voting” system: competitive traits nominate potential dominants, while rare taxa vote for the ultimate winner through their complex interactions. Recognizing this hidden but decisive role of rare microbes provides a new perspective on community assembly and underscores how subtle ecological interactions shape community outcomes. This assembly framework offers new opportunities for the prediction, manipulation, and stabilization of agriculture, health, and environmental microbiomes.

Background Inherent characteristics and changes in the physiology of rice as it attains salt tolerance affect the colonizing bacterial endophytic communities of the rice seeds. These transmissible endophytes also serve as a source of the plant’s microbial community and concurrently respond to the host and environmental conditions. This study explores the influence of the rice host as well as the impact of soil salinity on the community structure and diversity of seed bacterial endophytes of rice with varying tolerance to salt stress. Endophytic bacterial diversity was studied through culture-dependent technique and Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis. Results Results revealed considerably diverse communities of bacterial endophytes in the interior of rice seeds. The overall endophytic bacterial communities of the indica rice seeds based on 16S rRNA analysis of clones and isolates are dominated by phylum Proteobacteria followed by Actinobacteria and Firmicutes. Community profiles show common ribotypes found in all cultivars of the indica subspecies representing potential core microbiota belonging to Curtobacterium , Flavobacterium , Enterobacter , Xanthomonas , Herbaspirillum , Microbacterium and Stenotrophomonas . Clustering analysis shows that the host genotype mainly influences the seed endophytic community of the different rice cultivars. Under salt stress conditions, endophytic communities of the salt-sensitive and salt-tolerant rice cultivars shift their dominance to bacterial groups belonging to Flavobacterium , Pantoea , Enterobacter , Microbacterium , Kosakonia and Curtobacterium . Conclusion The endophytic communities of rice indica seeds are shaped by the hosts’ genotype, their physiological adaptation to salt stress and phylogenetic relatedness. Under salt stress conditions, a few groups of bacterial communities become prominent causing a shift in bacterial diversity and dominance.

Background and aimsKarst rocky desertification (KRD) influences soil properties and plant species. Soil microbes are important factors in maintaining ecosystem stability. However, little is known about the role of fungi in adaptation of plants to KRD.MethodsFungi colonized in bulk soil, rhizosphere, and roots of Themeda japonica at strong and slight KRD were analyzed by ITS2 amplicon sequencing. The relationship between soil nutrients and fungal diversity was estimated by redundancy analysis (RDA) and Spearman analysis.ResultsAN, NN, SOC, TN, TP content and pH in strong KRD soil were higher than those with slight KRD. Rhizosphere with slight KRD had higher fungal richness and diversity than it with strong KRD, but there was no difference in root endophyte between KRD grades. The bulk soil with slight KRD had higher fungal richness compare to strong KRD. The fungal communities in bulk soil, rhizosphere, and root between plants at different KRD grades were significantly different. In addition, the fungal communities of rhizosphere were sensitive to the change of KRD environment. Ascomycota and Basidiomycota were the predominant phyla in bulk soil, rhizosphere and root endophyte at strong and slight KRD. SOC, AN and pH influenced the composition of fungal communities at strong KRD. In contrast, TN and AN had a negative impact on richness.ConclusionOur results suggest that fungal communities of rhizosphere may play a role in adaptation of T. japonica to KRD and may contribute to promote plant growth and ecological performance in karst areas.

Biochar amendment has been proposed as a strategy to improve acidic soils after overuse of nitrogen fertilizers. However, little is known of the role of biochar in soil microbial biomass carbon (MBC) and bacterial community structure and diversity after soil acidification induced by nitrogen (N) deposition. Using high-throughput sequencing of the 16S rRNA gene, we determined the effects of biochar amendment (BC0, 0 t bamboo biochar ha−1; BC20, 20 t bamboo biochar ha−1; and BC40, 40 t bamboo biochar ha−1) on the soil bacterial community structure and diversity in Moso bamboo plantations that had received simulated N deposition (N30, 30 kg N ha−1 yr−1; N60, 60 kg N ha−1 yr−1; N90, 90 kg N ha−1 yr−1; and N-free) for 21 months. After treatment of N-free plots, BC20 significantly increased soil MBC and bacterial diversity, while BC40 significantly decreased soil MBC but increased bacterial diversity. When used to amend N30 and N60 plots, biochar significantly decreased soil MBC and the reducing effect increased with biochar amendment amount. However, these significant effects were not observed in N90 plots. Under N deposition, biochar amendment largely increased soil bacterial diversity, and these effects depended on the rates of N deposition and biochar amendment. Soil bacterial diversity was significantly related to the soil C/N ratio, pH, and soil organic carbon content. These findings suggest an optimal approach for using biochar to offset the effects of N deposition in plantation soils and provide a new perspective for understanding the potential role of biochar amendments in plantation soil.

Soybean continuous cropping (SC) leads to continuous cropping obstacles, and soil-borne fungal diseases occur frequently. Rotation can alleviate continuous cropping obstacles. However, the long-term effects of continuous cropping and rotation on the structure and function of the fungal community in soil are not clear. In this study, five cropping systems, SC, fallow (CK), fallow-soybean (FS), corn–soybean (CS), and wheat–soybean (WS), were implemented in the long-term continuous cropping area of soybean. After 13 years of planting, high-throughput sequencing was used to evaluate the structure and diversity of soil fungal communities and to study the relationship between fungal communities and soil environmental factors. The results showed that the abundance and diversity of fungal flora in SC soil were the highest. There were significant differences in the formation of soil fungal communities between soybean continuous cropping and the other treatments. There were 355 species of endemic fungi in SC soil. There were 231 and 120 endemic species in WS and CS, respectively. The relative abundance of the potential pathogens Lectera , Gibberella , and Fusarium in the SC treatment soil was significantly high, and the abundance of all potential pathogens in CK was significantly the lowest. The abundance of Lectera and Fusarium in CS was significantly the lowest. There was a positive correlation between potential pathogens in the soil. The relative abundance of potential pathogens in the soil was significantly positively correlated with the relative abundance of Ascomycetes and negatively correlated with the relative abundance of Basidiomycetes. Potential pathogenic genera had a significant negative correlation with soil OM, available Mn, K and soil pH and a significant positive correlation with the contents of soil available Cu, Fe, and Zn. In general, the fungal communities of SC, FS, WS, and CS were divided into one group, which was significantly different from CK. WS and CS were more similar in fungal community structure. The CK and CS treatments reduced the relative abundance of soil fungi and potential pathogens. Our study shows that SC and FS lead to selective stress on fungi and pathogenic fungi and lead to the development of fungal community abundance and diversity, while CK and CS can reduce this development, which is conducive to plant health.

Background The shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf ( Ophiopogon japonicus , OJ) and shade-intolerant perennial turf-type ryegrass ( Lolium perenne , LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing. Results OJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria . Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO 3 − -N, NH 4 + -N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion Soil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.

Boundaries between environments provide important insight into how ecological communities are structured across broader landscapes. Of particular interest is how communities assemble within the transition zone constituting the boundary (i.e., where the transition in environmental variables occurs) and whether transitions in community composition parallel transitions in environmental variables. While ecological boundaries have a long history in classic ecology, similar concepts have recently emerged in microbiota literature. Currently, however, most studies of microbial ecological boundaries focus on environmental microbiota, rather than host-associated (HA) microbiota. This is likely because it is unclear what constitutes an ecological boundary in HA microbiota systems. We propose hybrid hosts as an HA analog for environmental ecological boundaries. Specifically, we outline how different types of hybrid hosts serve as models for different types of ecological boundaries. We then outline how the ecological boundary framework can be used to interpret HA microbial community coalescence (i.e., mixing) across host species. Finally, we suggest that many hybrid hosts reside within the transition zones of larger scale ecological boundaries. When this happens, hybrid hosts can be used to examine a novel phenomenon that we term a “multiscale ecological boundary.”

Understanding microbiome dynamics requires capturing not only changes in microbial composition but also interactions between community members. Traditional approaches frequently overlook microbe-microbe interactions, limiting their ecological interpretation. Here, we introduce a novel computational framework that integrates compositional data with network-based analyses, significantly improving the detection of biologically meaningful patterns in community variation. By applying this framework to a large data set from the plant microbiota, we identify representative groups of interacting microbes driving differences across microhabitats and environmental conditions. Our analysis framework, implemented in an R package “mina,” provides robust tools allowing researchers to assess statistical differences between microbial networks and detect condition-specific interactions. Broadly applicable to microbiome data sets, our framework is aimed at enabling advances in our understanding of microbial interactions within complex communities.

PurposeRare-earth elements (REEs) have been listed as emerging pollutants, and REEs often occur together with heavy metals (HMs) in the environment. Large amounts of REEs and their coexisting HMs enter into the surrounding soils through dust, surface runoff, and leachate, causing serious REE and HM co-contamination and resulting in ecological crisis. The ecological effects caused by REEs have been gradually concerned, but ignore the synergistic effect of coexistence with HMs. Soil microorganisms are closely related to the soil ecosystem stability. At present, under long-term REE–HM disturbance, the response of bacterial and fungal communities and the effects of community functions remain unclear. In this study, the response of bacterial and fungal communities to different REE and HM co-contamination levels and the community predicted function were analyzed.Methods16S rRNA and ITS1 high-throughput sequencing were performed for bacteria and fungi, respectively. The bacteria community functions were predicted using the PICRUSt2 method.ResultsThe co-contamination caused decreases in bacterial and fungal community richness and diversity, with significant changes in community structure and composition, especially in the most serious co-contaminated soils. With the increase in the pollution levels, the bacterial communities became reorganize, whereas fungal communities had a certain buffer capacity. The microbial symbiotic pattern changed under severe co-contamination conditions, and microorganisms enhanced interactions to advance the dominant taxa adaptability or resistance. Bacterial communities developed more competitive relationships, whereas fungal communities developed more symbiotic relationships. Thus, bacteria are more sensitive than fungi. PICRUSt2 prediction results showed that bacterial community could resist cell damage caused by exotic REEs and HMs by strengthening the efflux transport system, DNA repair function, cell defense mechanism, and detoxification mechanism. The co-contamination might enhance bacterial antibiotic resistance; dissimilatory and assimilatory nitrate reduction and denitrification might be the nitrogen metabolic predominant processes.ConclusionFor the first time, we systematically confirmed that bacteria and fungi respond differently under long-term REE and HM exposure: bacterial are more sensitive than fungi. The ecological functions of bacterial community were changed, and the ecological risk of desert steppe soil environment might be increased. Our results have important significance for ecological risk assessments in co-contamination environment.