Relationships between plant diversity and soil microbial diversity vary across taxonomic groups and spatial scales

Soil Fungal Diversity, Community Structure, and Network Stability in the Southwestern Tibetan Plateau

Despite substantial research on how environmental factors affect fungal diversity, the mechanisms shaping regional-scale diversity patterns remain poorly understood. This study employed ITS high-throughput sequencing to evaluate soil fungal diversity, community composition, and co-occurrence networks across alpine meadows, desert steppes, and alpine shrublands in the southwestern Tibetan Plateau. We found significantly higher fungal α-diversity in alpine meadows and desert steppes than in alpine shrublands. Random forest and CAP analyses identified the mean annual temperature (MAT) and normalized difference vegetation index (NDVI) as major ecological drivers. Mantel tests revealed that soil physicochemical properties explained more variation than climate, indicating an indirect climatic influence via soil characteristics. Distance-decay relationships suggested that environmental heterogeneity and species interactions drive community isolation. Structural equation modeling confirmed that the MAT and NDVI regulate soil pH and carbon/nitrogen availability, thereby influencing fungal richness. The highly modular fungal co-occurrence network depended on key nodes for connectivity. Vegetation coverage correlated positively with network structure, while soil pH strongly affected network stability. Spatial heterogeneity constrained stability and diversity through resource distribution and niche segregation, whereas stable networks concentrated resources among dominant species. These findings enhance our understanding of fungal assemblage processes at a regional scale, providing a scientific basis for the management of soil fungal resources in plateau ecosystems.

Impacts of forest expansion on microbial diversity and community assembly in fragmented mountain ecosystems

Under the influence of global climate change and human activities, forest expansion has become increasingly significant in shaping ecosystems. However, its effects on soil microbial communities remain poorly understood. This study investigates the impacts of forest expansion on soil bacteria, fungi, and protists within mountaintop forest ecosystems. Soil samples were collected from three forest habitats: non-forest expansion mountaintops (NFE-Top), forest expansion mountaintops (FE-Top) and mountain bottoms (FE-Bottom). This study revealed that forest expansion promoted microbial sharing between mountaintop and bottom forests, resulting in greater community similarity between FE-Top and FE-Bottom compared to NFE-Top and FE-Bottom. Notably, forest expansion significantly reduced microbial diversity and altered community composition, particularly within bacterial communities. Microbial network analyses indicated that forest expansion mountaintops were more stable, with higher robustness, and lower vulnerability than non-forest expansion mountaintops. Stochastic assembly processes dominated the microbial communities across all forest habitats, with their relative importance increasing after forest expansion. Furthermore, forest expansion decreased the community-level habitat niche breadth of microbial communities. Distinct environmental factors were the primary indicators of microbial community dissimilarities across different habitats, with TP, pH, and moisture acting as key indicators of these differences in NFE-Top, FE-Top, and FE-Bottom, respectively. These findings highlight the important role of forest expansion in shaping microbial community dynamics and emphasize the potential of microbial communities as indicators of ecosystem changes.

Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures

Introduction

The production environment of extensively raised village chickens necessitates their adaptability to low-resource systems. The gut microbiome plays a critical role in supporting this adaptability by influencing health and productivity. This study aimed to investigate the diversity and functional capacities of the faecal microbiome in village chickens from Limpopo and KwaZulu-Natal provinces of South Africa.

Methods

Using a combination of 16S rRNA gene sequencing and shotgun metagenomic sequencing technologies, we analysed 98 16S rRNA and 72 metagenomic datasets. Taxonomic profiles and functional gene annotations were derived, focusing on microbial diversity, antibiotic resistance genes (ARGs), and potential zoonotic pathogens.

Results

Taxonomic analysis showed that the predominant phyla in both provinces were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. At the genus level, Escherichia and Shigella were prevalent, with Escherichia coli and Shigella dysenteriae identified as major contributors to the gut microbiome. ARGs were identified, with MarA, PmrF, and AcrE detected in KwaZulu-Natal, and cpxA, mdtG, and TolA in Limpopo. These genes primarily mediate antibiotic efflux and alteration.

Discussion

The detection of zoonotic bacteria such as Escherichia coli and Streptococcus spp. highlights potential health risks to humans through the food chain, emphasizing the importance of improved household hygiene practices. This study underscores the role of the gut microbiome in village chicken health and adaptability, linking microbial diversity to production efficiency in low-resource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.

Effects of alligator weed invasion on wetlands in protected areas: A case study of Lishui Jiulong National Wetland Park

Wetlands are one of the ecosystems most easily and severely invaded by alien species. Biological invasions can have significant impacts on local plant communities and ecosystem functioning. While numerous studies have assessed the impacts of biological invasions on wetlands, relatively few have been conducted in protected areas such as national wetland parks. We conducted a field survey to investigate the effects of the invasive herb Alternanthera philoxeroides (alligator weed) on the productivity and structure of plant communities and soil microbial communities in the Lishui Jiulong National Wetland Park in Zhejiang, China. We also examined the potential influence of the distance to the river edge on the impact of the alligator weed invasion. The alligator weed invasion significantly altered the plant community structure. It reduced the coverage of co-occurring plant species, including native (-31.2 %), invasive (-70.1 %), and non-invasive alien plants (-58.4 %). However, it increased species richness by 50 %, Pielou's evenness by 20 %, and Simpson's diversity index by 29.1 % for the overall plant community. Furthermore, within the community not invaded by alligator weed, increasing the distance to the river edge decreased the number of native plants by 57.0 % and the aboveground biomass of other invasive plants by 78.6 %. Contrary to expectations, no effects of the alligator weed invasion were observed on soil fungal and bacterial communities. Therefore, the impacts of the alligator weed invasion varied with spatial context and plant category, emphasizing the need to consider multiple scales and environmental factors when assessing the effects of invasive species on plant biodiversity. These insights enhance our understanding of plant invasions in wetlands and can guide the development of effective management strategies for these important ecosystems.

Molecular Diversity of Ectomycorrhizal Fungi in Relation to the Diversity of Neighboring Plant Species

(1) Background: Plant diversity has long been assumed to predict soil microbial diversity. The mutualistic symbiosis between forest trees and ectomycorrhizal (EM) fungi favors strong correlations of EM fungal diversity with host density in terrestrial ecosystems. Nevertheless, in contrast with host tree effects, neighboring plant effects are less well studied. (2) Methods: In the study presented herein, we examined the α-diversity, community composition, and co-occurrence patterns of EM fungi in Quercus acutissima across different forest types (pure forests, mixed forests with Pinus tabuliformis, and mixed forests with other broadleaved species) to ascertain how the EM fungi of focal trees are related to their neighboring plants and to identify the underlying mechanisms that contribute to this relationship. (3) Results: The EM fungal community exhibited an overall modest but positive correlation with neighboring plant richness, with the associations being more pronounced in mixed forests. This neighboring effect was mediated by altered abiotic (i.e., SOC, TN, LC, and LP) and biotic (i.e., bacterial community) factors in rhizosphere soil. Further analysis revealed that Tomentella_badia, Tomentella_galzinii, and Sebacina_incrustans exhibited the most significant correlations with plant and EM fungal diversity. These keystone taxa featured low relative abundance and clear habitat preferences and shared similar physiological traits that promote nutrient uptake through contact, short-distance and medium-distance smooth contact-based exploration types, thereby enhancing the potential correlations between EM fungi and the neighboring plant community. (4) Conclusions: Our findings contribute to the comprehension of the effect of neighboring plants on the EM fungal community of focal trees of different forest communities and the biodiversity sensitivity to environmental change.

The effect of successive summer drought periods on bacterial diversity along a plant species richness gradient

Drought is a major stressor to soil microbial communities, and the intensification of climate change is predicted to increase hydric stress worldwide in the coming decades. As a possible mitigating factor for the consequences of prolonged drought periods, above and belowground biodiversity can increase ecosystem resistance and resilience by improving metabolic redundancy and complementarity as biodiversity increases. Here, we investigated the interaction effect between plant richness and successive, simulated summer drought on soil microbial communities during a period of 9 years.To do that, we made use of a well-established biodiversity experiment (The Jena Experiment) to investigate the response of microbial richness and community composition to successive drought periods alongside a plant richness gradient, which covers 1-, 2-, 4-, 8-, 16-, and 60-species plant communities. Plots were covered from natural precipitation by installing rain shelters 6 weeks every summer. Bulk soil samples were collected 1 year after the last summer drought was simulated. Our data indicate that bacterial richness increased after successive exposure to drought, with the increase being stable along the plant richness gradient. We identified a significant effect of plant species richness on the soil microbial community composition and determined the taxa significantly impacted by drought at each plant richness level. Our data successfully demonstrates that summer drought might have a legacy effect on soil bacterial communities.

In the Qaidam Basin, Soil Nutrients Directly or Indirectly Affect Desert Ecosystem Stability under Drought Stress through Plant Nutrients

The low nutrient content of soil in desert ecosystems results in unique physiological and ecological characteristics of plants under long-term water and nutrient stress, which is the basis for the productivity and stability maintenance of the desert ecosystem. However, the relationship between the soil and the plant nutrient elements in the desert ecosystem and its mechanism for maintaining ecosystem stability is still unclear. In this study, 35 sampling sites were established in an area with typical desert vegetation in the Qaidam Basin, based on a drought gradient. A total of 90 soil samples and 100 plant samples were collected, and the soil's physico-chemical properties, as well as the nutrient elements in the plant leaves, were measured. Regression analysis, redundancy analysis (RDA), the Theil-Sen Median and Mann-Kendall methods, the structural equation model (SEM), and other methods were employed to analyze the distribution characteristics of the soil and plant nutrient elements along the drought gradient and the relationship between the soil and leaf nutrient elements and its impact on ecosystem stability. The results provided the following conclusions: Compared with the nutrient elements in plant leaves, the soil's nutrient elements had a more obvious regularity of distribution along the drought gradient. A strong correlation was observed between the soil and leaf nutrient elements, with soil organic carbon and alkali-hydrolyzed nitrogen identified as important factors influencing the leaf nutrient content. The SEM showed that the soil's organic carbon had a positive effect on ecosystem stability by influencing the leaf carbon, while the soil's available phosphorus and the mean annual temperature had a direct positive effect on stability, and the soil's total nitrogen had a negative effect on stability. In general, the soil nutrient content was high in areas with a low mean annual temperature and high precipitation, and the ecosystem stability in the area distribution of typical desert vegetation in the Qaidam Basin was low. These findings reveal that soil nutrients affect the stability of desert ecosystems directly or indirectly through plant nutrients in the Qaidam Basin, which is crucial for maintaining the stability of desert ecosystems with the background of climate change.

Contrasting roles of plant, bacterial, and fungal diversity in soil organic carbon accrual during ecosystem restoration: A meta-analysis

Plant and microbial diversity plays vital roles in soil organic carbon (SOC) accumulation during ecosystem restoration. However, how soil microbial diversity mediates the positive effects of plant diversity on carbon accumulation during vegetation restoration remains unclear. We conducted a large-scale meta-analysis with 353 paired observations from 65 studies to examine how plant and microbial diversity changed over 0-160 years of natural restoration and its connection to SOC accrual in the topsoil (0-10 cm). Results showed that natural restoration significantly increased plant aboveground biomass (122.09 %), belowground biomass (153.05 %), and richness (21.99 %) and SOC accumulation (32.34 %) but had no significant impact on microbial diversity. Over time, bacterial and fungal richness increased and then decreased. The responses of major microbial phyla, in terms of relative abundance, varied across restoration and ecosystem types. Specifically, Ascomycota and Zygomycota decreased more under farmland abandonment than under grazing exclusion. In forest, Bacteroidetes, Ascomycota, and Zygomycota significantly decreased after natural restoration. The increase in SOC and Basidiomycota was higher in forest than in grassland. Based on standardized estimates, structural equation modeling showed that plant diversity had the highest positive effect (0.55) on SOC accrual, and while fungal diversity (0.15) also had a positive effective, bacterial diversity (-0.20) had a negative effect. Plant diversity promoted SOC accumulation by directly impacting biomass and soil moisture and total nitrogen and indirectly influencing soil microbial richness. This meta-analysis highlights the significant roles of plant diversity and microbial diversity in carbon accumulation during natural restoration and elucidates their relative contributions to carbon accumulation, thereby aiding in more precise predictions of soil carbon sequestration.

Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region

A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.

Response of microbial communities to the changes in grazing intensity and season in a typical steppe

Livestock grazing is an influencing factor playing a key role in shaping the plant community, microbial community, and soil properties in grassland ecosystems. Northern China's Loess Plateau has been used for livestock grazing for centuries and is a vulnerable ecosystem. In this study, the fates of bacterial and fungal communities of the typical steppe of the Loess Plateau were investigated under increasing grazing intensities practiced in summer and winter seasons. The results revealed changes in soil physiochemical properties, plant community properties, and microbial diversity in response to alterations in the grazing intensity. The alpha diversity of microbial communities (including bacteria and fungi) exhibited an uneven trend during summer grazing due to an increase in grazing intensity, but it decreased during winter grazing; however, the observed changes were not significant. The beta diversity of the bacterial community was highly influenced by grazing intensity, the summer community clustered near nongrazing, and the winter community presented significantly different results. The beta diversity of the fungal community was not influenced by grazing intensity or season. Grazing induced the growth of fast-growing bacteria (such as Actinobacteria and Firmicutes) and saprophytic fungi and a reduction in overall pathogenic traits. Co-occurrence network analysis and a structural equation model revealed changes in soil and plant properties (such as soil nitrogen level, soil organic carbon level, aboveground biomass, and litter biomass), with an increase in grazing intensity contributing to alterations in bacterial and fungal diversities. This finding demonstrates that grazing intensity can directly affect soil microbes and play an indirect role by modifying soil nutrients and reducing plant biomass, which eventually contributes to changes in microbial communities. Overall, implementing low grazing intensity is suggested for maintaining the microbial community structure the same as that of the native microbiome (ungrazed) in the steppe ecosystems.

Beneath the blooms: Unearthing the effect of rhizospheric bacteria on floral signals and pollinator preferences

The relationship between plants and pollinators is known to be influenced by ecological interactions with other community members. While most research has focused on aboveground communities affecting plant-pollinator interactions, it is increasingly recognized that soil-dwelling organisms can directly or indirectly impact these interactions. Although studies have examined the effects of arbuscular mycorrhizal fungi on floral traits, there is a gap in research regarding similar effects associated with plant growth-promoting rhizobacteria (PGPR), particularly concerning floral scent. Our study aimed to investigate the influence of the PGPR Bacillus amyloliquefaciens on the floral traits of wild (Solanum habrochaites, Solanum pimpinellifolium and Solanum peruvianum) and cultivated tomato (Solanum lycopersicum), as well as the impact of microbially-driven changes in floral scent on the foraging behaviour of the stingless bee Melipona quadrifasciata. Our findings revealed that inoculating tomatoes with PGPR led to an increased number of flowers and enhanced overall floral volatile emission. Additionally, we observed higher flower biomass and pollen levels in all species, except S. peruvianum. Importantly, these changes in volatile emissions influenced the foraging behaviour of M. quadrifasciata significantly. Our results highlight the impact of beneficial soil microbes on plant-pollinator interactions, shedding light on the multiple effects that plant-microbial interactions can have on aboveground organisms.

The invasive legume Lupinus polyphyllus has minor site-specific impacts on the composition of soil bacterial communities

Plant invasions can have major impacts on ecosystems, both above- and belowground. In particular, invasions by legumes, which often host nitrogen-fixing symbionts (rhizobia), are known to modify soil bacterial communities. Here, we examined the effect of the invasive herbaceous legume Lupinus polyphyllus on the alpha diversity and community composition of soil bacteria. We also explored the relationships between these bacterial communities and vegetation cover, the cover of other (non-invasive) legumes, or the number of vascular plants present. For this, we sampled rhizosphere soil and surveyed vegetation from ten paired sites (uninvaded versus invaded more than 10 years ago) in southwestern Finland, and identified bacterial DNA using 16S rRNA gene amplicon sequencing. The presence of the plant invader and the three vegetation variables considered had no effect on the alpha diversity of soil bacteria in terms of bacterial richness or Shannon and Inverse Simpson diversity indices. However, the composition of soil bacterial communities differed between invaded and uninvaded soils at four out of the ten sites. Interestingly, the relative abundances of the top bacterial families in invaded and uninvaded soils were inconsistent across sites, including for legume-associated rhizobia in the family Bradyrhizobiaceae. Other factors-such as vegetation cover, legume cover (excluding L. polyphyllus), number of plant species-also explained a small proportion of the variation in bacterial community composition. Our findings indicate that L. polyphyllus has the potential to modify the composition of local soil bacterial community, at least in sites where it has been present for more than a decade.

Mapping wild vascular plant species diversity in urban areas in California using crowdsourcing data by regression kriging: Examining socioeconomic disparities

Biodiversity is crucial for human health, but previous methods of measuring biodiversity require intensive resources and have other limitations. Crowdsourced datasets from citizen scientists offer a cost-effective solution for characterizing biodiversity on a large spatial scale. This study has two aims: 1) to generate fine-resolution plant species diversity maps in California urban areas using crowdsourced data and extrapolation methods; and 2) to examine their associations with sociodemographic factors and identify subpopulations with low biodiversity exposure. We used iNaturalist observations from 2019 to 2022 to calculate species diversity metrics by exploring the sampling completeness in a 5 × 5-km2 grid and then computing species diversity metrics for grid cells with at least 80 % sample completeness (841 out of 4755 grid cells). A generalized additive model with ordinary kriging (GAM OK) provided moderately reliable estimates, with correlations of 0.64-0.66 between observed and extrapolated metrics, relative mean absolute errors of 21 %-23 %, and relative root mean squared errors of 27 %-30 % for grid cells with ≥80 % sample completeness from 10-fold cross-validation. GAM OK was further applied to extrapolate species diversity metrics from saturated grid cells (N = 841) to the remaining grid cells with <80 % sample completeness (N = 3914) and generate diversity maps that cover the grid. Further, generalized linear mixed models were used to examine the associations between species diversity and sociodemographic indicators at census tract level. The wild vascular plant species diversity metrics were inversely associated with neighborhood socioeconomic status (i.e., unemployment, linguistic isolation, educational attainment, and poverty rate). Minority populations (i.e., African American, Asian American, and Hispanic) and children had significantly lower diversity exposure in their neighborhoods. Crowdsourcing data offers a cost-effective solution for characterizing large-scale biodiversity in urban areas.

Structure of plant-associated microeukaryotes in roots and leaves of aquatic and terrestrial plants revealed by blocking peptide-nucleic acid (PNA) amplification

Studies of plant-microbe interactions, including mutualistic, antagonistic, parasitic, or commensal microbes, have greatly benefited our understanding of ecosystem functioning. New molecular identification tools have increasingly revealed the association patterns between microorganisms and plants. Here, we integrated long-read PacBio single-molecule sequencing technology with a blocking protein-nucleic acid (PNA) approach to minimise plant amplicons in a survey of plant-eukaryotic microbe relationships in roots and leaves of different aquatic and terrestrial plants to determine patterns of organ, host, and habitat preferences. The PNA approach reduced the samples' relative amounts of plant reads and did not distort the fungal and other microeukaryotic composition. Our analyses revealed that the eukaryotic microbiomes associated with leaves and roots of aquatic plants exhibit a much larger proportion of non-fungal microorganisms than terrestrial plants, and leaf and root microbiomes are similar. Terrestrial plants had much stronger differentiation of leaf and root microbiomes and stronger partner specificity than aquatic plants.

Improved description of terrestrial habitat types by including microbial communities as indicators

Soils host diverse communities of microorganisms essential for ecosystem functions and soil health. Despite their importance, microorganisms are not covered by legislation protecting biodiversity or habitats, such as the Habitats Directive. Advances in molecular methods have caused breakthroughs in microbial community analysis, and recent studies have shown that parts of the communities are habitat-specific. If distinct microbial communities are present in the habitat types defined in the Habitats Directive, the Directive may be improved by including these communities. Thus, monitoring and reporting of biodiversity and conservation status of habitat types could be based not only on plant communities but also on microbial communities. In the present study, bacterial and plant communities were examined in six habitat types defined in the Habitats Directive by conducting botanical surveys and collecting soil samples for amplicon sequencing across 19 sites in Denmark. Furthermore, selected physico-chemical properties expected to differ between habitat types and explain variations in community composition of bacteria and vegetation were analysed (pH, electrical conductivity (EC), soil texture, soil water repellency, soil organic carbon content (OC), inorganic nitrogen, and in-situ water content (SWC)). Despite some variations within the same habitat type and overlaps between habitat types, habitat-specific communities were observed for both bacterial and plant communities, but no correlation was observed between the alpha diversity of vegetation and bacteria. PERMANOVA analysis was used to evaluate the variables best able to explain variation in the community composition of vegetation and bacteria. Habitat type alone could explain 46% and 47% of the variation in bacterial and plant communities, respectively. Excluding habitat type as a variable, the best model (pH, SWC, OC, fine silt, and Shannon's diversity index for vegetation) could explain 37% of the variation for bacteria. For vegetation, the best model (pH, EC, ammonium content and Shannon's diversity index for bacteria) could explain 25% of the variation. Based on these results, bacterial communities could be included in the Habitats Directive to improve the monitoring, as microorganisms are more sensitive to changes in the environment compared to vegetation, which the current monitoring is based on.

Contrasting effects of bioenergy crops on biodiversity

Agriculture is driving biodiversity loss, and future bioenergy cropping systems have the potential to ameliorate or exacerbate these effects. Using a long-term experimental array of 10 bioenergy cropping systems, we quantified diversity of plants, invertebrates, vertebrates, and microbes in each crop. For many taxonomic groups, alternative annual cropping systems provided no biodiversity benefits when compared to corn (the business-as-usual bioenergy crop in the United States), and simple perennial grass-based systems provided only modest gains. In contrast, for most animal groups, richness in plant-diverse perennial systems was much higher than in annual crops or simple perennial systems. Microbial richness patterns were more eclectic, although some groups responded positively to plant diversity. Future agricultural landscapes incorporating plant-diverse perennial bioenergy cropping systems could be of high conservation value. However, increased use of annual crops will continue to have negative effects, and simple perennial grass systems may provide little improvement over annual crops.

Comparative analysis of microbial community structure in different times of Panax ginseng Rhizosphere microbiome and soil properties under larch forest

BACKGROUND

Panax ginseng cultivated under the forest is popular because its shape and effective ingredients are similar to wild ginseng. The growth of P. ginseng in the larch forest is generally better than in the broad-leaved forest, and the incidence rate of diseases is low. Therefore, the selection of forest species is one of the basic factors in the successful cropping of P. ginseng.

METHODS

Illumina HiSeq high-throughput sequencing was used to analyze the 16S rRNA/ITS gene sequence of P. ginseng rhizosphere soil under larch forest to study the rhizosphere microbiome's diversity and community composition structure.

RESULTS

The species classification and richness of rhizosphere bacterial and fungal communities in the same-aged P. ginseng were similar. Consistent with the soil system of commonly cultivated crops, Proteobacteria, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, Chloroflexi, and Basidiomycota, Ascomycota were the dominant phylum of bacteria and fungi, respectively. Compared with the soil without planting P. ginseng, the diversity of microorganisms and community structure of continuous planting for 2 years, 5 years, and 18 years of P. ginseng rhizosphere soil had little change. The accumulation levels of Ilyonectria, Fusarium, Gibberella, and Cylindrocarpon were not significantly increased with planting P. ginseng and the increased age of cropping P. ginseng.

CONCLUSIONS

The results of this study showed that the soil function of the larch forest was good, which provided a theoretical basis for the land selection and soil improvement of cultivating P. ginseng under the larch forest.

Biogeography of Fungal Communities Associated with Pinus sylvestris L. and Picea abies (L.) H. Karst. along the Latitudinal Gradient in Europe

We assessed the diversity and composition of fungal communities in different functional tissues and the rhizosphere soil of Pinus sylvestris and Picea abies stands along the latitudinal gradient of these tree species distributions in Europe to model possible changes in fungal communities imposed by climate change. For each tree species, living needles, shoots, roots, and the rhizosphere soil were sampled and subjected to high-throughput sequencing. Results showed that the latitude and the host tree species had a limited effect on the diversity and composition of fungal communities, which were largely explained by the environmental variables of each site and the substrate they colonize. The mean annual temperature and mean annual precipitation had a strong effect on root fungal communities, isothermality on needle fungal communities, mean temperature of the warmest quarter and precipitation of the driest month on shoot fungal communities, and precipitation seasonality on soil fungal communities. Fungal communities of both tree species are predicted to shift to habitats with a lower annual temperature amplitude and with increasing precipitation during the driest month, but the suitability of these habitats as compared to the present conditions is predicted to decrease in the future.

Composition, Abundance, and Diversity of the Soil Microbiome Associated with the Halophytic Plants Tamarix aphylla and Halopeplis perfoliata on Jeddah Seacoast, Saudi Arabia

The coast of the Red Sea in Jeddah City is home to a unique microbial community that has adapted to extreme environmental conditions. Therefore, it is essential to characterize the microbial community in this unique microbiome to predict how environmental changes will affect it. The aim of this study was to conduct metagenomic sequencing of 16S rRNA and ITS rRNA genes for the taxonomic classification of the microbial community in soil samples associated with the halophytic plants Tamarix aphylla and Halopeplis perfoliata. Fifteen soil samples were collected in triplicate to enhance robustness and minimize sampling bias. Firstly, to identify novel microbial candidates, the gDNAs were isolated from the saline soil samples surrounding each plant, and then bacterial 16S (V3-V4) and fungal ITS1 regions were sequenced utilizing a high-throughput approach (next-generation sequencing; NGS) on an Illumina MiSeq platform. Quality assessment of the constructed amplicon libraries was conducted using Agilent Bioanalyzer and fluorometric quantification methods. The raw data were processed and analyzed using the Pipeline (Nova Lifetech, Singapore) for bioinformatics analysis. Based on the total number of readings, it was determined that the phylum Actinobacteriota was the most prevalent in the soil samples examined, followed by the phylum Proteobacteria. Based on ITS rRNA gene analysis, the alpha and beta fungal diversity in the studied soil samples revealed that the fungal population is structured into various groups according to the crust (c) and/or rhizosphere (r) plant parts. Fungal communities in the soil samples indicated that Ascomycota and Basidiomycota were the two most abundant phyla based on the total amount of sequence reads. Secondly, heat-map analysis of the diversity indices showed that the bacterial alpha diversity, as measured by Shannon, Simpson, and InvSimpson, was associated with soil crust (Hc and Tc enclosing H. perfoliata and T. aphylla, respectively) and that the soil rhizosphere (Hr and Tr) was strongly correlated with bacterial beta diversity. Finally, fungal-associated Tc and Hc samples clustered together, according to observations made using the Fisher and Chao1 methods, and Hr and Tr samples clustered together according to Shannon, Simpson, and InvSimpson analyses. As a result of the soil investigation, potential agents that have been identified could lead to innovative agricultural, medical, and industrial applications.

Above- and belowground linkages during extreme moisture excess: leveraging knowledge from natural ecosystems to better understand implications for row-crop agroecosystems

Above- and belowground linkages are responsible for some of the most important ecosystem processes in unmanaged terrestrial systems including net primary production, decomposition, and carbon sequestration. Global change biology is currently altering above- and belowground interactions, reducing ecosystem services provided by natural systems. Less is known regarding how above- and belowground linkages impact climate resilience, especially in intentionally managed cropping systems. Waterlogged or flooded conditions will continue to increase across the Midwestern USA due to climate change. The objective of this paper is to explore what is currently known regarding above- and belowground linkages and how they impact biological, biochemical, and physiological processes in systems experiencing waterlogged conditions. We also identify key above- and belowground processes that are critical for climate resilience in Midwestern cropping systems by exploring various interactions that occur within unmanaged landscapes. Above- and belowground interactions that support plant growth and development, foster multi-trophic-level interactions, and stimulate balanced nutrient cycling are critical for crops experiencing waterlogged conditions. Moreover, incorporating ecological principles such as increasing plant diversity by incorporating crop rotations and adaptive management via delayed planting dates and adjustments in nutrient management will be critical for fostering climate resilience in row-crop agriculture moving forward.

Soil Bacterial Assemblage Across a Production Landscape: Agriculture Increases Diversity While Revegetation Recovers Community Composition

Aboveground ecological impacts associated with agricultural land use change are evident as natural plant communities are replaced with managed production systems. These impacts have been extensively studied, unlike those belowground, which remain poorly understood. Soil bacteria are good candidates to monitor belowground ecological dynamics due to their prevalence within the soil system and ability to survive under harsh and changing conditions. Here, we use soil physicochemical assessment and 16S rRNA gene sequencing to investigate the soil physical and bacterial assemblage changes across a mixed-use agricultural landscape. We assess soil from remnant vegetation (Eucalyptus mallee), new and old vineyards, old pasture, and recently revegetated areas. Elevated concentrations of nitrogen (NO₃^-) and plant-available (Colwell) phosphorus were identified in the managed vineyard systems, highlighting the impact of agricultural inputs on soil nutrition. Alpha diversity comparison revealed a significant difference between the remnant mallee vegetation and the vineyard systems, with vineyards supporting highest bacterial diversity. Bacterial community composition of recently revegetated areas was similar to remnant vegetation systems, suggesting that bacterial communities can respond quickly to aboveground changes, and that actions taken to restore native plant communities may also act to recover natural microbial communities, with implications for soil and plant health. Findings here suggest that agriculture may disrupt the correlation between above- and belowground diversities by altering the natural processes that otherwise govern this relationship (e.g. disturbance, plant production, diversity of inputs), leading to the promotion of belowground microbial diversity in agricultural systems.

Carbon source utilization pattern of soil bacterial microbiome of bambara groundnut rhizosphere at the different growth stages determines soil fertility

The diversity of microbes in the soil of plants is important for sustainable agriculture as these microbes are important in carrying out different functional processes to improve the soil and invariably plant growth. Inversely the presence of the crop also affects the types of microbial communities in the soil. In this study, bambara groundnut was grown during the planting season in South Africa, from November to March 2014/2015 and 2015/2016 and soil samples were taken after every 4 weeks after planting. Soil samples were taken 15 cm deep from 2 different landraces named VBR and VL. Microbial diversity was determined by soil microbial Carbon Source Utilization Profiles (CSUP) using BIOLOG™ GN2 plates. The abundance and richness of the soil microbes was also determined using the Shannon-Weaver and Evenness diversity indices. The diversity of the soil microbial population changed over the stages of plant growth, according to cluster analysis. Bacterial abundance and diversity were higher at 4 and 8 weeks after planting (WAP). The microbial abundance (richness index) in this study ranged from 0.64 to 0.94 with cultivar VL2 at 8 WAP being the highest while bulk soil (control), R2 was the lowest. The Shannon-Weaver index varied between 2.19 and 4.00 with the lowest corresponding to control while the highest was VL2 at 8 WAP. Carbon sources utilized by bacterial communities spread across the 96 carbon sources. The highest utilization of carboxylic acids, ester, amino acids and polymers and carbohydrates was found in the bacterial communities of the different landraces across growth stages. The highest utilization of alcohols, amides, amines, aromatic chemicals, brominated chemicals and phosphorylated chemicals was found in the control landraces. This indicates that the soil samples between 4 WAP and 12 WAP were richer in diversity of microbial species and their abundance. This soil diversity and richness is an indicator of the quality of the soil in order to increase crop yields and agricultural production.

Actinobacteria-Plant Interactions in Alleviating Abiotic Stress

Abiotic stressors, such as drought, flooding, extreme temperature, soil salinity, and metal toxicity, are the most important factors limiting crop productivity. Plants use their innate biological systems to overcome these abiotic stresses caused by environmental and edaphic conditions. Microorganisms that live in and around plant systems have incredible metabolic abilities in mitigating abiotic stress. Recent advances in multi-omics methods, such as metagenomics, genomics, transcriptomics, and proteomics, have helped to understand how plants interact with microbes and their environment. These methods aid in the construction of various metabolic models of microbes and plants, resulting in a better knowledge of all metabolic exchanges engaged during interactions. Actinobacteria are ubiquitous and are excellent candidates for plant growth promotion because of their prevalence in soil, the rhizosphere, their capacity to colonize plant roots and surfaces, and their ability to produce various secondary metabolites. Mechanisms by which actinobacteria overcome abiotic stress include the production of osmolytes, plant hormones, and enzymes, maintaining osmotic balance, and enhancing nutrient availability. With these characteristics, actinobacteria members are the most promising candidates as microbial inoculants. This review focuses on actinobacterial diversity in various plant regions as well as the impact of abiotic stress on plant-associated actinobacterial diversity and actinobacteria-mediated stress mitigation processes. The study discusses the role of multi-omics techniques in expanding plant-actinobacteria interactions, which aid plants in overcoming abiotic stresses and aims to encourage further investigations into what may be considered a relatively unexplored area of research.

Genome of Hippophae rhamnoides provides insights into a conserved molecular mechanism in actinorhizal and rhizobial symbioses

Sea buckthorn (Hippophae rhamnoides), a horticulturally multipurpose species in the family Elaeagnaceae, can build associations with Frankia actinomycetes to enable symbiotic nitrogen-fixing. Currently, no high-quality reference genome is available for an actinorhizal plant, which greatly hinders the study of actinorhizal symbiotic nodulation. Here, by combining short-read, long-read and Hi-C sequencing technologies, we generated a chromosome-level reference genome of H. rhamnoides (scaffold N50: 65 Mb, and genome size: 730 Mb) and predicted 30 812 protein-coding genes mainly on 12 pseudochromosomes. Hippophae rhamnoides was found to share a high proportion of symbiotic nodulation genes with Medicago truncatula, implying a shared molecular mechanism between actinorhizal and rhizobial symbioses. Phylogenetic analysis clustered the three paralogous NODULE INCEPTION (NIN) genes of H. rhamnoides with those of other nodulating species, forming the NIN group that most likely evolved from the ancestral NLP group. The genome of H. rhamnoides will help us to decipher the underlying genetic programming of actinorhizal symbiosis, and our high-quality genome and transcriptomic resources will make H. rhamnoides a new excellent model plant for actinorhizal symbiosis research.

Drought soil legacy alters drivers of plant diversity-productivity relationships in oldfield systems

Ecosystem functions are threatened by both recurrent droughts and declines in biodiversity at a global scale, but the drought dependency of diversity-productivity relationships remains poorly understood. Here, we use a two-phase mesocosm experiment with simulated drought and model oldfield communities (360 experimental mesocosms/plant communities) to examine drought-induced changes in soil microbial communities along a plant species richness gradient and to assess interactions between past drought (soil legacies) and subsequent drought on plant diversity-productivity relationships. We show that (i) drought decreases bacterial and fungal richness and modifies relationships between plant species richness and microbial groups; (ii) drought soil legacy increases net biodiversity effects, but responses of net biodiversity effects to plant species richness are unaffected; and (iii) linkages between plant species richness and complementarity/selection effects vary depending on past and subsequent drought. These results provide mechanistic insight into biodiversity-productivity relationships in a changing environment, with implications for the stability of ecosystem function under climate change.

Biochar-Based Compost Affects Bacterial Community Structure and Induces a Priming Effect on Soil Organic Carbon Mineralization

Urban forests are key to mitigating the Urban Heat Island Effect, which contributes to temperature increases in urban areas. However, the trees in these forests are usually under stress because urban soil is typically degraded. Biochar/compost amendments help with soil management by improving the physiochemical properties and bacterial communities of soil. Here, we compared the physiochemical properties and bacterial communities before and after (1) biochar-only and (2) biochar-based compost amendments. Our results suggested that biochar-only application did not improve soil properties after 1 year of treatment, whereas in the biochar-based compost treatment, the soil properties and bacterial communities changed after just four months. The increase in potassium and decrease in organic material, calcium, and available phosphorus in the soil of the former treatment indicated that the nutrient uptake of its trees had improved. Although there was no significant variation in the soil’s total nitrogen, the higher abundance of potential nitrogen-fixing bacteria in the biochar-based treatment suggested that the soil contained a supplement to nitrogen. Our results show that biochar-based compost amendment improves soil quality and associated bacterial communities in urban forest management.

Roles of Arbuscular Mycorrhizal Fungi on Soil Fertility: Contribution in the Improvement of Physical, Chemical, and Biological Properties of the Soil

Many of the world's soils are experiencing degradation at an alarming rate. Climate change and some agricultural management practices, such as tillage and excessive use of chemicals, have all contributed to the degradation of soil fertility. Arbuscular Mycorrhizal Fungi (AMFs) contribute to the improvement of soil fertility. Here, a short review focusing on the role of AMF in improving soil fertility is presented. The aim of this review was to explore the role of AMF in improving the chemical, physical, and biological properties of the soil. We highlight some beneficial effects of AMF on soil carbon sequestration, nutrient contents, microbial activities, and soil structure. AMF has a positive impact on the soil by producing organic acids and glomalin, which protect from soil erosion, chelate heavy metals, improve carbon sequestration, and stabilize soil macro-aggregation. AMF also recruits bacteria that produce alkaline phosphatase, a mineralization soil enzyme associated with organic phosphorus availability. Moreover, AMFs influence the composition, diversity, and activity of microbial communities in the soil through mechanisms of antagonism or cooperation. All of these AMF activities contribute to improve soil fertility. Knowledge gaps are identified and discussed in the context of future research in this review. This will help us better understand AMF, stimulate further research, and help in sustaining the soil fertility.

Can Model Experiments Give Insight into the Response of the Soil Environment to Flooding? A Comparison of Microcosm and Natural Event

Studies using soil microcosms are very common, but few involve flooded soils, and comparing the results from such an experiment with natural conditions is unheard of. In the present study, we investigated the biological activity of soil (pH value, dehydrogenases and phosphatase activities) and the metabolic potential (EcoPlate™ Biolog®) of soil microorganisms in three fluvisol subjected to flooding under laboratory and natural conditions. The results indicate that soil flooding under both natural and laboratory conditions affected soil pH, enzymatic activity and metabolic potential (AWCD, average well colour development) of soil microorganisms. Changes in these parameters are more pronounced in the microcosmic experiment than in the field conditions. Furthermore, depending on the characteristics of the soil (i.e., its type, structure, vegetation) some of the soil quality parameters may return to their preflood state. Microcosm studies are needed in environmental ecology and microbiology to predict changes due to various factors, but their scale and course must be carefully planned.

Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: A field-based experiment

Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting, we found that bacterial community composition differed among R. mangle maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of R. mangle. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.