Integrated network analysis reveals the importance of microbial interactions for maize growth

Dynamic responses of soil microbial communities to long-term co-contamination with PBAT and cadmium

The co-contamination of plastics and heavy metals poses novel challenges to agricultural soil ecosystems. However, research into the long-term effects of such co-contamination on soil microbial communities remains limited. This study, through a 540-day incubation experiment, investigated the impacts of poly(butylene adipate-co-terephthalate) (PBAT) and cadmium (Cd) co-contamination on the structure and function of soil microbial communities. The findings revealed that co-contamination significantly altered soil nitrate and ammonium nitrogen levels. Furthermore, the co-contamination continuously and significantly reduced bacterial diversity, producing a more pronounced negative impact compared to single pollution. Key microbial groups such as Proteobacteria, acting as core microorganisms, were significantly enriched under co-contamination conditions, with their relative abundance increasing significantly by 40.0 %. This indicates their potential role in plastic degradation and heavy metal resistance. In addition, the co-contamination also drove the shift of bacterial and fungal community assembly from deterministic processes to stochastic processes. These insights not only fill the research gap regarding the effects of long-term co-contamination on soil microorganisms but also provide a scientific foundation for the development of targeted soil management and remediation strategies, especially in regions where plastic and heavy metal pollution coexist.

Biophysical investigation of metal-substituted D-2-hydroxyglutarate dehydrogenase

D-2-Hydroxyglutarate dehydrogenase from Pseudomonas aeruginosa PAO1 (EC: 1.1.99.39; Uniprot ID: Q9I6H4) is a metallo-flavoenzyme that utilizes Zn2+ and FAD to catalyze the conversion of D-2-hydroxyglutarate to 2-ketoglutarate. The enzyme utilizes Co2+, Ni2+, Mn2+, and Cd2+ as alternative metal cofactors. To study how metal substitution impacts flavin properties, the enzyme was purified with different metal ions or treated with EDTA to generate the metallo-apoenzyme (EFAD-apo). Fluorescence assays revealed distinct metal ion binding sites in the enzyme: concentrations of metal ions up to ∼0.40 mM increased flavin fluorescence at 531 nm, whereas concentrations above ∼0.40 mM quenched flavin fluorescence with a 2-6 nm bathochromic shift. Concomitantly, enzyme-specific activity exhibited a sigmoidal increase, indicating a metal-induced conformational change. CD spectra showed no significant shifts at ∼209 and ∼220 nm but a ≤ 2-fold increase in mean residue ellipticity compared to EFAD-apo. Metal binding also caused a 2-9 nm bathochromic shift in flavin absorption and emission maxima, indicating stabilization of the excited-state flavin π-electron system. The binding of Zn2+, Co2+, Mn2+, or Cd2+ to the enzyme increased by ∼1 unit of the pKa value of the flavin N3 atom compared to the EFAD-apo, consistent with metal-hydrate perturbing flavin electronic properties. In contrast, Ni2+ binding decreased the pKa value, consistent with flavin N3 atom deprotonating before the Ni2+-hydrate in the enzyme active site. These findings reveal that metal ion substitution has minimal impact on the electronic properties of the flavin and the overall structural integrity of the enzyme, highlighting the potential use of metal-substituted variants of the enzyme as biomimetic catalysts.

Microbiome Analysis of Area in Proximity to White Spot Lesions Reveals More Harmful Plant Pathogens in Maize

Plant microbiomes play a major role in plant health, growth, and development, enhancing resistance to pathogen invasion. However, despite the extensive research on the phyllosphere microbiome, it remains unclear how the microbiome of leaves in proximity to diseased leaves responds to pathogen invasion. We investigate the response of the maize phyllosphere microbiome to maize white spot by assessing the microbiome dynamics associated with the white spot portion and the area in proximity using 16S and ITS high-throughput sequencing analysis. Our results showed that the bacterial diversities were higher in the diseased portion and area in proximity to the spot than those in healthy plants. At the same time, lower fungal diversity was recorded in the diseased portion compared to portions in proximity to it and healthy leaves. The spot portion had a significant influence on the microbial composition. The diseased portion, the area in proximity to it, and the healthy leaves were dominated by the bacterial genera Sphingomonas, Delftia, Chryseobacterium, Stenotrophomonas, Methylobacterium-methylorubrum, and Bacteroides. Still, the abundance of Sphingomonas decreased in the healthy leaves with a corresponding increase in Stenotrophomonas. Conversely, the fungal genus Setophoma dominated the diseased portion, while the fungal pathogens Cladosporium, Alternaria, and Exserohilum were highly abundant in the samples from the area in proximity to it. In addition, a co-occurrence network analysis revealed a complex fungal network in healthy leaves and those in proximity to leaves infected with white spot compared to the diseased portion. This study suggests that the area in proximity to the maize leaf infected with white spot disease is colonized by more harmful plant pathogenic fungi for disease progression.

Soil fungal networks exhibit sparser interactions than bacterial networks in diseased banana plantations

Soil microorganisms play a crucial role in suppressing soil-borne diseases. Although the composition of microbial communities in healthy versus diseased soils is somewhat understood, the interplay between microbial interactions and disease incidence remains unclear. This study used 16S rRNA and fungal internal transcribed spacer (ITS) sequencing to investigate the bacterial and fungal community composition in three soil types: forest soil (Z), soil from healthy banana plantations (H), and soil from diseased banana plantations (D). Principal coordinate analysis revealed significant differences among the bacterial and fungal community structures of the three soil types. Compared with those in forest soil, bacterial and fungal diversities significantly decreased in diseased banana soil. Key microorganisms, including the bacteria Chloroflexi and Pseudonocardia and the fungi Mortierellomycota and Moesziomyces, were significantly increased in soil from diseased banana plantations. Redundancy analysis revealed that total nitrogen and available phosphorus were the primary drivers of the soil microbial community structure. The neutral community model posited that the bacterial community assembly in banana plantations is predominantly governed by stochastic processes, whereas the fungal community assembly in banana plantations is primarily driven by deterministic processes. Furthermore, co-occurrence network analysis revealed that the proportion of positive edges in the fungal network of soil from diseased banana plantations was 5.92 times lower than that in soil from healthy banana plantations, and its fungal network structure was sparse and simple. In conclusion, reduced interactions within the fungal network were significantly linked to the epidemiology of Fusarium wilt. These findings underscore the critical role of soil fungal communities in modulating pathogens.

IMPORTANCE

Soil microorganisms are pivotal in mitigating soil-borne diseases. The intricate mechanisms underlying the interactions among microbes and their impact on disease occurrence remain enigmatic. This study underscores that a reduction in fungal network interactions correlates with the incidence of soil-borne Fusarium wilt.

Insights into the interactions of plant-associated bacteria and their role in the transfer of antibiotic resistance genes from soil to plant

This study discussed the role of plant-associated microbiome in regulating ARG transfer in soil-plant systems. Results showed that target ARGs in plants were mainly derived from rhizosphere soil. Cooperative interactions among bacteria in rhizosphere soil, plant-roots, plant-shoots, and soil-roots-shoots systems occurred during ARG transfer. The number of modules and keystone taxa identified as positively correlated with ARG transfer in rhizosphere soil, roots, and shoots was 3 and 49, 3 and 41, 2 and 5, respectively. Among these modules, module 3 in roots was significantly positively correlated with module 3 in rhizosphere soils and module 2 in shoots, indicating that module 3 in roots played central hub roles in ARG transfer from rhizosphere soil to roost and shoots. This may be because module 3 in roots increased cell motility and xenobiotics biodegradation and metabolism. These keystone taxa mainly belonged to Proteobacteria that can carry ARGs to transfer in soil-plant systems, especially Clostridium-sensu_stricito and Pseudomonas in rhizosphere soil carried ARGs into the shoot. Additionally, they promoted ARG transfer by increasing plant biomass, net photosynthetic rate and water use efficiency. The findings helped reveal the mechanism of plant-associated bacterial interactions and provided understanding for potential risks of ARG transfer from soil to plants.

Enhanced mobilization of soil heavy metals by the enantioselective herbicide R-napropamide compared to its S-isomer: Analyses of abiotic and biotic drivers

Chiral herbicides applied to agricultural soils are typically mildly to moderately contaminated with heavy metals (HMs), necessitating a thorough investigation into their effects on soil HMs availability. This study evaluated the effect of the chiral herbicide napropamide (NAP) on HMs bioavailability in different soil types, including weakly alkaline clay in Northeast China, neutral sandy loam in Zhejiang, and weakly acidic clay loam in Sichuan, China. The results demonstrate significant differences in the availability of HMs (Cd, Pb, Zn, and Ni) in the soil following enantiomer treatments, with variation ranges of 4.57-45.67 %, 5.03-96.21 %, 2.92-52.30 %, and 10.57-29.79 %, respectively. Overall, R-NAP enhanced the bioavailability of HMs more effectively than S-NAP, specifically by significantly activating available iron 3.33-191.97 % and markedly affecting soil pH and cation exchange capacity. Additionally, R-NAP influenced biotic processes by enriching dominant microbial communities, such as Chitinophaga, Niabella, and Promicromonospora, and by constructing more stable microbial networks. Notably, bioavailable Fe plays a dual regulatory role, affecting both the abiotic and biotic processes affected by soil NAP. In summary, although R-NAP is commonly used in agriculture, it poses a greater risk of HMs contamination in crops, highlighting the need for careful application and management. This study provides a fundamental theoretical basis for the judicious use of chiral herbicides in agricultural soils with mild-to-moderate HMs contamination.

Significant correlations between heavy metals and prokaryotes in the Okinawa Trough hydrothermal sediments

Prokaryotes play crucial roles in hydrothermal vent ecosystems, yet their interactions with heavy metals are not well understood. This study explored the diversity of prokaryotic communities and their correlations with heavy metals and nutrient elements in hydrothermal sediments from Okinawa Trough. A total of 117 bacterial genera in 26 bacterial phyla and 10 archaeal classes in 3 archaeal phyla were identified, including dominant prokaryotic phyla Planctomycetes, Acidobacteria, Verrucomicrobia, and Euryarchaeota. Furthermore, Fe (39.61 mg/g), Mn (2.84 mg/g) and Ba (0.36 mg/g) were found to be the most abundant heavy metals in the Okinawa hydrothermal sediments. Notably, the concentrations of Zn, Ba, Mn, total organic carbon, and total nitrogen significantly increased, whereas the total sulfur concentration distinctively decreased at sampling sites farther from hydrothermal vents. These changes corresponded with reductions in prokaryotic abundance and diversity. Most heavy metals, including Mn, Fe, Co, Cu and As, presented significant positive correlations with a number of prokaryotic genera in the nearby sediment samples. In contrast, both positive and negative correlations with prokaryotes were observed in remote sediment. The keystone taxa include Magnetospirillum, GOUTA19, Lysobacter, Kaistobacter, Treponema, and Clostridium were detected through prokaryote interspecies interactions. The functional predictions revealed significant genes involved in carbon fixation, nitrogen/sulfur cycling, heat shock protein, and metal resistance pathways. Structural equation modeling confirmed that metal and nutrient elements directly influence the composition of prokaryotic communities, which in turn affects the relative abundance of functional genes.

Synergistic effects of yeast and plant growth-promoting bacteria on Tobacco growth and soil-borne disease suppression: evidence from pot and field experiments

Background

Tobacco (Nicotiana tabacum L.) is an important economic crop, and the use of plant growth-promoting bacteria (PGPB) to enhance its growth and suppress soil-borne diseases has garnered considerable research interest. However, the potential of yeast to augment the growth-promoting and disease-suppressing effects of PGPB on tobacco remains unclear.

Methods

This study investigated the effects of Pichia sp. microbial fertilizer (J1), PGPB-Klebsiella oxytoca microbial fertilizer (ZS4), and their composite fertilizer (JZ) on tobacco growth indexes, soil properties, and soil microbial community through a pot experiment. Additionally, field experiments were conducted to further assess the efficacy of the composite microbial fertilizer on tobacco growth and the incidences of soil-borne diseases, including tobacco bacterial wilt (TBW) and tobacco black shank (TBS).

Results and discussions

In the pot experiment, application of the microbial fertilizers significantly enhanced soil organic matter (OM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available phosphorus (AP), and available potassium (AK) levels. Compared to the control group (CK), J1, ZS4, and JZ microbial fertilizers significantly promoted tobacco growth, and the composite microbial fertilizers demonstrated superior to the individual microbial fertilizers. We found that the application of microbial fertilizer led to significant alterations in the structure and composition of the bacterial and fungal communities based on the high-throughput sequencing of 16S rRNA and internal transcribed spacer (ITS) regions. The bacterial and fungal diversity indexes showed a decreasing trend. Key microorganisms such as Sphingomonas, Kitasatospora, Nitrosospira, Mortierella, and Trichoderma were identified as influential in regulating soil physicochemical parameters to enhance tobacco growth. Functional prediction further demonstrated a significant increase in the relative abundances of certain enzymes, including Alkaline phosphatase, 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase), and Peroxidase, as well as antimicrobial substances like Tetracycline, Isoquinoline alkaloid, and Phenylpropanoids, following inoculation with the fertilizer. Besides, field experiments revealed that the JZ fertilizer significantly promoted tobacco growth and reduced the incidence of TBW and TBS, indicating its potential for further application in tobacco cultivation.

Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.

Deciphering the role of rhizosphere microbiota in modulating disease resistance in cabbage varieties

BACKGROUND

Cabbage Fusarium wilt (CFW) is a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. conglutinans (Foc). One of the optimal measures for managing CFW is the employment of tolerant/resistant cabbage varieties. However, the interplay between plant genotypes and the pathogen Foc in shaping the rhizosphere microbial community, and the consequent influence of these microbial assemblages on biological resistance, remains inadequately understood.

RESULTS

Based on amplicon metabarcoding data, we observed distinct differences in the fungal alpha diversity index (Shannon index) and beta diversity index (unweighted Bray-Curtis dissimilarity) within the rhizosphere of the YR (resistant to Foc) and ZG (susceptible to Foc) cabbage varieties, irrespective of Foc inoculation. Notably, the Shannon diversity shifts in the resistant YR variety were more pronounced following Foc inoculation. Disease-resistant plant variety demonstrate a higher propensity for harboring beneficial microorganisms, such as Pseudomonas, and exhibit superior capabilities in evading harmful microorganisms, in contrast to their disease-susceptible counterparts. Furthermore, the network analysis was performed on rhizosphere-associated microorganisms, including both bacteria and fungi. The networks of association recovered from YR exhibited greater complexity, robustness, and density, regardless of Foc inoculation. Following Foc infection in the YR rhizosphere, there was a notable increase in the dominant bacterium NA13, which is also a hub taxon in the microbial network. Reintroducing NA13 into the soil significantly improved disease resistance in the susceptible ZG variety, by directly inhibiting Foc and triggering defense mechanisms in the roots.

CONCLUSIONS

The rhizosphere microbial communities of these two cabbage varieties are markedly distinct, with the introduction of the pathogen eliciting significant alterations in their microbial networks which is correlated with susceptibility or resistance to soil-borne pathogens. Furthermore, we identified a rhizobacteria species that significantly boosts disease resistance in susceptible cabbages. Our results indicated that the induction of resistance genes leading to varied responses in microbial communities to pathogens may partly explain the differing susceptibilities of the cabbage varieties tested to CFW. Video Abstract.

Mediterranean pine forest decline: A matter of root-associated microbiota and climate change

Forest ecosystems worldwide currently face worrying episodes of forest decline, which have boosted weakening and mortality of the trees. In the Mediterranean region, especially in the southeast Iberian Peninsula, Pinus sylvestris forests are severely affected by this phenomenon, and it has been commonly attributed to drought events. Remarkably, the role of root microbiota on pine decline has been overlooked and remains unclear. We therefore used metabarcoding to identify the belowground microbial communities of decline-affected and unaffected pine trees. Taxonomic composition of bacterial and fungal rhizosphere communities, and fungal populations dwelling in root endosphere showed different profiles depending on the health status of the trees. The root endosphere of asymptomatic trees was as strongly dominated by 'Candidatus Phytoplasma pini' as the root of decline-affected pines, accounting for >99 % of the total bacterial sequences in some samples. Notwithstanding, the titer of this phytopathogen was four-fold higher in symptomatic trees than in symptomless ones. Furthermore, the microbiota inhabiting the root endosphere of decline-affected trees assembled into a less complex and more modularized network. Thus, the observed changes in the microbial communities could be a cause or a consequence of forest decline phenomenon. Moreover, 'Ca. Phytoplasma pini' is positively correlated to Pinus sylvestris decline events, either as the primary cause of pine decline or as an opportunistic pathogen exacerbating the process once the tree has been weaken by other factors.

The color of biodegradable mulch films is associated with differences in peanut yield and bacterial communities

Biodegradable mulch films (BDMs) are increasingly used in agricultural production as desirable alternatives to the current widespread use of polyethylene (PE) mulch films in China. However, potential effects of different colors of BDMs on field crop production and microbiomes remain unexplored. Here, the differences in bacterial communities of peanut rhizosphere soil (RS) and bulk soil (BS) under non-mulching (CK), PE, and three different colors of BDMs were studied. The results indicated that all treatments could increase the soil temperature, which positively affected the growth of the peanut plants. Moreover, mulching affected the bacterial community structure in RS and BS compared to CK. Furthermore, certain BDM treatments significantly enriched N-fixing bacteria (Bradyrhizobium and Mesorhizobium) and functional groups, increased the closeness of bacterial networks, and harbored more beneficial bacteria as keystone taxa in the RS. This in turn facilitated the growth and development of the peanut plants under field conditions. Our study provides new insights into the micro-ecological effects of mulch films, which can be affected by both the mulch type and color. The observed effects are likely caused by temperature and prevalence of specific microbial functions under the employed films and could guide the development of optimized mulching materials.

The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis

Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.

Deciphering core microbiota in rhizosphere soil and roots of healthy and Rhizoctonia solani-infected potato plants from various locations

Black scurf caused by Rhizoctonia solani severely affects potato production. Through amplification of V3-V4 and ITS1-5f variable regions of 16S and internal transcribed spacer (ITS) rRNA, the study was based on the location (Kunming, Qujing, and Zhaotong), plant components (rhizosphere soil and roots), and sample types (healthy and diseased) to assess the diversity of bacterial and fungal communities. We found plant components significantly influence microbial diversity, with rhizosphere soil being more diverse than roots, and the microbial community in the root is mainly derived from the rhizosphere soil. Moreover, the rhizosphere soil and roots of healthy potato plants exhibit greater microbial diversity compared to those of potato plants infected by Rhizoctonia solani. Bacterial phyla Actinobacteriota and Acidobacteriota were enriched in rhizosphere soil compared to that of roots, whereas Proteobacteria and Cyanobacteria showed the opposite trend. Fungal phylum Ascomycota was found in low relative abundance in rhizosphere soil than in roots, whereas Basidiomycota showed the opposite trend. Bacterial genera including Streptomyces, Lysobacter, Bacillus, Pseudomonas, Ensifer, Enterobacter, and the Rhizobium group (Allorhizobium, Neorhizobium, Pararhizobium, Rhizobium), along with fungal genera such as Aspergillus, Penicillium, Purpureocillium, and Gibberella moniliformis, have the potential ability of plant growth promotion and disease resistance. However, most fungal species and some bacterial species are pathogenic to potato and could provide a conducive environment for black scurf infection. Interaction within the bacterial network increased in healthy plants, contrasting with the trend in the fungal network. Our findings indicate that R. solani significantly alters potato plant microbial diversity, underscoring the complexity and potential interactions between bacterial and fungal communities for promoting potato plant health and resistance against black scurf.

Functional keystone taxa promote N and P removal of the constructed wetland to mitigate agricultural nonpoint source pollution

Characterized by irregular spatial and temporal variations of pollutant loading and complex occurrence mechanisms, agricultural nonpoint source pollution (ANPSP) has always been a great challenge in field restoration worldwide. Returning farmlands to wetlands (RFWs) as an ecological restoration mode among various constructed wetlands was selected to manage ANPSP in this study. Triarrhena lutarioriparia, Nelumbo nucifera and Zizania latifolia monocultures were designed and the water pollutants was monitored. N. nucifera and Z. latifolia could reach the highest TN (53.28 %) and TP (53.22 %) removal efficiency, respectively. By 16s high-throughput sequencing of rhizosphere bacteria, 45 functional species were the main contributors for efficient N and P removal, and 38 functional keystone taxa (FKT) were found with significant ecological niche roles and metabolic functions. To our knowledge, this is the first study to explore the microbial driving N and P removal mechanism in response to ANPSP treated by field scale RFWs.

Similarity of Chinese and Pakistani oral microbiome

Oral microbiota is vital for human health and can be affected by various factors (i.e. diets, ethnicity). However, few studies have compared oral microbiota of individuals from different nationalities in the same environment. Here, we explored the assembly and interaction of oral microbial communities of Chinese and Pakistanis in one university. Firmicutes and Proteobacteria were the predominant microorganisms in the oral cavity of Chinese and Pakistanis. Streptococcus and Neisseria were the dominant genera of China, while Streptococcus and Haemophilus were the dominant genera of Pakistanis. In addition, the oral community membership and structure were not influenced by season, Chinese/Pakistani student and gender, reflecting the stability of the human oral microbiome. The beta diversity of oral microbiomes between Chinese and Pakistanis significantly differed in winter, but not in spring. The alpha diversity of Chinese students and Pakistani students was similar. Moreover, oral microbial community of both Chinese and Pakistani students was mainly driven by stochastic processes. The microbial network of Chinese was more complexity and stability than that of Pakistanis. Our study uncovers the characteristics of human oral microbiota, which is of great significance for oral and human health.

Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum

Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.

Co-Occurrence Patterns of Soil Fungal and Bacterial Communities in Subtropical Forest-Transforming Areas

Soil microbial communities are engineers of important biogeochemical processes and play a critical role in regulating the functions and stability of forest ecosystem. However, few studies have assessed microbial interactions during forest conversion, which is essential to the understanding of the structure and function of soil microbiome. Herein, we investigated the co-occurrence network pattern and putative functions of fungal and bacterial communities in forest-transforming areas (five sites that cover the typical forests) using high-throughput sequencing of the ITS genes and 16S rRNA. Our study showed that the bacterial network had higher average connectivity and more links than fungal network, which might indicate that the bacterial community had more complex internal interactions compared with fungal one. Alphaproteobacteria_unclassfied, Telmatobacter, 0319-6A21 and Latescibacteria_unclassfied were the keystone taxa in bacterial network. For the fungal community network, the keystone taxon was Ceratobasidium. A structural equation model indicated that the available potassium and total organic carbon were important soil environmental factors, which affected all microbial modules, including bacterial and fungi. Total nitrogen had significant effects on the bacterial module that contains a relatively rich group of nitrogen cycling functions, and pH influenced the bacterial module which have higher potential functions of carbon cycling. And, more fungal modules were directly affected by forest structure (S Tree) compared with bacterial ones. This study provides new insights into our understanding of the feedback of underground creatures to forest conversion and highlights the importance of microbial modules in the nutrient cycling process.

Indirect regulation of topsoil nutrient cycling by groundwater depth: impacts on sand-fixing vegetation and rhizosphere bacterial communities

Introduction

The impact of groundwater table depth (GTD) on bacterial communities and soil nutrition in revegetated areas remains unclear.

Methods

We investigated the impacts of plant growth and soil physicochemical factors on rhizosphere bacterial communities under different GTD.

Results

The four plant growth indices (Pielou, Margalef, Simpson, and Shannon-Wiener indices) and soil water content (SWC) at the Artem and Salix sites all showed a decreasing trend with increasing GTD. Salix had a higher nutrient content than Artem. The response of plant rhizosphere bacterial communities to GTD changes were as follows. Rhizosphere bacteria at the Artem and Salix sites exhibited higher relative abundance and alpha diversity in SW (GTD < 5 m) compared than in DW (GTD > 5 m). Functional microbial predictions indicated that the rhizosphere bacterial communities of Artem and Salix promoted carbon metabolism in the SW. In contrast, Artem facilitated nitrogen cycling, whereas Salix enhanced both nitrogen cycling and phototrophic metabolism in the DW.

Discussion

Mantel test analysis revealed that in the SW of Artem sites, SWC primarily governed the diversity of rhizosphere and functional bacteria involved in the nitrogen cycle by affecting plant growth. In DW, functional bacteria increase soil organic carbon (SOC) to meet nutrient demands. However, higher carbon and nitrogen availability in the rhizosphere soil was observed in the SW of the Salix sites, whereas in DW, carbon nutrient availability correlated with keystone bacteria, and changes in nitrogen content could be attributed to nitrogen mineralization. This indicates that fluctuations in the groundwater table play a role in regulating microbes and the distribution of soil carbon and nitrogen nutrients in arid environments.

Confronting stresses affecting olive cultivation from the holobiont perspective

The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.

Differentiated responses of the phyllosphere bacterial community of the yellowhorn tree to precipitation and temperature regimes across Northern China

Introduction

As an ephemeral and oligotrophic environment, the phyllosphere harbors many highly diverse microorganisms. Importantly, it is known that their colonization of plant leaf surfaces is considerably influenced by a few abiotic factors related to climatic conditions. Yet how the dynamics of phyllosphere bacterial community assembly are shaped by detailed climatological elements, such as various bioclimatic variables, remains poorly understood.

Methods

Using high-throughput 16S rRNA gene amplicon sequencing technology, we analyzed the bacterial communities inhabiting the leaf surfaces of an oilseed tree, yellowhorn (Xanthoceras sorbifolium), grown at four sites (Yinchuan, Otogqianqi, Tongliao, and Zhangwu) whose climatic status differs in northern China.

Results and Discussion

We found that the yellowhorn phyllosphere's bacterial community was generally dominated by four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Nevertheless, bacterial community composition differed significantly among the four sampled site regions, indicating the possible impact of climatological factors upon the phyllosphere microbiome. Interestingly, we also noted that the α-diversities of phyllosphere microbiota showed strong positive or negative correlation with 13 bioclimatic factors (including 7 precipitation factors and 6 temperature factors). Furthermore, the relative abundances of 55 amplicon sequence variants (ASVs), including three ASVs representing two keystone taxa (the genera Curtobacterium and Streptomyces), exhibited significant yet contrary responses to the precipitation and temperature climatic variables. That pattern was consistent with all ASVs' trends of possessing opposite correlations to those two parameter classes. In addition, the total number of links and nodes, which conveys community network complexity, increased with rising values of most temperature variables. Besides that, remarkably positive relevance was found between average clustering coefficient and most precipitation variables. Altogether, these results suggest the yellowhorn phyllosphere bacterial community is capable of responding to variation in rainfall and temperature regimes in distinctive ways.

Reed restoration decreased nutrients in wetlands with dredged sediments: Microbial community assembly and function in rhizosphere

Using dredged sediments as substrate for aquatic plants is a low-cost and ecological friendly way for in situ aquatic ecological restoration. However, the limited information available about how aquatic plant restoration affects the microbial ecology and nutrients in dredged sediments. In this study, nutrient contents, enzyme activities, and bacterial and archaeal communities in vertical sediment layers were determined in bulk and reed zones of wetlands constructed with dredged sediments in west Lake Taihu for three years. Reed restoration significantly decreased total nitrogen, total phosphorus, and organic carbon contents and increased alkaline phosphatase, urease, and sucrase activities compared to bulk area. Bacterial communities in vertical sediment layers had higher similarity in reed zone in comparison to bulk zone, and many bacterial and archaeal genera were only detected in reed rhizosphere zones. Compared with the bulk zone, the reed restoration area has a higher abundance of phylum Actinobacteriota, Hydrothermarchaeota, and class α-proteobacteria. The assembly process of the bacterial and archaeal communities was primarily shaped by dispersal limitation (67.03% and 32.97%, respectively), and stochastic processes were enhanced in the reed recovery area. Network analysis show that there were more complicated interactions among bacteria and archaea and low-abundance taxa were crucial in maintaining the microbial community stability in rhizosphere of reed zone. PICRUST2 analysis demonstrate that reed restoration promotes metabolic pathways related to C and N cycle in dredged sediments. These data highlight that using dredged sediments as substrates for aquatic plants can transform waste material into a valuable resource, enhancing the benefits to the environment.

Distinct prokaryotic and eukaryotic communities and networks in two agricultural fields of central Japan with different histories of maize-cabbage rotation

Crop rotation is an important agricultural practice for homeostatic crop cultivation. Here, we applied high-throughput sequencing of ribosomal RNA gene amplicons to investigate soil biota in two fields of central Japan with different histories of maize-cabbage rotation. We identified 3086 eukaryotic and 17,069 prokaryotic sequence variants (SVs) from soil samples from two fields rotating two crops at three different growth stages. The eukaryotic and prokaryotic communities in the four sample groups of two crops and two fields were clearly distinguished using β-diversity analysis. Redundancy analysis showed the relationships of the communities in the fields to pH and nutrient, humus, and/or water content. The complexity of eukaryotic and prokaryotic networks was apparently higher in the cabbage-cultivated soils than those in the maize-cultivated soils. The node SVs (nSVs) of the networks were mainly derived from two eukaryotic phyla: Ascomycota and Cercozoa, and four prokaryotic phyla: Pseudomonadota, Acidobacteriota, Actinomycetota, and Gemmatimonadota. The networks were complexed by cropping from maize to cabbage, suggesting the formation of a flexible network under crop rotation. Ten out of the 16 eukaryotic nSVs were specifically found in the cabbage-cultivated soils were derived from protists, indicating the potential contribution of protists to the formation of complex eukaryotic networks.

Bacterial inoculation of Quercus pyrenaica trees alters co-occurrence patterns but not the composition of the rhizosphere bacteriome in wild conditions

Quercus pyrenaica is a woody species of high landscape value, however, its forests show an advanced state of degradation in the Iberian Peninsula. Afforestation typically has low success, thus, it is necessary to improve the fitness of oaks plantlets to be transplanted, for instance, by inoculating beneficial microorganisms. In adding microorganisms to ecosystems, there must be balanced efficacy with potential effects on native microbial communities. We addressed changes in diversity, richness, composition and co-occurrence networks of prokaryotic communities in the rhizosphere of inoculated and control trees outplanted to three different sites located in the Sierra Nevada National and Natural Park (Spain). After 18 months in wild conditions, we did not detect changes due to the inoculation in the richness, diversity and structure in none of the sites. However, we observed an increase in the complexity of the co-occurrence networks in two experimental areas. Modularization of the networks changed as a result of the inoculation, although the sense of the change depended on the site. Although it was impossible to unravel the effect of bacterial inoculation, our results highlighted that inoculation alters the association of rhizosphere bacteria without entailing other changes, so networks should be analysed prior to inoculating the plantlets.

Thriving beneath olive trees: The influence of organic farming on microbial communities

Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 10⁶ ± 1.62 × 10⁵ (CM) to 4.54 × 10⁶ ± 8.07 × 10⁵ (OM) copies of the 18 S rRNA gene g^-1 soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.

Aerobic denitrifying bacterial-fungal consortium mediating nitrate removal: Dynamics, network patterns and interactions

In recent years, nitrogen removal by mixed microbial cultures has received increasing attention owing to cooperative metabolism. A natural bacterial-fungal consortium was isolated from mariculture, which exhibited an excellent aerobic denitrification capacity. Under aerobic conditions, nitrate removal and denitrification efficiencies were up to 100% and 44.27%, respectively. High-throughput sequencing and network analysis suggested that aerobic denitrification was potentially driven by the co-occurrence of the following bacterial and fungal genera: Vibrio, Fusarium, Gibberella, Meyerozyma, Exophiala and Pseudoalteromonas, with the dominance of Vibrio and Fusarium in bacterial and fungal communities, respectively. In addition, the isolated consortium had a high steady aerobic denitrification performance in our sub-culturing experiments. Our results provide new insights on the dynamics, network patterns and interactions of aerobic denitrifying microbial consortia with a high potential for new biotechnology applications.

Azithromycin Exposure Induces Transient Microbial Composition Shifts and Decreases the Airway Microbiota Resilience from Outdoor PM2.5 Stress in Healthy Adults: a Randomized, Double-Blind, Placebo-Controlled Trial

Inappropriate antibiotic prescriptions are common for patients with upper respiratory tract infections (URTIs). Few data exist regarding the effects of antibiotic administration on airway microbiota among healthy adults. We conducted a randomized, double-blind, placebo-controlled trial to characterize the airway microbiota longitudinally in healthy adults using 16S rRNA gene sequencing and quantification. Both the induced sputum and oral wash samples were collected over a 60-day period following a 3-day intervention with 500 mg azithromycin or placebo. Environmental information, including air quality data (particulate matter [PM2.5] and PM10, air quality index [AQI] values), were also collected during the study. A total of 48 healthy volunteers were enrolled and randomly assigned into two groups. Azithromycin did not alter bacterial load but significantly reduced species richness and Shannon index. Azithromycin exposure resulted in a decrease in the detection rate and relative abundance of different genera belonging to Veillonellaceae, Leptotrichia, Fusobacterium, Neisseria, and Haemophilus. In contrast, the relative abundance of taxa belonging to Streptococcus increased immediately after azithromycin intervention. The shifts in the diversity of the microbiology composition took between 14 and 60 days to recover, depending on the measure used: either UniFrac phylogenetic distance or α-diversity. Outdoor environmental perturbations, especially the high concentration of PM2.5, contributed to novel variability in microbial community composition of the azithromycin group at D30 (30 days after baseline). The network analysis found that azithromycin altered the microbial interactions within airway microbiota. The influence was still obvious at D14 when the relative abundance of most taxa had returned to the baseline level. Compared to the sputum microbiota, oral cavity microbiota had a different pattern of change over time. The induced sputum microbial data can represent the airway microbiota composition in healthy adults. Azithromycin may have transient effects in the airway microbiota of healthy adults and decrease the airway microbiota resilience against outdoor environmental stress. The influence of azithromycin on microbial interactions is noteworthy, although the airway microbiota has returned to a near-baseline level. IMPORTANCE The influence of antibiotic administration on the airway microbiota of healthy adults remains unknown. This study is a randomized, double-blind, placebo-controlled trial aiming to investigate the microbial shifts in airways after exposure to azithromycin among heathy adults. We find that azithromycin changes the airway microbial community composition of healthy adults and decreases the airway microbiota resilience against outdoor environmental stress. This study depicts the longitudinal recovery trajectory of airway microbiota after the antibiotic perturbation and may provide reference for appropriate antibiotic prescription.

Bio-organic fertilizer promoted phytoremediation using native plant leymus chinensis in heavy Metal(loid)s contaminated saline soil

Heavy metal(loid)s (HMs) contaminated saline soil appeared around the world, however, remediation regarding these collected from field conditions remains unknown. Native plants cultivation and bio-organic fertilizer (BOF) application were two efficient tools for soil amelioration. Herein, a pot experiment was conducted to examine the feasibility of a native plant (Leymus chinensis) for phytoremediation, and investigate the impacts of lignite based bio-organic fertilizer (LBOF) and manure based bio-organic fertilizer (MBOF) on phytoremediation of the soil contaminated by Pb, Cd, As, Zn, Cu, Ca²⁺, and SO₄^2-. The results demonstrated the effectiveness of L. chinensis and highlighted the positive impacts of BOF according to the improved plant growth, HMs phytostabilization, salt removal, and soil properties. LBOF and MBOF changed soil microbiome to assist phytoremediation in addition to physiological modulation. Having enhanced fungal and bacterial richness respectively, LBOF and MBOF recruited various plant growth promoting rhizobacteria with different functions, and shifted microbial co-occurrence networks and keystone taxa towards these different but beneficial forms. Structural equation models comprehensively reveled the strategy discrepancy of LBOF and MBOF to regulate the plant biomass, HMs uptake, and soil salt. In summary, L. chinensis coupled with BOF, especially LBOF, was a effective strategy to remediate HMs contaminated saline soil.

Effect of long-term application of bioorganic fertilizer on the soil property and bacteria in rice paddy

The application of novel bioorganic fertilizer (BIO) has been established as a weed biocontrol strategy, and reduce herbicides pollution and negatively effects on agricultural ecosystems. However, its long-term influences on soil bacterial communities are unknown. Here, 16 S rRNA sequencing to identify the changes that occur in soil bacterial community and enzyme under BIO treatments after five years in a field experiment. BIO application effectively controlled weeds, however no obvious differences between treatments were observed under BIO-50, BIO-100, BIO-200 and BIO-400 treatment. Anaeromyxobacter and Clostridium_ sensu_ stricto_1 were the two dominant genera among BIO-treated soil samples. The BIO-800 treatment had a slight influence on the species diversity index, which was more remarkable after five years. The seven significantly-different genera between BIO-800 treatment and untreated soils included C._sensu_stricto_1, Syntrophorhabdus, Candidatus_Koribacter, Rhodanobacter, Bryobacter, Haliangium, Anaeromyxobacter. In addition, BIO application had different effects on soil enzymatic activities and chemical properties. The extractable P and pH saliency correlated with Haliangium and C._Koribacter, and C._sensu_stricto_1 observably correlated with exchangeable K, hydrolytic N and organic matter. Taken together, our data suggest that BIO application effectively controlled weeds and a slight influence on soil bacterial communities and enzymes. These findings expand our knowledge of the application of BIO as widely used as a sustainable weed control in rice paddy.

Organic Matter Decomposition in River Ecosystems: Microbial Interactions Influenced by Total Nitrogen and Temperature in River Water

Microbes contribute to the organic matter decomposition (OMD) in river ecosystems. This study considers two aspects of OMD in river ecosystems which have not been examined in scientific studies previously, and these are the microbial interactions in OMD and the influence of environmental factors on microbial interactions. Cotton strip (CS), as a substitute for organic matter, was introduced to Luanhe River Basin in China. The results of CS assay, microbial sequencing, and redundancy analysis (RDA) showed that CS selectively enriched bacterial and fungal groups related to cellulose decomposition, achieving cotton strip decomposition (CSD). Bacterial phylum Proteobacteria and fungal phyla Rozellomycota and Ascomycota were the dominant groups associated with CSD. Network analysis and Mantel test results indicated that bacteria and fungi on CS cooperatively formed an interaction network to achieve the CSD. In the network, modules 2 and 4 were significantly positively associated with CSD, which were considered as the key modules in this study. The key modules were mainly composed of phyla Proteobacteria and Ascomycota, indicating that microbes in key modules were the effective decomposers of CS. Although keystone taxa were not directly associated with CSD, they may regulate the genera in key modules to achieve the CSD, since some keystone taxa were linked with the microbial genera associated with CSD in the key modules. Total nitrogen (TN) and temperature in water were the dominant environmental factors positively influenced CSD. The key modules 2 and 4 were positively influenced by water temperature and TN in water, respectively, and two keystone taxa were positively associated with TN. This profoundly revealed that water temperature and TN influenced the OMD through acting on the keystone taxa and key modules in microbial interactions. The research findings help us to understand the microbial interactions influenced by environmental factors in OMD in river ecosystems.

Metabarcoding reveals response of rice rhizosphere bacterial community to rice bacterial leaf blight

Rice bacterial leaf blight (BLB) is a major disease affecting cultivated rice and caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). It is well established that rhizosphere microorganisms could help improve the adaptability of plants to biotic stresses. However, it is still unclear about the response mechanism of rice rhizosphere microbial community to BLB infection. Here, we used 16S rRNA gene amplicon sequencing to explore the effect of BLB on the rice rhizosphere microbial community. The results show that the alpha diversity index of the rice rhizosphere microbial community decreased significantly at the onset of BLB and then gradually recovered to normal levels. Beta diversity analysis indicated that BLB significantly affected community composition. In addition, there were significant differences in the taxonomic composition between healthy and diseased groups. For example, ceretain genera were more abundant in diseased rhizospheres, namely Streptomyces, Sphingomonas, and Flavobacterium, among others. In addition, the size and complexity of the rhizosphere co-occurrence network increased after disease onset compared to healthy groups. Also, hub microbe Rhizobiaceae and Gemmatimonadaceae were identified in the diseased rhizosphere co-occurrence network, and these hub microbes played an important role in maintaining network stability. In conclusion, our results provide important insights into the rhizosphere microbial community response to BLB and also provide important data and ideas in using rhizosphere microbes to control BLB.

Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria

BACKGROUND

Verticillium wilt of olive (VWO), caused by Verticillium dahliae Kleb, is one of the most threatening diseases affecting olive cultivation. An integrated disease management strategy is recommended for the effective control of VWO. Within this framework, the use of biological control agents (BCAs) is a sustainable and environmentally friendly approach. No studies are available on the impact that the introduction of BCAs has on the resident microbiota of olive roots. Pseudomonas simiae PICF7 and Paenibacillus polymyxa PIC73 are two BCAs effective against VWO. We examined the effects of the introduction of these BCAs on the structure, composition and co-occurrence networks of the olive (cv. Picual) root-associated microbial communities. The consequences of the subsequent inoculation with V. dahliae on BCA-treated plants were also assessed.

RESULTS

Inoculation with any of the BCAs did not produce significant changes in the structure or the taxonomic composition of the 'Picual' root-associated microbiota. However, significant and distinctive alterations were observed in the topologies of the co-occurrence networks. The introduction of PIC73 provoked a diminution of positive interactions within the 'Picual' microbial community; instead, PICF7 inoculation increased the microbiota's compartmentalization. Upon pathogen inoculation, the network of PIC73-treated plants decreased the number of interactions and showed a switch of keystone species, including taxa belonging to minor abundant phyla (Chloroflexi and Planctomycetes). Conversely, the inoculation of V. dahliae in PICF7-treated plants significantly increased the complexity of the network and the number of links among their modules, suggestive of a more stable network. No changes in their keystone taxa were detected.

CONCLUSION

The absence of significant modifications on the structure and composition of the 'Picual' belowground microbiota due to the introduction of the tested BCAs underlines the low/null environmental impact of these rhizobacteria. These findings may have important practical consequences regarding future field applications of these BCAs. Furthermore, each BCA altered the interactions among the components of the olive belowground microbiota in idiosyncratic ways (i.e. PIC73 strongly modified the number of positive relations in the 'Picual' microbiota whereas PICF7 mostly affected the network stability). These modifications may provide clues on the biocontrol strategies used by these BCAs.

Increased Leaf Bacterial Network Complexity along the Native Plant Diversity Gradient Facilitates Plant Invasion?

Understanding the mechanisms of biological invasion is critical to biodiversity protection. Previous studies have produced inconsistent relationships between native species richness and invasibility, referred to as the invasion paradox. Although facilitative interactions among species have been proposed to explain the non-negative diversity-invasibility relationship, little is known about the facilitation of plant-associated microbes in invasions. We established a two-year field biodiversity experiment with a native plant species richness gradient (1, 2, 4, or 8 species) and analyzed the effects of community structure and network complexity of leaf bacteria on invasion success. Our results indicated a positive relationship between invasibility and network complexity of leaf bacteria of the invader. Consistent with previous studies, we also found that native plant species richness increased the leaf bacterial diversity and network complexity. Moreover, the results of the leaf bacteria community assembly of the invader suggested that the complex bacteria community resulted from higher native diversity rather than higher invader biomass. We concluded that increased leaf bacterial network complexity along the native plant diversity gradient likely facilitated plant invasion. Our findings provided evidence of a potential mechanism by which microbes may affect the plant community invasibility, hopefully helping to explain the non-negative relationship between native diversity and invasibility.

Mixed organic and inorganic amendments enhance soil microbial interactions and environmental stress resistance of Tibetan barley on plateau farmland

Sufficient crop yield while maintaining soil health and sustainable agricultural development is a global objective, serving a special challenge to certain climate-sensitive plateau areas. Despite conducting trails on a variety of soil amendments in plateau areas, systematic research is lacking regarding the influences of organic and inorganic amendments on soil quality, particularly soil microbiome. To our knowledge, this was the first study that compared the effects of inorganic, organic, and mixed amendments on typical plateau crop hulless barley (Hordeum vulgare L. var. Nudum, also known as "Qingke" in Chinese) over the course of tillering, jointing, and ripening. Microbial communities and their responses to amendments, soil properties and Tibetan hulless barley growth, yield were investigated. Results indicated that mixed organic and inorganic amendments promoted the abundance of rhizosphere microorganisms, enhancing the rhizosphere root-microbes interactions and resistance to pathogenic bacteria and environmental stresses. The rhizosphere abundant and significantly different genera Arthrobacter, Rhodanobacter, Sphingomona, Nocardioides and so on demonstrated their unique adaptation to the plateau environment based on the results of metagenomic binning. The abundance of 23 genes about plant growth and environmental adaptations in the mixed amendment soil were significantly higher than other treatments. Findings from this study suggest that the mixed organic/inorganic amendments can help establish a healthy microbiome and increase soil quality while achieving sufficient hulless barley yields in Tibet and presumably other similar geographic areas of high altitude.

Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event

Even if Archaea deliver important ecosystem services and are major players in global biogeochemical cycles, they remain poorly understood in freshwater ecosystems. To our knowledge, no studies specifically address the direct impact of xenobiotics on the riverine archaeome. Using environmental DNA metabarcoding of the 16S ribosomal gene, we previously demonstrated bacterial communities significant shifts linked to pollutant mixtures during an extreme flood in a typical Mediterranean coastal watercourse. Here, using the same methodology, we sought to determine whether archaeal community shifts coincided with the delivery of environmental stressors during the same flood. Further, we wanted to determine how archaea taxa compared at different seasons. In contrast to the bacteriome, the archaeome showed a specific community in summer compared to winter and autumn. We also identified a significant relationship between in situ archaeome shifts and changes in physicochemical parameters along the flood, but a less marked link to those parameters correlated to river hydrodynamics than bacteria. New urban-specific archaeal taxa significantly related to multiple stressors were identified. Through statistical modeling of both domains, our results demonstrate that Archaea, seldom considered as bioindicators of water quality, have the potential to improve monitoring methods of watersheds.

Soil amendment with cow dung modifies the soil nutrition and microbiota to reduce the ginseng replanting problem

Ginseng is a profitable crop worldwide; however, the ginseng replanting problem (GRP) is a major threat to its production. Soil amendment is a non-chemical method that is gaining popularity for alleviating continuous cropping obstacles, such as GRP. However, the impact of soil amendment with either cow dung or canola on GRP reduction and the associated soil microbiota remains unclear. In the present study, we evaluated the effect of soil amendment with cow dung, canola seed powder, and without amendment (control), on the survival of ginseng seedling transplants, the soil bacterial and fungal communities, and their associated metabolic functions. The results showed that cow dung increased ginseng seedling survival rate by 100 percent and had a remarkable positive effect on ginseng plant growth compared to control, whereas canola did not. Cow dung improved soil nutritional status in terms of pH, electrical conductivity, NO 3 - , total carbon, total phosphorus, and available phosphorus. The amplicon sequencing results using Illumina MiSeq showed that canola had the strongest negative effect in reducing soil bacterial and fungal diversity. On the other hand, cow dung stimulated beneficial soil microbes, including Bacillus, Rhodanobacter, Streptomyces, and Chaetomium, while suppressing Acidobacteriota. Community-level physiological profiling analysis using Biolog Ecoplates containing 31 different carbon sources showed that cow dung soil had a different metabolic activity with higher utilization rates of carbohydrates and polymer carbon sources, mainly Tween 40 and beta-methyl-d-glucoside. These carbon sources were most highly associated with Bacillota. Furthermore, predicted ecological function analyses of bacterial and fungal communities showed that cow dung had a higher predicted function of fermentation and fewer functions related to plant pathogens and fungal parasites, signifying its potential to enhance soil suppressiveness. Co-occurrence network analysis based on random matrix theory (RMT) revealed that cow dung transformed the soil microbial network into a highly connected and complex network. This study is the first to report the alleviation of GRP using cow dung as a soil amendment, and the study contributes significantly to our understanding of how the soil microbiota and metabolic alterations via cow dung can aid in GRP alleviation.

Role of the rhizosphere bacterial community in assisting phytoremediation in a lead-zinc area

Heavy metals (HMs) contamination and vegetation destruction in the mining area caused by mining activities are severely increasing. It is urgent to restore vegetation and stabilize HMs. In this study, we compared the ability of HMs phytoextraction/phytostabilization of three dominant plants, including Artemisia argyi (LA), Miscanthus floridulus (LM), and Boehmeria nivea (LZ) in a lead-zinc mining area in Huayuan County (China). We also explored the role of the rhizosphere bacterial community in assisting phytoremediation using 16S rRNA sequencing technology. Bioconcentration factor (BCF) and translocation factor (TF) analysis showed that LA preferred accumulating Cd, LZ preferred accumulating Cr and Sb, and LM preferred accumulating Cr and Ni. Significant (p < 0.05) differences were found among the rhizosphere soil microbial communities of these three plants. The key genera of LA were Truepera and Anderseniella, that of LM were Paracoccus and Erythrobacter, and of LZ was Novosphingobium. Correlation analysis showed some rhizosphere bacterial taxa (e.g., Actinomarinicola, Bacillariophyta and Oscillochloris) affected some soil physicochemical parameters (e.g., organic matter and pH) of the rhizosphere soil and enhanced the TF of metals. Functional prediction analysis of soil bacterial community showed that the relative abundances of genes related to the synthesis of some proteins (e.g., manganese/zinc-transporting P-type ATPase C, nickel transport protein and 1-aminocyclopropane-1-carboxylate deaminase) was positively correlated with the phytoextraction/phytostabilization capacity of plants for heavy metals. This study provided theoretical guidance on selecting appropriate plants for different metal remediation applications. We also found some rhizosphere bacteria might enhance the phytoremediation of multi-metals, which could provide a reference for subsequent research.

Root-Zone Restriction Regulates Soil Factors and Bacterial Community Assembly of Grapevine

Root-zone restriction induces physiological stress on roots, thus limiting the vegetative and enhancing reproductive development, which promotes fruit quality and growth. Numerous bacterial-related growth-promoting, stress-mitigating, and disease-prevention activities have been described, but none in root-restricted cultivation. The study aimed to understand the activities of grapevine bacterial communities and plant-bacterial relationships to improve fruit quality. We used High-throughput sequencing, edaphic soil factors, and network analysis to explore the impact of restricted cultivation on the diversity, composition and network structure of bacterial communities of rhizosphere soil, roots, leaves, flowers and berries. The bacterial richness, diversity, and networking were indeed regulated by root-zone restriction at all phenological stages, with a peak at the veraison stage, yielding superior fruit quality compared to control plants. Moreover, it also handled the nutrient availability in treated plants, such as available nitrogen (AN) was 3.5, 5.7 and 0.9 folds scarcer at full bloom, veraison and maturity stages, respectively, compared to control plants. Biochemical indicators of the berry have proved that high-quality berry is yielded in association with the bacteria. Cyanobacteria were most abundant in the phyllosphere, Proteobacteria in the rhizosphere, and Firmicutes and Bacteroidetes in the endosphere. These bacterial phyla were most correlated and influenced by different soil factors in control and treated plants. Our findings are a comprehensive approach to the implications of root-zone restriction on the bacterial microbiota, which will assist in directing a more focused procedure to uncover the precise mechanism, which is still undiscovered.

A field study on the composition, structure, and function of endophytic bacterial community of Robinia pseudoacacia at a composite heavy metals tailing

Robinia pseudoacacia (R. pseudoacacia) is a well reported plant species for heavy metal phytoremediation, and it was capable to improve Cd uptake efficiency after inoculated with plant growth promoting endophytes. However, the knowledge on R. pseudoacacia associated endophytes in field condition and the relationship between these microbial communities and heavy metal uptake capacities are still scarce. In this study, the characteristics of heavy metal bioaccumulation and translocation in R. pseudoacacia, and the structure and function of its endophytic bacterial communities were revealed. The results showed that heavy metal pollution made microbes more sensitive to the environment as the diversity (Shannon) of endophyte community decreased but the abundance (Chao) increased. Redundancy analysis (RDA) also showed that heavy metals were the key factor affecting the composition of endophyte. In the co-occurrence network, 27 keystone taxa mainly from Actinobacteria, Proteobacteria and Firmicutes occupied the dominant niches, among which 16 OTUs mainly from lactobacillus, bacteroides, staphylococcus, methylorubrum and bifidobacterium were positively related to bioaccumulation and translocation of Cd, Cu, Pb and Zn. Besides, heavy metal stress enhanced the functional adaptability of endophytic bacteria community. Related predicted genes were enriched in immune response, physiological metabolism pathway and stress-resistant enzyme synthesis. This study showed that heavy metal stress enhanced the structural and functional adaptability of endophyte community and keystone taxa played significant role in improving the efficiency of phytoremediation.

Alhagi sparsifolia Harbors a Different Root-Associated Mycobiome during Different Development Stages

The mycobiome in the rhizosphere and within the roots benefits the nutrition and function of host plants. However, compared with the bacterial community, root-associated mycobiomes of desert plants and the forces that drive their assemblage are limited. Here, we investigated the mycobiomes in bulk soil, rhizosphere, and root compartments of Alhagi sparsifolia Shap., a phreatophyte species dominating in Central Asia. The internal transcribed spacer (ITS) gene phylogenetic profiles displayed significantly diverse mycobiomes across three compartments and host growth times, together explaining 31.45% of the variation in the community composition. The community structure of the perennial stage was markedly different from that of other stages (30 days to 2 years old). Along the soil-plant continuum, the α-diversity (estimated by Chao1) decreased gradually, while concomitantly increasing the community dissimilarity and the influence of edaphic factors. Specific leaf area, soil water content, and soil organic matter levels were common factors driving the composition of the three mycobiome communities. A more complex and connected network was observed in the root community compared with the other compartments. Overall, our work suggests that an age-sensitive host effect restructured the desert-plant-root-associated mycobiome, and that edaphic factors and host growth strategy may play potential roles in this process.

Changes in soil fungal communities after onset of wheat yellow mosaic virus disease

Rhizosphere-associated microbes have important implications for plant health, but knowledge of the association between the pathological conditions of soil-borne virus-infected wheat and soil microbial communities, especially changes in fungal communities, remains limited. We investigated the succession of fungal communities from bulk soil to wheat rhizosphere soil in both infected and healthy plants using amplicon sequencing methods, and assessed their potential role in plant health. The results showed that the diversity of fungi in wheat rhizosphere and bulk soils significantly differed post wheat yellow mosaic virus disease onset. The structure differences in fungal community at the two wheat health states or two compartment niches were evident, soil physicochemical properties (i.e., NH4 +) contribute to differences in fungal community structure and alpha diversity. Comparison analysis showed Mortierellomycetes and Dothideomycetes as dominant communities in healthy wheat soils at class level. The genus Pyronemataceae and Solicoccozyma were significantly are significantly enriched in rhizosphere soil of diseased plant, the genus Cystofilobasidium, Cladosporium, Mortierella, and Stephanonectria are significantly enriched in bulk soil of healthy plant. Co-occurrence network analysis showed that the fungi in healthy wheat soil has higher mutual benefit and connectivity compared with diseased wheat. The results of this study demonstrated that the occurrence of wheat yellow mosaic virus diseases altered both fungal community diversity and composition, and that NH4 + is the most important soil physicochemical factor influencing fungal diversity and community composition.

Liquid Organic Fertilizer Amendment Alters Rhizosphere Microbial Community Structure and Co-occurrence Patterns and Improves Sunflower Yield Under Salinity-Alkalinity Stress

Response of rhizosphere microbial community structure and co-occurrence patterns to liquid organic fertilizer in sunflower cropland was investigated. Moderate and severe saline-alkaline soils were treated with liquid organic fertilizer containing mainly small molecular organic compounds (450 g L^-1) at a rate of 4500 L ha^-1 year^-1 over 2 years. Compared with the untreated soils, organic fertilizer treatment increased soil nutrient concentrations by 13.8-137.1% while reducing soil pH and salinity by 5.6% and 54.7%, respectively. Organic fertilizer treatment also improved sunflower yield, plant number, and plant height by 28.6-67.3%. Following organic fertilizer treatment, fungal α-diversity was increased, and the effects of salinity-alkalinity stress on rhizosphere microbial communities were alleviated. The relative abundances of some halotolerant microbes and phytopathogenic fungi were reduced in organic fertilizer-treated soils, in contrast to increases in the relative abundances of plant growth-promoting microbes and organic matter decomposers, such as Nocardioides, Rhizophagus, and Stachybotrys. Network analysis revealed that severe salinity-alkalinity stress stimulated cooperation among bacteria, while organic fertilizer treatment tended to stimulate the ecosystem functions of fungi with higher proportions of fungi-bacteria and fungi-fungi links. More keystone taxa (e.g., Amycolatopsis, Variovorax, and Gemmatimonas) were positively correlated with soil nutrient concentrations and crop yield-related traits in organic fertilizer-treated soils. Overall, liquid organic fertilizer amendment could attenuate the adverse effects of salinity-alkalinity stress on sunflower yield by improving soil quality and optimizing rhizosphere microbial community structure and co-occurrence patterns.

Integrated network analysis reveals that exogenous cadmium-tolerant endophytic bacteria inhibit cadmium uptake in rice

Most previous studies have focused on the diversity and species richness of microbial communities, however, understanding the interactions between species and detecting key functional members of the community can help us better understand how microorganisms perform their functions. In this study, the response of the rice plant microbial community to the inoculation of cadmium-resistant endophytic bacterium R5 (Stenotrophomonas) was investigated for the first time using a microbial phylogenetic molecular ecological network. The results showed that inoculation of R5 changed the topological characteristics of the microbial network in rice plants, with the resulting network displaying stronger complexity and interaction in roots and aboveground parts, indicating that inoculation of R5 provided favorable conditions for microbial interactions. In addition, these interactions may be related to the absorption and transportation of cadmium by rice. Under the exogenous addition of R5, the network interactions of the rice plant microbial community were more inclined to cooperation. Both in the roots and aboveground parts of rice, the plant Cd content showed a decrease as the complexity and connectivity of the network increased, suggesting that complex microbial networks may be more beneficial to rice than simple microbial networks because as they were more adaptive and resistant to unfavorable environments. After inoculation with the R5 strain, the negative interaction with Cd content in rice plants increased significantly, and there might be more synergy between the microbial community and plants to jointly inhibit the absorption and transportation of Cd.

Correlating the above- and belowground genotype of Pinus pinaster trees and rhizosphere bacterial communities under drought conditions

Increasing temperatures along with severe droughts are factors that may jeopardize the survival of the forests in the Mediterranean basin. In this region, Pinus pinaster is a common conifer species, that has been used as a model species in evolutionary studies due to its adaptive response to changing environments. Although its drought tolerance mechanisms are already known, knowledge about the dynamics of its root microbiota is still scarce. We aimed to decipher the structural (bacterial abundance), compositional, functional and associative changes of the P. pinaster rhizosphere bacterial communities in spring and summer, at DNA and RNA level (environmental DNA, live and dead cells, and those synthesizing proteins). A fundamental aspect of root microbiome-based approaches is to guarantee the correct origin of the samples. Thus, we assessed the genotype of host needles and roots from which rhizosphere samples were obtained. For more than 50% of the selected trees, genotype discrepancies were found and in three cases the plant species could not be determined. Rhizosphere bacterial communities were homogeneous with respect to diversity and structural levels regardless of the host genotype in both seasons. Nonetheless, significant changes were seen in the taxonomic profiles depending on the season. Seasonal changes were also evident in the bacterial co-occurrence patterns, both in DNA and RNA libraries. While spring communities switched to more complex networks, summer populations resulted in more compartmentalized networks, suggesting that these communities were facing a disturbance. These results may mirror the future status of bacterial communities in a context of climate change. A keystone hub was ascribed to the genus Phenylobacterium in the functional network calculated for summer. Overall, it is important to validate the origin and identity of plant samples in any plant-microbiota study so that more reliable ecological analyses are performed.

Specific Plant Mycorrhizal Responses Are Linked to Mycorrhizal Fungal Species Interactions

Effects of arbuscular mycorrhizal fungi (AMF) on plants span the continuum from mutualism to parasitism due to the plant-AMF specificity, which obscures the utilization of AMF in the restoration of degraded lands. Caragana korshinskii, Hedysarum laeve, Caragana microphylla, and Poa annua are the most frequently used plants for revegetation in Kubuqi Desert, China, and the influence of AMF on their re-establishment remains to be explored further. Herein, using a greenhouse experiment, we tested the plant-AMF feedbacks between the four plant species and their conspecific or heterospecific AMF, retrieved from their rhizosphere in the Kubuqi Desert. AMF showed beneficial effects on plant growth for all these plant-AMF pairs. Generally, AMF increased the biomass of C. korshinskii, H. laeve, C. microphylla, and P. annua by 97.6, 50.6, 46.5, and 381.1%, respectively, relative to control. In addition, the AMF-plant specificity was detected. P. annua grew best, but C. microphylla grew worst with conspecific AMF communities. AMF community from P. annua showed the largest beneficial effect on all the plants (with biomass increased by 63.9-734.4%), while the AMF community from C. microphylla showed the least beneficial effect on all the plants (with biomass increased by 9.9-59.1%), except for P. annua (a 292.4% increase in biomass). The magnitude of AMF effects on plant growth was negatively correlated with the complexity of the corresponding AMF co-occurrence networks. Overall, this study suggests that AMF effects on plant growth vary due to plant-AMF specificity. We also observed the broad-spectrum benefits of the native AMF from P. annua, which indicates its potential utilization in the restoration of the desert vegetation.

Insights into the Interactions Between Root Phenotypic Traits and the Rhizosphere Bacterial Community

The root phenotypic traits have been considered as important factors in shaping the rhizosphere microbiome and regulating plant growth. However, the relationships between root phenotypic traits and the rhizosphere bacterial community remain unclear. We investigated two fields with different developing tobacco roots by a long-term positioning test in Hengshi. The well-developed root system (WDR) showed much more superiority in root phenotypic traits, including total root length, total projection area, surface area, and root tip number, than the underdeveloped root system. The specific root traits in WDR provided more ecological niches for the rhizosphere microorganisms, contributing to a more diverse microbial community and a more complex microbial network. The total root length and root tip number were the key factors shaping bacterial communities in the rhizosphere. In turn, the phyla Acidobacteria and Bacteroidetes might play vital roles in modifying root development and promoting plant growth according to their positive correlation with root phenotypic traits. Linking root phenotypic traits to the microbiome may enhance our understanding of rhizospheric interactions and their roles in developing rhizosphere ecosystems.

Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses

The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified-the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants.

Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars

The microbial community within the root system, the rhizosphere closely connected to the root, and their symbiotic relationship with the host are increasingly seen as possible drivers of natural pathogen resistance. Resistant cultivars have the most effective strategy in controlling the Chinese wheat yellow mosaic disease, but the roles of the root and rhizosphere microbial interactions among different taxonomic levels of resistant cultivars are still unknown. Thus, we aimed to investigate whether these microbial community composition and network characteristics are related to disease resistance and to analyze the belowground plant-associated microflora. Relatively high microbial diversity and stable community structure for the resistant cultivars were detected. Comparison analysis showed that some bacterial phyla were significantly enriched in the wheat root or rhizosphere of the resistant wheat cultivar. Furthermore, the root and rhizosphere of the resistant cultivars greatly recruited many known beneficial bacterial and fungal taxa. In contrast, the relative abundance of potential pathogens was higher for the susceptible cultivar than for the resistant cultivar. Network co-occurrence analysis revealed that a much more complex, more mutually beneficial, and a higher number of bacterial keystone taxa in belowground microbial networks were displayed in the resistant cultivar, which may have been responsible for maintaining the stability and ecological balance of the microbial community. Overall, compared with the susceptible cultivar, the resistant cultivar tends to recruit more potential beneficial microbial groups for plant and rhizosphere microbial community interactions. These findings indicate that beneficial rhizosphere microbiomes for cultivars should be targeted and evaluated using community compositional profiles. KEY POINTS: • Different resistance levels in cultivars affect the rhizosphere microbiome.. • Resistant cultivars tend to recruit more potential beneficial microbial groups. • Bacteria occupy a high proportion and core position in the microflora network.