Rare taxa maintain the stability of crop mycobiomes and ecosystem functions

Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota

BACKGROUND

Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.

RESULTS

This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.

CONCLUSIONS

Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.

A novel method for achieving ecological indicator based on vertical soil bacterial communities coupled with machine learning: A case study of a typical tropical site in China

Global industrialization has resulted in severe contamination of soil with heavy metals (HMs). Nevertheless, it is unclear if it affects the depth-resolved bacterial communities. Herein, we collected soil samples at different depths from a typical HM-contaminated site and used amplicon sequencing to determine the differences in depth-resolved bacterial communities and to assess the thresholds and ecological impacts of HMs. Results revealed that HM levels reduced markedly with soil depth. The bacteria in upper soil exhibited higher community diversity and a more complex and stable ecological network structure. As depth increased, the proportion of negative interactions gradually elevated, indicating more competitive interspecies behavior. Threshold analyses based on machine learning revealed that arsenic (As) and copper (Cu) exhibited nonlinear impacts on ecosystems. Cu demonstrated a low-threshold effect, with its ecological consequences manifested at extremely low concentrations. Our results highlighted the utility of microbial monitoring in assessing the adverse effects of HMs on soil health to support environmental management and ecological restoration.

Relative importance of microbial abundance and taxonomic types in driving the processes and functions of coral reef seawater in the Wuzhizhou Island

Abundant and rare taxa of diverse microbial groups may play different roles in coral reefs, yet comprehensive and fine - scale analyses are still lacking. Using high-throughput sequencing methods, we investigated the microbial community and function of impacted reef seawater. Here, we focused on the effects of distinct microbial abundance (abundant versus rare biospheres) and taxonomic types (prokaryotic versus eukaryotic communities). Our study revealed that community assembly processes were more closely related to microbial abundance than to taxonomic types. Rare taxa increased partial functional redundancy compared to the abundant taxa, and bacterial composition had stronger associations with the overall functional attributes than the microeukaryotic taxa. We further demonstrated that taxonomic signatures were more sensitive to temperature and nutrient dynamics in the impacted coral reef than other functional features. These results suggest that community assembly and functional response are highly correlated with microbial abundance and taxonomic types, and that they have different sensitivities as potential indicators of environmental changes. Our findings can promote understanding about community assembly and promising indicators related to microbial abundance and taxonomic types in coral reefs.

Differentiation and Interconnection of the Bacterial Community Associated with Silene nigrescens Along the Soil-To-Plant Continuum in the Sub-Nival Belt of the Qiangyong Glacier

Plant microbiomes provide significant fitness advantages to their plant hosts, especially in the sub-nival belt. Studies to date have primarily focused on belowground communities in this region. Here, we utilized high-throughput DNA sequencing to quantify bacterial communities in the rhizosphere soil as well as in the root and leaf endosphere compartments of Silene nigrescens to uncover the differentiation and interconnections of these bacterial communities along the soil-to-plant continuum. Our findings reveal that the bacterial communities exhibit notable variation across different plant compartment niches: the rhizosphere soil, root endosphere, and leaf endosphere. There was a progressive decline in diversity, network complexity, network modularity, and niche breadth from the rhizosphere soil to the root endosphere, and further to the leaf endosphere. Conversely, both the host plant selection effect and the stability of these communities showed an increasing trend. Total nitrogen and total potassium emerged as crucial factors accounting for the observed differences in diversity and composition, respectively. Additionally, 3.6% of the total amplicon sequence variants (ASVs) were shared across the rhizosphere soil, root endosphere, and leaf endosphere. Source-tracking analysis further revealed bacterial community migration among these compartments. The genera Pseudomonas, IMCC26256, Mycobacterium, Phyllobacterium, and Sphingomonas constituted the core of the bacterial microbiome. These taxa are shared across all three compartment niches and function as key connector species. Notably, Pseudomonas stands out as the predominant taxon among these bacteria, with nitrogen being the most significant factor influencing its relative abundance. These findings deepen our understanding of the assembly principles and ecological dynamics of the plant microbiome in the sub-nival belt, offering an integrated framework for its study.

Plant-microbiome interactions and their impacts on plant adaptation to climate change

Plants have co-evolved with a wide range of microbial communities over hundreds of millions of years, this has drastically influenced their adaptation to biotic and abiotic stress. The rapid development of multi-omics approaches has greatly improved our understanding of the diversity, composition, and functions of plant microbiomes, but how global climate change affects the assembly of plant microbiomes and their roles in regulating host plant adaptation to changing environmental conditions is not fully known. In this review, we summarize recent advancements in the community assembly of plant microbiomes, and their responses to climate change factors such as elevated CO2 levels, warming, and drought. We further delineate the research trends and hotspots in plant-microbiome interactions in the context of climate change, and summarize the key mechanisms by which plant microbiomes influence plant adaptation to the changing climate. We propose that future research is urgently needed to unravel the impact of key plant genes and signal molecules modulated by climate change on microbial communities, to elucidate the evolutionary response of plant-microbe interactions at the community level, and to engineer synthetic microbial communities to mitigate the effects of climate change on plant fitness.

Exposure to thiazole pesticides disrupts pathogens and undermines keystone status of rare taxa within bacterial ecological networks

Considering the sensitivity of rare microbial taxa to environmental disturbances and their critical roles in ecosystems, it is essential to investigate how soil microbial communities (particularly rare microbes) respond to pesticide exposure. In this study, we found that thiazole pesticides significantly reduced the severity of potato common scab and effectively disrupted the pathogen's cell membrane integrity. Notably, hierarchical partitioning analysis indicated that the rare microbial taxa in potato geocaulosphere soil constitute key clusters influencing disease incidence. Within bacterial molecular ecological networks, nodes corresponding to these rare taxa generally exhibited higher degrees compared to those of more abundant taxa. However, pesticide exposure reduced the number of keystone nodes and substantially weakened the hub status of rare bacterial taxa in these networks. These findings suggest that, although thiazole pesticides effectively eradicate pathogens, they may also pose a non-negligible potential risk to rare taxa in agricultural ecosystems.

Plant diversity increases diversity and network complexity rather than alters community assembly processes of leaf-associated fungi in a subtropical forest

Plant diversity significantly impacts ecosystem processes and functions, yet its influence on the community assembly of leaf fungi remains poorly understood. In this study, we investigated leaf epiphytic and endophytic fungal communities in a Chinese subtropical tree species richness experiment, ranging from 1 to 16 species, using amplicon sequencing to target the internal transcribed spacer 1 region of the rDNA. We found that the community assembly of epiphytic and endophytic fungi was predominantly governed by stochastic processes, with a higher contribution of dispersal limitation on epiphytic than on endophytic fungal communities but a higher contribution of selection on endophytic than on epiphytic fungal communities. The plant-epiphytic fungus interaction network was more complex (e.g., more highly connected and strongly nested but less specialized and modularized) than the plant-endophytic fungus interaction network. Additionally, tree species richness was positively correlated with the network complexity and diversity of epiphytic (α-, β- and γ-diversity) and endophytic (β- and γ-diversity) fungi, but was not associated with the contribution of the stochastic and deterministic processes on the community assembly of epiphytic and endophytic fungi. This study highlights that tree species diversity enhances the diversity and network complexity, rather than alters the ecological processes in community assembly of leaf-associated fungi.

Nonlinear relationship between diversity of rare and common species and ecosystem multifunctionality in alpine meadows along an altitude gradient

Biodiversity is closely related to ecosystem multifunctionality (EMF), and both are affected by environmental change. However, little is known about the impact of specific components of a biome (e.g., rare and common species) on EMF. This limits our understanding of protecting rare and common species and better utilizing multiple ecosystem services. In this study, we established 15 study plots at different elevation gradients (ranging from 2010 m to 3931 m) in the northeastern Tibetan Plateau to analyze the changes in species diversity of rare and common species in alpine meadows and their contributions to EMF. The results showed that (1) the functional richness (FRic), functional evenness (FEve), and species richness (SR) of rare species were significantly higher than those of common species. (2) The diversity of both rare and common species was significantly positively correlated with EMF across the entire elevation gradient, with the FRic of rare species explaining more of the variation in EMF (R2 = 0.73, P < 0.001). (3) EMF showed a significant negative correlation with elevation (F = -14.67, P < 0.001), with elevation explaining 88 % and 81 % of the variation in EMF in the regions with elevation <3100 m and elevation >3100 m, respectively. (4) The relationship between rare species diversity and EMF changed around 3100 m above sea level. At lower altitudes (<3000 m), common species diversity was positively correlated with EMF, while at higher altitudes (>3150 m), the positive impact of rare species diversity on EMF was more significant. This study helps to understand more carefully how rare and common species affect EMF in the context of climate change and, for the first time, emphasizes the potential and role of rare species in predicting and regulating ecosystem functions, productivity, and functional trade-offs. It is recommended to designate alpine meadow areas as protected areas, strengthen the protection of rare species in high-altitude meadows, and establish seed banks of rare species for artificial restoration. In low-altitude regions, the diversity of common species should be maintained through reasonable grazing, grazing bans and rotations, and organic fertilizers.

Culture-dependent and -independent analyses reveal unique community structure and function in the external mycelial cortices of Ophiocordyceps sinensis

Ophiocordyceps sinensis, also known as DongChong XiaCao (DCXC) in China, is a complex of the parasitic fungus Hirsutella sinensis and its caterpillars host living in extreme alpine environments on the Qinghai-Tibetan Plateau. Wild resources of O. sinensis are threatened by over-harvesting due to its perceived high medicinal value. In recent years, numerous studies have pointed out that endofungal bacteria play an important role in fungal spore germination and zygote formation. In this sense, studying the endofungal bacteria of O. sinensis is of great interest regarding the conservation of this species. In this study, we investigated the community structure (abundance and rare sub-communities) and function of the soil-mycelial-sclerotia-stromata continuum endofungal bacteria in O. sinensis from the Qilian Mountain region of the Tibetan Plateau by using amplicon and macro-genome sequencing technologies. Based on the results, rare taxa exhibited more differences among the components, and enrichment and co-occurrence network analyses revealed that abundant taxa played a more important role. We further found that endofungal bacteria in external mycelial cortices have unique community structures and functions. In particular, they play an important role in material cycling, potentially providing essential nutrients during the lifecycle of O. sinensis. We successfully isolated 52 endofungal bacterial strains using high-throughput isolation techniques, some of them were undetected by high-throughput sequencing. We systematically investigated the structure and function of endofungal bacteria of the O. sinensis, providing a solid foundation for the cultivation and conservation of wild resources of this species at an industrial scale.

Four birds with one stone: applying nitrification inhibitor on the basis of percarbamide restores yield, decreases fungicide residue, enhances soil multifunctionality and stimulates bacterial community

BACKGROUND

Fungicide residues were frequently detected in vegetables and soils, which severely affected crop yields and qualities. Reasonable nitrogen management might promote yields and decrease fungicide carbendazim residues in plant-soil systems. Current study explores comprehensive relationships among carbendazim residues, crop yields, soil multifunctionalities and endophytic and soil bacterial communities after applying nitrification inhibitors (3,4-dimethylpyrazole phosphate and dicyandiamide) and percarbamide to different soils.

RESULTS

Combined nitrification inhibitor and percarbamide additions produced multi-effects on restoring yields, declining fungicide residues, promoting soil multifunctionalities and stimulating bacterial communities. Relative to the control, percarbamide application promoted carbendazim dissipations in upland soils but decreased bacterial community diversities and stabilities in different soils. Compared to exclusive percarbamide, extra dicyandiamide applications decreased carbendazim residues by 25.8% in upland soils and 70.2% in paddy soils, declined carbendazim residues in carrots via improving soil pH, ammonium nitrogen (NH4 +-N) and Proteobacteria ratios. Relative to percarbamide application alone, extra dicyandiamide addition promoted the dry carrot yields by 133.2% in upland soils and 33.5% in paddy soils via promoting soil NH4 +-N, Acidobacteriota and Actinobacteriota ratios and bacterial community diversities and stabilities. Upland soil multifunctionality improvements diminished soil carbendazim residues via promoting soil pH and NH4 +-N, and paddy soil multifunctionalities and endophytic bacterial community structures generated negative influences on carrot carbendazim residues.

CONCLUSION

Our study suggested that nitrification inhibitor on the basis of percarbamide generated multi-effects on the different crop-soil systems: restoring carrot yields, reducing carbendazim contents, promoting soil multifunctionalities and stimulating bacterial community diversities and stabilities. © 2024 Society of Chemical Industry.

Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration

The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.

Evaluating the stability of nursery-established arbuscular mycorrhizal fungal associations in apple rootstocks

Arbuscular mycorrhizal fungi (AMF) are promoted as commercial bioinoculants for sustainable agriculture. Little is known, however, about the survival of AMF inoculants in soil and their impacts on native or pre-established AMF communities in root tissue. The current study was designed to assess the stability of pre-existing/nursery-derived AMF in apple rootstocks after being planted into soil containing a known community of AMF with a limited number of species. Root-associated endophytic communities (bacteria and fungi) are known to differ depending on apple rootstock genotype. Thus, an additional aim of this study was to explore the effect of apple rootstock genotype on AMF community structure. A greenhouse experiment was conducted in which a variety of apple rootstock genotypes (G.890, G.935, M.26, and M.7) were inoculated with a commercially available, multi-species AMF consortium. Nursery-derived AMF communities were sequenced, and changes to AMF community structure following cultivation in pasteurized soil (inoculated and non-inoculated) were assessed using a Glomeromycota-specific phylogenetic tree, which included 91 different AMF species from 24 genera. Results show that inoculant colonization potential was limited and that apple rootstocks serve as a significant source of inoculum from the nursery where they are produced. Rootstocks established relationships with introduced AMF in a genotype-specific manner. Regardless of colonization success, however, the inoculant caused alterations to the resident AMF communities of both Geneva and Malling rootstocks, particularly low abundance taxa. In addition, phylogeny-based analysis revealed a unique, well-supported clade of unknown taxonomy, highlighting the importance of using phylogenetic-based classification for accurate characterization of AMF communities.IMPORTANCEUnderstanding the impacts of introduced AMF on residential AMF communities is essential to improving plant productivity in nursery and orchard systems. In general, there is a dearth of data on the interactions of commercial AMF inoculants with pre-established AMF communities living in symbiosis with the host plant. The interplay between apple rootstock genotype and the endophytic root microbiome is also an area where more research is needed. This study demonstrates the potential for nursery-established AMF associations to be maintained when transplanted into the field. In addition to providing insight into rootstock/AMF associations, our study calls attention to the current issues attendant with relying on web-based databases for determining AMF identity. The use of phylogenetic tools represents one possible solution and may be of value to industry practitioners in terms of improving product composition and consistency.

The process of nitrogen-adaptation root endophytic bacterial rather than phosphorus-adaptation fungal subcommunities construction unveiled the tomato yield improvement under long-term fertilization

Interactions between endophytes (endophytic bacteria and fungi) and plants are crucial in maintaining crop fitness in agricultural systems, particularly in relation to abundant and rare subcommunities involved in community construction. However, the influence of long-term fertilization on heterogeneous rhizosphere nitrogen and phosphorus environments and how these conditions affect the key subcommunities of root endophytes and their community assembly mechanisms remain unclear. We studied the 26th year of a field experiment conducted in a greenhouse with varying levels of nitrogen and phosphorus (CKP0, CKP1, CNP0, CNP1, ONP0, and ONP1) to assess the composition of tomato root endophytes and their impact on yield. We employed 16S rRNA and fungal ITS region amplicon sequencing to investigate the assembly mechanisms of abundant and rare endophytic subcommunities, network correlations, core subcommunity structures, and key species that enhance crop yield. The results indicated that organic manure and phosphorus fertilizers significantly increased the rhizosphere soil nitrogen content, phosphorus content, and phosphorus availability (labile P, moderately labile P, and non-labile P). These fertilizers also significantly affected the composition (based on Bray-Curtis distance) and community assembly processes (βNTI) of endophytic microbial subcommunities. The assembly of both bacterial and fungal subcommunities was primarily governed by dispersal limitation, with community structures being significantly regulated by the content of rhizosphere soil available nitrogen (AN) and moderately labile P (MLP). Rare bacterial and fungal subcommunities complemented the ecological niches of abundant subcommunities in the co-occurrence network, supporting community functions and enhancing network stability. Nitrogen-adapting abundant and rare bacterial subcommunities provided a stronger predictive correlation for tomato yield than phosphorus-adapting fungal subcommunities. Additionally, three core genera of rare endophytic bacteria such as Arthrobacter, Microbacterium, and Sphingobium were identified as potentially involved in improving crop yield improvement. These findings revealed the distinct assembly mechanisms of endophytic microbial subcommunities affected by fertilization, enhancing our understanding of better management practices and controlling endophytes to improve crop yield in intensive agricultural ecosystems.

Variability of microbiomes in winter rye, wheat, and triticale affected by snow mold: predicting promising microorganisms for the disease control

BACKGROUND

Snow mold caused by different psychrophilic phytopathogenic fungi is a devastating disease of winter cereals. The variability of the snow mold pathocomplex (the quantitative composition of snow mold fungi) has not been evaluated across different crops or different agrocenoses, and no microbial taxa have been predicted at the whole-microbiome level as potential effective snow mold control agents. Our study aimed to assess the variability of the snow mold pathocomplex in different winter cereal crops (rye, wheat, and triticale) in different agrocenoses following the peak disease progression and to arrange a hierarchical list of microbial taxa predicted to be the main candidates to prevent or, conversely, stimulate the development of snow mold pathogens.

RESULTS

The variability of microbiomes between different crops within a particular agrocenosis was largely determined by fungal communities, whereas the variability of microbiomes of a particular crop in different agrocenoses was largely determined by bacterial communities. The snow mold pathocomplex was the most "constant" in rye, with the lowest level of between-replicate variability and between-agrocenoses variability and (similar to the triticale snow mold pathocomplex) strong dominance of Microdochium over other snow mold fungi. The wheat snow mold pathocomplex was represented by different snow mold fungi, including poorly investigated Phoma sclerotioides. To predict snow mold-control microorganisms, a conveyor of statistical methods was formed and applied; this conveyor enables considering not only the correlation between the abundance of target taxa and a phytopathogen but also the stability and fitness of taxa within plant-associated communities and the reproducibility of the predicted effect of taxa under different conditions. This conveyor can be widely used to search for biological agents against various plant infectious diseases.

CONCLUSIONS

The top indicator microbial taxa for winter wheat and rye following the winter period were Ph. sclerotioides and Microdochium, respectively, both of which are causal agents of snow mold disease. Bacteria from the Cellulomonas, Lechevalieria, and Pseudoxanthomonas genera and fungi from the Cladosporium, Entimomentora, Pseudogymnoascus, and Cistella genera are prime candidates for testing their plant-protective properties against Microdochium-induced snow mold disease and for further use in agricultural practice.

From nature to urbanity: exploring phyllosphere microbiome and functional gene responses to the Anthropocene

The Anthropocene exerts various pressures and influences on the stability and function of the Earth's ecosystems. However, our understanding of how the microbiome responds in form and function to these disturbances is still limited, particularly when considering the phyllosphere, which represents one of the largest microbial reservoirs in the terrestrial ecosystem. In this study, we comprehensively characterized tree phyllosphere bacteria and associated nutrient-cycling genes in natural, rural, suburban, and urban habitats in China. Results revealed that phyllosphere bacterial community diversity, richness, stability, and composition heterogeneity were greatest at the most disturbed sites. Stochastic processes primarily governed the assembly of phyllosphere bacterial communities, although the role of deterministic processes (environmental selection) in shaping these communities gradually increased as we moved from rural to urban sites. Our findings also suggest that human disturbance is associated with the reduced influence of drift as increasingly layered environmental filters deterministically constrain phyllosphere bacterial communities. The intensification of human activity was mirrored in changes in functional gene expression within the phyllosphere microbiome, resulting in enhanced gene abundance, diversity, and compositional variation in highly human-driven disturbed environments. Furthermore, we found that while the relative proportion of core microbial taxa decreased in disturbed habitats, a core set of microbial taxa shaped the distributional characteristics of both microbiomes and functional genes at all levels of disturbance. In sum, this study offers valuable insights into how anthropogenic disturbance may influence phyllosphere microbial dynamics and improves our understanding of the intricate relationship between environmental stressors, microbial communities, and plant function within the Anthropocene.

DNA and RNA sequencing reveal the role of rare bacterial taxa in constructed wetlands: Insights into community activities, ecological functions, and assembly processes

Microorganisms are essential for the functioning of constructed wetlands (CWs), yet the role of rare bacterial taxa in CWs remains poorly understood. In this study, the community structure, metabolic activities, ecological functions, and assembly processes of abundant and rare bacterial taxa in CWs were examined using DNA and RNA high-throughput sequencing. Our results revealed that Gammaproteobacteria, Alphaproteobacteria, Bacteroidia, and Actinobacteria exhibited high diversity and sequence abundance. Retention in CWs generally reduced the metabolic activities of bacterial communities, with intermediate and rare taxa showing significantly lower activity compared to those in the influent. Despite their low abundance, functional groups involved in nitrogen and phosphorus removal exhibited high metabolic activities, highlighting their crucial role in these processes. Co-occurrence network analysis showed that non-rare taxa interacted more frequently with rare taxa than with conspecifics, and that keystone species included comparable numbers of both abundant and rare species. These highlight the importance of rare taxa in ecological functions and maintaining the stability of bacterial community structure in CWs. The assembly of bacterial communities was driven by both deterministic and stochastic processes, with stochastic processes predominantly shaping the rare taxa and deterministic processes primarily influencing the abundant taxa. Overall, this study provides novel insights into bacterial community structure, metabolic activity, and assembly processes in CWs, particularly the ecological roles of rare taxa.

Fungal communities are more sensitive to mildew than bacterial communities during tobacco storage processes

Mildew poses a significant threat to tobacco production; however, there is limited information on the structure of the abundant and rare microbial subcommunities in moldy tobacco leaves. In this study, we employed high-throughput sequencing technology to discern the disparities in the composition, diversity, and co-occurrence patterns of abundant and rare fungal and bacterial subcommunities between moldy and normal tobacco leaves collected from Guizhou, Shanghai, and Jilin provinces, China. Furthermore, we explored the correlation between microorganisms and metabolites by integrating the metabolic profiles of moldy and normal tobacco leaves. The results showed that the fungi are more sensitive to mildew than bacteria, and that the fungal abundant taxa exhibit greater resistance and environmental adaptability than the rare taxa. The loss of rare taxa results in irreversible changes in the diversity, richness, and composition of the fungal community. Moreover, rare fungal taxa and abundant bacterial taxa played crucial roles in maintaining the stability and functionality of the tobacco microecosystem. In moldy tobacco, however, the disappearance of rare taxa as key nodes resulted in reduced connectivity and stability within the fungal network. In addition, metabolomic analysis showed that the contents of indoles, pyridines, polyketones, phenols, and peptides were significantly enriched in the moldy tobacco leaves, while the contents of amino acids, carbohydrates, lipids, and other compounds were significantly reduced in these leaves. Most metabolites showed negative correlations with Dothideomycetes, Alphaproteobacteria, and Gammaproteobacteria, but showed positive correlations with Eurotiales and Bacilli. This study has demonstrated that abundant fungal taxa are the predominant biological agents responsible for tobacco mildew, while bacteria may indirectly contribute to this process through the production and degradation of metabolites. KEY POINTS: • Fungi exhibited greater sensitivity to mildew of tobacco leaf compared to bacteria • Rare fungal taxa underwent significant damage during the mildew process • Mildew may damage the defense system of the tobacco leaf microecosystem.

Stochasticity-dominated rare fungal endophytes contribute to coexistence stability and saponin accumulation in Panax species

Fungal communities inhabiting plant tissues are complex systems of inter-species interactions, consisting of both the "abundant biosphere" and "rare biosphere". However, the composition, assembly, and stability of these subcommunities, as well as their contributions to productivity remain unclear. In this study, the taxonomic and functional composition, co-occurrence, and ecological assembly of abundant and rare fungal subcommunities in different tissues of three Panax species were investigated. Abundant subcommunities were dominated by potential plant pathogens belonging to Microbotryomycetes, while saprotrophic fungi like Agaricomycetes and Mortierellomycetes were more prevalent in rare subcommunities. The rare taxa played a central role in upholding the stability of the fungal networks as driven by Dothideomycetes and Sordariomycetes. Homogeneous selection played a larger role in the assembly of abundant fungal subcommunities compared to the rare counterparts, which was more dominated by stochastically ecological drift in all plant species. Rare biospheres played a larger role in the accumulation of saponin compared to their abundant counterparts, especially in the leaf endosphere, which was mainly affected by environmental factors (Mg, pH, OC, and etc.). Furthermore, we found that rare species belonging to unidentified saprotrophs were associated with saponin formation. This study provides hypotheses for future experiments to understand mechanisms accounting for the variations in the composition and function of rare fungal subcommunities across different Panax species.

Distribution and diversity of cultured endophytic fungi in Gentiana straminea Maxim. at different altitudes on the northeastern Qinghai-Tibetan Plateau

Endophytic fungi are a crucial microbial resource that can influence plant growth and development through their interactions with host plants. Gentiana straminea Maxim. is an important traditional Tibetan herb used to treat a range of diseases in the Qinghai-Tibetan region. However, the diversity and community structure of endophytic fungi in the species remain poorly understood. In this study, a total of 944 strains of endophytic fungi were isolated from the roots, stems, and leaves of G. straminea from four different altitudes. A total of 87 OTUs were identified through sequence alignment, comprising 6 classes, 15 orders, 25 families, and 44 genera. The colonization rate and diversity of endophytic fungi were affected by tissue type and altitude. With the exception of Xining, the endophytic fungi colonization rate of tissues was roots>leaves>stems. Moreover, the α-diversity of endophytic fungi among different tissues was leaves>stems>roots. Notably, the phylogenetic diversity index in leaves was significantly higher than that in roots. In addition, the colonization rate and diversity of endophytic fungi in leaves and stems demonstrated a decline with the increasing altitude. The β-diversity analysis revealed significant differences in the endophytic fungi of G. straminea at varying altitudes. In roots, geographical factors, such as latitude and longitude, were the primary drivers of variation, whereas environmental factors, including temperature and precipitation, had a greater influence on endophytes in leaves and stems. In addition, the results of the endophytic fungi association preference, linear discriminant analysis effect size (LEfSe), and co-network analysis indicated that these differential endophytic fungi may play a significant role in the authenticity and stress resistance of G. straminea.

Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils

Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.

Assembly processes and co-occurrence of bacterial communities in tree rhizosphere under Pb-Zn contamination

Rhizosphere bacteria are critical for supporting plant performance in stressful environments. Understanding the assembly and co-occurrence of rhizosphere bacterial communities contributes significantly to both plant growth and heavy metal accumulation. In this study, Ligustrum lucidum and Melia azedarach were planted in soils with simulated varying levels of Pb-Zn contamination. The Rhizosphere bacterial communities were investigated by using 16S rRNA gene sequencing. The impacts of Pb-Zn contamination on the diversity and structure of the rhizosphere bacterial community were found to be greater than those of both tree species. The variation in bacterial community structure in both trees was mainly driven by the combinations of Pb-Zn and soil properties. Deterministic processes (non-planted, 82 %; L. lucidum, 73 %; M. azedarach, 55 %) proved to be the most important assembly processes for soil bacterial communities, but both trees increased the importance of stochastic processes (18 %, 27 %, 45 %). The rhizosphere co-occurrence networks exhibited greater stability compared to the non-planted soil networks. Rare taxa played a dominant role in maintaining the stability of rhizosphere networks, as most of the keystone taxa within rhizosphere networks belonged to rare taxa. Dissimilarities in the structure and network complexity of rhizosphere bacterial communities were significantly associated with differences in tree biomass and metal accumulation. These variations in response varied between both trees, with L. lucidum exhibiting greater potential for phytoremediation in its rhizosphere compared to M. azedarach. Our results offer valuable insights for designing effective microbe-assisted phytoremediation systems.

Differential responses of the phyllosphere abundant and rare microbes of Eucommia ulmoides to phytohormones

Phyllosphere microbiota play a crucial role in plant productivity and adaptation, and the abundant and rare microbial taxa often possess distinct characteristics and ecological functions. However, it is unclear whether the different subcommunities of phyllosphere microbiota respond variably to the factors that influence their formation, which limits the understanding of community assembly. The effects of two phytohormones, namely, indole-3-acetic acid (IAA) and N6-(delta 2-isopentenyl)-adenine (IP), on the phyllosphere microbial subcommunities of Eucommia ulmoides were investigated using potted experiments. The results demonstrated that the phytohormones induced significant variations in the composition, diversity, and function of the abundant microbial subcommunity in the phyllosphere of E. ulmoides, however, their effects on the rare subcommunity were negligible, and their effects on the moderate subcommunity were between those of the abundant and rare taxa. The phytohormones also induced significant alterations in the phenotypic and physiological properties of E. ulmoides, which indirectly affected the phyllosphere microbial community. Leaf thickness and average leaf area were the main phenotypic variables that affected the composition of the phyllosphere microbial community. The total alkaloid content and activity of superoxide dismutase (SOD) were the main physiological variables that affected the composition of the phyllosphere microbial community. The phenotypic and physiological indices of E. ulmoides explained the variations in the phyllosphere microbial subcommunities in descending order: abundant > moderate > rare taxa. These variables explained a significant proportion of the variations in the abundant taxa, and an insignificant proportion of the variations in the rare taxa. This study improves our understanding of the assembly of the phyllosphere microbiota, which provides important theoretical knowledge for future sustainable agriculture and forestry management based on the precise regulation of phyllosphere microbiota.

Distinct strategies of the habitat generalists and specialists in the Arctic sediments: Assembly processes, co-occurrence patterns, and environmental implications

Microorganisms could be classified as habitat generalists and specialists according to their niche breadth, uncovering their survival strategy is a crucial topic in ecology. Here, differences in environmental adaptation, community assemblies, co-occurrence patterns, and ecological functions between generalists and specialists were explored in the Arctic marine sediments. Compared to specialists, generalists showed lower alpha diversity but stronger environmental adaption, and dispersal limitation contributed more to the community assembly of specialists (74 %) than generalists (46 %). Furthermore, the neutral theory model demonstrated that generalists (m = 0.20) had a higher immigration rate than specialists (m = 0.02), but specialists exhibited more complex co-occurrence patterns than generalists. Our results also found that generalists may play more important roles in C, N, S metabolism but are weaker in carbon fixation and xenobiotic biodegradation and metabolism. This study would broaden our understanding of bacterial generalists' and specialists' survival strategies, and further reveal their ecological functions in marine sediments.

Ms gene and Mr gene: Microbial-mediated spatiotemporal communication between plants

Within dynamic agroecosystems, microbes can act as key intermediaries, facilitating spatiotemporal communication among plants. Future research could categorize key plant genes involved in plant-microbe interactions into microbiome-shaping genes (Ms genes) and microbiome-responsive genes (Mr genes), potentially leading to the construction of spatiotemporal molecular networks with microbes as intermediaries.

Bacterial abundant taxa exhibit stronger environmental adaption than rare taxa in the Arctic Ocean sediments

Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. However, little is known about the survival strategies of their abundant and rare taxa, especially in polar marine environments. Here, bacterial environmental adaptation, community assembly processes, and co-occurrence patterns between abundant and rare taxa were compared in the Arctic Ocean sediments. Results indicated that the diversity of rare taxa is significantly higher than that of abundant taxa, whereas the distance-decay rate of rare taxa community similarity is over 1.5 times higher than that of abundant taxa. Furthermore, abundant taxa exhibited broader environmental breadth and stronger phylogenetic signals compared to rare taxa. Additionally, the community assembly processes of the abundant taxa were predominantly governed by 81% dispersal limitation, while rare taxa were primarily influenced by 48% heterogeneous selection. The co-occurrence network further revealed the abundant taxa formed a more complex network to enhance their environmental adaptability. This study revealed the differences in environmental responses and community assembly processes between bacterial abundant and rare taxa in polar ocean sediments, providing some valuable insights for understanding their environmental adaptation strategies in marine ecosystems.

Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities

The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.

Impacts of fertilization methods on Salvia miltiorrhiza quality and characteristics of the epiphytic microbial community

Plant epiphytic microorganisms have established a unique symbiotic relationship with plants, which has a significant impact on their growth, immune defense, and environmental adaptation. However, the impact of fertilization methods on the epiphytic microbial community and their correlation with the yield and quality of medicinal plant was still unclear. In current study, we conducted a field fertilization experiment and analyzed the composition of epiphytic bacterial and fungal communities employing high throughput sequencing data in different organs (roots, stems, and leaves) of Salvia miltiorrhiza, as well as their correlation with plant growth. The results showed that fertilization significantly affected the active ingredients and hormone content, soil physicochemical properties, and the composition of epiphytic microbial communities. After fertilization, the plant surface was enriched with a core microbial community mainly composed of bacteria from Firmicutes, Proteobacteria, and Actinobacteria, as well as fungi from Zygomycota and Ascomycota. Additionally, plant growth hormones were the principal factors leading to alterations in the epiphytic microbial community of S. miltiorrhiza. Thus, the most effective method of fertilization involved the application of base fertilizer in combination with foliar fertilizer. This study provides a new perspective for studying the correlation between microbial community function and the quality of S. miltiorrhiza, and also provides a theoretical basis for the cultivation and sustainable development of high-quality medicinal plants.

Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland

The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant-microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.

The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil-Root Continuum Niche Gradient

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil-root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil-root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root-soil continuum.

Rare subcommunity maintains the stability of ecosystem multifunctionality by deterministic assembly processes in subtropical estuaries

Microorganisms, especially rare microbial species, are crucial in estuarine ecosystems for driving biogeochemical processes and preserving biodiversity. However, the understanding of the links between ecosystem multifunctionality (EMF) and the diversity of rare bacterial taxa in estuary ecosystems remains limited. Employing high-throughput sequencing and a variety of statistical methods, we assessed the diversities and assembly process of abundant and rare bacterioplankton and their contributions to EMF in a subtropical estuary. Taxonomic analysis revealed Proteobacteria as the predominant phylum among both abundant and rare bacterial taxa. Notably, rare taxa demonstrated significantly higher taxonomic diversity and a larger species pool than abundant taxa. Additionally, our findings highlighted that deterministic assembly processes predominantly shape microbial communities, with heterogeneous selection exerting a stronger influence on rare taxa. Further analysis reveals that rare bacterial beta-diversity significantly impacts to EMF, whereas alpha diversity did not. The partial least squares path modeling (PLS-PM) analysis demonstrated that the beta diversity of abundant and rare taxa, as the main biotic factor, directly affected EMF, while temperature and total organic carbon (TOC) were additional key factors to determine the relationship between beta diversity and EMF. These findings advance our understanding of the distribution features and ecological knowledge of the abundant and rare taxa in EMF in subtropical estuaries, and provide a reference for exploring the multifunctionality of different biospheres in aquatic environments.

Singh B, Zhu YG, Hu HW, Li PP, Han YL, Han LL, Zhang QB, Wang JT, Liu SY, Wu CF, Ge AH, Zhang LM, He JZ. Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development

Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.

Keystone taxa enhance the stability of soil bacterial communities and multifunctionality under steelworks disturbance

Continuous discharge of wastewater, emissions, and solid wastes from steelworks poses environmental risks to ecosystems. However, the role of keystone taxa in maintaining multifunctional stability during environmental disturbances remains poorly understood. To address this, we investigated the community diversity, assembly mechanisms, and soil multifunctionality of soils collected from within the steelworks (I), within 2.5 km radius from the steelworks (E), and from an undisturbed area (CK) in Jiangsu Province, China, via 16 S rRNA sequencing. Significant differences were found in the Chao1 and the richness indexes of the total taxa (p < 0.05), while the diversity of keystone taxa was not significant at each site (p > 0.05). The deterministic processes for total taxa were 42.9%, 61.9% and 47.7% in CK, E, and I, respectively. Steelworks stress increased the deterministicity of keystone taxa from 52.3% in CK to 61.9% in E and I soils. The average multifunctionality indices were 0.518, 0.506 and 0.513 for CK, E and I, respectively. Although the soil multifunctionality was positive correlated with α diversity of both the total and keystone taxa, the average degree of keystone taxa in functional network increased significantly (79.96 and 65.58, respectively), while the average degree of total taxa decreased (44.59 and 51.25, respectively) in the E and I. This suggests keystone taxa contribute to promoting the stability of ecosystems. With increasing disturbance, keystone taxa shift their function from basic metabolism (ribosome biogenesis) to detoxification (xenobiotics biodegradation, metabolism, and benzoate degradation). Here we show that keystone taxa are the most important factor in maintaining stable microbial communities and functions, providing new insights for mitigating pollution stress and soil health protection.

Strategies for regulating the intensity of different cyanobacterial blooms: Insights from the dynamics and stability of bacterioplankton communities

The occurrence of cyanobacterial blooms is increasing in frequency and magnitude due to climate change and human activities, which poses a direct threat to drinking water security. The impacts of abiotic and biotic factors on the development of blooms have been well studied; however, control strategies for different bloom intensities have rarely been explored from the perspective of the dynamics and stability of bacterioplankton communities. Here, a network analysis was used to investigate the interactions and stability of microbial communities during different periods of R. raciborskii bloom in an inland freshwater lake. The abundance and diversity of rare taxa were significantly higher than that of abundant taxa throughout the bloom cycle. At the pre-bloom (PB) stage, microbial interactions among the different bacterial groups were weak but strongly negatively correlated, indicating low robustness and weak disturbance resistance within the community. However, community stability was better, and microbial interactions became more complicated at the high-bloom (HB) and low-bloom (LB) stages. Interestingly, rare taxa were significantly responsible for community stability and connectivity despite their low relative abundance. The Mantel test revealed that Secchi depth (SD), orthophosphate (PO43--P), and dissolved oxygen (DO) were significantly positively correlated with abundant taxa, rare taxa and PB. DO was significantly positively correlated with HB, intermediate taxa, and rare taxa, while water temperature (WT), N/P and total nitrogen (TN) were significantly positively correlated with LB, abundant taxa, intermediate taxa, and rare taxa. These findings suggest that reducing the PO43--P concentration at the PB stage may be an effective approach to preventing the development of R. raciborskii blooms, while regulating rare taxa at the HB and LB stages may be a key factor in controlling R. raciborskii blooms.

Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease

Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.

Assemblages of rhizospheric and root endospheric mycobiota and their ecological associations with functional traits of rice

The soil-root interface harbors complex fungal communities that play vital roles in the fitness of host plants. However, little is known about the assembly rules and potential functions of rhizospheric and endospheric mycobiota. A greenhouse experiment was conducted to explore the fungal communities inhabiting the rhizosphere and roots of 87 rice cultivars at the tillering stage via amplicon sequencing of the fungal internal transcribed spacer 1 region. The potential relationships between these communities and host plant functional traits were also investigated using Procrustes analysis, generalized additive model fitting, and correlation analysis. The fungal microbiota exhibited greater richness, higher diversity, and lower structural variability in the rhizosphere than in the root endosphere. Compared with the root endosphere, the rhizosphere supported a larger coabundance network, with greater connectivity and stronger cohesion. Null model-based analyses revealed that dispersal limitation was primarily responsible for rhizosphere fungal community assembly, while ecological drift was the dominant process in the root endosphere. The community composition of fungi in the rhizosphere was shown to be more related to plant functional traits, such as the root/whole plant biomass, root:shoot biomass ratio, root/shoot nitrogen (N) content, and root/shoot/whole plant N accumulation, than to that in the root endosphere. Overall, at the early stage of rice growth, diverse and complex rhizospheric fungal communities are shaped by stochastic-based processes and exhibit stronger associations with plant functional traits.

IMPORTANCE

The assembly processes and functions of root-associated mycobiota are among the most fascinating yet elusive topics in microbial ecology. Our results revealed that stochastic forces (dispersal limitation or ecological drift) act on fungal community assembly in both the rice rhizosphere and root endosphere at the early stage of plant growth. In addition, high covariations between the rhizosphere fungal community compositions and plant functional trait profiles were clearly demonstrated in the present study. This work provides empirical evidence of the root-associated fungal assembly principles and ecological relationships of plant functional traits with rhizospheric and root endospheric mycobiota, thereby potentially providing novel perspectives for enhancing plant performance.

Chemical composition of soil carbon is governed by microbial diversity during understory fern removal in subtropical pine forests

Understory vegetation has an important impact on soil organic carbon (SOC) accumulation. However, little is known about how understory vegetation alters soil microbial community composition and how microbial diversity contributes to SOC chemical composition and persistence during subtropical forest restoration. In this study, removal treatments of an understory fern (Dicranopteris dichotoma) were carried out within pine (Pinus massoniana) plantations restored in different years in subtropical China. Soil microbial community composition and microbial diversity were measured using phospholipid fatty acids (PLFAs) biomarkers and high-throughput sequencing, respectively. The chemical composition of SOC was also measured via solid-state 13C nuclear magnetic resonance (13C NMR). Our results showed that fern removal decreased alkyl C by 4.2 % but increased O-alkyl C by 15.6 % on average, leading to a decline of alkyl C/O-alkyl C ratio, suggesting altered chemical composition of SOC and lowered SOC recalcitrance without fern. Fern removal significantly lowered the fungi-to-bacteria ratio, and it also reduced fungal and bacterial diversity. Partial correlation analysis revealed that soil nitrogen availability was a key factor influencing microbial diversity. Bacterial diversity showed a close relationship with the Alkyl C/O-alkyl C ratio following fern removal. Furthermore, the microbial community structure and bacterial diversity were responsible for 18 % and 55 % of the explained variance in the chemical composition of SOC, respectively. Taken together, these analyses jointly suggest that bacterial diversity exerts a greater role than microbial community structure in supporting SOC persistence during understory fern removal. Our study emphasizes the significance of understory ferns in supporting microbial abundance and diversity as a means of altering SOC persistence during subtropical forest restoration.

Ecological and functional differences of abundant and rare sub-communities in wastewater treatment plants across China

The microbial community in activated sludge is composed of a small number of abundant sub-community with high abundance and a large number of rare sub-community with limited abundance. Our knowledge regarding the ecological properties of both abundant and rare sub-communities in activated sludge is limited. This article presented an analysis of functional prediction, assembly mechanisms, and biogeographic distribution characteristics of abundant and rare sub-communities in 211 activated sludge samples from 60 wastewater treatment plants across China. Moreover, this study investigated the dominant factors influencing the community structure of these two microbial groups. The results showed that the functions associated with carbon and nitrogen cycling were primarily detected in abundant sub-community, while rare sub-community were primarily involved in sulfur cycling. Both microbial groups were mainly influenced by dispersal limitation, which, to some extent, resulted in a distance-decay relationship in their biogeographic distribution. Moreover, a higher spatial turnover rate of rare sub-communities (0.0887) suggested that spatial differences in microbial community structure among different WWTPs may mainly result from rare sub-community. Moreover, SEM showed that geographic locations affected rare sub-communities greatly, which agreed with their higher dispersal limitation and turnover rate. In contrast, influent characteristics showed stronger correlations with abundant sub-communities, suggesting that abundant sub-community may contribute more to the removal of pollutants. This study enhanced our understanding of abundant and rare microorganisms in activated sludge especially the role of rare species and provided scientific evidence for precise regulation and control of wastewater treatment plants.

Habitat-specific patterns of bacterial communities in a glacier-fed lake on the Tibetan Plateau

Different types of inlet water are expected to affect microbial communities of lake ecosystems due to changing environmental conditions and the dispersal of species. However, knowledge of the effects of changes in environmental conditions and export of microbial assemblages on lake ecosystems is limited, especially for glacier-fed lakes. Here, we collected water samples from the surface water of a glacier-fed lake and its two fed streams on the Tibetan Plateau to investigate the importance of glacial and non-glacial streams as sources of diversity for lake bacterial communities. Results showed that the glacial stream was an important source of microorganisms in the studied lake, contributing 45.53% to the total bacterial community in the lake water, while only 19.14% of bacterial community in the lake water was seeded by the non-glacial stream. Bacterial communities were significantly different between the glacier-fed lake and its two fed streams. pH, conductivity, total dissolved solids, water temperature and total nitrogen had a significant effect on bacterial spatial turnover, and together explained 36.2% of the variation of bacterial distribution among habitats. Moreover, bacterial co-occurrence associations tended to be stronger in the lake water than in stream habitats. Collectively, this study may provide an important reference for assessing the contributions of different inlet water sources to glacier-fed lakes.

Intermediate irrigation with low fertilization promotes soil nutrient cycling and reduces CO2 and CH4 emissions via regulating fungal communities in arid agroecosystems

The field practices, including irrigation and fertilization, strongly affect greenhouse gas emissions and soil nutrient cycling from agriculture. Understanding the underlying mechanism of greenhouse gas emissions, soil nutrient cycling, and their impact factors (fungal diversity, network characteristics, soil pH, salt, and moisture) is essential for efficiently managing global greenhouse gas mitigation and agricultural production. By considering abundant and rare taxa, we determine the identities and relative importance of ecological processes that modulate the fungal communities and identify whether they are crucial contributors to soil nutrient cycling and greenhouse gas emissions. The research is based on a 4-year field fertigation experiment with low (300 kg/ha P2O5 with 150 kg/ha urea) and high (600 kg/ha P2O5 with 300 kg/ha urea) fertilization level and three irrigation levels, that is, low (200 mm), medium (300 mm), and high (400 mm). The α-diversity (richness and Shannon index) of fungal subcommunities was significantly higher under medium irrigation (300 mm) and low fertilization (300 kg/ha P2O5 with 150 kg/ha urea) than under other treatments. Intermediate irrigation with low fertilization treatment yielded the most significant higher multinutrient cycling index and the lowest CO2 and CH4 emissions. The null model indicated that abundant taxa are mainly regulated by stochastic processes (dispersal limitation), and rare taxa are mainly regulated by environmental selection, especially by soil salinity. The co-occurrence network of rare taxa explained the changes in the entire fungal network stability. The abundant taxa played vital roles in regulating soil nutrient status, owing to the stronger association between their network and multinutrient cycling index. Furthermore, we have confirmed that soil moisture and fungal network stability are crucial factors affecting greenhouse gas emissions. Together, these results provide a deep understanding of the mechanisms that reveal fungal community assembly and soil fungal-driven variations in nutrient status and network stability, link fungal network characteristics to ecosystem functions, and reveal the factors that influence greenhouse gas emissions.

Rare and abundant bacterial communities in poplar rhizosphere soils respond differently to genetic effects

Interactions between plants and soil microbes are important to plant hybrid breeding under global change. However, the relationship between host plants and rhizosphere soil microorganisms has not been fully elucidated. Understanding the rhizosphere microbial structure of parents and progenies would provide a deeper insight into how genetic effects modulate the relationship between plants and soil. In this study, two family groups of poplar trees (A: parents and their two progenies; B: parents and their one progeny) with different genetic backgrounds (including seven genotypes) were selected from a common garden, and their rhizobacterial communities were analyzed to explore parent-progeny relationships. Our results showed significant differences in phylogenetic diversity, the number of 16S genes and the structure of rhizosphere bacterial communities (Adonis: R2 = 0.166, P < 0.01) between different family groups. Rhizosphere bacterial community structure was significantly dominated by genetic effects. Compared with abundant taxa, genetic effects were more powerful drivers of rare taxa. In addition, bacterial communities of hybrid progenies were all significantly more similar to their parents compared to the other group of parents, especially among rare taxa. The two poplar family groups exhibited differences between their rhizosphere bacterial co-occurrence networks. Group B had a relatively complex network with 2380 edges and 468 nodes, while group A had 1829 edges and 304 nodes. Soil organic carbon and carbon to nitrogen ratio (C/N) also influenced the rhizosphere bacterial community assembly. This was especially true for soil C/N, which explained 23 % of the β-nearest taxon index (βNTI) variation in rare taxa. Our results reveal the relationship of rhizosphere microorganisms between parents and progenies. This can help facilitate an understanding of the combination of plant breeding with microbes resource utilization and provide a theoretical basis for scientific advancement to support the development of forestry industry.

Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health

Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.

Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe

Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.

Seasonal dynamics of phyllosphere epiphytic microbial communities of medicinal plants in farmland environment

Introduction

The phyllosphere of plants is inhabited by various microorganisms, which play a crucial role in plant physiological metabolism. Currently, there is limited research on the dynamic effects of species and seasons on plant phyllosphere microbial community diversity and microbial interactions.

Methods

In this study, high-throughput sequencing technology was used to sequence the leaf surface parasitic microorganisms of five medicinal plants (Bupleurum chinense, Atractylodes lancea, Salvia miltiorrhiza, Astragalus membranaceus, and Lonicera japonica).

Results

The results showed that bacteria and fungi clustered into 3,898 and 1,572 operational taxonomic units (OTUs), respectively. Compared to host species, seasons had a more significant impact on the a diversity of bacteria and fungi. The heterogeneity of phyllosphere microbial communities was greater in winter compared to summer. Key species analysis at the OTU level and Spearman correlation analysis demonstrated significant preferences in microbial interactions under plant and seasonal backgrounds. The network connections between bacterial and fungal communities significantly increased during seasonal transitions compared to connections with plants.

Discussion

This study enhances our understanding of the composition and ecological roles of plant-associated microbial communities in small-scale agricultural environments. Additionally, it provides valuable insights for assessing the biodiversity of medicinal plants.

Application of culturomics in fungal isolation from mangrove sediments

BACKGROUND

Fungi play a crucial role in ecosystems, and they have been widely considered a promising source for natural compounds that are crucial for drug discovery. Fungi have a high diversity, but about 95% of them remain unknown to science. The description rate of fungi is very low, mainly due to the inability of most fungi to grow in artificial media, which could not provide a sufficiently similar environment to their natural habitats. Moreover, many species in nature are in a state of low metabolic activity which cannot readily proliferate without proper resuscitation. Previously developed culturomics techniques are mostly designed and applicable for bacteria, with few attempts for fungal isolation because of their significantly larger cell size and hyphal growth properties.

RESULTS

This study attempted to isolate previously uncultured and rare fungi from mangrove sediments using newly developed fungal enrichment culture method (FECM) and fungal isolation chips (FiChips). Comparison of fungal community composition at different enrichment stages showed that FECM had great influence on fungal community composition, with rare taxa increased significantly, thus improving the isolation efficiency of previously uncultured fungi. Similarly, in situ cultivation using FiChips has a significant advantage in detecting and culturing rare fungi, as compared to the conventional dilution plate method (DPM). In addition, based on morphological comparisons and phylogenetic analyses, we described and proposed 38 new ascomycetous taxa, including three new families, eight new genera, 25 new species, and two new combinations (presented in additional file 1).

CONCLUSIONS

Our study demonstrated that mangrove sediments harbor a high diversity of fungi, and our new isolation approaches (FECM and FiChips) presented a high efficiency in isolating hitherto uncultured fungi, which is potentially usable for fungal isolation in other similar environments. Video Abstract.

Changes in soil stoichiometry, soil organic carbon mineralization and bacterial community assembly processes across soil profiles

Soil organic carbon (SOC) mineralization is essential to biogeochemical recycling in terrestrial ecosystem. However, the microbial mechanisms underlying the nutrient-induced SOC mineralization remain uncertain. Here, we investigated how SOC mineralization was linked to microbial assembly processes as well as soil nutrient availability and stoichiometric ratio in a paddy rice ecosystem at four soil profile levels. Our results showed a sharp decrease in SOC mineralization from topsoil (112.61-146.34 mg CO2 kg-1 day-1) to subsoil (33.51-61.41 mg CO2 kg-1 day-1). High-throughput sequencing showed that both abundance and diversity of specialist microorganisms (Chao1: 1244.30-1341.35) significantly increased along the soil profile, while the generalist microorganisms (Chao1: 427.67-616.15; Shannon: 7.46-7.97) showed the opposite trend. Correspondingly, the proportion of deterministic processes that regulate specialist (9.64-21.59 %) and generalist microorganisms (21.17-53.53 %) increased and decreased from topsoil to subsoil, respectively. Linear regression modeling and partial least squares path modeling indicated that SOC mineralization was primarily controlled by the assembly processes of specialist microorganisms, which was significantly mediated by available soil C:N:P stoichiometry. This study highlighted the importance of soil stoichiometry-mediated bacterial community assembly processes in regulating SOC mineralization. Our results have an important implication for the integration of bacterial community assembly processes into the prediction of SOC dynamics.

Dynamics of Endophytic Fungal Communities Associated with Cultivated Medicinal Plants in Farmland Ecosystem

Microorganisms are an important component of global biodiversity and play an important role in plant growth and development and the protection of host plants from various biotic and abiotic stresses. However, little is known about the identities and communities of endophytic fungi inhabiting cultivated medicinal plants in the farmland ecosystem. The diversity and community composition of the endophytic fungi of cultivated medicinal plants in different hosts, tissue niches, and seasonal effects in the farmland of Northern China were examined using the next-generation sequencing technique. In addition, the ecological functions of the endophytic fungal communities were investigated by combining the sequence classification information and fungal taxonomic function annotation. A total of 1025 operational taxonomic units (OTUs) of endophytic fungi were obtained at a 97% sequence similarity level; they were dominated by Dothideomycetes and Pleosporales. Host factors (species identities and tissue niches) and season had significant effects on the community composition of endophytic fungi, and endophytic fungi assembly was shaped more strongly by host than by season. In summer, endophytic fungal diversity was higher in the root than in the leaf, whereas opposite trends were observed in winter. Network analysis showed that network connectivity was more complex in the leaf than in the root, and the interspecific relationship between endophytic fungal OTUs in the network structure was mainly positive rather than negative. The functional predications of fungi revealed that the pathotrophic types of endophytic fungi decreased and the saprotrophic types increased from summer to winter in the root, while both pathotrophic and saprotrophic types of endophytic fungi increased in the leaf. This study improves our understanding of the community composition and ecological distribution of endophytic fungi inhabiting scattered niches in the farmland ecosystem. In addition, the study provides insight into the biodiversity assessment and management of cultivated medicinal plants.

Core taxa drive microeukaryotic community stability of a deep subtropical reservoir after complete mixing

Microeukaryotes are key for predicting the change of ecosystem processes in the face of a disturbance. However, their vertical responses to multiple interconnected factors caused by water mixing remain unknown. Here, we conducted a 12-month high-frequency study to compare the impacts of mixing disturbances on microeukaryotic community structure and stability over different depths in a stratified reservoir. We demonstrate that core and satellite microeukaryotic compositions and interactions in surface waters were not resistant to water mixing, but significantly recovered. This was because the water temperature rebounded to the pre-mixing level. Core microeukaryotes maintained community stability in surface waters with high recovery capacity after water mixing. In contrast, the changes in water temperature, chlorophyll-a, and nutrients resulted in steep and prolonged variations in the bottom core and satellite microeukaryotic compositions and interactions. Under low environmental fluctuation, the recovery of microbial communities did not affect nutrient cycling in surface waters. Under high environmental fluctuation, core and satellite microeukaryotic compositions in bottom waters were significantly correlated with the multi-nutrient cycling index. Our findings shed light on different mechanisms of plankton community resilience in reservoir ecosystems to a major disturbance over depths, highlighting the role of bottom microeukaryotes in nutrient cycling.

Distinct responses of airborne abundant and rare microbial communities to atmospheric changes associated with Chinese New Year

Airborne microorganisms, including pathogens, would change with surrounding environments and become issues of global concern due to their threats to human health. Microbial communities typically contain a few abundant but many rare species. However, how the airborne abundant and rare microbial communities respond to environmental changes is still unclear, especially at hour scale. Here, we used a sequencing approach based on bacterial 16S rRNA genes and fungal ITS2 regions to investigate the high time-resolved dynamics of airborne bacteria and fungi and to explore the responses of abundant and rare microbes to the atmospheric changes. Our results showed that air pollutants and microbial communities were significantly affected by human activities related to the Chinese New Year (CNY). Before CNY, significant hour-scale changes in both abundant and rare subcommunities were observed, while only abundant bacterial subcommunity changed with hour time series during CNY. Air pollutants and meteorological parameters explained 61.5%-74.2% variations of abundant community but only 13.3%-21.6% variations of rare communities. These results suggested that abundant species were more sensitive to environmental changes than rare taxa. Stochastic processes predominated in the assembly of abundant communities, but deterministic processes determined the assembly of rare communities. Potential bacterial pathogens during CNY were the highest, suggesting an increased health risk of airborne microbes during CNY. Overall, our findings highlighted the "holiday effect" of CNY on airborne microbes and expanded the current understanding of the ecological mechanisms and health risks of microbes in a changing atmosphere.

Different responses of abundant and rare bacterial composition to groundwater depth and reduced nitrogen application in summer maize field

Introduction

It is well known that reduced nitrogen application and groundwater depth can change soil microbial communities, but the associated difference in the response of abundant and rare bacterial composition to these local environmental changes remains unclear.

Methods

In this study a lysimeter experiment was carried out to examine the impact of reduced nitrogen and groundwater depth on the composition of abundant and rare bacteria.

Results and discussion

Our results demonstrated that the summer maize field soil species composition of rare bacterial sub-communities was significantly regulated by reduced nitrogen application, groundwater depth change and their interactions. However, only reduced nitrogen application had a significant influence on the species composition of abundant bacterial sub-communities. The structural equation model (SEM) indicated that reduced nitrogen application and groundwater depth change also could indirectly regulate the species composition of abundant and rare bacteria by altering soil attributes. The changes in soil pH and TSN had the most significant effects on the community composition of abundant and rare bacteria, respectively. More importantly, rare bacterial sub-communities were more sensitive to the changes in nitrogen input, groundwater depth and soil factors. Collectively, our study first demonstrated that abundant and rare microbial sub-communities responded differently to reduced nitrogen application and groundwater depth change. This study highlights that summer maize farmland production management should take nitrogen input and groundwater depth into consideration to maintain the compositional stability of soil rare microbial sub-communities.

Phyllosphere Microbiome in Plant Health and Disease

The phyllosphere refers to the aboveground surface of plants colonized by diverse microorganisms. Microbes inhabiting this environment play an important role in enhancing the host's genomic and metabolic capabilities, including defense against pathogens. Compared to the large volume of studies on rhizosphere microbiome for plant health and defense, our understanding of phyllosphere microbiome remains in its infancy. In this review, we aim to explore the mechanisms that govern the phyllosphere assembly and their function in host defence, as well as highlight the knowledge gaps. These efforts will help develop strategies to harness the phyllosphere microbiome toward sustainable crop production.