Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

Environmental microbes promote phenotypic plasticity in reproduction and sleep behaviour

The microbiome has been hypothesized as a driving force of phenotypic variation in host organisms that is capable of extending metabolic processes, altering development and in some cases, conferring novel functions that are critical for survival. Only a few studies have directly shown a causal role for the environmental microbiome in altering host phenotypic features. To assess the extent to which environmental microbes induce variation in host life-history traits and behaviour, we inoculated axenic Drosophila melanogaster with microbes isolated from drosophilid populations collected from two different field sites and generated two populations with distinct bacterial and fungal profiles. We show that microbes isolated from environmental sites with modest abiotic differences induce large variation in host reproduction, fatty acid levels, stress tolerance and sleep behaviour. Importantly, clearing microbes from each experimental population removed the phenotypic differences. The results support the causal role of environmental microbes as drivers of host phenotypic plasticity and potentially, rapid adaptation and evolution.

Soybean and Cotton Spermosphere Soil Microbiome Shows Dominance of Soilborne Copiotrophs

The spermosphere is the transient, immediate zone of soil around imbibing and germinating seeds. It represents a habitat where there is contact between seed-associated microbes and soil microbes, but it is studied less than other plant habitats. Previous studies on spermosphere microbiology were primarily culture based or did not sample the spermosphere soil as initially defined in space and time. Thus, the objectives of this study were to develop an efficient strategy to collect spermosphere soils around imbibing soybean and cotton in nonsterile soil and investigate changes in microbial communities. The method employed sufficiently collected spermosphere soil as initially defined in space by constraining the soil sampled with a cork borer and confining the soil to a 12-well microtiter plate. Spermosphere prokaryote composition changed over time and depended on the crop within 6 h after seeds were sown. By 12 to 18 h, crops had unique microbial communities in spermosphere soils. Prokaryote evenness dropped following seed imbibition, with the proliferation of copiotrophic soil bacteria. Due to their long history of plant growth promotion, prokaryote operational taxonomic units (OTUs) in Bacillus, Paenibacillus, Burkholderia, Massilia, Azospirillum, and Pseudomonas were notable organisms enriched. Fungi and prokaryotes were hub taxa in cotton and soybean spermosphere networks. Additionally, the enriched taxa were not hubs in networks, suggesting that other taxa besides those enriched may be important for spermosphere communities. Overall, this study advances knowledge in the assembly of the plant microbiome early in a plant's life, which may have plant health implications in more mature plant growth stages. IMPORTANCE The central hypothesis of this research was that plant species and seed exudate release would alter the assembly of microbes in the spermosphere soil. Our research investigated the response of microbes to the initial burst of nutrients into the spermosphere soil, filling knowledge gaps from previous studies that pregerminated seeds under sterile conditions. We identified several copiotrophic bacterial lineages with a long history of plant growth promotion proliferating in response to the initial exudate release. With a comparative network approach, we show that these copiotrophic bacteria are not central to networks, demonstrating that other microbes (including fungi) may be important for community structure. This study improves knowledge on microbial dynamics in the understudied spermosphere and helps inform solutions for biologically or ecologically motivated solutions to spermosphere pathogens.

Limited Impact of Soil Microorganisms on the Endophytic Bacteria of Tartary Buckwheat (Fagopyrum tataricum)

Soil has been considered the main microbial reservoir for plants, but the robustness of the plant microbiome when the soil resource is removed has not been greatly considered. In the present study, we tested the robustness of the microbiota recruited by Tartary buckwheat (Fagopyrum tataricum Gaertn.), grown on sterile humus soil and irrigated with sterile water. Our results showed that the microbiomes of the leaf, stem, root and next-generation seeds were comparable between treated (grown in sterile soil) and control plants (grown in non-sterile soil), indicating that the plants had alternative robust ways to shape their microbiome. Seed microbiota contributed greatly to endophyte communities in the phyllosphere, rhizosphere and next-generation seeds. The microbiome originated from the seeds conferred clear benefits to seedling growth because seedling height and the number of leaves were significantly increased when grown in sterilized soil. The overall microbiome of the plant was affected very little by the removal of the soil microbial resource. The microbial co-occurrence network exhibited more interactions, and Proteobacteria was enriched in the root of Tartary buckwheat planted in sterilized soil. Our research broadens the understanding of the general principles governing microbiome assembly and is widely applicable to both microbiome modeling and sustainable agriculture.

The Use of Synthetic Microbial Communities to Improve Plant Health

Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.

Weather factors, soil microbiome, and bacteria-fungi interactions as drivers of the epiphytic phyllosphere communities of romaine lettuce

Lettuce is associated with seasonal outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections. Little is known about how various biotic and abiotic factors affect the lettuce microbiome, which in turn impacts STEC colonization. We characterized the lettuce phyllosphere and surface soil bacterial, fungal, and oomycete communities at harvest in late-spring and -fall in California using metagenomics. Harvest season and field type, but not cultivar, significantly influenced the microbiome composition of leaves and surface soil near plants. Phyllosphere and soil microbiome compositions were correlated with specific weather factors. The relative abundance of Enterobacteriaceae, but not E. coli, was enriched on leaves (5.2%) compared to soil (0.4%) and correlated positively with minimum air temperature and wind speed. Co-occurrence networks revealed seasonal trends in fungi-bacteria interactions on leaves. These associations represented 39%-44% of the correlations between species. All significant E. coli co-occurrences with fungi were positive, while all negative associations were with bacteria. A large proportion of the leaf bacterial species was shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings provide new insight into factors that shape lettuce microbial communities and the microbial context of foodborne pathogen immigration events in the lettuce phyllosphere.

AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning?

Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.

Rickettsial pathogens drive microbiota assembly in Hyalomma marginatum and Rhipicephalus bursa ticks

Most tick-borne pathogens (TBPs) are secondarily acquired by ticks during feeding on infected hosts, which imposes 'priority effect' constraints, as arrival order influences the establishment of new species in a microbial community. Here we tested whether once acquired, TBPs contribute to bacterial microbiota functioning by increasing community stability. For this, we used Hyalomma marginatum and Rhipicephalus bursa ticks collected from cattle in different locations of Corsica and combined 16S rRNA amplicon sequencing and co-occurrence network analysis, with high-throughput pathogen detection, and in silico removal of nodes to test for impact of rickettsial pathogens on network properties. Despite its low centrality, Rickettsia showed preferential connections in the networks, notably with a keystone taxon in H. marginatum, suggesting facilitation of Rickettsia colonisation by the keystone taxon. In addition, conserved patterns of community assembly in both tick species were affected by Rickettsia removal, suggesting that privileged connections of Rickettsia in the networks make this taxon a driver of community assembly. However, Rickettsia removal had minor impact on the conserved 'core bacterial microbiota' of H. marginatum and R. bursa. Interestingly, networks of the two tick species with Rickettsia have similar node centrality distribution, a property that is lost after Rickettsia removal, suggesting that this taxon drives specific hierarchical interactions between bacterial microbes in the microbiota. The study indicates that tick-borne Rickettsia play a significant role in the tick bacterial microbiota, despite their low centrality. These bacteria are influential and contribute to the conservation of the 'core bacterial microbiota' while also promoting community stability.

Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils

Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.

Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome

BACKGROUND

Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome.

RESULTS

We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in.

CONCLUSIONS

Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.

Connect the dots: sketching out microbiome interactions through networking approaches

Microbiome networking analysis has emerged as a powerful tool for studying the complex interactions among microorganisms in various ecological niches, including the human body and several environments. This analysis has been used extensively in both human and environmental studies, revealing key taxa and functional units peculiar to the ecosystem considered. In particular, it has been mainly used to investigate the effects of environmental stressors, such as pollution, climate change or therapies, on host-associated microbial communities and ecosystem function. In this review, we discuss the latest advances in microbiome networking analysis, including methods for constructing and analyzing microbiome networks, and provide a case study on how to use these tools. These analyses typically involve constructing a network that represents interactions among microbial taxa or functional units, such as genes or metabolic pathways. Such networks can be based on a variety of data sources, including 16S rRNA sequencing, metagenomic sequencing, and metabolomics data. Once constructed, these networks can be analyzed to identify key nodes or modules important for the stability and function of the microbiome. By providing insights into essential ecological features of microbial communities, microbiome networking analysis has the potential to transform our understanding of the microbial world and its impact on human health and the environment.

Microbial composition and diversity of the tobacco leaf phyllosphere during plant development

Phyllosphere-associated microorganisms affect host plant's nutrients availability, its growth and ecological functions. Tobacco leaves provide a wide-area habitat for microbial life. Previous studies have mainly focused on phyllosphere microbiota at one time point of tobacco growth process, but more is unknown about dynamic changes in phyllospheric microbial composition from earlier to the late stage of plant development. In the current study, we had determined the bacterial and fungal communities succession of tobacco growth stages (i.e., seedling, squaring, and maturing) by using both 16S rRNA sequencing for bacterial and ITS sequencing for fungi. Our results demonstrated that among tobacco growth stages, the phyllospheric bacterial communities went through more distinct succession than the fungal communities did. Proteobacteria and Actinobacteria exerted the most influence in tobacco development from seedling to squaring stages. At maturing stage, Proteobacteria and Actinobacteria dominance was gradually replaced by Firmicutes and Bacteroidetes. Network analysis revealed that Proteobacteria, as the core phyllospheric microbia, played essential role in stabilizing the whole bacterial network during tobacco development, and consequently rendered it to more profound ecological functions. During tobacco development, the contents of leaf sugar, nicotine, nitrogen and potassium were significantly correlated with either bacterial or fungal communities, and these abiotic factors accounted for 39.3 and 51.5% of the total variation, respectively. We overall evinced that the development of tobacco phyllosphere is accompanied by variant dynamics of phyllospheric microbial community.

Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding

Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen-one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estimating their relative abundance based on mock communities and (ii) the degree of taxonomic resolution using phylogenetic trees. Furthermore, our pipelines were also applied to DNA sequences from symptomatic walnut husks and twigs. Overall, our results showed that the ITS2 region was a better barcode than ITS1 and ITS, resulting in significantly higher sensitivity and/or similarity of composition values. The ITS3/ITS4_KYO1 primer set allowed to cover a wider range of fungal diversity, compared to the other primer sets also targeting the ITS2 region, namely, GTAA and GTAAm. Adding an extraction step to the ITS2 sequence influenced both positively and negatively the taxonomic resolution at the genus and species level, depending on the primer pair considered. Taken together, these results suggested that Kyo set without ITS2 extraction was the best pipeline to assess the broadest fungal diversity, with a more accurate taxonomic assignment, in walnut organs with dieback symptoms.

Ozone pollution, water deficit stress and time drive poplar phyllospheric bacterial community structure

Ground-level ozone (O₃) pollution often rise in the summer and coincide with drought stress, which alters the relationships between trees and associated microbial communities in a manner that can have pronounced effects on associated biological activity and ecosystem integrity. Discerning the responses of phyllosphere microbial communities to O₃ and water deficit could highlight the ability of plant-microbe interactions to either exacerbate or mitigate the effects of these stressors. Accordingly, this study was designed as the first report to specifically interrogate the impacts of elevated O₃ and water deficit stress on phyllospheric bacterial community composition and diversity in hybrid poplar saplings. Significant reductions in phyllospheric bacterial alpha diversity indices were observed, with clear evidence of significant time × water deficit stress interactions. The combination of elevated O₃ and water deficit stress shifted in the bacterial community composition over sampling time, resulted in significant increases in the relative abundance of the dominant Gammaproteobacteria phyla together with reductions in Betaproteobacteria. An increased prevalence of Gammaproteobacteria may represent a potential diagnostic dysbiosis-related biosignature associated with poplar disease risk. Significant positive correlations were observed between both Betaproteobacteria abundance and diversity indices and key foliar photosynthetic traits and isoprene emissions, whereas these parameters were negatively correlated with Gammaproteobacteria abundance. These findings suggest that the photosynthesis-related properties in plant leaves are closely related to the makeup of the phyllosphere bacterial community. These data provide novel insight into how plant-associated microbes can help maintain plant health and the stability of the local ecosystem in O₃-polluted and dried environments.

Distinct Features Based on Partitioning of the Endophytic Fungi of Cereals and Other Grasses

Endophytic fungi form a significant part of the plant mycobiome. Defining core members is crucial to understanding the assembly mechanism of fungal endophytic communities (FECs) and identifying functionally important community members. We conducted a meta-analysis of FECs in stems of wheat and five wild cereal species and generated a landscape of the fungal endophytic assemblages in this group of plants. The analysis revealed that several Ascomycota members and basidiomycetous yeasts formed an important compartment of the FECs in these plants. We observed a weak spatial autocorrelation at the regional scale and high intrahost variations in the FECs, suggesting a space-related heterogeneity. Accordingly, we propose that the heterogeneity among subcommunities should be a criterion to define the core endophytic members. Analysis of the subcommunities and meta-communities showed that the core and noncore members had distinct roles in various assembly processes, such as stochasticity, universal dynamics, and network characteristics, within each host. The distinct features identified between the community partitions of endophytes aid in understanding the principles that govern the assembly and function of natural communities. These findings can assist in designing synthetic microbiomes. IMPORTANCE This study proposes a novel method for diagnosing core microbiotas based on prevalence of community members in a meta-community, which could be determined and supported statistically. Using this approach, the study found stratification in community assembly processes within fungal endophyte communities (FECs) in the stems of wheat and cereal-related wild species. The core and noncore partitions of the FECs exhibited certain degrees of determinism from different aspects. Further analysis revealed abundant and consistent interactions between rare taxa, which might contribute to the determinism process in noncore partitions. Despite minor differences in FEC compositions, wheat FECs showed distinct patterns in community assembly processes compared to wild species, suggesting the effects of domestication on FECs. Overall, our study provided a new approach for identifying core microbiota and provides insights into the community assembly processes within FECs in wheat and related wild species.

Microbial Diversity and Enzyme Activity as Indicators of Permethrin-Exposed Soil Health

Owing to their wide range of applications in the control of ticks and insects in horticulture, forestry, agriculture and food production, pyrethroids pose a significant threat to the environment, including a risk to human health. Hence, it is extremely important to gain a sound understanding of the response of plants and changes in the soil microbiome induced by permethrin. The purpose of this study has been to show the diversity of microorganisms, activity of soil enzymes and growth of Zea mays following the application of permethrin. This article presents the results of the identification of microorganisms with the NGS sequencing method, and of isolated colonies of microorganisms on selective microbiological substrates. Furthermore, the activity of several soil enzymes, such as dehydrogenases (Deh), urease (Ure), catalase (Cat), acid phosphatase (Pac), alkaline phosphatase (Pal), β-glucosidase (Glu) and arylsulfatase (Aryl), as well as the growth of Zea mays and its greenness indicators (SPAD), after 60 days of growth following the application of permethrin, were presented. The research results indicate that permethrin does not have a negative effect on the growth of plants. The metagenomic studies showed that the application of permethrin increases the abundance of Proteobacteria, but decreases the counts of Actinobacteria and Ascomycota. The application of permethrin raised to the highest degree the abundance of bacteria of the genera Cellulomonas, Kaistobacter, Pseudomonas, Rhodanobacter and fungi of the genera Penicillium, Humicola, Iodophanus, Meyerozyma. It has been determined that permethrin stimulates the multiplication of organotrophic bacteria and actinomycetes, decreases the counts of fungi and depresses the activity of all soil enzymes in unseeded soil. Zea mays is able to mitigate the effect of permethrin and can therefore be used as an effective phytoremediation plant.

Evolutionary implications of host genetic control for engineering beneficial microbiomes

Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.

Selection of rhizosphere communities of diverse rotation crops reveals unique core microbiome associated with reduced banana Fusarium wilt disease

Crop rotation can assemble distinct core microbiota as functionally specific barriers against the invasion of banana Fusarium oxysporum pathogens. However, the taxonomic identity of rotation-unique core taxa and their legacy effects are poorly understood under field conditions. Pepper and eggplant rotations were employed to reveal rotation crop- and banana-unique antagonistic core taxa by in situ tracking of the soil microbiome assembly patterns for 2 yr. The rotation crop-unique antagonistic taxa were isolated and functionally verified by culture-dependent techniques, high-throughput sequencing, and pot experiments. Pepper and eggplant rotations resulted in eight and one rotation-unique antagonistic core taxa out of 12 507 microbial taxa, respectively. These nine antagonistic taxa were retained the following year and significantly decreased banana wilt disease incidence via legacy effects, although the cultivated strains were exclusively of the genera Bacillus and Pseudomonas. The fermentation broth and volatiles of these two taxa showed strong antagonistic activity, and pot experiments demonstrated high suppression of wilt disease and significant promotion of banana growth. Our study provides a mechanistic understanding of the identification of rotation crop-unique antagonistic taxa and highlights the importance of targeted cultivation of beneficial microorganisms for optimizing crop rotation-based scenarios in support of banana agriculture sustainability.

Evolution of fungal and non-fungal eukaryotic communities in response to thermophilic co-composting of various nitrogen-rich green feedstocks

Thermophilic composting is a promising soil and waste management approach involving diverse micro and macro-organisms, including eukaryotes. Due to sub-optimal amounts of nutrients in manure, supplemental feedstock materials such as Lantana camara, and Tithonia diversifolia twigs are used in composting. These materials have, however, been reported to have antimicrobial activity in in-vitro experiments. Furthermore, the phytochemical analysis has shown differences in their complexities, thus possibly requiring various periods to break down. Therefore, it is necessary to understand these materials' influence on the biological and physical-chemical stability of compost. Most compost microbiome studies have been bacterial-centric, leaving out eukaryotes despite their critical role in the environment. Here, the influence of different green feedstock on the fungal and non-fungal eukaryotic community structure in a thermophilic compost environment was examined. Total community fungal and non-fungal eukaryotic DNA was recovered from triplicate compost samples of four experimental regimes. Sequencing for fungal ITS and non-fungal eukaryotes; 18S rDNA was done under the Illumina Miseq platform, and bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 workflow in R version 4.1. Samples of mixed compost and composting day 84 recorded significantly (P<0.05) higher overall fungal populations, while Lantana-based compost and composting day 84 revealed the highest fungal community diversity. Non-fungal eukaryotic richness was significantly (P< 0.05) more abundant in Tithonia-based compost and composting day 21. The most diverse non-fungal eukaryotic biome was in the Tithonia-based compost and composting day 84. Sordariomycetes and Holozoa were the most contributors to the fungal and non-fungal community interactions in the compost environment, respectively. The findings of this study unravel the inherent influence of diverse composting materials and days on the eukaryotic community structure and compost's biological and chemical stability.

Accurate prediction of huanglongbing occurrence in citrus plants by machine learning-based analysis of symbiotic bacteria

Huanglongbing (HLB), the most prevalent citrus disease worldwide, is responsible for substantial yield and economic losses. Phytobiomes, which have critical effects on plant health, are associated with HLB outcomes. The development of a refined model for predicting HLB outbreaks based on phytobiome markers may facilitate early disease detection, thus enabling growers to minimize damages. Although some investigations have focused on differences in the phytobiomes of HLB-infected citrus plants and healthy ones, individual studies are inappropriate for generating common biomarkers useful for detecting HLB on a global scale. In this study, we therefore obtained bacterial information from several independent datasets representing hundreds of citrus samples from six continents and used these data to construct HLB prediction models based on 10 machine learning algorithms. We detected clear differences in the phyllosphere and rhizosphere microbiomes of HLB-infected and healthy citrus samples. Moreover, phytobiome alpha diversity indices were consistently higher for healthy samples. Furthermore, the contribution of stochastic processes to citrus rhizosphere and phyllosphere microbiome assemblies decreased in response to HLB. Comparison of all constructed models indicated that a random forest model based on 28 bacterial genera in the rhizosphere and a bagging model based on 17 bacterial species in the phyllosphere predicted the health status of citrus plants with almost 100% accuracy. Our results thus demonstrate that machine learning models and phytobiome biomarkers may be applied to evaluate the health status of citrus plants.

Past microbial stress benefits tree resilience

Soil microbiota from stressful environments provide an avenue for climate resilience.

Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau

In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.

Plant-microbe interactions: Mining heritable root-associated microbiota across environments

The root-associated microbiota represents an untapped reservoir of beneficial functions for plants. A new study begins unravelling the host genetic determinants governing these interactions across environments, which will be a key step towards the development of novel climate-smart crops.

Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem

BACKGROUND

Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta.

RESULTS

We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages.

CONCLUSIONS

Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.

Core microbiota of wheat rhizosphere under Upper Indo-Gangetic plains and their response to soil physicochemical properties

Wheat is widely cultivated in the Indo-Gangetic plains of India and forms the major staple food in the region. Understanding microbial community structure in wheat rhizosphere along the Indo-Gangetic plain and their association with soil properties can be an important base for developing strategies for microbial formulations. In the present study, an attempt was made to identify the core microbiota of wheat rhizosphere through a culture-independent approach. Rhizospheric soil samples were collected from 20 different sites along the upper Indo-Gangetic plains and their bacterial community composition was analyzed based on sequencing of the V3-V4 region of the 16S rRNA gene. Diversity analysis has shown significant variation in bacterial diversity among the sites. The taxonomic profile identified Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Planctomycetes, Verrucomicrobia, Firmicutes, and Cyanobacteria as the most dominant phyla in the wheat rhizosphere in the region. Core microbiota analysis revealed 188 taxa as core microbiota of wheat rhizosphere with eight genera recording more than 0.5% relative abundance. The order of most abundant genera in the core microbiota is Roseiflexus> Flavobacterium> Gemmatimonas> Haliangium> Iamia> Flavisolibacter> Ohtaekwangia> Herpetosiphon. Flavobacterium, Thermomonas, Massilia, Unclassified Rhizobiaceae, and Unclassified Crenarchaeota were identified as keystone taxa of the wheat rhizosphere. Correlation studies revealed, pH, organic carbon content, and contents of available nitrogen, phosphorus, and iron as the major factors driving bacterial diversity in the wheat rhizosphere. Redundancy analysis has shown the impact of different soil properties on the relative abundance of different genera of the core microbiota. The results of the present study can be used as a prelude to be developing microbial formulations based on core microbiota.

Current Viewpoint on Female Urogenital Microbiome-The Cause or the Consequence?

An increasing amount of evidence implies that native microbiota is a constituent part of a healthy urinary tract (UT), making it an ecosystem on its own. What is still not clear is whether the origin of the urinary microbial community is the indirect consequence of the more abundant gut microbiota or a more distinct separation exists between these two systems. Another area of uncertainty is the existence of a link between the shifts in UT microbial composition and both the onset and persistence of cystitis symptoms. Cystitis is one of the most common reasons for antimicrobial drugs prescriptions in primary and secondary care and an important contributor to the problem of antimicrobial resistance. Despite this fact, we still have trouble distinguishing whether the primary cause of the majority of cystitis cases is a single pathogen overgrowth or a systemic disorder affecting the entire urinary microbiota. There is an increasing trend in studies monitoring changes and dynamics of UT microbiota, but this field of research is still in its infancy. Using NGS and bioinformatics, it is possible to obtain microbiota taxonomic profiles directly from urine samples, which can provide a window into microbial diversity (or the lack of) underlying each patient's cystitis symptoms. However, while microbiota refers to the living collection of microorganisms, an interchangeably used term microbiome referring to the genetic material of the microbiota is more often used in conjunction with sequencing data. It is this vast amount of sequences, which are truly "Big Data", that allow us to create models that describe interactions between different species contributing to an UT ecosystem, when coupled with machine-learning techniques. Although in a simplified predator-prey form these multi-species interaction models have the potential to further validate or disprove current beliefs; whether it is the presence or the absence of particular key players in a UT microbial ecosystem, the exact cause or consequence of the otherwise unknown etiology in the majority of cystitis cases. These insights might prove to be vital in our ongoing struggle against pathogen resistance and offer us new and promising clinical markers.

Gambierone and Sodium Channel Specific Bioactivity Are Associated with the Extracellular Metabolite Pool of the Marine Dinoflagellate Coolia palmyrensis

Tropical epibenthic dinoflagellate communities produce a plethora of bioactive secondary metabolites, including the toxins ciguatoxins (CTXs) and potentially gambierones, that can contaminate fishes, leading to ciguatera poisoning (CP) when consumed by humans. Many studies have assessed the cellular toxicity of causative dinoflagellate species to better understand the dynamics of CP outbreaks. However, few studies have explored extracellular toxin pools which may also enter the food web, including through alternative and unanticipated routes of exposure. Additionally, the extracellular exhibition of toxins would suggest an ecological function and may prove important to the ecology of the CP-associated dinoflagellate species. In this study, semi-purified extracts obtained from the media of a Coolia palmyrensis strain (DISL57) isolated from the U.S. Virgin Islands were assessed for bioactivity via a sodium channel specific mouse neuroblastoma cell viability assay and associated metabolites evaluated by targeted and non-targeted liquid chromatography tandem and high-resolution mass spectrometry. We found that extracts of C. palmyrensis media exhibit both veratrine enhancing bioactivity and non-specific bioactivity. LC-HR-MS analysis of the same extract fractions identified gambierone and multiple undescribed peaks with mass spectral characteristics suggestive of structural similarities to polyether compounds. These findings implicate C. palmyrensis as a potential contributor to CP and highlight extracellular toxin pools as a potentially significant source of toxins that may enter the food web through multiple exposure pathways.

Plant-microbiome crosstalk and disease development

Plants harbor a complex immune system to fight off invaders and prevent diseases. For decades, the interactions between plants and pathogens have been investigated primarily through the lens of binary interactions, largely neglecting the diversity of microbes that naturally inhabit plant tissues. Recent research, however, demonstrates that resident microbes are more than mere spectators. Instead, the plant microbiome extends host immune function and influences the outcome of a pathogen infection. Both plants and the interacting microbes produce a large diversity of metabolites that form an intricate chemical network of nutrients, signals, and antimicrobial molecules. In this review, we discuss the involvement of the plant microbiome in disease development, focusing on the biochemical conversation that occurs between plants and their associated microbiota before, during and after infection. We also highlight outstanding questions and possible directions for future research.

Plant species shape the bacterial communities on the phyllosphere in a hyper-arid desert

Microorganisms are an important component of global biodiversity. However, they are vulnerable to hyper-arid climates in desert regions. Xerophytes are desert vegetation with unique biodiversity. However, little is known about the identities and communities of phyllosphere epiphytic microorganisms inhabiting the xerophyte leaf surface in the hot and dry environment. The diversity and community composition of phyllosphere epiphytes on different desert plants in Gansu, China, was investigated using the next-generation sequencing technique, revealing the diversity and community composition of the phyllosphere epiphytic bacteria associated with desert xerophytes. In addition, the ecological functions of the bacterial communities were investigated by combining the sequence classification information and prokaryotic taxonomic function annotation (FAPROTAX). This study determined the phyllosphere bacterial community composition, microbial interactions, and their functions. Despite harsh environments in the arid desert, we found that there are still diverse epiphytic bacteria on the leaves of desert plants. The bacterial communities mainly included Actinobacteria (52.79%), Firmicutes (31.62%), and Proteobacteria (12.20%). Further comparisons revealed different microbial communities, including Firmicutes at the phylum and Paenibacillaceae at the family level, in the phyllosphere among different plants, suggesting that the host plants had strong filter effects on bacteria. Co-occurrence network analysis revealed positive relationships were dominant among different bacterial taxa. The abundance of Actinobacteria and Proteobacteria was positively correlated, demonstrating their mutual relationship. On the other hand, the abundance of Firmicutes was negatively correlated, which suggested that they inhibit the growth of other bacterial taxa. FAPROTAX prediction revealed that chemoheterotrophy (accounting for 39.02% of the community) and aerobic chemoheterotrophy (37.01%) were the main functions of the leaf epiphytic bacteria on desert plants. This study improves our understanding of the community composition and ecological functions of plant-associated microbial communities inhabiting scattered niches in the desert ecosystem. In addition, the study provides insight into the biodiversity assessment in the desert region.

Identifying keystone species in microbial communities using deep learning

Previous studies suggested that microbial communities harbor keystone species whose removal can cause a dramatic shift in microbiome structure and functioning. Yet, an efficient method to systematically identify keystone species in microbial communities is still lacking. This is mainly due to our limited knowledge of microbial dynamics and the experimental and ethical difficulties of manipulating microbial communities. Here, we propose a Data-driven Keystone species Identification (DKI) framework based on deep learning to resolve this challenge. Our key idea is to implicitly learn the assembly rules of microbial communities from a particular habitat by training a deep learning model using microbiome samples collected from this habitat. The well-trained deep learning model enables us to quantify the community-specific keystoneness of each species in any microbiome sample from this habitat by conducting a thought experiment on species removal. We systematically validated this DKI framework using synthetic data generated from a classical population dynamics model in community ecology. We then applied DKI to analyze human gut, oral microbiome, soil, and coral microbiome data. We found that those taxa with high median keystoneness across different communities display strong community specificity, and many of them have been reported as keystone taxa in literature. The presented DKI framework demonstrates the power of machine learning in tackling a fundamental problem in community ecology, paving the way for the data-driven management of complex microbial communities.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species

Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.

Composition and variability of core phyllosphere fungal mycobiota on field-grown broccoli

BACKGROUND

Fresh vegetables harbor an assemblage of different microorganisms on their surfaces. The phyllosphere microbiota is important for maintaining plant health and managing crop quality before and after harvest. However, the diversity and ecology of fungal communities are largely unexplored in fresh vegetables. This study investigated the phyllosphere mycobiota of field-grown broccoli florets (n = 66) collected from 22 farms across four regions in Korea, using culturing, amplicon sequencing of the internal transcribed spacer region, and microbial network analysis.

RESULTS

Microbial network analysis identified core genera (Purpureocillium, Filobasidium, Cystofilobasidium, Papiliotrema, Aureobasidium, and unclassified genera of Capnodiales) specific to the broccoli phyllosphere. The composition and network complexity of core and unique populations varied among farming regions, and was associated with local agro-meteorological conditions. The complexity of microbial associations was higher in mature communities than in immature communities, but complexity was lost upon development of plant pathogenic disease. Broccoli mycobiota were classified according to the dominance of Purpurecillium. While Purpurecillium-type microbiota were prevalent in normal samples, Filobasidium-type microbiota were frequently observed in immature, damaged, or postharvest samples.

CONCLUSIONS

Together, fungal communities were important components of phyllosphere microbiota on fresh vegetables, and have substantial potential for exploitation to enhance and stabilize plant health and growth.

Habitats Within the Plant Root Differ in Bacterial Network Topology and Taxonomic Assortativity

The root microbiome is composed of distinct epiphytic (rhizosphere) and endophytic (endosphere) habitats. Differences in abiotic and biotic factors drive differences in microbial community diversity and composition between these habitats, though how they shape the interactions among community members is unknown. Here, we coupled a large-scale characterization of the rhizosphere and endosphere bacterial communities of 30 plant species across two watering treatments with co-occurrence network analysis to understand how root habitats and soil moisture shape root bacterial network properties. We used a novel bootstrapping procedure and null network modeling to overcome some of the limitations associated with microbial co-occurrence network construction and analysis. Endosphere networks had elevated node betweenness centrality versus the rhizosphere, indicating greater overall connectivity among core bacterial members of the root endosphere. Taxonomic assortativity was higher in the endosphere, whereby positive co-occurrence was more likely between bacteria within the same phylum while negative co-occurrence was more likely between bacterial taxa from different phyla. This taxonomic assortativity could be driven by positive and negative interactions among members of the same or different phylum, respectively, or by similar niche preferences associated with phylum rank among root inhabiting bacteria across plant host species. In contrast to the large differences between root habitats, drought had limited effects on network properties but did result in a higher proportion of shared co-occurrences between rhizosphere and endosphere networks. Our study points to fundamentally different ecological processes shaping bacterial co-occurrence across root habitats. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

From guest to host: parasite Cistanche deserticola shapes and dominates bacterial and fungal community structure and network complexity

BACKGROUND

Rhizosphere and plant microbiota are assumed to play an essential role in deciding the well-being of hosts, but effects of parasites on their host microbiota have been rarely studied. Also, the characteristics of the rhizosphere and root microbiota of parasites and hosts under parasitism is relatively unknown. In this study, we used Cistanche deserticola and Haloxylon ammodendron from cultivated populations as our model parasites and host plants, respectively. We collected samples from BULK soil (BULK), rhizosphere soil of H. ammodendron not parasitized (NCD) and parasitized (RHA) to study how the parasite influenced the rhizosphere microbiota of the host. We also collected samples from the rhizosphere soil and roots of C. deserticola (RCD and ECD) and Haloxylon ammodendron (RHA and EHA) to explore the difference between the microbiota of the parasite and its host under parasitism.

RESULTS

The parasite reduced the compositional and co-occurrence network complexities of bacterial and fungal microbiota of RHA. Additionally, the parasite increased the proportion of stochastic processes mainly belonging to dispersal limitation in the bacterial microbiota of RHA. Based on the PCoA ordinations and permutational multivariate analysis of variance, the dissimilarity between microbiota of C. deserticola and H. ammodendron were rarely evident (bacteria, R² = 0.29971; fungi, R² = 0.15631). Interestingly, four hub nodes of H. ammodendron in endosphere fungal microbiota were identified, while one hub node of C. deserticola in endosphere fungal microbiota was identified. It indicated that H. ammodendron played a predominant role in the co-occurrence network of endosphere fungal microbiota. Source model of plant microbiome suggested the potential source percentage from the parasite to the host (bacteria: 52.1%; fungi: 16.7%) was lower than host-to-parasite (bacteria: 76.5%; fungi: 34.3%), illustrating that microbial communication was bidirectional, mainly from the host to the parasite.

CONCLUSIONS

Collectively, our results suggested that the parasite C. deserticola shaped the diversity, composition, co-occurrence network, and community assembly mechanisms of the rhizosphere microbiota of H. ammodendron. Additionally, the microbiota of C. deserticola and H. ammodendron were highly similar and shared. Our findings on parasite and host microbiota provided a novel line of evidence supporting the influence of parasites on the microbiota of their hosts.

Comparative Analysis of the Symbiotic Microbiota in the Chinese Mitten Crab (Eriocheir sinensis): Microbial Structure, Co-Occurrence Patterns, and Predictive Functions

Symbiotic microorganisms in the digestive and circulatory systems are found in various crustaceans, and their essential roles in crustacean health, nutrition, and disease have attracted considerable interest. Although the intestinal microbiota of the Chinese mitten crab (Eriocheir sinensis) has been extensively studied, information on the symbiotic microbiota at various sites of this aquatic economic species, particularly the hepatopancreas and hemolymph, is lacking. This study aimed to comprehensively characterize the hemolymph, hepatopancreas, and intestinal microbiota of Chinese mitten crab through the high-throughput sequencing of the 16S rRNA gene. Results showed no significant difference in microbial diversity between the hemolymph and hepatopancreas (Welch t-test; p > 0.05), but their microbial diversity was significantly higher than that in the intestine (p < 0.05). Distinct differences were found in the structure, composition, and predicted function of the symbiotic microbiota at these sites. At the phylum level, the hemolymph and hepatopancreas microbiota were dominated by Proteobacteria, Firmicutes, and Acidobacteriota, followed by Bacteroidota and Actinobacteriota, whereas the gut microbiota was mainly composed of Firmicutes, Proteobacteria, and Bacteroidota. At the genus level, Candidatus Hepatoplasma, Shewanella, and Aeromonas were dominant in the hepatopancreas; Candidatus Bacilloplasma, Roseimarinus, and Vibrio were dominant in the intestine; Enterobacter, norank_Vicinamibacterales, and Pseudomonas were relatively high-abundance genera in the hemolymph. The composition and abundance of symbiotic microbiota in the hemolymph and hepatopancreas were extremely similar (p > 0.05), and no significant difference in functional prediction was found (p > 0.05). Comparing the hemolymph in the intestine and hepatopancreas, the hemolymph had lower variation in bacterial composition among individuals, having a more uniform abundance of major bacterial taxa, a smaller coefficient of variation, and the highest proportion of shared genera. Network complexity varied greatly among the three sites. The hepatopancreas microbiota was the most complex, followed by the hemolymph microbiota, and the intestinal microbiota had the simplest network. This study revealed the taxonomic and functional characteristics of the hemolymph, hepatopancreas, and gut microbiota in Chinese mitten crab. The results expanded our understanding of the symbiotic microbiota in crustaceans, providing potential indicators for assessing the health status of Chinese mitten crab.

Microbial communities in tree root-compartment niches under Cd and Zn pollution: Structure, assembly process and co-occurrence relationship

Woody plants have showed great potential in remediating severely contaminated soils by heavy metals (HMs) due to their cost-efficient and ecologically friendly trait. It is believed the root-associated microbiota plays a vital role in phytoremediation for HMs. However, the ecological process controlling the assembly and composition of tree root-associated microbial communities under HMs stress remains poorly understood. Herein, we profiled the bulk soil, rhizosphere and endosphere microbial communities of trees growing in heavily Cd and Zn polluted soil. The microbiota was gradually filtered from bulk soil to the tree roots and was selectively enriched in roots with specific taxa, such as Proteobacteria and Ascomycota. The microbial community assembly along the soil-root continuum was mainly controlled by deterministic processes from bulk soil to the endosphere, with the normalized stochasticity ratio (NST) indices of 67.16-31.05 % and 30.37-15.02 % for bacteria and fungi, respectively. Plant selection pressure sequentially increased from bulk soil to rhizosphere to endosphere, with the reduced bacterial alpha diversity accompanying the consequently reduced complexity of the co-occurrence network. Together, the findings provide new evidence for horizontal transmission of endophytic microbiome from soil to the host, which can shed light on the future screening and application of microbial-assisted phytoremediation.

Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees

Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.

The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions

As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.

Ecological Processes of Bacterial and Fungal Communities Associated with Typha orientalis Roots in Wetlands Were Distinct during Plant Development

Root-associated microbiomes are essential for the ecological function of the root system. However, their assembly mechanisms in wetland are poorly understood. In this study, we explored and compared the ecological processes of bacterial and fungal communities in water, bulk soil, rhizosphere soil, and root endosphere niches for 3 developmental stages of Typha orientalis at different wetland sites, and assessed the potential functions of root endosphere microbiomes with function prediction. Our findings suggest that the microbial diversity, composition, and interaction networks along the water-soil-plant continuum are shaped predominantly by compartment niche and developmental stage, rather than by wetland site. Source tracking analysis indicated that T. orientalis' root endosphere is derived primarily from the rhizosphere soil (bacteria 39.9%, fungi 27.3%) and water (bacteria 18.9%, fungi 19.1%) niches. In addition, we found that the assembly of bacterial communities is driven primarily by deterministic processes and fungal communities by stochastic processes. The interaction network among microbes varies at different developmental stages of T. orientalis, and is accompanied by changes in microbial keystone taxa. The functional prediction data supports the distribution pattern of the bacterial and fungal microbiomes, which have different ecological roles at different plant developmental stages, where more beneficial bacterial taxa are observed in the root endosphere in the early stages, but more saprophytic fungi in the late stages. Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities and have significant implications for the future applications of plant microbiomes in the wetland ecosystem. IMPORTANCE Our findings provide empirical evidence for the assembly, sources, interactions, and potential functions of wetland plant root microbial communities, and have significant implications for the future applications of plant microbiomes in the wetland ecosystem.

Root Exudates of Ginger Induced by Ralstonia solanacearum Infection Could Inhibit Bacterial Wilt

Bacterial wilt caused by Ralstonia solanacearum (Rs) is one of the most important diseases found in ginger; however, the disease resistance mechanisms dependent on root bacteria and exudates are unclear. In the present study, we analyzed the changes in the composition of rhizobacteria, endobacteria, and root exudates during the pathogenesis of bacterial wilt using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS). Rs caused bacterial wilt in ginger with an incidence of 50.00% and changed the bacterial community composition in both endosphere and rhizosphere. It significantly reduced bacterial α-diversity but increased the abundance of beneficial and stress-tolerant bacteria, such as Lysobacter, Ramlibacter, Pseudomonas, and Azospirillum. Moreover, the change in rhizobacterial composition induced the changes in endobacterial and root exudate compositions. Moreover, the upregulated exudates inhibited ginger bacterial wilt, with the initial disease index (77.50%) being reduced to 40.00%, suggesting that ginger secretes antibacterial compounds for defense against bacterial pathogens.

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites

Plant genotypes shape root-associated microbiota that affect plant nutrient acquisition and productivity. It is unclear how maize hybrids modify root-associated microbiota and their functions and relationship with nitrogen use efficiency (NUE) by regulating rhizosphere soil metabolites. Here, two N-efficient (NE) (ZD958, DMY3) and two N-inefficient (NIE) maize hybrids (YD9953, LY99) were used to investigate this issue under low N (60 kg N ha^-1 , LN) and high N (180 kg N ha^-1 , HN) field conditions. NE hybrids had higher yield than NIE hybrids under LN but not HN. NE and NIE hybrids recruited only distinct root-associated bacterial microbiota in LN. The bacterial network stability was stronger in NE than NIE hybrids. Compared with NIE hybrids, NE hybrids recruited more bacterial taxa that have been described as plant growth-promoting rhizobacteria (PGPR), and less related to denitrification and N competition; this resulted in low N₂ O emission and high rhizosphere NO₃ ^- -N accumulation. NE and NIE hybrids had distinct rhizosphere soil metabolite patterns, and their specific metabolites were closely related to microbiota and specific genera under LN. Our findings reveal the relationships among plant NUE, rhizosphere soil metabolites, root-associated microbiota, and soil nutrient cycling, and this information is informative for breeding NE crops.

Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche

Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria-bacteria links with increasing depth in all crops, particularly in the root microbiome.

Microbiome-mediated signal transduction within the plant holobiont

Microorganisms colonizing the plant rhizosphere and phyllosphere play crucial roles in plant growth and health. Recent studies provide new insights into long-distance communication from plant roots to shoots in association with their commensal microbiome. In brief, these recent advances suggest that specific plant-associated microbial taxa can contribute to systemic plant responses associated with the enhancement of plant health and performance in face of a variety of biotic and abiotic stresses. However, most of the mechanisms associated with microbiome-mediated signal transduction in plants remain poorly understood. In this review, we provide an overview of long-distance signaling mechanisms within plants mediated by the commensal plant-associated microbiomes. We advocate the view of plants and microbes as a holobiont and explore key molecules and mechanisms associated with plant-microbe interactions and changes in plant physiology activated by signal transduction.

The root enrichment of bacteria is consistent across different stress-resistant plant species

Bacteria, inhabiting around and in plant roots, confer many beneficial traits to promote plant growth and health. The secretion of root exudates modulates the nutritional state of the rhizosphere and root area, further selecting specific bacteria taxa and shaping the bacteria communities. Many studies of the rhizosphere effects have demonstrated that selection by the plant rhizosphere consistently enriches a set of bacteria taxa, and this is conserved across different plant species. Root selection effects are considered to be stronger than the rhizosphere selection effects, yet studies are limited. Here, we focus on the root selection effects across a group of 11 stress-resistant plant species. We found that the root selection consistently reduced the alpha diversity (represented by total number of observed species, Shannon's diversity, and phylogenetic diversity) and altered the structure and composition of bacteria communities. Furthermore, root selection tended to enrich for clusters of bacteria genera including Pantoea, Akkermansia, Blautia, Acinetobacter, Burkholderia-Paraburkholderia, Novosphingobium, Massilia, Pseudomonas, Chryseobacterium, and Stenotrophomonas. Our study offers some basic knowledge for understanding the microbial ecology of the plant root, and suggests that several bacteria genera are of interest for future studies.

Above- and below-ground microbiome in the annual developmental cycle of two olive tree varieties

The olive tree is a hallmark crop in the Mediterranean region. Its cultivation is characterized by an enormous variability in existing genotypes and geographical areas. As regards the associated microbial communities of the olive tree, despite progress, we still lack comprehensive knowledge in the description of these key determinants of plant health and productivity. Here, we determined the prokaryotic, fungal and arbuscular mycorrhizal fungal (AMF) microbiome in below- (rhizospheric soil, roots) and above-ground (phyllosphere and carposphere) plant compartments of two olive varieties 'Koroneiki' and 'Chondrolia Chalkidikis' grown in Southern and Northern Greece respectively, in five developmental stages along a full fruit-bearing season. Distinct microbial communities were supported in above- and below-ground plant parts; while the former tended to be similar between the two varieties/locations, the latter were location specific. In both varieties/locations, a seasonally stable root microbiome was observed over time; in contrast the plant microbiome in the other compartments were prone to changes over time, which may be related to seasonal environmental change and/or to plant developmental stage. We noted that olive roots exhibited an AMF-specific filtering effect (not observed for bacteria and general fungi) onto the rhizosphere AMF communities of the two olive varieties/locations/, leading to the assemblage of homogenous intraradical AMF communities. Finally, shared microbiome members between the two olive varieties/locations include bacterial and fungal taxa with putative functional attributes that may contribute to olive tree tolerance to abiotic and biotic stress.

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering

In recent years, unsupervised analysis of microbiome data, such as microbial network analysis and clustering, has increased in popularity. Many new statistical and computational methods have been proposed for these tasks. This multiplicity of analysis strategies poses a challenge for researchers, who are often unsure which method(s) to use and might be tempted to try different methods on their dataset to look for the "best" ones. However, if only the best results are selectively reported, this may cause over-optimism: the "best" method is overly fitted to the specific dataset, and the results might be non-replicable on validation data. Such effects will ultimately hinder research progress. Yet so far, these topics have been given little attention in the context of unsupervised microbiome analysis. In our illustrative study, we aim to quantify over-optimism effects in this context. We model the approach of a hypothetical microbiome researcher who undertakes four unsupervised research tasks: clustering of bacterial genera, hub detection in microbial networks, differential microbial network analysis, and clustering of samples. While these tasks are unsupervised, the researcher might still have certain expectations as to what constitutes interesting results. We translate these expectations into concrete evaluation criteria that the hypothetical researcher might want to optimize. We then randomly split an exemplary dataset from the American Gut Project into discovery and validation sets multiple times. For each research task, multiple method combinations (e.g., methods for data normalization, network generation, and/or clustering) are tried on the discovery data, and the combination that yields the best result according to the evaluation criterion is chosen. While the hypothetical researcher might only report this result, we also apply the "best" method combination to the validation dataset. The results are then compared between discovery and validation data. In all four research tasks, there are notable over-optimism effects; the results on the validation data set are worse compared to the discovery data, averaged over multiple random splits into discovery/validation data. Our study thus highlights the importance of validation and replication in microbiome analysis to obtain reliable results and demonstrates that the issue of over-optimism goes beyond the context of statistical testing and fishing for significance.

Effect of disease severity on the structure and diversity of the phyllosphere microbial community in tobacco

Tobacco target spot is a serious fungal disease and it is important to study the similarities and differences between fungal and bacterial community under different disease severities to provide guidance for the biological control of tobacco target spot. In this study, tobacco leaves at disease severity level of 1, 5, 7 and 9 (S1, S5, S7, and S9) were collected, both healthy and diseased leaf tissues for each level were sampled. The community structure and diversity of fungi and bacteria in tobacco leaves with different disease severities were compared using high-throughput sequencing technology. The results indicated that there was a significant differences in the community structure of fungi and bacteria for both healthy and diseased samples depending on the disease severity. In both healthy and diseased tobacco leaves for all four different disease severities, the most dominant fungal phylum was Basidiomycota with a high prevalence of genus Thanatephorus. The relative abundance of Thanatephorus was most found at S9 diseased samples. Proteobacteria represent the most prominent bacterial phylum, with Pseudomonas as predominant genus, followed by Pantoea. The relative abundance of Pseudomonas was most found at S7 healthy samples. In fungal community, the Alpha-diversity of healthy samples was higher than that of diseased samples. In contrast, in bacterial community, the Alpha-diversity of healthy samples was lower than that of diseased samples. LEfSe analysis showed that the most enrich fungal biomarker was Thanatephorus cucumeris in diseased samples. Clostridium disporicum and Ralstonia pickettii were the most enrich bacterial biomarker in healthy samples. FUNGuild analysis showed that the pathotroph mode was the most abundant trophic modes. The relative abundance of pathotroph mode in diseased samples changes insignificantly, but a peak at S5 was observed for healthy samples. PICRUSt analysis showed that most bacterial gene sequences seem to be independent of the disease severity. The results of this study provide scientific references for future studies on tobacco phyllosphere microecology aiming at prevention and control of tobacco target spot.

Distinct Phyllosphere Microbiome of Wild Tomato Species in Central Peru upon Dysbiosis

Plants are colonized by myriads of microbes across kingdoms, which affect host development, fitness, and reproduction. Hence, plant microbiomes have been explored across a broad range of host species, including model organisms, crops, and trees under controlled and natural conditions. Tomato is one of the world's most important vegetable crops; however, little is known about the microbiota of wild tomato species. To obtain insights into the tomato microbiota occurring in natural environments, we sampled epiphytic microbes from leaves of four tomato species, Solanum habrochaites, S. corneliomulleri, S. peruvianum, and S. pimpinellifolium, from two geographical locations within the Lima region of Peru over 2 consecutive years. Here, a high-throughput sequencing approach was applied to investigate microbial compositions including bacteria, fungi, and eukaryotes across tomato species and geographical locations. The phyllosphere microbiome composition varies between hosts and location. Yet, we identified persistent microbes across tomato species that form the tomato microbial core community. In addition, we phenotypically defined healthy and dysbiotic samples and performed a downstream analysis to reveal the impact on microbial community structures. To do so, we compared microbial diversities, unique OTUs, relative abundances of core taxa, and microbial hub taxa, as well as co-occurrence network characteristics in healthy and dysbiotic tomato leaves and found that dysbiosis affects the phyllosphere microbial composition in a host species-dependent manner. Yet, overall, the present data suggests an enrichment of plant-promoting microbial taxa in healthy leaves, whereas numerous microbial taxa containing plant pathogens occurred in dysbiotic leaves.Concluding, we identify the core phyllosphere microbiome of wild tomato species, and show that the overall phyllosphere microbiome can be impacted by sampling time point, geographical location, host genotype, and plant health. Future studies in these components will help understand the microbial contribution to plant health in natural systems and can be of use in cultivated tomatoes.

Seasonal characterization of the prokaryotic microbiota of full-scale anaerobic UASB reactors treating domestic sewage in southern Brazil

Upflow Anaerobic Sludge Blanket (UASB) reactors are alternatives in the anaerobic treatment of sanitary sewage in different parts of the world; however, in temperate environments, they are subject to strong seasonal influence. Understanding the dynamics of the microbial community in these systems is essential to propose operational alternatives, improve projects and increase the quality of treated effluents. In this study, for one year, high-performance sequencing, associated with bioinformatics tools for taxonomic annotation and functional prediction was used to characterize the microbial community present in the sludge of biodigesters on full-scale, treating domestic sewage at ambient temperature. Among the most representative phyla stood out Desulfobacterota (20.21-28.64%), Proteobacteria (7.48-24.90%), Bacteroidota (10.05-18.37%), Caldisericota (9.49-17.20%), and Halobacterota (3.23-6.55%). By performing a Canonical Correspondence Analysis (CCA), Methanolinea was correlated to the efficiency in removing Chemical Oxygen Demand (COD), Bacteroidetes_VadinHA17 to the production of volatile fatty acids (VFAs), and CI75cm.2.12 at temperature. On the other hand, Desulfovibrio, Spirochaetaceae_uncultured, Methanosaeta, Lentimicrobiaceae_unclassified, and ADurb.Bin063-1 were relevant in shaping the microbial community in a co-occurrence network. Diversity analyses showed greater richness and evenness for the colder seasons, possibly, due to the lesser influence of dominant taxa. Among the principal metabolic functions associated with the community, the metabolism of proteins and amino acids stood out (7.74-8.00%), and the genes related to the synthesis of VFAs presented higher relative abundance for the autumn and winter. Despite the differences in diversity and taxonomic composition, no significant changes were observed in the efficiency of the biodigesters.