Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists

Planting halophytes increases the rhizosphere ecosystem multifunctionality via reducing soil salinity

Soil salinization poses a significant global challenge, exerting adverse effects on both agriculture and ecosystems. Planting halophytes has the potential ability to improve saline-alkali land and enhance ecosystem multifunctionality (EMF). However, it remains unclear which halophytes are effective in improving saline-alkali land and what impact they have on the rhizosphere microbial communities and EMF. In this study, we evaluated the Na+ absorption capability of five halophytes (Grubovia dasyphylla, Halogeton glomeratus, Suaeda salsa, Bassia scoparia, and Reaumuria songarica) and assessed their rhizosphere microbial communities and EMF. The results showed that S. salsa possessed the highest shoot (3.13 mmol g-1) and root (0.92 mmol g-1) Na+ content, and its soil Na+ absorption, along with B. scoparia, was significantly higher than that of other plants. The soil pH, salinity, and Na+ content of the halophyte rhizospheres decreased by 6.21%, 23.49%, and 64.29%, respectively, when compared to the bulk soil. Extracellular enzymes in the halophyte rhizosphere soil, including α-glucosidase, β-glucosidase, β-1,4-N-acetyl-glucosaminidase, neutral phosphatase, and alkaline phosphatase, increased by 70.1%, 78.4%, 38.5%, 79.1%, and 64.9%, respectively. Furthermore, the halophyte rhizosphere exhibited higher network complexity of bacteria and fungi and EMF than bulk soil. The relative abundance of the dominant phyla Proteobacteria, Firmicutes, and Ascomycota in the halophyte rhizosphere soil increased by 9.4%, 8.3%, and 22.25%, respectively, and showed higher microbial network complexity compared to the bulk soil. Additionally, keystone taxa, including Muricauda, Nocardioides, and Pontibacter, were identified with notable effects on EMF. This study confirmed that euhalophytes are the best choice for saline-alkali land restoration. These findings provided a theoretical basis for the sustainable use of saline-alkali cultivated land.

The impact of kaolin mining activities on bacterial diversity and community structure in the rhizosphere soil of three local plants

Introduction

Thus far, the impact of kaolin mining activities on the surrounding native plants and rhizosphere microecology has not been fully understood.

Methods

In this study, we used 16S rRNA high-throughput sequencing to examine the impact of kaolin mining on the rhizosphere bacterial communities and functions of three local plant species: Conyza bonariensis, Artemisia annua, and Dodonaea viscosa.

Results

The results showed that kaolin mining significantly reduced the diversity of rhizosphere bacteria in these plants, as indicated by the Shannon, Simpson, Chao1, and observed species indices (p < 0.05). Kaolin mining had an impact on the recruitment of three rhizosphere bacteria native to the area: Actinoplanes, RB41, and Mycobacterium. These bacteria were found to be more abundant in the rhizosphere soil of three local plants than in bulk soil, yet the mining of kaolin caused a decrease in their abundance (p < 0.05). Interestingly, Ralstonia was enriched in the rhizosphere of these plants found in kaolin mining areas, suggesting its resilience to environmental stress. Furthermore, the three plants had different dominant rhizosphere bacterial populations in kaolin mining areas, such as Nocardioides, Pseudarthrobacter, and Sphingomonas, likely due to the unique microecology of the plant rhizosphere. Kaolin mining activities also caused a shift in the functional diversity of rhizosphere bacteria in the three local plants, with each plant displaying different functions to cope with kaolin mining-induced stress, such as increased abundance of the GlpM family and glucan-binding domain.

Discussion

This study is the first to investigate the effects of kaolin mining on the rhizosphere microecology of local plants, thus contributing to the establishment of soil microecological health monitoring indicators to better control soil pollution in kaolin mining areas.

A Comprehensive Review of Climate Change and Plant Diseases in Brazil

Analyzing the impacts of climate change on phytosanitary problems in Brazil is crucial due to the country's special role in global food security as one of the largest producers of essential commodities. This review focuses on the effects of climate change on plant diseases and discusses its main challenges in light of Brazil's diverse agricultural landscape. To assess the risk of diseases caused by fungi, bacteria, viruses, oomycetes, nematodes, and spiroplasms, we surveyed 304 pathosystems across 32 crops of economic importance from 2005 to 2022. Results show that diseases caused by fungi account for 79% of the pathosystems evaluated. Predicting the occurrence of diseases in a changing climate is a complex challenge, and the continuity of this work is strategic for Brazil's agricultural defense. The future risk scenarios analyzed here aim to help guide disease mitigation for cropping systems. Despite substantial progress and ongoing efforts, further research will be needed to effectively prevent economic and environmental damage.

Distinct changes in tomato-associated multi-kingdom microbiomes during Meloidogyne incognita parasitism

BACKGROUND

The interplay between root-knot nematode (RKN) parasitism and the complex web of host-associated microbiota has been recognized as pivotal for effective management of the pest. However, studies assessing this relationship have focussed on the bacterial and fungal communities, neglecting the unicellular eukaryotic members. Here, we employed amplicon sequencing analysis of the bacterial 16S rRNA, fungal ITS and eukaryotic 18S rRNA genes, and comprehensively examined how the microbiome composition, diversity and networking developed with time in the rhizospheres and roots of RKN-inoculated and non-inoculated tomato plants.

RESULTS

As expected, infection with the RKN Meloidogyne incognita decreased plant growth. At individual timepoints, we found distinct bacterial, fungal and eukaryote community structures in the RKN-inoculated and non-inoculated rhizospheres and roots, and RKN inoculation affected several taxa in the root-associated microbiome differentially. Correlation analysis revealed several bacterial and fungal and few protist taxa that correlated negatively or positively with M. incognita. Moreover, network analysis using bacterial, fungal and eukaryotic data revealed more dynamic networks with higher robustness to disturbances in the RKN-inoculated than in the non-inoculated rhizospheres/roots. Hub taxa displayed a noticeable successional pattern that coincided with different phases of M. incognita parasitism. We found that fungal hubs had strong negative correlations with bacteria and eukaryotes, while positive correlations characterized hub members within individual kingdoms.

CONCLUSION

Our results reveal dynamic tomato-associated microbiomes that develop along different trajectories in plants suffering M. incognita infestation and non-infested plants. Overall, the results identify stronger associations between RKN and bacterial and fungal taxa than between eukaryotic taxa and RKN, suggesting that fungal and bacterial communities could play a larger role in the regulation of RKN. The study identifies several putative RKN-antagonistic bacterial and fungal taxa and confirms the antagonistic potential previously identified in other taxa.

Draft genome sequences of Streptomyces virginiae strain CMAA1738, Paenibacillus ottowii strain CMAA1739 and Pseudomonas inefficax strain CMAA1741, isolated from rhizosphere of wheat landraces

In this study, we have identified and characterized three genomes from bacteria isolated from the rhizosphere of Triticum aestivum. Streptomyces virginiae CMAA1738 and Paenibacillus ottowii CMAA1739 were obtained from the wheat landrace Iran 1-29-11334, and Pseudomonas inefficax CMAA1741 was isolated from the wheat landrace Karakilcik.

Domestication caused taxonomical and functional shifts in the wheat rhizosphere microbiota, and weakened the natural bacterial biocontrol against fungal pathogens

Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial-fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.

The impact of various forms of silver nanoparticles on the rhizosphere of wheat (Triticum aestivum L.) - Shifts in microbiome structure and predicted microbial metabolic functions

The study investigated the effects of different silver nanoparticles (AgNPs) on the soil microbiome and wheat growth. For comparison purposes, a commercial fungicide and silver nitrate (AgNO3) were used. The results revealed three distinct groups of nanoparticles based on their impacts. Small-size AgNPs (10 nm) with a negative charge, as well as fungicide had limited effects on the microbiome, similar to the no-treatment control. Bigger in size (30-60 nm) and a negative charge AgNPs showed the most beneficial effects on soil microbiota shifts. These AgNPs increased the abundance of bacteria with beneficial traits such as nitrogen-fixing, urease, protease, and lignin degradation bacteria. The third type of AgNPs had a positive charge of nanostructure and influenced specific microbial populations, increasing the abundance of anaerobic and autotrophic groups of microorganisms, which could be assessed as a harmful shift for plants growth promotions and was similar to the AgNO3 treatment. Overall, the study emphasized the potential of AgNPs in agriculture not only as biocidal. The conducted study proved that AgNPs with bigger size/negative charge, used in low concentration can have a surprisingly stimulating effect on the positive characteristics of the rhizosphere microbiome. Moreover, the surface charge of AgNPs is a significant factor affecting microbial activity of wheat rhizosphere soil, which in this treatment is significantly similar to the AgNO3 treatment.

Biotic interactions explain seasonal dynamics of the alpine soil microbiome

While it is acknowledged that alpine soil bacterial communities are primarily driven by season and elevation, there is no consensus on the factors influencing fungi and protists. Here we used a holistic approach of the microbiome to investigate the seasonal dynamics in alpine grasslands, focusing on soil food web interactions. We collected 158 soil samples along elevation transects from three mountains in the Alps, in spring during snowmelt and in the following summer. Using metatranscriptomics, we simultaneously assessed prokaryotic and eukaryotic communities, further classified into trophic guilds. Our findings reveal that the consumers' pressure increases from spring to summer, leading to more diverse and evenly distributed prey communities. Consequently, consumers effectively maintain the diverse soil bacterial and fungal communities essential for ecosystem functioning. Our research highlights the significance of biotic interactions in understanding the distribution and dynamics of alpine microbial communities.

Influence of rice-wheat and sugarcane-wheat rotations on microbial diversity and plant growth promoting bacteria: Insights from high-throughput sequencing and soil analysis

Wheat is a staple food crop, primarily grown in India's Indo-Gangetic plains, crucial for sustaining the region. Soil quality, vitality, and microbial inhabitants' interplay are pivotal. However, very little information is available on the impacts of agricultural practices, such as crop rotation and cropping systems, on the diversity of both bulk soil (BS) and rhizospheric soil (RS) microbiota. The impact of two different cropping systems, rice-wheat (RW) and sugarcane-wheat (SW) on soil properties, microbial diversity, and plant growth-promoting bacteria (PGPB) in wheat cultivation was investigated in the Indo-Gangetic plains of India. Microbial richness and diversity were analyzed using 16S rRNA sequencing, which reveals distinct clustering patterns between RS and BS, with higher diversity in BS of RW and higher richness in RS of SW. Notably, Proteobacteria dominated across all samples, along with Chloroflexi, Actinobacteria, Bacteroidetes, Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Firmicutes, Planctomycetes, candidate division TM7, Cyanobacteria, and Nitrospirae. Intriguingly, the RS associated with the SW system exhibited the presence of 67 distinct genera, whereas the RS under the RW system showed 48 such genera. Within the realm of specific microbial genera exhibiting plant growth-promoting (PGP) activity, a higher abundance was noted in the RS (17.48%), as opposed to the BS (15.21%). Moreover, certain genera such as Haliangium, Iamia, Bacillus, Gaiella, Candidatus_Entotheonella, Anaerolinea, and Anaeromyxobacter, were found to be positively correlated with the availability of nitrogen, phosphorus, potassium, iron, and sulfur. The study sheds light on the intricate relationships between cropping practices, soil properties, and microbial dynamics, contributing to the development of sustainable agricultural practices for wheat cultivation.

Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness

BACKGROUND

Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.

RESULTS

The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.

CONCLUSION

Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.

Rhizosphere shapes the associations between protistan predators and bacteria within microbiomes through the deterministic selection on bacterial communities

The assembly of bacterial communities in the rhizosphere is well-documented and plays a crucial role in supporting plant performance. However, we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rhizosphere selection. To address this, we examined bacterial and protistan taxa from 443 agricultural soil samples including bulk and rhizosphere soils. Our results presented distinct patterns of bacteria and protistan predators in rhizosphere microbiome assembly. Community assembly of protistan predators was determined by a stochastic process in the rhizosphere and the diversity of protistan predators was reduced in the rhizosphere compared to bulk soils, these may be attributed to the indirect impacts from the altered bacterial communities that showed deterministic process assembly in the rhizosphere. Interestingly, we observed that the plant rhizosphere facilitates more close interrelationships between protistan predators and bacterial communities, which might promote a healthy rhizosphere microbial community for plant growth. Overall, our findings indicate that the potential predator-prey relationships within the microbiome, mediated by plant rhizosphere, might contribute to plant performance in agricultural ecosystems.

Phosphorus Fertilization Boosts Mineral-Associated Soil Organic Carbon Formation Associated with Phagotrophic Protists

Long-term fertilization affects soil organic C accumulation. A growing body of research has revealed critical roles of bacteria in soil organic C accumulation, particularly through mineral-associated organic C (MAOC) formation. Protists are essential components of soil microbiome, but the relationships between MAOC formation and protists under long-term fertilization remain unclear. Here, we used cropland soil from a long-term fertilization field trial and conducted two microcosm experiments with 13C-glucose addition to investigate the effects of N and P fertilizations on MAOC formation and the relationships with protists. The results showed that long-term fertilization (especially P fertilization) significantly (P < 0.05) increased 13C-MAOC content. Compared with P-deficient treatment, P replenishment enriched the number of protists (mainly Amoebozoa and Cercozoa) and bacteria (mainly Acidobacteriota, Bacteroidota, and Gammaproteobacteria), and significantly (P < 0.001) promoted the abundances of bacterial functional genes controlling C, N, P, and S metabolisms. The community composition of phagotrophic protists prominently (P < 0.001) correlated with the bacterial community composition, bacterial functional gene abundance, and 13C-MAOC content. Co-occurrence networks of phagotrophic protists and bacteria were more connected in soil with the N inoculum added than in soil with the NP inoculum added. P replenishment strengthened bacterial 13C assimilation (i.e., 13C-phospholipid fatty acid content), which negatively (P < 0.05) correlated with the number and relative abundance of phagotrophic Cercozoa. Together, these results suggested that P fertilization boosts MAOC formation associated with phagotrophic protists. Our study paves the way for future research to harness the potential of protists to promote belowground C accrual in agroecosystems.

Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere

BACKGROUND

Plant-beneficial bacterial inoculants are of great interest in agriculture as they have the potential to promote plant growth and health. However, the inoculation of the rhizosphere microbiome often results in a suboptimal or transient colonization, which is due to a variety of factors that influence the fate of the inoculant. To better understand the fate of plant-beneficial inoculants in complex rhizosphere microbiomes, composed by hundreds of genotypes and multifactorial selection mechanisms, controlled studies with high-complexity soil microbiomes are needed.

RESULTS

We analysed early compositional changes in a taxa-rich natural soil bacterial community under both exponential nutrient-rich and stationary nutrient-limited growth conditions (i.e. growing and stable communities, respectively) following inoculation with the plant-beneficial bacterium Pseudomonas protegens in a bulk soil or a wheat rhizosphere environment. P. protegens successfully established under all conditions tested and was more abundant in the rhizosphere of the stable community. Nutrient availability was a major factor driving microbiome composition and structure as well as the underlying assembly processes. While access to nutrients resulted in communities assembled mainly by homogeneous selection, stochastic processes dominated under the nutrient-deprived conditions. We also observed an increased rhizosphere selection effect under nutrient-limited conditions, resulting in a higher number of amplicon sequence variants (ASVs) whose relative abundance was enriched. The inoculation with P. protegens produced discrete changes, some of which involved other Pseudomonas. Direct competition between Pseudomonas strains partially failed to replicate the observed differences in the microbiome and pointed to a more complex interaction network.

CONCLUSIONS

The results of this study show that nutrient availability is a major driving force of microbiome composition, structure and diversity in both the bulk soil and the wheat rhizosphere and determines the assembly processes that govern early microbiome development. The successful establishment of the inoculant was facilitated by the wheat rhizosphere and produced discrete changes among other members of the microbiome. Direct competition between Pseudomonas strains only partially explained the microbiome changes, indicating that indirect interactions or spatial distribution in the rhizosphere or soil interface may be crucial for the survival of certain bacteria. Video Abstract.

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

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

Ecological Diversity of Bacterial Rhizomicrobiome Core during the Growth of Selected Wheat Cultivars

One of the latest ecological concepts is the occurrence of a biased rhizosphere of microorganisms recruited mostly through interactions among various components of the rhizosphere, including plant roots and the bulk soil microbiome. We compared the diverse attributes of the core microbiome of wheat rhizosphere communities with wheat (W) and legume (L) forecrops determined by three different methods in this study (membership, composition, and functionality). The conclusions of the three methods of microbiome core definition suggest the presence of generalists, i.e., some representative microorganisms from Proteobacteria, Actinobacteria, Hypomicrobiaceae, Bradyrhizobiaceae, Sphingomonas sp., in the wheat rhizomicrobiome. The relative abundance of the core microbiome accounted for 0.1976% (W) and 0.334% (L)-membership method and 6.425% (W) and 4.253% (L)-composition method. Additionally, bacteria of the specialist group, such as Rhodoplanes sp., are functionally important in the rhizomicrobiome core. This small community is strongly connected with other microbes and is essential for maintenance of the sustainability of certain metabolic pathways.

Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum

Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.

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.

Domestication of Lima Bean (Phaseolus lunatus) Changes the Microbial Communities in the Rhizosphere

Plants modulate the soil microbiota and select a specific microbial community in the rhizosphere. However, plant domestication reduces genetic diversity, changes plant physiology, and could have an impact on the associated microbiome assembly. Here, we used 16S rRNA gene sequencing to assess the microbial community in the bulk soil and rhizosphere of wild, semi-domesticated, and domesticated genotypes of lima bean (Phaseolus lunatus), to investigate the effect of plant domestication on microbial community assembly. In general, rhizosphere communities were more diverse than bulk soil, but no differences were found among genotypes. Our results showed that the microbial community's structure was different from wild and semi-domesticated as compared to domesticated genotypes. The community similarity decreased 57.67% from wild to domesticated genotypes. In general, the most abundant phyla were Actinobacteria (21.9%), Proteobacteria (20.7%), Acidobacteria (14%), and Firmicutes (9.7%). Comparing the different genotypes, the analysis showed that Firmicutes (Bacillus) was abundant in the rhizosphere of the wild genotypes, while Acidobacteria dominated semi-domesticated plants, and Proteobacteria (including rhizobia) was enriched in domesticated P. lunatus rhizosphere. The domestication process also affected the microbial community network, in which the complexity of connections decreased from wild to domesticated genotypes in the rhizosphere. Together, our work showed that the domestication of P. lunatus shaped rhizosphere microbial communities from taxonomic to a functional level, changing the abundance of specific microbial groups and decreasing the complexity of interactions among them.

Core root-associated prokaryotic community and its relationship to host traits across wheat varieties

The root-associated microbiomes play important roles in plant growth. However, it is largely unknown how wheat variety evolutionary relatedness shapes each subcommunity in the root microbiome and, in turn, how these microbes affect wheat yield and quality. Here we studied the prokaryotic communities associated with the rhizosphere and root endosphere in 95 wheat varieties at regreening and heading stages. The results indicated that the less diverse but abundant core prokaryotic taxa occurred among all varieties. Among these core taxa, we identified 49 and 108 heritable amplicon sequence variants, whose variations in relative abundances across the root endosphere and rhizosphere samples were significantly affected by wheat variety. The significant correlations between phylogenetic distance of wheat varieties and prokaryotic community dissimilarity were only observed in non-core and abundant subcommunities in the endosphere samples. Again, wheat yield was only significantly associated with root endosphere microbiota at the heading stage. Additionally, wheat yield could be predicted using the total abundance of 94 prokaryotic taxa as an indicator. Our results demonstrated that the prokaryotic communities in the root endosphere had higher correlations with wheat yield and quality than those in the rhizosphere; thus, managing root endosphere microbiota, especially core taxa, through agronomic practices and crop breeding, is important for promoting wheat yield and quality.

Plant domestication shapes rhizosphere microbiome assembly and metabolic functions

BACKGROUND

The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments.

RESULTS

Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status.

CONCLUSIONS

Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.

Plant genotype influence the structure of cereal seed fungal microbiome

Plant genotype is a crucial factor for the assembly of the plant-associated microbial communities. However, we still know little about the variation of diversity and structure of plant microbiomes across host species and genotypes. Here, we used six species of cereals (Avena sativa, Hordeum vulgare, Secale cereale, Triticum aestivum, Triticum polonicum, and Triticum turgidum) to test whether the plant fungal microbiome varies across species, and whether plant species use different mechanisms for microbiome assembly focusing on the plant ears. Using ITS2 amplicon metagenomics, we found that host species influences the diversity and structure of the seed-associated fungal communities. Then, we tested whether plant genotype influences the structure of seed fungal communities across different cultivars of T. aestivum (Aristato, Bologna, Rosia, and Vernia) and T. turgidum (Capeiti, Cappelli, Mazzancoio, Trinakria, and Timilia). We found that cultivar influences the seed fungal microbiome in both species. We found that in T. aestivum the seed fungal microbiota is more influenced by stochastic processes, while in T. turgidum selection plays a major role. Collectively, our results contribute to fill the knowledge gap on the wheat seed microbiome assembly and, together with other studies, might contribute to understand how we can manipulate this process to improve agriculture sustainability.

Comparison of the diversity and structure of the rhizosphere microbial community between the straight and twisted trunk types of Pinus yunnanensis

Background

Pinus yunnanensis is a major silvicultural species in Southwest China. Currently, large areas of twisted-trunk Pinus yunnanensis stands severely restrict its productivity. Different categories of rhizosphere microbes evolve alongside plants and environments and play an important role in the growth and ecological fitness of their host plant. However, the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types-straight and twisted-remain unclear.

Methods

We collected the rhizosphere soil of 5 trees with the straight and 5 trees with the twisted trunk type in each of three sites in Yunnan province. We assessed and compared the diversity and structure of the rhizosphere microbial communities between P. yunnanensis with two different trunk types by Illumina sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions.

Results

The available phosphorus in soil differed significantly between P. yunnanensis with straight and twisted trunks. Available potassium had a significant effect on fungi. Chloroflexi dominated the rhizosphere soils of the straight trunk type, while Proteobacteria was predominant in the rhizosphere soils of the twisted trunk type. Trunk types significantly explained 6.79% of the variance in bacterial communities.

Conclusion

This study revealed the composition and diversity of bacterial and fungal groups in the rhizosphere soil of P. yunnanensis with straight and twisted trunk types, providing proper microbial information for different plant phenotypes.

Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture

This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.

What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes

In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as 'protist microbiomes' in analogy to 'bacterial microbiomes'.

Distinct rhizosphere soil responses to nitrogen in relation to microbial biomass and community composition at initial flowering stages of alfalfa cultivars

In the long-term growth process, alfalfa rhizosphere forms specific microbiome to provide nutrition for its growth and development. However, the effects of different perennial alfalfa cultivars on changes in the rhizosphere soil characteristics and microbiome are not well understood. In this study, 12 perennial alfalfa cultivars were grown continuously for eight years. Rhizosphere samples were tested using Illumina sequencing of the 16S rRNA gene coupled with co-occurrence network analysis to explore the relationship between alfalfa (biomass and crude protein content), soil properties, and the microbial composition and diversity. Redundancy analysis showed SOC and pH had the greatest impact on the composition of the rhizosphere microbial community. Moreover, microbial diversity also contributes to microbial composition. Soil properties (AP, EC, SOC and pH) exhibited a significant positive correlation with soil bacterial communities, which was attributed to the differences between plant cultivars. Partial least squares path modeling (PLS-PM) revealed that microbial biomass and community composition rather than diversity, are the dominant determinants in the rhizosphere soil nitrogen content of perennial alfalfa. Our findings demonstrate that the soil microbial biomass and composition of rhizosphere bacterial communities are strongly affected by cultivar, driving the changes in soil nitrogen content, and variances in the selective capacities of plants.

Trichoderma atroviride seed dressing influenced the fungal community and pathogenic fungi in the wheat rhizosphere

Fusarium crown rot and wheat sharp eyespot are major soil-borne diseases of wheat, causing serious losses to wheat yield in China. We applied high-throughput sequencing combined with qPCR to determine the effect of winter wheat seed dressing, with either Trichoderma atroviride HB20111 spore suspension or a chemical fungicide consisting of 6% tebuconazole, on the fungal community composition and absolute content of pathogens Fusarium pseudograminearum and Rhizoctonia cerealis in the rhizosphere at 180 days after planting. The results showed that the Trichoderma and chemical fungicide significantly reduced the amount of F. pseudograminearum in the rhizosphere soil (p < 0.05), and also changed the composition and structure of the fungal community. In addition, field disease investigation and yield measurement showed that T. atroviride HB20111 treatment reduced the whiteheads with an average control effect of 60.1%, 14.9% higher than the chemical treatment; T. atroviride HB20111 increased yield by 7.7%, which was slightly more than the chemical treatment. Therefore, T. atroviride HB20111 was found to have the potential to replace chemical fungicides to control an extended range of soil-borne diseases of wheat and to improve wheat yield.

The methane-driven interaction network in terrestrial methane hotspots

BACKGROUND

Biological interaction affects diverse facets of microbial life by modulating the activity, diversity, abundance, and composition of microbial communities. Aerobic methane oxidation is a community function, with emergent community traits arising from the interaction of the methane-oxidizers (methanotrophs) and non-methanotrophs. Yet little is known of the spatial and temporal organization of these interaction networks in naturally-occurring complex communities. We hypothesized that the assembled bacterial community of the interaction network in methane hotspots would converge, driven by high substrate availability that favors specific methanotrophs, and in turn influences the recruitment of non-methanotrophs. These environments would also share more co-occurring than site-specific taxa.

RESULTS

We applied stable isotope probing (SIP) using ¹³C-CH₄ coupled to a co-occurrence network analysis to probe trophic interactions in widespread methane-emitting environments, and over time. Network analysis revealed predominantly unique co-occurring taxa from different environments, indicating distinctly co-evolved communities more strongly influenced by other parameters than high methane availability. Also, results showed a narrower network topology range over time than between environments. Co-occurrence pattern points to Chthoniobacter as a relevant yet-unrecognized interacting partner particularly of the gammaproteobacterial methanotrophs, deserving future attention. In almost all instances, the networks derived from the ¹³C-CH₄ incubation exhibited a less connected and complex topology than the networks derived from the ^unlabelledC-CH₄ incubations, likely attributable to the exclusion of the inactive microbial population and spurious connections; DNA-based networks (without SIP) may thus overestimate the methane-dependent network complexity.

CONCLUSION

We demonstrated that site-specific environmental parameters more strongly shaped the co-occurrence of bacterial taxa than substrate availability. Given that members of the interactome without the capacity to oxidize methane can exert interaction-induced effects on community function, understanding the co-occurrence pattern of the methane-driven interaction network is key to elucidating community function, which goes beyond relating activity to community composition, abundances, and diversity. More generally, we provide a methodological strategy that substantiates the ecological linkages between potentially interacting microorganisms with broad applications to elucidate the role of microbial interaction in community function.

Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere

Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.

18S rRNA gene amplicon sequencing combined with culture-based surveys of maize rhizosphere protists reveal dominant, plant-enriched and culturable community members

Protists play important roles in shaping the microbial community of the rhizosphere and defining these roles will require the study of protist isolates. However, there is still a limited understanding of how well protist isolation efforts can capture the diversity and composition of rhizosphere protistan communities. Here, we report a simultaneous isolation and 18S rRNA gene amplicon sequencing survey describing the protist diversity of maize rhizospheres in two climatically and pedologically distinct sites. We demonstrated that the maize rhizosphere exerted significant and site-dependent effects on the protistan community structure and defined a set of core and rhizosphere-enriched protists. From the same root samples, we generated a library of 103 protist isolates representing 46 18S rRNA gene sequence variants from six eukaryotic supergroups. While cultured isolates represented a small proportion of total protist diversity recovered by sequencing, they included taxa enriched in rhizosphere soils across all samples, encompassing 9% of all core sequence variants. The isolation approach also captured 17 protists not detected through 18S rRNA gene amplicon sequencing. This study demonstrated that maize roots select for distinct protistan communities, and established a diverse protist culture collection that can be used for future research linking protists to rhizosphere status and plant health.

Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields

The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank's and seed-originated microbiome recruitment depend on both plants' genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.

Significance of the Diversification of Wheat Species for the Assembly and Functioning of the Root-Associated Microbiome

Wheat, one of the major crops in the world, has had a complex history that includes genomic hybridizations between Triticum and Aegilops species and several domestication events, which resulted in various wild and domesticated species (especially Triticum aestivum and Triticum durum), many of them still existing today. The large body of information available on wheat-microbe interactions, however, was mostly obtained without considering the importance of wheat evolutionary history and its consequences for wheat microbial ecology. This review addresses our current understanding of the microbiome of wheat root and rhizosphere in light of the information available on pre- and post-domestication wheat history, including differences between wild and domesticated wheats, ancient and modern types of cultivars as well as individual cultivars within a given wheat species. This analysis highlighted two major trends. First, most data deal with the taxonomic diversity rather than the microbial functioning of root-associated wheat microbiota, with so far a bias toward bacteria and mycorrhizal fungi that will progressively attenuate thanks to the inclusion of markers encompassing other micro-eukaryotes and archaea. Second, the comparison of wheat genotypes has mostly focused on the comparison of T. aestivum cultivars, sometimes with little consideration for their particular genetic and physiological traits. It is expected that the development of current sequencing technologies will enable to revisit the diversity of the wheat microbiome. This will provide a renewed opportunity to better understand the significance of wheat evolutionary history, and also to obtain the baseline information needed to develop microbiome-based breeding strategies for sustainable wheat farming.

Fungi Inhabiting the Wheat Endosphere

Wheat production is influenced by changing environmental conditions, including climatic conditions, which results in the changing composition of microorganisms interacting with this cereal. The group of these microorganisms includes not only endophytic fungi associated with the wheat endosphere, both pathogenic and symbiotic, but also those with yet unrecognized functions and consequences for wheat. This paper reviews the literature in the context of the general characteristics of endophytic fungi inhabiting the internal tissues of wheat. In addition, the importance of epigenetic regulation in wheat-fungus interactions is recognized and the current state of knowledge is demonstrated. The possibilities of using symbiotic endophytic fungi in modern agronomy and wheat cultivation are also proposed. The fact that the current understanding of fungal endophytes in wheat is based on a rather small set of experimental conditions, including wheat genotypes, plant organs, plant tissues, plant development stage, or environmental conditions, is recognized. In addition, most of the research to date has been based on culture-dependent methods that exclude biotrophic and slow-growing species and favor the detection of fast-growing fungi. Additionally, only a few reports of studies on the entire wheat microbiome using high-throughput sequencing techniques exist. Conducting comprehensive research on the mycobiome of the endosphere of wheat, mainly in the context of the possibility of using this knowledge to improve the methods of wheat management, mainly the productivity and health of this cereal, is needed.

Microbial co-occurrence network and its key microorganisms in soil with permanent application of composted tannery sludge

Soil microbial communities act on important environmental processes, being sensitive to the application of wastes, mainly those potential contaminants, such as tannery sludge. Due to the microbiome complexity, graph-theoretical approaches have been applied to represent model microbial communities interactions and identify important taxa, mainly in contaminated soils. Herein, we performed network and statistical analyses into microbial 16S rRNA gene sequencing data from soil samples with the application of different levels of composted tannery sludge (CTS) to assess the most connected nodes and the nodes that act as bridges to identify key microbes within each community. The network analysis revealed hubs belonging to Proteobacteria in soil with lower CTS rates, while active degraders of recalcitrant and pollutant chemical hubs belonging to Proteobacteria and Actinobacteria were found in soils under the highest CTS rates. The majority of classified connectors belonged to Actinobacteria, but similarly to hubs taxa, they shifted from metabolic functional profile to taxa with abilities to degrade toxic compounds, revealing a soil perturbation with the CTS application on community organization, which also impacted the community modularity. Members of Actinobacteria and Acidobacteria were identified as both hub and connector suggesting their role as keystone groups. Thus, these results offered us interesting insights about crucial taxa, their response to environmental alterations, and possible implications for the ecosystem.

Taxonomic Compositions and Co-occurrence Relationships of Protists in Bulk Soil and Rhizosphere of Soybean Fields in Different Regions of China

As the main consumers of bacteria and fungi in farmed soils, protists remain poorly understood. The aim of this study was to explore protist community assembly and ecological roles in soybean fields. Here, we investigated differences in protist communities using high-throughput sequencing and their inferred potential interactions with bacteria and fungi between the bulk soil and rhizosphere compartments of three soybean cultivars collected from six ecological regions in China. Distinct protist community structures characterized the bulk soil and rhizosphere of soybean plants. A significantly higher relative abundance of phagotrophs was observed in the rhizosphere (25.1%) than in the bulk soil (11.3%). Spatial location (R 2 = 0.37-0.51) explained more of the variation in protist community structures of soybean fields than either the compartment (R 2 = 0.08-0.09) or cultivar type (R 2 = 0.02-0.03). The rhizosphere protist network (76 nodes and 414 edges) was smaller and less complex than the bulk soil network (147 nodes and 880 edges), indicating a smaller potential of niche overlap and interactions in the rhizosphere due to the increased resources in the rhizosphere. Furthermore, more inferred potential predator-prey interactions occur in the rhizosphere. We conclude that protists have a crucial ecological role to play as an integral part of microbial co-occurrence networks in soybean fields.

Culture-Based and Culture-Independent Assessments of Endophytic Fungal Diversity in Aquatic Plants in Southwest China

Aquatic ecosystems contain tremendous plant and microbial diversity. However, little is known about endophyte diversity in aquatic plants. In this study, we investigated the diversity of endophytic fungi in aquatic plants in southwest China using both culture-based and culture-independent high-throughput sequencing methods. A total of 1,689 fungal isolates belonging to three phyla and 154 genera were obtained from 15,373 plant tissue segments of 30 aquatic plant species. The most abundant endophytic fungi were those in ascomycete genera Aspergillus, Ceratophoma, Fusarium, Penicillium, Phoma and Plectosporium. No difference in fungal isolation rates was observed among tissues from roots, stems, and leaves. Twenty tissue samples from three most common plant species were further subjected to culture-independent meta-barcode sequencing. The sequence-based analyses revealed a total of 1,074 OTUs belonging to six fungal phyla and 194 genera. Among the three plants, Batrachium bungei harbored the highest number of OTUs. Besides, a total of 66 genera were detected by two methods. Both the culture-dependent and independent methods revealed that aquatic plants in southwest China have abundant endophytic fungal diversity. This study significantly expands our knowledge of the fungal community of aquatic plants.

The Rhizobacterium Pseudomonas alcaligenes AVO110 Induces the Expression of Biofilm-Related Genes in Response to Rosellinia necatrix Exudates

The rhizobacterium Pseudomonas alcaligenes AVO110 exhibits antagonism toward the phytopathogenic fungus Rosellinia necatrix. This strain efficiently colonizes R. necatrix hyphae and is able to feed on their exudates. Here, we report the complete genome sequence of P. alcaligenes AVO110. The phylogeny of all available P. alcaligenes genomes separates environmental isolates, including AVO110, from those obtained from infected human blood and oyster tissues, which cluster together with Pseudomonas otitidis. Core and pan-genome analyses showed that P. alcaligenes strains encode highly heterogenic gene pools, with the AVO110 genome encoding the largest and most exclusive variable region (~1.6 Mb, 1795 genes). The AVO110 singletons include a wide repertoire of genes related to biofilm formation, several of which are transcriptionally modulated by R. necatrix exudates. One of these genes (cmpA) encodes a GGDEF/EAL domain protein specific to Pseudomonas spp. strains isolated primarily from the rhizosphere of diverse plants, but also from soil and water samples. We also show that CmpA has a role in biofilm formation and that the integrity of its EAL domain is involved in this function. This study contributes to a better understanding of the niche-specific adaptations and lifestyles of P. alcaligenes, including the mycophagous behavior of strain AVO110.

Wheat Rhizosphere Metagenome Reveals Newfound Potential Soil Zn-Mobilizing Bacteria Contributing to Cultivars' Variation in Grain Zn Concentration

An effective solution to global human zinc (Zn) deficiency is Zn biofortification of staple food crops, which has been hindered by the low available Zn in calcareous soils worldwide. Many culturable soil microbes have been reported to increase Zn availability in the laboratory, while the status of these microbes in fields and whether there are unculturable Zn-mobilizing microbes remain unexplored. Here, we use the culture-independent metagenomic sequencing to investigate the rhizosphere microbiome of three high-Zn (HZn) and three low-Zn (LZn) wheat cultivars in a field experiment with calcareous soils. The average grain Zn concentration of HZn was higher than the Zn biofortification target 40 mg kg^–1, while that of LZn was lower than 40 mg kg^–1. Metagenomic sequencing and analysis showed large microbiome difference between wheat rhizosphere and bulk soil but small difference between HZn and LZn. Most of the rhizosphere-enriched microbes in HZn and LZn were in common, including many of the previously reported soil Zn-mobilizing microbes. Notably, 30 of the 32 rhizosphere-enriched species exhibiting different abundances between HZn and LZn possess the functional genes involved in soil Zn mobilization, especially the synthesis and exudation of organic acids and siderophores. Most of the abundant potential Zn-mobilizing species were positively correlated with grain Zn concentration and formed a module with strong interspecies relations in the co-occurrence network of abundant rhizosphere-enriched microbes. The potential Zn-mobilizing species, especially Massilia and Pseudomonas, may contribute to the cultivars’ variation in grain Zn concentration, and they deserve further investigation in future studies on Zn biofortification.

Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome

Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history.

Defining the physiological determinants of low nitrogen requirement in wheat

Nitrogen (N) is a major nutrient limiting productivity in many ecosystems. The large N demands associated with food crop production are met mainly through the provision of synthetic N fertiliser, leading to economic and ecological costs. Optimising the balance between N supply and demand is key to reducing N losses to the environment. Wheat (Triticum aestivum L.) production provides food for millions of people worldwide and is highly dependent on sufficient N supply. The size of the N sink, i.e. wheat grain (number, size, and protein content) is the main driver of high N requirement. Optimal functioning of temporary sinks, in particular the canopy, can also affect N requirement. N use efficiency (i.e. yield produced per unit of N available) tends to be lower under high N conditions, suggesting that wheat plants are more efficient under low N conditions and that there is an optimal functioning yet unattained under high N conditions. Understanding the determinants of low N requirement in wheat would provide the basis for the selection of genetic material suitable for sustainable cereal production. In this review, we dissect the drivers of N requirement at the plant level along with the temporal dynamics of supply and demand.

Spatiotemporal Dynamics of Maize (Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota

Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.

Assembly Patterns of the Rhizosphere Microbiome Along the Longitudinal Root Axis of Maize (Zea mays L.)

It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil - their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important.

Defining the wheat microbiome: Towards microbiome-facilitated crop production

Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.

Potentilla anserina L. developmental changes affect the rhizosphere prokaryotic community

Plant roots and soil prokaryotes primarily interact with each other in the rhizosphere. Changes in the rhizosphere prokaryotic structure are influenced by several factors. In this study, the community structure of the Potentilla anserina L. rhizosphere prokaryotes was identified and evaluated by high-throughput sequencing technology in different continuous cropping fields and developmental stages of the plant. In total, 2 archaeal (Euryarchaeota and Thaumarchaeota) and 26 bacterial phyla were identified in the P. anserina rhizosphere. The bacterial community was mainly composed of Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria, and Verrucomicrobia. Moreover, the prokaryotic community structure of the rhizosphere varied significantly during plant development. Our results provide new insights into the dynamics of the P. anserina rhizosphere prokaryotic community and may provide useful information for enhancing the growth and development of P. anserina through artificial control of the soil prokaryotes.

Effect of Inorganic N Top Dressing and Trichoderma harzianum Seed-Inoculation on Crop Yield and the Shaping of Root Microbial Communities of Wheat Plants Cultivated Under High Basal N Fertilization

Wheat crop production needs nitrogen (N) for ensuring yield and quality. High doses of inorganic N fertilizer are applied to soil before sowing (basal dressing), with additional doses supplied along the cultivation (top dressing). Here, a long-term wheat field trial (12 plots), including four conditions (control, N top dressing, Trichoderma harzianum T34 seed-inoculation, and top dressing plus T34) in triplicate, was performed to assess, under high basal N fertilization, the influence of these treatments on crop yield and root microbial community shaping. Crop yield was not affected by top dressing and T. harzianum T34, but top dressing significantly increased grain protein and gluten contents. Twenty-seven-week old wheat plants were collected at 12 days after top dressing application and sampled as bulk soil, rhizosphere and root endosphere compartments in order to analyze their bacterial and fungal assemblies by 16S rDNA and ITS2 high-throughput sequencing, respectively. Significant differences for bacterial and fungal richness and diversity were detected among the three compartments with a microbial decline from bulk soil to root endosphere. The most abundant wheat root phyla were Proteobacteria and Actinobacteria for bacteria, and Ascomycota and Basidiomycota for fungi. An enrichment of genera commonly associated with soils subjected to chemical N fertilization was observed: Kaistobacter, Mortierella, and Solicoccozyma in bulk soil, Olpidium in rhizosphere, and Janthinobacterium and Pedobacter in root endosphere. Taxa whose abundance significantly differed among conditions within each compartment were identified. Results show that: (i) single or strain T34-combined application of N top dressing affected to a greater extent the bulk soil bacterial levels than the use of T34 alone; (ii) when N top dressing and T34 were applied in combination, the N fertilizer played a more decisive role in the bacterial microbiome than T34; (iii) many genera of plant beneficial bacteria, negatively affected by N top dressing, were increased by the application of T34 alone; (iv) bulk soil and rhizosphere fungal microbiomes were affected by any of the three treatments assayed; and (v) all treatments reduced Claroideoglomus in bulk soil but the single application of T34 raised the rhizosphere levels of this mycorrhizal fungus.

What Drives the Diversity of the Most Abundant Terrestrial Cercozoan Family (Rhogostomidae, Cercozoa, Rhizaria)?

Environmental sequencing surveys of soils and freshwaters revealed high abundance and diversity of the Rhogostomidae, a group of omnivorous thecate amoebae. This is puzzling since only a few Rhogostomidae species have yet been described and only a handful of reports mention them in field surveys. We investigated the putative cryptic diversity of the Rhogostomidae by a critical re-evaluation of published environmental sequencing data and in-depth ecological and morphological trait analyses. The Rhogostomidae exhibit an amazing diversity of genetically distinct clades that occur in a variety of different environments. We further broadly sampled for Rhogostomidae species; based on these isolates, we describe eleven new species and highlight important morphological traits for species delimitation. The most important environmental drivers that shape the Rhogostomidae community were soil moisture, soil pH, and total plant biomass. The length/width ratio of the theca was a morphological trait related to the colonized habitats, but not the shape and size of the aperture that is often linked to moisture adaption in testate and thecate amoebae.