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Characterizing microbial communities associated with disease-suppressive soil is an important first step toward understanding the potential of microbiota to protect crops against plant pathogens. In the present study, we compared microbial communities in suppressive- and conducive-soils associated with Fusarium wilt disease in a vanilla long-term continuous cropping system. Suppressive soil was associated with higher fungal diversity and lower bacterial diversity. The fungal phyla Zygomycota and Basidiomycota , and the bacterial phyla Acidobacteria , Verrucomicrobia , Actinobacteria and Firmicutes were strongly enriched in the suppressive soil. Notably, suppressive soil was dominated by the fungal genus Mortierella , accounting for 37% of the total fungal sequences. The hyper-dominance of Mortierella spp. in suppressive soil suggests that this taxon may serve as an indicator and enhancer of Fusarium wilt disease suppression in vanilla. In addition, Molecular Ecological Network analysis revealed that fungal communities were more connected and showed more co-occurrence relationships in the suppressive versus conducive soils. Our results indicate that fungal communities may be important in the development of soil suppressiveness against vanilla Fusarium wilt disease. [ABSTRACT FROM AUTHOR]

The “energetic equivalence rule” predicts that abundance should always scale as the −3/4 power of body size within a trophic group, but if the body size–abundance allometry (BSA) of soil fauna in fact is labile then the relationship could potentially be used as a standard descriptor for shifts in community functional structure in response to environmental change. To assess the possibility that the BSA could serve as an index of community functional structure, we measured the effect of fertilization on the slope and intercept of the BSA in nematode communities in a rice–wheat crop rotation over three years. Fertilization increased the BSA intercept but did not affect the slope in either rice or wheat phases, which highlights the stable scaling of BSA. [ABSTRACT FROM AUTHOR]

Soil microbial communities mix and interact, a widespread phenomenon known as community coalescence. However, in the context of different coalescence degrees, the effects and potential applicability of soil mixing on plant disease resistance have not been studied. Here, we mixed soils from two habitats (healthy and diseased soils) at different mixing ratios for watermelon planting. Rhizosphere soils were collected for amplicon sequencing to study the effects of different degrees of bacterial community coalescence on plant growth and disease resistance, as well as on the characteristics, network complexity and stability of rhizosphere microbial communities. Combined with network and cohesion analyses, we found that mixing in more healthy soil reduced the plant disease index and increased biomass by improving the stability and complexity of the network; positive cohesion, reflecting degree of cooperation, was also negatively correlated with the plant disease index. The rhizosphere from healthy soils enriched the core taxa, Nitrospirillum and Singulisphaera. These core taxa were significantly associated with disease suppression and important for regulating the positive cohesion and modularity of the networks. Overall, these findings revealed that the soil bacterial community coalescence enhanced the stability and complexity of the rhizobacterial network, simultaneously core taxa enhanced microbial potential cooperation and network complexity, ultimately enhancing plant health and biomass. Our results provide insights into the understanding of microbial community coalescence as a potentially effective mechanism for improving plant microbial community function and suggest promising new tools for improving plant fitness via mixing soil microbiota. • Community coalescence by soil mixing had positive effects on plant growth and disease-suppression. • More healthy soils resulted in higher positive cohesion and network stability and complexity. • Cooperative behaviours among taxa improved plant resistance to disease. • Core bacterial species strengthen microbial cooperation and network complexity. [ABSTRACT FROM AUTHOR]

Plant-beneficial microbes improve while pathogens reduce plant performance. When introduced in soils, such microbes can induce entire microbiome changes. However, the impact of those microbial introductions on protists – key predators within the soil microbiome – remain unknown. Here, we tracked how soil protists respond to bacterial (Bacillus and Ralstonia) and fungal (Trichoderma and Fusarium) introductions, with both microbial groups represented by one beneficial and one pathogenic taxon. We found that plant-beneficial Bacillus bacteria change the protist community structure. This community-shift was likely induced by an increased fungi/bacteria ratio, supported by a negative correlation of the fungi/bacteria ratio with the relative abundance of phagotrophic protists across all treatments. Our results indicate that microbial introductions can impact protist communities, thereby altering microbiome-derived multi-functionality. • We tested how bacterial and fungal species introductions affect soil protists. • Introduced Bacillus bacteria changed the protist community. • Phagotrophic protists were negatively correlated with the fungi/bacteria ratio. [ABSTRACT FROM AUTHOR]

Abstract Fusarium wilt disease of banana, caused by the fungus Fusarium oxysporum f. sp. cubense race 4, is a serious soil-borne fungal disease that currently threatens worldwide banana production. No single agricultural practice has yet been developed to effectively manage this disease. In the present study, greenhouse experiments were conducted to evaluate the effect of an integrated biofertilizer application after ammonia fumigation to enhance control of Fusarium wilt disease in severely infected banana mono-cropped soils. Quantitative PCR and high-throughput sequencing were used to characterise soil microbial community structure and the results from both two-season experimental studies showed that biofertilizer application after ammonia fumigation significantly reduced the incidence of banana Panama disease by approximately 55% and promoted the plant biomass, compared to the control application of cow manure to non-fumigated soil. Ammonia fumigation significantly reduced total fungal and F. oxysporum abundances and bacterial and fungal diversities. Biofertilizer application after fumigation further depleted the abundance of the pathogen. Biofertilizer application and fumigation altered the soil microbial community composition with the bacterial community responding first to fumigation, while the fungal community responded first to fertilization. Although Bacillus , including our inoculated strain, was not enriched after biofertilization, putative beneficial microbes such as Paenibacillus , Virgibacillus , Nitrosomonas , and Nitrobacter , were significantly enriched by ammonia fumigation and biofertilizer application, and were significantly correlated with disease suppression or increased plant biomass. Furthermore, fumigation and biofertilization significantly increased the soil pH and nutrient contents, with concomitant effects on the microbial community. Overall, the observed disease suppression and increased plant biomass resulting from both soil fumigation and biofertilization after banana cropping can be attributed to the reduced abundance of F. oxysporum and general suppression from altered soil properties that may enable the establishment of a beneficial soil microbiome. Highlights • Integrated biofertilizer application and fumigation enhanced Fusarium wilt disease suppression. • Ammonia fumigation significantly reduced F. oxysporum abundance. • Biofertilizer application after fumigation further depleted the abundance of the pathogen. • An increase in the number of known beneficial microbes is correlated with disease suppression. [ABSTRACT FROM AUTHOR]

Although numerous studies suggest that organic amendments are better at maintaining soil fertility and crop production than mineral-only fertilization, it is unclear if this occurs in different agricultural systems on a global scale. Here we report a comprehensive meta-analysis of 690 independent experiments comparing the performance of organic amendments and mineral-only fertilization on crop yields, the soil organic carbon (SOC) and total nitrogen (TN) contents, soil nutrient dynamics and biological properties. Our analysis shows that organic amendments increased crop yields on average of 27% than mineral-only fertilization. Farmyard manure (FYM) had the highest effect (49% increase) and this was especially clear in wheat croplands (40% increase). Organic amendment increased the amount of SOC (38%), TN (20%), microbial biomass carbon (MBC; 51%) and microbial biomass nitrogen (MBN; 24%) than mineral-only fertilization. Organic amendments also increased the soil microbiome enzyme activity in terms of soil hydrolytic C acquisition (C-acq; 39%), N acquisition (N-acq; 22%), P acquisition (P-acq; 48%) and oxidative decomposition (OX; 58%). Increased nutrient acquisition and oxidative decomposition could explain the positive effects of organic amendment on crop yields. These observed patterns were consistent for most organic amendments and cropping systems in diverse regions of the world. In summary, our analysis suggests that organic amendments can improve microbe-mediated soil ecosystem functioning, long-term soil fertility and crop productivity, relative to mineral fertilization, on a global scale. [ABSTRACT FROM AUTHOR]

Paddy soils constitute the largest anthropogenic wetlands on earth. However, the biogeochemical cycles of iron (Fe) oxides and organic compounds at the redox interfaces in paddy soils are poorly understood. Here, we propose a conceptual mechanism based on our data set, which links seasonal turnover of soil aggregates and the organo-mineral associations at the aggregate interfaces in the rice-wheat cropping system. Our results showed that the application of organic amendments significantly ( P  < 0.05) increased the aggregate mean weight diameter (MWD) compared to chemical fertilization alone. The aggregate MWD was always higher after the wheat harvest than after the rice harvest from 2013 to 2015, indicating a seasonal dynamic management-induced process of aggregation, disaggregation and re-aggregation. The oxalate-extractable Fe oxides (Feo) may preferentially retain aromatic organic compounds as indicated by the significant positive correlation between Feo and the percentage of aromatic carbon (C). Furthermore, the specific surface area of the ferrihydrite significantly increased after the microbial reduction, showing the potential of adsorbing more aromatic organic compounds. Moreover, there were more aromatic organic compounds at the aggregate surfaces than in the entire entities, suggesting that aromatic organic compounds were selectively preserved at the aggregate interfaces possibly by forming aromatic-Fe complexes. Therefore, soil disaggregation coupled with the anaerobic conditions exposed more fresh surfaces for C accumulation by forming aromatic-Fe complexes, which were subsequently protected by soil re-aggregation in the aerobic conditions. Organic fertilization improved soil aggregation and promoted the organo-mineral interactions, thus contributing to C sequestration in the rice-wheat cropping system. [ABSTRACT FROM AUTHOR]

Plant pathogen invasions are often associated with changes in physical environmental conditions and the composition of host-associated rhizosphere microbiome. It is however unclear how these factors interact and correlate with each other in determining plant disease dynamics in natural field conditions. To study this, we temporally sampled the rhizosphere of tomato plants that were exposed to moderate to aggressive Ralstonia solanacearum pathogen invasions over one crop season. We found that physiochemical soil properties correlated weakly with the severity of pathogen invasion apart from the water-soluble nitrogen concentration, which increased more clearly during the aggressive invasion. Instead, a much stronger link was found between pathogen invasion and reduced abundance and diversity of various rhizosphere bacterial taxa, simplification of bacterial interaction networks and loss of several predicted functional genes. We further verified our results in a separate greenhouse experiment to show that pathogen invasion causally drives similar changes in rhizosphere microbiome diversity and composition under controlled environmental conditions. Our results suggest that R. solanacearum invasion disrupts rhizosphere bacterial communities leading to clear reduction in the diversity and abundance of non-pathogenic bacteria. These changes could potentially affect the likelihood of secondary pathogen invasions during following crop seasons as less diverse microbial communities are also often less resistant to invasions. Strong negative correlation between pathogen and non-pathogenic bacterial densities further suggest that relative pathogen abundance could better predict the severity of bacterial wilt disease outbreaks compared to absolute pathogen abundance. Monitoring the dynamics of whole microbiomes could thus open new avenues for more accurate disease diagnostics in the future. [ABSTRACT FROM AUTHOR]

Although the precipitation and dissolution of iron (Fe)-containing-minerals are driven by microbially-mediated iron-redox cycling, we still have a limited understanding of complex response of such microbial communities to fertilisation. Here, using chemical and synchrotron-based spectral analyses, we show that the distribution of poorly crystalline Fe minerals and crystalline Fe minerals is different in organically- and inorganically-fertilised soils, and that compared to no fertilisation (Control), Fe redox cycling bacteria were present at higher abundance and diversity in organically-fertilised soils but lower in inorganically-fertilised soil. During Fe(III) reduction, Geobacter were important active Fe(III) reducers, with a higher relative abundance in both organically- and inorganically-fertilised soils than in Control, and their higher abundance was responsible for greater dissolution of ferrihydrite in inorganically-fertilised soil than in organically-fertilised soil. However, during the Fe(II) oxidation, Pseudomonas and Anaerolinea were more abundant, and produced higher levels of poorly crystalline Fe oxides under organic fertilisation. Thus, for the first time, we demonstrate that inorganic and organic fertilisation regimes have contrasting effects on the Fe redox bacterial communities, which then influence Fe cycling in soils. [ABSTRACT FROM AUTHOR]

Even though organic fertilization is known to promote soil nitrogen cycling ( N -cycling), it is unclear how this effect is mediated. Here we studied the potential roles of soil physiochemical properties and soil particle-size fraction (PSF) in relation to the diversity and abundance of N -cycling-related prokaryotes by sampling field sites that had been subjected to either mineral or organic fertilization for over 30 years (two independent fields subjected to both fertilization treatments). We found that organic fertilization increased the 63–200 μm sized soil fraction and the abundance of various N -cycling-related prokaryotes including diazotrophs, ammonia-oxidizers and denitrifiers. Moreover, increase in the abundance of different N -cycling-related prokaryotes varied between different size fractions: the abundance of ammonia-oxidizers and nitrate-reducers was the highest in the 63–200 μm size fraction, while the abundance of diazotrophs, ammonifiers and denitrifiers was the highest in the 200–2000 μm, 2–63 μm and 0.1–2 μm size fractions, respectively. According to structural equation modelling (SEM), soil PSF, physiochemical properties and the community structure of N -cycling-related prokaryotes within different PSFs were associated with the abundance of N -cycling-related prokaryotes in non-fractionated bulk soils. In conclusion, these results suggest that organic, but not mineral, fertilization can support the abundance of N -cycling-related prokaryotes and that the strength of the effects depends on their association with specific particle-size fractions. [ABSTRACT FROM AUTHOR]

Ammonia oxidation, the primary and rate-limiting step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the dominant environmental driver of the activity, abundance, diversity and composition of ammonia-oxidizers has not been well understood enough, and the relative contribution of AOA and AOB to nitrification is still under debate. Soils treated with different fertilization regimes in an over 35-year field experiment were collected to explore the variation in function and structure of ammonia-oxidizer communities and corresponding driver. The highest nitrification activity (44.49 mg N kg −1 soil d −1 ) was found in only organic fertilizer (O) treated soil, whereas the lowest activity (2.81 mg N kg −1 soil d −1 ) was observed in only mineral fertilizer (NPK) treated soil. Moreover, as 1-octyne was employed to discriminate AOA- and AOB-supported nitrification, AOA dominated (93.53%) the nitrification in the Control soil, while AOB contributed dominantly (84.73–89.10%) in all of the organic amended soils, and NPK-treated soil showed an almost equal contribution to AOA (45.79%) and AOB (54.21%). Compared with the Control soil, AOA abundance increased in soils with organic and low chemical fertilizer but decreased in only chemically treated soil, whereas the AOB abundance in all fertilized soils was greatly enhanced. The AOA activity was linearly dependent on AOA abundance, whereas the AOB activity was exponentially correlated with AOB abundance. The sequences of AOA and AOB in the Control soil were mostly affiliated with group I.1b thaumarchaeota and genus Nitrosospira clusters 3a.1. Soil treated with NPK increased the abundance of AOA that belonged to group I.1a-associated lineage, whereas more abundant AOB was related to Nitrosospira clusters 3a.2 and 8b. In contrast, the O-treated soil showed more abundant AOB that belonged to Nitrosospira clusters 3b and 8b. As revealed by aggregated boosted tree analysis, the soil ammonium (NH 4 + ) content was identified as the dominant driver of activity and diversity of AOA, and soil pH was considered to be the major influencing factor in abundance and composition of AOA; the AOB composition was mainly affected by soil NH 4 + content, the relative activity and diversity by soil pH, and the relative abundance by soil electrical conductivity (EC). Collectively, different fertilization regimes will result in variations in activity, abundance, diversity and composition of ammonia-oxidizers with distinct drivers. Our research could be helpful to identify better strategies for the mitigation of nitrate production in agricultural soils. [ABSTRACT FROM AUTHOR]

Fusarium wilt disease is a growing problem in agriculture systems. Application of bio-fertilizers containing beneficial microbes represents a promising disease control strategy. However, the mechanisms underlying disease suppression remain elusive. Here, in order to assess the importance of direct antagonism and modified soil microbiota on suppression of Fusarium wilt disease, we conducted a pot experiment with chemical, organic and biologically enhanced fertilizers, we tracked the impact of those fertilizer amendments on disease incidence, and measured the pathogen density and changes in soil microbiota. Alterations in bacterial abundance and community structure after bio-fertilizers application were determined to be key factors in constraining the pathogen, Fusarium oxysporum . In particular, bio-fertilizer application increased the abundance of indigenous microbial groups with reported antifungal activity, such as Lysobacter spp., which could play a keystone role in controlling this pathogen. The microbes introduced in the bio-fertilizer treatments ( e.g. Bacillus and Trichoderma spp.) induced suppressiveness via alteration of the soil microbiome rather than direct pathogen inhibition. These results contrast with the commonly held paradigm of disease suppression using beneficial microbes and open up new perspectives for the promotion of soil health. In addition to seeking antagonistic microbes based on their direct inhibitory activity, disease suppression may also be achieved by introducing keystone species that reshape soil microbiome structure and function. [ABSTRACT FROM AUTHOR]

High-throughput sequencing technologies have recently made it possible to interrogate the phylogenetic diversity of soils at considerable depth. This ability has led to the development of many computational tools to infer interaction networks from environmental samples. Although such tools have widely been used, they have more often served as a visual means to compare microbial communities across environmental gradients than as a means to appreciate microbial interactions associated with certain ecological processes. Previous studies have often regarded a subnetwork (module) as a functional unit but its functionality in ecological context has never been evidenced. To make better use of these tools in appreciating microbial interactions, we propose the combinational use of different inference tools. This ensemble approach permits the use of more independent predictors and the removal of tool-specific predictions in order to increase prediction accuracy. The purpose of the present study is to identify ecologically meaningful bacterial associations using multi-tool approach. Soil samples were collected in time series from experimental paddy rice plots. Bacterial communities were characterized by high-throughput tag sequencing of 16S rRNA gene fragments. We used three tools, Co-occurrence Network inference (CoNet), Molecular Ecological Network Analysis (MENA) and extended Local Similarity Analysis (eLSA), to infer networks from abundance profiles, partitioned the networks into modules, screened for the modules with ≥50% of genus-/species-level nodes, captured the modules that were derived from different tools and shared ≥ 50% of order-level nodes (tool-agreed modules) and tested their robustness against the changes in the tool parameters. By these procedures, two three-tool-agreed modules were found. One represented a guild that is phenotypically associated with aerobic respiration and fermentation and the other represented a guild phenotypically associated with metal/sulphur cycles, all of which are essential processes of water-submerged paddy soils that are mediated by bacteria. These data suggested that the linked members in a module were functionally associated taxa that work together to achieve a distinct function or an ecological process, and thus were ecologically meaningful to the environment. We selected three linked species from a three-tool-agreed module and validated their interactions using co-culture methods. Results showed that the interaction type between Janthinobacterium lividum and Leuconostoc lactis in the two-species mixture was validated to be ambivalent, positive for one partner and negative for the other. However, this type of interaction was not retained when a third party Lactococcus piscium was introduced, signifying the complexity of multi-species interactions. Validation results suggested that the selected species were interacting partners in laboratory but the validated interaction types were different from those inferred. By multi-tool approach, we also found that highly linked nodes, which are often referred to as “keystone species” and are frequently interpreted as the species playing important roles in soils, are tool dependent. Among top ten highly linked nodes, only four are conserved across three tools. These results suggest more research is required on the ecological significance of degree-based identification of keystone species. Overall, the present study highlights the potential utility of combined use of inference tools to identify ecologically meaningful bacterial associations in soils and other environmental samples. It is interesting to see what type of ecologically meaningful bacterial associations can be found in other soils. [ABSTRACT FROM AUTHOR]

Worldwide, banana production is severely hindered by Fusarium wilt, a devastating disease caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). With no widely adopted efficient method of control or prevention, the emergence of a new Foc variant, tropical race 4 (Foc TR4), has led to the widespread destruction of plantations in Cavendish-producing areas. Recently, banana Fusarium wilt has been controlled by the consecutive application of biofertilizer (BIO) in newly reclaimed fields. In this study we examine the temporal effects of BIO versus compost application in newly converted banana fields on the composition and abundance of the rhizosphere bacterial and fungal communities and the survival of the biocontrol inoculant, Bacillus amyloliquefaciens NJN-6. Our findings show that BIO-amended rhizosphere soils increased the abundance of bacteria while decreasing fungal abundance. This corresponded to higher bacterial richness and diversity in the BIO amendment, while no trends were observed with the fungal community. Rhizosphere soil bacterial and fungal community composition were significantly different between BIO and compost amendment and treatment, not time, exhibited the largest impact. Other potential taxa involved in disease suppression were also identified, such as increased abundances of Sphingobium , Dyadobacter , and Cryptococcus and lower abundances of Fusarium , Ralstonia , and Burkholderia . Overall, decreased abundances of F . oxysporum and a lack of variability in the abundance of the biocontrol agent NJN-6 over three years contributed to disease suppression, in combination with alterations in fungal and bacterial composition and abundance, pointing to the sustainability of BIO as an amendment for disease suppression. [ABSTRACT FROM AUTHOR]

Significant differences in the microbial biomass and diversity in soil have been observed following long-term fertilization, but little research has explored the co-occurrence patterns among microbial taxa or functions. Soil samples from four long-term experiments in China were collected, and an Illumina amplicon sequencing of 16S rDNA amplicon was performed to decipher the differences in interactions and network organization arising from fertilization with organic amendment (OA) or chemical fertilizer (CF) across the sampling sites. We thus aimed to extend the analysis beyond the basic inventory descriptions of the composition and diversity of the microbiome and toward an assessment of relationships and effects. Nonmetric multidimensional scaling analysis revealed a clear difference between the soil microbiomes associated with the OA and CF treatments. Fertilization can interact with the soil chemical properties and sampling site, thereby significantly impacting the associated soil microbiome. Distinct network structures indicated that the OA network was characterized by more functionally interrelated operational taxonomic units (OTUs) than the CF network. The topological roles of individual OTUs and key microbial populations were distinctly different, although the generalists mainly belonging to Actinobacteria and Proteobacteria were observed in both networks. The different fertilization treatments had distinct effects on the soil pH, which represented a key variable to impact the associated microbial community modularity. Most functional groups involving carbon-, nitrogen- and phosphorus-related metabolism and recycling and antibiotic biosynthesis were present at significantly high abundance in the organic-amended soils. All of the functions with statistical significance could be traced to corresponding responsible major modules in the CF network, but it was not the case in OA soil. These results suggested that the soil functions were decentralized and assigned to small groups in OA soil. Overall, we demonstrated that long-term organic amendment supports stronger functional potentials and more interactions within soil community relative to long-term chemical-only fertilization, which may be related to OA benefits to soil stability and buffering capacity. These results explore the correlations, inter-taxa and between major groups and functional traits, to gain a more integrated understanding of microbiome and ecological rules guiding soil community fostered by fertilization regimes. [ABSTRACT FROM AUTHOR]

Soil parent materials are potential arable land resources that have great value for utilization. Soil bacteria play vital roles in soil formation, and soil parent material provides the basic nutritional environment for the development of the microbial community. Due to the extremely limited available nutrients in most parent materials, fertilization management is important for providing necessary available nutrients and for enhancing the maturation process of the parent materials. After 30 years of artificial maturation driven by different fertilization treatments, the soil development of three different parental materials was evaluated, and the bacterial community compositions were investigated using a high-throughput nucleic acid sequencing approach. The results showed that fertilization management increased the soil fertility and microbial biomass and enhanced soil parent material maturation compared with cultivation alone. Supplying available nutrients via chemical fertilization was more effective than cultivation alone for soil nutrient accumulation, microbial biomass promotion, and copiotrophic bacterial enrichment during soil parent material development. The soil bacterial community structure was determined by both parent material and fertilization strategies. Compared to straw returning, chemical fertilization-driven parent material maturation decreased soil bacterial diversity and significantly changed the soil bacterial community structure. However, compared to chemical fertilization, straw returning had a less negative effect on soil bacterial diversity, but was not as efficient in resolving the nutrient limitation during soil parent material maturation. This study provided insight into the maturation of soil parent materials for agriculture production to support the ever constant need for food by an increasing human population. [ABSTRACT FROM AUTHOR]

We evaluated how fertilization impacted nematode trophic groups via changes in trophic resources (soil microbes, plant roots) and the soil environment in a 3-year fertilization experiment in a double-cropped paddy rice and upland wheat agroecosystem. Fertilization exerted a strong influence on bacterial- and fungal-feeding nematodes by changing soil microbes and the soil environment in both phases, whereas plant- and root-associated fungal-feeding nematodes were bottom-up controlled by plant roots in the upland wheat phase only. Also, fertilization-induced linkages between bacteria phyla and bacterial-feeding nematode genera were inconsistent across crop phases. Although fertilization results in bottom-up control of nematode feeding groups in well-drained soils, our findings suggest environmental filtering due to water management and crop species can be responsible for the abundance of dominant nematode genera. [ABSTRACT FROM AUTHOR]

The composition of microbial communities and the level of enzymatic activity in the soil are both important indicators of soil quality, but the mechanisms by which a soil bacterial community is generated and maintained are not yet fully understood. Two soil samples were collected from the same location, but each had been subjected to a different long-term fertilization treatment and was characterized by different microbial diversity, biomass and physicochemical properties. These samples were γ-sterilized and swap inoculated. Non-sterilized soil samples along with sterilized and inoculated soil samples were incubated for eight months before their nutrient content, microbial biomass, enzymatic activity and bacterial composition were analyzed. Total phosphorus, and potassium concentrations along with the overall organic matter content of the non-sterilized soil were all equal to those of the same soil that had been sterilized and self/swap inoculated. Additionally, the microbial biomass carbon concentration was not affected by the specific inoculum and varied only by soil type. The activities of catalase, invertase, urease, protease, acid phosphatase and phytase were smaller in the sterilized soils that had been inoculated with organisms from chemical fertilizer amended soil (NPK) when compared to sterilized soil inoculated with organisms from manure and chemical fertilizer amended soil (NPKM) and non-sterilized soil samples. Bacterial 16S rRNA examined by 454-pyrosequencing revealed that the composition of bacterial community reconstructed by immigrant microbial inoculum in the soil was mainly influenced by its physicochemical properties, although the microbial inoculum contained different abundances of bacterial taxa. For example, the pH of the soil was the dominant factor in reconstructing a new bacterial community. Taken together, these results demonstrated that both soil microbial composition and functionality were primarily determined by soil properties rather than the microbial inoculum, which contributed to our understanding of how soil microbial communities are generated and maintained. [ABSTRACT FROM AUTHOR]

Soil microbes live in close association with plants and are crucial for plant health and fitness. Recent literature revealed that specific microbes were cultured at distinct developmental stages of Arabidopsis . It is not clear how fast the roots, depending on their developmental stage, can alter the root-associated microbiome. In this study, Arabidopsis , grown under sterile conditions at precisely distinct developmental stages were supplied with a soil microbial slurry. Within four days, roots selected specific microorganisms depending on plant development, and Proteobacteria among other bacterial groups were found to colonize the roots irrespective of developmental stage. Moreover, exposure to a microbiome resulted in modulation of phytohormone levels at different stages of Arabidopsis . [ABSTRACT FROM AUTHOR]

Abstract: Most previous studies on soil microbial communities have been focused on species abundance and diversity, but not the interactions among species. In present study, the Molecular Ecological Network Analysis tool was used to study the interactions and network organizations of fungal communities in yield-invigorating (healthy) and -debilitating (diseased) soils induced by prolonged potato monoculture, based on the relative abundances of internal transcribed spacer sequences derived using pyrosequencing. An emphasis was placed on the differences between the healthy and diseased networks. The constructed healthy and diseased networks both showed scale-free, small world and modular properties. The key topological properties and phylogenetic composition of the two networks were similar. However, major differences included: a) the healthy network had more number of functionally interrelated operational taxonomic units (OTUs) than the diseased one; b) healthy network contained 6 (4%) generalist OTUs whereas the diseased contained only 1 (0.6%) marginal generalist OTU; and c) majority (55%) of OTUs in healthy soils were stimulated by a certain set of soil variables but the majorities (63%) in diseased soils were inhibited. Based on these data, a conceptual picture was synthesized: a healthy community was a better organized or a better operated community than the diseased one; a healthy soil was a soil with variables that encouraged majority of fungi whereas a diseased soil discouraged. By comparing the topological roles of different sets of shared OTUs between healthy and diseased networks, it was found that role-shifts prevailed among the network members such as generalists/specialists, significant module memberships and the OTU sets irresponsive to soil variables in one network but responsive in the counterpart network. Soil organic matter was the key variable associated with healthy community, whereas ammonium nitrogen (NH4 +–N) and Electrical conductivity (EC) were the key variables associated with diseased community. Major affected phylogenetic groups were Sordariales and Hypocreales. [Copyright &y& Elsevier]

Abstract: Watermelon is susceptible to Fusarium wilt in successively mono-cropped soil. Pot experiments were carried out to investigate the effect of intercropping with aerobic rice on Fusarium wilt in watermelon. The tested soil was classified as a loam soil, previously planted with watermelon and collected from Hexian county, Anhui province, China. The results obtained are listed as follows: (1) 66.7% of watermelon plants were infected with wilt disease and 44.4% died on 40 days after transplanting in mono-cropped soil, but plants were much less susceptible to infection when intercropped with rice; (2) the density of Fusarium oxysporum f. sp. niveum decreased by 91% in soil from the intercropped watermelon rhizosphere when compared with that from the mono-crop 40 days after transplanting; (3) densities of bacteria and actinomycetes increased, but fungal density decreased in rhizosphere soil from the intercrops in comparison with the mono-crop control; (4) compared to the control, the germinated Fusarium spores were decreased by 41.0% in the treatment with addition of 1.5ml rice root exudates. Adding 20ml of root exudates decreased Fusarium spore production by 76.4%; and (5) the activities of defense enzymes in the leaves and roots of watermelons in the intercropped system were significantly lower than those in the mono-cropped system. It is suggested that intercropping with aerobic rice alleviated Fusarium wilt in watermelon, by restraining the spore production of Fusarium and by changing the microbial communities in rhizosphere soil through the production of rice root exudates. [Copyright &y& Elsevier]

The rhizosphere microbiome plays a key role in plant nutrient provision. However, the impacts of the vertically transmitted seed microbiome on the assembly of the rhizosphere microbiome and consequently on the functional traits remain unclear. Here, to assess the role of seed-borne beneficial microbes on the assembly of rhizosphere microbiome, we conducted a guest-soil cultivation study using two maize cultivars and their corresponding native soils with different available nutrient contents. The assembly of the rhizosphere bacterial and fungal communities was assessed by amplicon DNA sequencing. Our results demonstrated that the soil microbiome dominates the assembly of the rhizosphere microbiome. A seed-borne beneficial bacterium, Burkholderia gladioli , was able to colonize the rhizosphere in great relative abundance, which significantly altered the assembly of the rhizosphere microbiome. Genome analysis demonstrated that this seed-borne beneficial bacterial species may contain extracellular phosphatase-encoding genes, and gene quantification confirmed their existence, suggesting the possible compensation of phosphate solubilizing function. This functional compensation, which is probably a response to the low concentration of soil available phosphorus, may consequently promote phosphorus acquisition of the host plant. Overall, this study provides new insights into our understanding of the assembly of the rhizosphere microbiome, suggesting that the seed microbiome serves as a functional compensation reservoir to enhance the fitness of progeny plants and highlighting the necessity to consider the seed microbiome during plant breeding. ●Plant seeds possess beneficial microbial storage as a functional compensation reservoir. ●Seed-borne bacteria contribute to the composition of the rhizosphere microbiome. ●A seed-borne P solubilizing bacterium improves rhizospheric function in low P soil. [ABSTRACT FROM AUTHOR]

Plant litter decomposition in the soil is governed by microorganisms such as bacteria and fungi that colonize lignocellulose residues during the decomposition process, and thus, the interplay of bacterial and fungal communities can yield insight into the lignocellulose decomposition dynamics. Previous studies have mainly investigated litter decomposing communities in microcosms or ex-situ conditions or at a single soil ecosystem. Here we conducted a 12 week-long litter decomposition experiment to explore how the temporal dynamics of soil enzyme activities and microbial communities are linked to litter decomposition under three different land use sites (forestland, farmland, and abandoned farmland) in Nanjing, China. We found that litter decomposition in the forestland was the highest among the three land use sites. Then, using a multifactorial approach, we showed that this higher decomposition rate in forest soils is determined by microbial communities with higher ligninolytic enzyme activities, higher diversity, and a less complex but more specialized network. Chryseobacterium in bacteria, and Fusarium , Aspergillus and Penicillium in fungi were the keystone taxa in networks across three land use types. We conducted subsequent culturing that further confirmed the strong decomposition ability and enzyme activities of these taxa, indicating their importance for microbial litter decomposition. As such, this is one of the first studies to validate the role of keystone taxa for litter decomposition, and it demonstrates that co-occurrence network scores can be used for statistical identification of putative keystone taxa for further screening and linking to microbiome functioning. Overall, we show that land use alters the composition and network structure of soil microbiota that determine the litter decomposition. Our study also reveals that specialized keystone taxa are involved in the decomposition dynamics, and highlights an opportunity of harnessing such taxa for manipulating lignocellulose decomposition in soil ecosystems. • Forestland had the highest litter decomposition and lignocellulolytic enzyme activities. • Forestland had greater microbial diversity and a specialized microbial network. • Culturing supported the role of keystone taxa in litter decomposition. [ABSTRACT FROM AUTHOR]

PhoD -harboring microorganisms are crucial for the regulation of soil phosphorus (P) cycling through the secretion of alkaline phosphomonoesterases and are also known to be sensitive to fertilizer inputs. However, the impacts of long-term mineral and organic fertilizer inputs on active phoD -harboring functional communities in soils remain largely unknown. In the present study, 18O-DNA-stable isotope probing coupled with high-throughput sequencing was utilized in order to characterize active phoD -harboring functional bacterial communities in soils subjected to long-term no-fertilizer (Control), mineral-only fertilizer (NPK), organic-only fertilizer (M), and the combination of mineral and organic fertilizer (NPKM) amendments. Total and active phoD gene abundance decreased in soils amended with long-term mineral fertilizer, but increased in soils under organic fertilizer amendment, compared with the non-fertilized soils. A total of 51 active phoD -harboring bacterial OTUs, mainly belonging to Actinobacteria, were identified in this study. Organically amended soils harbored a higher diversity of active bacterial community. In the active phoD -harboring functional community, Rhodococcus comprised approximately 99% of the total relative abundance in the unfertilized soil, whereas Nocardiopsis and Bacillus accounted for approximately 62% and 24%, respectively, in mineral-only fertilized soils. Active phoD -harboring communities were dominated by members of the genera Streptomyces (26–60%), Nocardia (5–9%) and Gordonia (23–41%) in all organically fertilized soils, including M and NPKM. Overall, these long-term fertilization regimes altered the abundance, richness and composition of the active phoD -harboring functional microbial community. This study provides novel insights into the responses of the active functional bacterial community that is responsible for soil P mineralization to differing long-term fertilization regimes. • The active phoD -harboring bacteria was identified by 18O-DNA-SIP technique. • Organic amendment increased the abundance and diversity of active phoD bacteria. • Different fertilization regimes shaped distinctive active phoD bacterial community. • The active phoD bacterial OTUs in fertilized soils was dominated by Actinobacteria. • In unfertilized soil, ~99% active phoD -harboring OTUs belonged to the Rhodococcus. [ABSTRACT FROM AUTHOR]

Plant rhizosphere microbes play a key role in plant-soil feedbacks. However, the intrinsic principles governing the assembly of the rhizosphere microbial community remain unclear. To understand these principles, we studied the taxonomical and functional characteristics of the reassembled maize rhizosphere bacterial communities after transplanting between soils. The composition of the rhizosphere bacterial community was measured by high-throughput amplicon-based Illumina MiSeq sequencing of the V4 region of the 16S ribosomal RNA (rRNA) gene. The rhizosphere functional profile was assessed using 16S rRNA data in the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved State) software. We found that the reassembled rhizosphere bacterial community was recruited from both soil and endosphere communities. The assembly and functional traits of the rhizosphere bacterial community were associated with the concentrations of soil available nutrients. The most important rhizospheric functions were to improve host stress tolerance, followed by nutrient cycling functions. The rhizosphere bacterial taxa that improved host stress tolerance were in low abundance and were primarily derived from the surrounding bulk soil. Moreover, the rhizosphere nutrient cycling functions were marginalized in nutrient-excessive soils. Plants may sacrifice stress tolerance functions and enhance compensatory colonization of nutrient cycling-related endophytes in the rhizosphere in nutrient-deficient soils. Our results demonstrate that the levels of soil available nutrients mediate the assembly of rhizosphere bacterial communities to satisfy plant-required functions. This assembly principle is useful for manipulating the bacterial communities of plant roots to improve agricultural sustainability. • The rhizosphere bacterial community is recruited from both soil and endosphere communities. • The rhizosphere bacterial communities are compositionally divergent among soils. • The rhizosphere bacterial communities are functionally less divergent among soils. • Soil available nutrient concentrations drive the assembly of rhizosphere microbiome. [ABSTRACT FROM AUTHOR]