Elucidating the temporal dynamics of arbuscular mycorrhizal (AM) fungi is critical for understanding their functions. Furthermore, research investigating the temporal dynamics of AM fungi in response to agricultural practices remain in its infancy. We investigated the effect of nitrogen fertilization and watering reduction on the temporal dynamics of AM fungi, across the lifespan of wheat. Nitrogen fertilization decreased AM fungal spore density, extra-radical hyphal density, and intra-radical colonization rate in both watering conditions. Nitrogen fertilization affected AM fungal community composition in soil but not in roots, regardless of watering conditions. The temporal analysis revealed that AM fungal extra-radical hyphal density and intra-radical colonization rate were higher under conventional watering and lower under reduced watering in March than in other growth stages at low (≤ 70 kg N ha yr ) but not at high (≥ 140) nitrogen fertilization levels. AM fungal spore density was lower in June than in other growth stages and community composition varied with plant development at all nitrogen fertilization levels, regardless of watering conditions. This study demonstrates that high nitrogen fertilization levels disrupt the temporal dynamics of AM fungal hyphal growth but not sporulation and community composition.This article is protected by copyright. All rights reserved.

Background: During the last 15 years the internal transcribed spacer (ITS) of nuclear DNA has been used as a target for analyzing fungal diversity in environmental samples, and has recently been selected as the standard marker for fungal DNA barcoding. In this study we explored the potential amplification biases that various commonly utilized ITS primers might introduce during amplification of different parts of the ITS region in samples containing mixed templates ('environmental barcoding'). We performed in silico PCR analyses with commonly used primer combinations using various ITS datasets obtained from public databases as templates. Results: Some of the ITS primers, such as ITS1-F, were hampered with a high proportion of mismatches relative to the target sequences, and most of them appeared to introduce taxonomic biases during PCR. Some primers, e. g. ITS1-F, ITS1 and ITS5, were biased towards amplification of basidiomycetes, whereas others, e.g. ITS2, ITS3 and ITS4, were biased towards ascomycetes. The assumed basidiomycete-specific primer ITS4-B only amplified a minor proportion of basidiomycete ITS sequences, even under relaxed PCR conditions. Due to systematic length differences in the ITS2 region as well as the entire ITS, we found that ascomycetes will more easily amplify than basidiomycetes using these regions as targets. This bias can be avoided by using primers amplifying ITS1 only, but this would imply preferential amplification of 'non-dikarya' fungi. Conclusions: We conclude that ITS primers have to be selected carefully, especially when used for high-throughput sequencing of environmental samples. We suggest that different primer combinations or different parts of the ITS region should be analyzed in parallel, or that alternative ITS primers should be searched for.

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

The rhizosphere is of central importance not only for plant nutrition, health and quality but also for microorganism-driven carbon sequestration, ecosystem functioning and nutrient cycling in terrestrial ecosystems. A multitude of biotic and abiotic factors are assumed to influence the structural and functional diversity of microbial communities in the rhizosphere. In this review, recent studies on the influence of the two factors, plant species and soil type, on rhizosphere-associated microbial communities are discussed. Root exudates and the response of microorganisms to the latter as well as to root morphology were shown to shape rhizosphere microbial communities. All studies revealed that soil is the main reservoir for rhizosphere microorganisms. Many secrets of microbial life in the rhizosphere were recently uncovered due to the enormous progress in molecular and microscopic tools. Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented here. Furthermore, implications for agriculture, nature conservation and biotechnology will also be discussed.

The aim of this research was to isolate and characterize bacteria from spores of arbuscular mycorrhizal fungi (AMF). We designated these bacteria 'probable endobacteria' (PE). Three bacterial strains were isolated from approximately 500 spores of Gigaspora margarita (Becker and Hall) using a hypodermic needle (diameter, 200 μm). The bacteria were identified by morphological methods and on the basis of ribosomal gene sequences as Bacillus sp. (KTCIGM01), Bacillus thuringiensis (KTCIGM02), and Paenibacillus rhizospherae (KTCIGM03). We evaluated the effect of these probable endobacteria on antagonistic activity to the soil-borne plant pathogens (SBPPs) Fusarium oxysporum f. sp. lactucae MAFF 744088, Rosellinia necatrix, Rhizoctonia solani MAFF 237426, and Pythium ultimum NBRC 100123. We also tested whether these probable endobacteria affected phosphorus solubilization, ethylene production, nitrogenase activity (NA), and stimulation of AMF hyphal growth. In addition, fresh samples of spores and hyphae were photographed using an in situ scanning electron microscope (SEM) (Quanta 250FEG; FEI Co., Japan). Bacterial aggregates (BAs), structures similar to biofilms, could be detected on the surface of hyphae and spores. We demonstrate that using extraction with an ultrathin needle, it is possible to isolate AMF-associated bacterial species that are likely derived from inside the fungal spores.

Bacteria, as the key component of soil ecosystems, participate in nutrient cycling and organic matter decomposition. However, how fertilization regime affects the rhizospheric bacterial community of reddish paddy soil remains unclear. Here, a long-term fertilization experiment initiated in 1982 was employed to explore the impacts of different fertilization regimes on physicochemical properties and bacterial communities of reddish paddy rhizospheric soil in Central South China by sequencing the 16S rRNA gene. The results showed that long-term fertilization improved the soil nutrient status and shaped the distinct rhizospheric bacterial communities. Particularly, chemical NPK fertilizers application significantly declined the richness of the bacterial community by 7.32%, whereas the application of manure alone or combined with chemical NPK fertilizers significantly increased the biodiversity of the bacterial community by 1.45%, 1.87% compared with no fertilization, respectively. Moreover, LEfSe indicated that application of chemical NPK fertilizers significantly enhanced the abundances of Verrucomicrobia and Nitrospiraceae, while manure significantly increased the abundances of Deltaproteobacteria and Myxococcales, but the most abundant Actinobacteria and Planctomycetes were detected in the treatment that combined application of manure and chemical NPK fertilizers. Furthermore, canonical correspondence analysis (CCA) and the Mantel test clarified that exchangeable Mg2+ (E-Mg2+), soil organic carbon (SOC) and alkali-hydrolyzable nitrogen (AN) are the key driving factors for shaping bacterial communities in the rhizosphere. Our results suggested that long-term balanced using of manure and chemical fertilizers not only increased organic material pools and nutrient availability but also enhanced the biodiversity of the rhizospheric bacterial community and the abundance of Actinobacteria, which contribute to the sustainable development of agro-ecosystems.

Long-term elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long-term N input alone or in combination with phosphorus (P) and potassium (K) is poorly understood. We explored the effect of long-term N and NPK fertilization on soil bacterial diversity and community composition using meta-analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effect of N fertilization on bacterial diversity varied with soil texture and water management, but was independent of crop type or N application rate. Changes in bacterial diversity were positively related to both soil pH and organic C content under N fertilization alone, but only to soil organic C under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long-term N fertilization. Nitrogen fertilization increased the relative abundance of Proteobacteria and Actinobacteria, but reduced the abundance of Acidobacteria, consistent with the general life history strategy theory for bacteria. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long-term N and NPK fertilization that differentially affects bacterial diversity and community composition provides a reference for nutrient management strategies for maintaining belowground microbial diversity in agro-ecosystems worldwide.© 2018 John Wiley & Sons Ltd.

The visual deficiency symptoms developing on plants constitute the ultimate manifestation of suboptimal nutrient supply. In classical plant nutrition, these symptoms have been extensively used as a tool to characterise the nutritional status of plants and to optimise fertilisation. Here we expand this concept by bridging the typical deficiency symptoms for each of the six essential macronutrients to their molecular and physiological functionalities in higher plants. We focus on the most recent insights obtained during the last decade, which now allow us to better understand the links between symptom and function for each element. A deep understanding of the mechanisms underlying the visual deficiency symptoms enables us to thoroughly understand how plants react to nutrient limitations and how these disturbances may affect the productivity and biodiversity of terrestrial ecosystems. A proper interpretation of visual deficiency symptoms will support the potential for sustainable crop intensification through the development of new technologies that facilitate automatised management practices based on imaging technologies, remote sensing and in-field sensors, thereby providing the basis for timely application of nutrients via smart and more efficient fertilisation.© 2020 The Authors New Phytologist © 2020 New Phytologist Foundation.

It is well established that resource quantity and elemental stoichiometry play major roles in shaping below and aboveground plant biodiversity, but their importance for shaping microbial diversity in soil remains unclear. Here, we used statistical modeling on a regional database covering 179 locations and six ecosystem types across Scotland to evaluate the roles of total carbon (C), nitrogen (N) and phosphorus (P) availabilities and ratios, together with land use, climate and biotic and abiotic factors, in determining regional scale patterns of soil bacterial diversity. We found that bacterial diversity and composition were primarily driven by variation in soil resource stoichiometry (total C:N:P ratios), itself linked to different land uses, and secondarily driven by other important biodiversity drivers such as climate, soil spatial heterogeneity, soil pH, root influence (plant-soil microbe interactions) and microbial biomass (soil microbe-microbe interactions). In aggregate, these findings provide evidence that nutrient stoichiometry is a strong predictor of bacterial diversity and composition at a regional scale.© 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

The shifts in adaptive strategies revealed by ecological succession and the mechanisms that facilitate these shifts are fundamental to ecology. These adaptive strategies could be particularly important in communities of arbuscular mycorrhizal fungi (AMF) mutualistic with sorghum, where strong AMF succession replaces initially ruderal species with competitive ones and where the strongest plant response to drought is to manage these AMF. Although most studies of agriculturally important fungi focus on parasites, the mutualistic symbionts, AMF, constitute a research system of human-associated fungi whose relative simplicity and synchrony are conducive to experimental ecology. First, we hypothesize that, when irrigation is stopped to mimic drought, competitive AMF species should be replaced by AMF species tolerant to drought stress. We then, for the first time, correlate AMF abundance and host plant transcription to test two novel hypotheses about the mechanisms behind the shift from ruderal to competitive AMF. Surprisingly, despite imposing drought stress, we found no stress-tolerant AMF, probably due to our agricultural system having been irrigated for nearly six decades. Remarkably, we found strong and differential correlation between the successional shift from ruderal to competitive AMF and sorghum genes whose products (i) produce and release strigolactone signals, (ii) perceive mycorrhizal-lipochitinoligosaccharide (Myc-LCO) signals, (iii) provide plant lipid and sugar to AMF, and (iv) import minerals and water provided by AMF. These novel insights frame new hypotheses about AMF adaptive evolution and suggest a rationale for selecting AMF to reduce inputs and maximize yields in commercial agriculture.© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.

生态群落中不同物种间发生多样化的相互作用, 形成了复杂的种间互作网络。复杂生态网络的结构如何影响群落的生态系统功能及稳定性是群落生态学的核心问题之一。种间互作直接影响到物质和能量在生态系统不同组分之间的流动和循环以及群落构建过程, 使得网络结构与生态系统功能和群落稳定性密切相关。在群落及生态系统水平上开展种间互作网络研究将为群落的构建机制、生物多样性维持、生态系统稳定性、物种协同进化和性状分化等领域提供新的视野。当前生物多样性及生态系统功能受到全球变化的极大影响, 研究种间互作网络的拓扑结构、构建机制、稳定性和生态功能也可为生物多样性的保护和管理提供依据。该文从网络结构、构建机制、网络结构和稳定性关系、种间互作对生态系统功能的影响等4个方面综述当前种间网络研究进展, 并提出在今后的研究中利用机器学习和多层网络等来探究环境变化对种间互作网络结构和功能的影响, 并实现理论和实证研究的有效整合。

The application of bioorganic fertilizer affects rhizosphere microbes and further improves soil fertility in farmlands. However, the effects of different fertilizers on rhizosphere bacterial community diversity and structure of winter wheat remains unclear. In this study, we explored the effects of different fertilization treatments (no fertilizer added, CK; nitrogen fertilizer, NF; bioorganic fertilizer, BOF) on the rhizosphere bacterial community of winter wheat in the North China Plain. Rhizosphere soil treated with BOF had a higher Shannon index than that of CK and NF. The relative abundance of the Proteobacteria treated with BOF was significantly higher than that of NF, while the Acidobacteria and Planctomycetes were significantly lower. The redundancy analysis (RDA) and Mantel test showed that soil bacterial communities were significantly correlated with pH, nitrate, available phosphorus (AP), and available potassium (AK). Our findings indicated that BOF increased bacterial diversity and the relative abundance of copiotrophic bacteria in rhizosphere soil, while NF reduced bacterial diversity and increased the relative abundance of oligotrophic bacteria. The increase in copiotrophic bacteria in the rhizosphere of winter wheat could indicate an increase in soil nutrient availability, which might have positive implications for soil fertility and crop production.

In this study, the effect of mineral fertilizer and organic manure were evaluated on soil microbial biomass, dehydrogenase activity, bacterial and fungal community structure in a long-term (33 years) field experiment. Except for the mineral nitrogen fertilizer (N) treatment, long-term fertilization greatly increased soil microbial biomass carbon (SMBC) and dehydrogenase activity. Organic manure had a significantly greater impact on SMBC and dehydrogenase activity, compared with mineral fertilizers. Bacterial and fungal community structure was analyzed by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE). Long-term fertilization increased bacterial and fungal ribotype diversity. Total soil nitrogen (TN) and phosphorus (TP), soil organic carbon (SOC) and available phosphorus (AP) had a similar level of influence on bacterial ribotypes while TN, SOC and AP had a larger influence than alkali-hydrolyzable nitrogen (AHN) on fungal ribotypes. Our results suggested that long-term P-deficiency fertilization can significantly decrease soil microbial biomass, dehydrogenase activity and bacterial diversity. N-fertilizer and SOC have an important influence on bacterial and fungal communities.

The advancement of DNA/RNA, proteins, and metabolite analytical platforms, combined with increased computing technologies, has transformed the field of microbial community analysis. This transformation is evident by the exponential increase in the number of publications describing the composition and structure, and sometimes function, of the microbial communities inhabiting the human body. This rapid evolution of the field has been accompanied by confusion in the vocabulary used to describe different aspects of these communities and their environments. The misuse of terms such as microbiome, microbiota, metabolomic, and metagenome and metagenomics among others has contributed to misunderstanding of many study results by the scientific community and the general public alike. A few review articles have previously defined those terms, but mainly as sidebars, and no clear definitions or use cases have been published. In this editorial, we aim to propose clear definitions of each of these terms, which we would implore scientists in the field to adopt and perfect.

Fungi play important roles as decomposers, plant symbionts and pathogens in soils. The structure of fungal communities in the rhizosphere is the result of complex interactions among selection factors that may favour beneficial or detrimental relationships. Using culture-independent fungal community profiling, we have investigated the effects of nitrogen fertilizer dosage on fungal communities in soil and rhizosphere of field-grown sugarcane. The results show that the concentration of nitrogen fertilizer strongly modifies the composition but not the taxon richness of fungal communities in soil and rhizosphere. Increased nitrogen fertilizer dosage has a potential negative impact on carbon cycling in soil and promotes fungal genera with known pathogenic traits, uncovering a negative effect of intensive fertilization.

Boreal forests harbour diverse fungal communities with decisive roles in decomposition and plant nutrition. Although changes in boreal plant communities along gradients in soil acidity and nitrogen (N) availability are well described, less is known about how fungal taxonomic and functional groups respond to soil fertility factors. We analysed fungal communities in humus and litter from 25 Swedish old-growth forests, ranging from N-rich Picea abies stands to acidic and N-poor Pinus sylvestris stands. 454-pyrosequencing of ITS2 amplicons was used to analyse community composition, and biomass was estimated by ergosterol analysis. Fungal community composition was significantly related to soil fertility at the levels of species, genera/orders and functional groups. Ascomycetes dominated in less fertile forests, whereas basidiomycetes increased in abundance in more fertile forests, both in litter and humus. The relative abundance of mycorrhizal fungi in the humus layer remained high even in the most fertile soils. Tolerance to acidity and nitrogen deficiency seems to be of greater importance than plant carbon (C) allocation patterns in determining responses of fungal communities to soil fertility, in old-growth boreal forests. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8-year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant-soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top-down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop-associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.

Shifts in fungal community structure are suggested to be induced by excessive application of nitrogen (N) with implications in soil quality and consequently in production. It is imperative to know how N-rich soil influences the responses of soil microbial community to N fertilization. In this study we employed the Nutrient Expert (NE) fertilizer management approach and compared it with the traditional farmer's practice (FP) fertilizer management in the intensively cultivated fluvo-aquic soil of North-central China and black soil of Northeast China and explored the effect of NE and FP management on crop yield, fungal diversity and community composition. The results revealed that maize yield was successfully increased in the NE management as compared with FP. Both the NE and FP management result in increased fungal diversity in fluvo-aquic soil. In black soil, NE management maintained fungal diversity, whereas FP management decreased fungal diversity. Meanwhile, soil pH and NO3-N significantly linked with fungal diversity and community composition across the two soils. Our study demonstrates that the NE management is a sustainable agricultural approach with higher crop yield and at the same time maintaining soil microbial diversity.

Shifts in soil bacterial diversity and community composition are suggested to be induced by elevated input of nitrogen (N) fertilization with implications for soil quality, and consequently production. In this study, we evaluated the impacts of recommended fertilization (RF) and conventional fertilization (CF) on soil chemical properties, crop yield, bacterial diversity, and community composition from two long-term experiments conducted in fluvo-aquic soil and black soil of China. Each site comprised of four treatments, i.e., RF N−, RF N+, CF N−, CF N+. No N fertilization was indicated by N− and N fertilization was indicated by N+. Across both sites, N fertilization significantly increased crop yield compared with no N fertilization and RF successfully enhanced crop yield over CF. Interestingly, the RF maintained bacterial diversity, while CF depressed bacterial diversity in the two soils. Microbial taxa performing important ecological roles such as order Rhodospirillales and Bacillales were significantly enhanced in the RF approach, while Rhizobiales declined under CF. Furthermore, the results of partial least square path modeling revealed that soil available phosphorus (AP) negatively affected bacterial diversity while it positively affected bacterial community structure in fluvo-aquic soils. In contrast, soil pH was positively linked with both bacterial diversity and community structure in black soil. Overall, our study demonstrated that RF is an environmentally friendly approach which not only maintained above ground plant productivity, but also preserved belowground microbial populations and important soil variables regulating bacterial communities varied in different soil types.

Despite their importance, how plant communities and soil microorganisms interact to determine the capacity of ecosystems to provide multiple functions simultaneously (multifunctionality) under climate change is poorly known. We conducted a common garden experiment using grassland species to evaluate how plant functional structure and soil microbial (bacteria and protists) diversity and abundance regulate soil multifunctionality responses to joint changes in plant species richness (one, three and six species) and simulated climate change (3°C warming and 35% rainfall reduction). The effects of species richness and climate on soil multifunctionality were indirectly driven via changes in plant functional structure and their relationships with the abundance and diversity of soil bacteria and protists. More specifically, warming selected for the larger and most productive plant species, increasing the average size within communities and leading to reductions in functional plant diversity. These changes increased the total abundance of bacteria that, in turn, increased that of protists, ultimately promoting soil multifunctionality. Our work suggests that cascading effects between plant functional traits and the abundance of multitrophic soil organisms largely regulate the response of soil multifunctionality to simulated climate change, and ultimately provides novel experimental insights into the mechanisms underlying the effects of biodiversity and climate change on ecosystem functioning.© 2018 John Wiley & Sons Ltd.

The soil microbiome is highly diverse and comprises up to one quarter of Earth's diversity. Yet, how such a diverse and functionally complex microbiome influences ecosystem functioning remains unclear. Here we manipulated the soil microbiome in experimental grassland ecosystems and observed that microbiome diversity and microbial network complexity positively influenced multiple ecosystem functions related to nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed microbial networks and reduced microbial richness had the lowest multifunctionality due to fewer taxa present that support the same function (redundancy) and lower diversity of taxa that support different functions (reduced  functional uniqueness). Moreover, different microbial taxa explained different ecosystem functions pointing to the significance of functional diversity in microbial communities. These findings indicate the importance of microbial interactions within and among fungal and bacterial communities for enhancing ecosystem performance and demonstrate that the extinction of complex ecological associations belowground can impair ecosystem functioning.

Microbes play vital roles in soil quality; however, their response to N (nitrogen) and P (phosphorus) fertilization in acidic paddy soils of subtropical China remains poorly understood. Here, a 10-year field experiment was conducted to evaluate the effects of different fertilization treatments on microbial communities by Illumina MiSeq sequencing. The results showed that different fertilization treatments did not exert a significant effect on microbial alpha diversity, but altered soil properties, and thus affected microbial community composition. The microbial communities in the T1 (optimized N and P fertilizer) and T2 (excessive N fertilizer) treated soils differed from those in the T0 (no N and P fertilizer) and T3 (excessive P fertilizer) treated soils. In addition, the bacterial phyla Proteobacteria, Chloroflexi, and Acidobacteria, and the fungal phyla Ascomycota and Basidiomycota dominated all the fertilized treatments. Soil total potassium (TK) concentration was the most important factor driving the variation in bacterial community structure under different fertilization regimes, while the major factors shaping fungal community structure were soil TN and NO3–-N (nitrate N). These findings indicate that optimization of N and P application rates might result in variations in soil properties, which changed the microbial community structure in the present study.

Soil carbon (C) and nitrogen (N) stoichiometry is a main driver of ecosystem functioning. Global N enrichment has greatly changed soil C : N ratios, but how altered resource stoichiometry influences the complexity of direct and indirect interactions among plants, soils, and microbial communities has rarely been explored. Here, we investigated the responses of the plant-soil-microbe system to multi-level N additions and the role of dissolved organic carbon (DOC) and inorganic N stoichiometry in regulating microbial biomass in semiarid grassland in northern China. We documented a significant positive correlation between DOC and inorganic N across the N addition gradient, which contradicts the negative nonlinear correlation between nitrate accrual and DOC availability commonly observed in natural ecosystems. Using hierarchical structural equation modeling, we found that soil acidification resulting from N addition, rather than changes in the plant community, was most closely related to shifts in soil microbial community composition and decline of microbial respiration. These findings indicate a down-regulating effect of high N availability on plant-microbe interactions. That is, with the limiting factor for microbial biomass shifting from resource stoichiometry to soil acidity, N enrichment weakens the bottom-up control of soil microorganisms by plant-derived C sources. These results highlight the importance of integratively studying the plant-soil-microbe system in improving our understanding of ecosystem functioning under conditions of global N enrichment.© 2013 John Wiley & Sons Ltd.

Fertilization typically reduces ectomycorrhizal diversity shortly after its application but less is known about its longer-term influence on fungal species. Long-term effects are important in forests where fertilizer is rarely applied. We compared fungal species composition in western hemlock control plots with plots last fertilized 7 years ago with nitrogen (N) or nitrogen plus phosphorus (N + P). The N + P fertilization had a significant lingering effect, increasing the tree size and foliar P content of the western hemlocks. From ectomycorrhizal roots of 24-year-old trees from northern Vancouver Island, Canada, we identified fungi from 12 samples per treatment, by amplifying, cloning, and sequencing fungal ribosomal DNA fragments, placing sequences with 97% or more identity in the same operational taxonomic unit (OTU). Diversity was high across treatments; we detected 77 fungal OTUs, 52 from ectomycorrhizal genera, among 922 clone sequences. The five most frequent OTUs were similar in abundance across treatments. Only 19 OTUs matched any of the 197 previously reported ectomycorrhizal species of western hemlock. Species composition but not diversity in nitrogen plus phosphorus plots differed significantly from control or nitrogen plots. Two Cortinarius OTUs were indicator species for nitrogen plus phosphorus plots and presence of Cortinarius cinnamomeus was correlated with control or nitrogen plots. After 7 years, fertilization history had made no detectable difference in ectomycorrhizal fungal diversity, but long-lasting changes in environment resulting from fertilization had a lingering effect on fungal ectomycorrhizal species composition.

Soil fungi fill pivotal ecological roles in biogeochemical processes, particularly dominating decomposition of lignin. Little is known, however, about the responses of different fungal groups to climate warming with respect to bacteria. In this study, using barcode pyrosequencing, we showed that short-term (15 months) of field exposure of an alpine meadow to warming (elevated 1 and 2 °C) did not markedly alter the overall soil fungal community structures and α-diversity on Tibetan Plateau, but the average β-diversity dramatically decreased in response to warming. However, soil respiration rates were stimulated in the growing season, which significantly (P < 0.001) correlated with soil temperature. Particularly, warming triggered dramatic shifts in the community structure of dominate Ascomycota and rare taxa (relative abundance < 0.1 %). In addition, the abundances of specific Basidiomycota-affiliated members significantly increased, while Ascomycota showed a range of responses to warming. Collectively, we conclude that the fungal communities are resistant to short-term warming, though variations are observed in certain species and rare taxa. This report indicates that changes in a relatively small subset of the soil fungal community are sufficient to produce substantial changes in function, such as CO(2) efflux rates.

Soil bacteria are key components of the soil microbial community contributing to soil health. Nitrogen (N) fertilization is an important factor that affects soil microbial community and cereal production. This study aims to explore the impact of long-term N fertilization on soil bacterial diversity, nitrogen use efficiency (NUE), and the grain yield of wheat in the semiarid region of Loess Plateau, China. The field experiment was conducted from 2003 to 2018 including five N treatments: 0 (N0), 52.5 (N52.5), 105 (N105), 157.5 (N157.5), and 210 (N210) kg N ha−1 yr−1. The soil pH was decreased by the N fertilization, while the soil ammonium, nitrate, and available phosphorus were increased. The N uptake and grain yield of wheat were significantly increased with N and the highest NUE (28%) and grain yield (44% higher than control) were observed at 105 kg N ha−1, but no significant increase in yield was observed by further increasing N rate. The bacterial diversity was significantly increased at N105. Soil bacteria community was strongly related to soil chemical properties and ammonium content was the most important contributor. The dominant soil bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Bacteroidetes, Nitrospirae, Verrucomicrobia, and Planctomycetes. The higher grain yield of wheat was related to the higher class Gammaproteobacteria and Sphingobacteriia abundance, and lower class Acidobacteria and Chloroflexia abundance. In summary, 105 kg ha−1 yr−1 was the optimum rate of N for diversified soil bacterial community and wheat yield for sustainable wheat production in semiarid Loess Plateau of China, whose higher N use efficiency was attributed to the higher phyla Verrucomicrobia and Planctomycetes, and lower Proteobacteria abundance.

Strigolactones (SLs) are essential host recognition signals for both root parasitic plants and arbuscular mycorrhizal fungi, and SLs or their metabolites function as a novel class of plant hormones regulating shoot and root architecture. Our previous study indicated that nitrogen (N) deficiency as well as phosphorus (P) deficiency in sorghum enhanced root content and exudation of 5-deoxystrigol, one of the major SLs produced by sorghum. In the present study, we examined how N and P fertilization affects SL production and exudation in sorghum plants subjected to short- (5 days) or long-term (10 days) N or P deficiency and demonstrated their common and distinct features. The root contents and exudation of SLs in the N- or P-deficient sorghum plants grown for 6, 12 or 24 h with or without N or P fertilization were quantified by LC-MS/MS. In general, without fertilization, root contents and exudation of SLs stayed at similar levels at 6 and 12 h and then significantly increased at 24 h. The production of SLs responded more quickly to P fertilization than the secretion of SLs, while regulation of SL secretion began earlier after N fertilization. It is suggested that sorghum plants regulate SL production and exudation when they are subjected to nutrient deficiencies depending on the type of nutrient and degree of deficiency.

Microbiomes are important for crop performance. However, a deeper knowledge of crop-associated microbial communities is needed to harness beneficial host-microbe interactions. Here, by assessing the assembly and functions of maize microbiomes across soil types, climate zones, and genotypes, we found that the stem xylem selectively recruits highly conserved microbes dominated by Gammaproteobacteria. We showed that the proportion of bacterial taxa carrying the nitrogenase gene (nifH) was larger in stem xylem than in other organs such as root and leaf endosphere. Of the 25 core bacterial taxa identified in xylem sap, several isolated strains were confirmed to be active nitrogen-fixers or to assist with biological nitrogen fixation. On this basis, we established synthetic communities (SynComs) consisting of two core diazotrophs and two helpers. GFP-tagged strains and N isotopic dilution method demonstrated that these SynComs do thrive and contribute, through biological nitrogen fixation, 11.8% of the total N accumulated in maize stems. These core taxa in xylem sap represent an untapped resource that can be exploited to increase crop productivity.© 2022. The Author(s).

A novel polymer-coated nitrogen (N) fertilizer was developed using bio-based polyurethane (PU) derived from liquefied locust sawdust as the coating material. The bio-based PU was successfully coated on the surface of the urea fertilizer prills to form polymer-coated urea (PCU) fertilizer for controlled N release. Epoxy resin (EP) was also used to further modify the bio-based PU to synthesize the interpenetrating network (IPN), enhancing the slow-release properties of the PCU. The N release characteristics of the EP-modified PCU (EMPCU) in water were determine at 25 °C and compared to that of PCU and EP-coated urea (ECU). The results showed that the EP modification reduced the N release rate and increased the longevity of the fertilizer coated with bio-based PU. A corn growth study was conducted to further evaluate the filed application of the EMPCU. In comparison to commercial PCU and conventional urea fertilizer, EMPCU was more effective and increased the yield and total dry matter accumulation of the corn. Findings from this work indicated that bio-based PU derived from sawdust can be used as coating materials for PCU, particularly after EP modification. The resulting EMPCU was more environmentally friendly and cost-effective than conventional urea fertilizers coated by EP.