Soil fertility matters! A new conceptual model for carbon stewardship in neotropical croplands taking climate-smart agricultural practices into account

Mismanagement of agroecosystems in Neotropical regions threatens global security, accelerating the transgression of planetary boundaries. Therefore, understanding carbon (C) stewardship and how climate-smart agriculture (CSA) practices change nutrient availability plays a central role. Here, we analyzed nutrient availability, nitrogen (N) inputs, climate, and soil texture influence C flow into particulate (POC) and mineral-associated organic carbon (MAOC) pools to support sustainable C management in neotropical agroecosystems. To test our hypothesis data were collected from three field experimental agroecosystem sites and a literature overview. Our machine learning models estimated that nutrient availability, notably zinc (Zn), and soil texture, regulate C flow into POC and MAOC pools in agroecosystems. The climate variables exhibited minimal effects. There was no MAOC C saturation in neotropical agroecosystems, with an upper boundary of 36 g C kg-1. This demonstrates the potential of nature-based solutions for C storage in tropical soils. Synthetic N fertilization was not a key driver of C flow into POC and MAOC pools in these agroecosystems; however, organic N inputs, such as those from legumes, showed significant potential in increasing soil C and reducing carbon-to‑nitrogen ratio. Our main finding reveals soil fertility as a key regulator of C flow into POC and MAOC pools in Neotropical agroecosystems. Additionally, nature-based solutions from CSA are viable for atmospheric carbon removal strategies in Neotropical areas. Thus, by integrating experimental and simulated insights, we propose a new conceptual model linking nutrient availability to C stewardship in neotropical agroecosystems, outlining existing knowledge gaps and suggesting directions for future research toward climate-smart agriculture.

Continuous Rice Cultivation Increases Celery Yield by Enhancing Plant Beneficial Bacteria in Rice-Celery Rotations

The sustainable management of crops is a fundamental challenge as the human population and demand for food increase. Crop rotation, a practice that has been used for centuries, offers a sustainable solution with minimal environmental impact. However, our understanding of how microbial diversity changes during rotation and how microbially mediated functions enhance plant production remains limited. In our study, we combined field surveys of rice-celery rotations with greenhouse experiments. We found that crop rotation increased yield by increasing the presence of plant-beneficial bacteria, including a novel strain named Acinetobacter bohemicus HfQ1. Bacteria that promote plant growth are enriched under crop rotation, leading to increased ammonia oxidation, siderophore production and indole-3-acetic acid synthesis. These beneficial ecological consequences of crop rotation were consistent across various crops during our metadata analysis. Our study provides new insights into the development of innovative crop rotation models and effective strategies to safeguard food production and advance sustainable agriculture. Additionally, the Acinetobacter strain may serve as a potential microbial agent to replace chemical fertilisers, further supporting sustainable agricultural practices.

Impact of organic liquid fertilizer on plant growth of Chinese cabbage and soil bacterial communities

Organic liquid fertilizers from livestock manure are increasingly recognized as sustainable amendments influencing soil bacterial communities. Yet, their direct impacts on bacterial composition and crop functionality remain unclear. Addressing this gap, we developed a bio-liquid fertilizer (LBF) by culturing Chlorella fusca in a purified pig manure-based medium. We compared its effects with chemical (CLF) and fermented (FLM) liquid fertilizers on Chinese cabbage (Brassica rapa subsp. pekinensis). We aimed to determine how organic bio-liquid fertilizers enhance crop health and soil bacterial balance, contributing to sustainable agricultural practices. Although LBF did not surpass CLF in promoting growth, it significantly increased antioxidant compounds (polyphenols, flavonoids), sugars, and antioxidant activities, including nitrite-scavenging capacity and reducing power. Soil bacterial communities were strongly correlated with key chemical properties (Na, K, NO3--N, Ca, pH). Notably, Litorilinea decreased under CLF, and Sphingomonas and Nocardioides declined under FLM, whereas LBF treatment increased all three genera, suggesting improved bacterial conditions. These findings demonstrate that a well-designed organic bio-liquid fertilizer can bridge knowledge gaps by enhancing plant functionality and promoting beneficial soil bacteria. This approach supports more efficient nutrient recycling and may foster greater resilience and sustainability in modern farming systems.

Sustainable Management of Major Fungal Phytopathogens in Sorghum (Sorghum bicolor L.) for Food Security: A Comprehensive Review

Sorghum (Sorghum bicolor L.) is a globally important energy and food crop that is becoming increasingly integral to food security and the environment. However, its production is significantly hampered by various fungal phytopathogens that affect its yield and quality. This review aimed to provide a comprehensive overview of the major fungal phytopathogens affecting sorghum, their impact, current management strategies, and potential future directions. The major diseases covered include anthracnose, grain mold complex, charcoal rot, downy mildew, and rust, with an emphasis on their pathogenesis, symptomatology, and overall economic, social, and environmental impacts. From the initial use of fungicides to the shift to biocontrol, crop rotation, intercropping, and modern tactics of breeding resistant cultivars against mentioned diseases are discussed. In addition, this review explores the future of disease management, with a particular focus on the role of technology, including digital agriculture, predictive modeling, remote sensing, and IoT devices, in early warning, detection, and disease management. It also provide key policy recommendations to support farmers and advance research on disease management, thus emphasizing the need for increased investment in research, strengthening extension services, facilitating access to necessary inputs, and implementing effective regulatory policies. The review concluded that although fungal phytopathogens pose significant challenges, a combined effort of technology, research, innovative disease management, and effective policies can significantly mitigate these issues, enhance the resilience of sorghum production to facilitate global food security issues.

Cover Cropping Attenuates Population Growth of Macrophomina phaseolina by Limiting Weed Biomass, Despite Asymptomatic Colonization of Cover Crops

Macrophomina phaseolina is a fungus that causes charcoal rot in strawberry and a wide variety of crop species. Little is known about its potential to asymptomatically colonize crop plants or grow saprophytically on their tissues, both of which would create a potential for alternate, asymptomatic hosts to lead to increases in inoculum. To test the impact of cover cropping on M. phaseolina abundance, we conducted randomized-block field experiments in soils infested by M. phaseolina. None of the 15 cover crop varieties showed symptoms of charcoal rot. All Fabaceae and Brassicaceae varieties were asymptomatically colonized at varying rates, but among Poaceae M. phaseolina was recovered from only one individual oat plant. Soil samples collected at the time of planting, tillage, and 8 weeks after tillage showed that cover cropping attenuated the growth of M. phaseolina relative to fallow plots harboring the weedy legume Medicago polymorpha. This weed species was abundantly colonized by this pathogen in both living root samples and plant residue collected 8 weeks after tillage. Cover cropping also influenced the diversity and composition of bulk soil bacterial and fungal communities, but these effects were not associated with M. phaseolina population density. Although M. phaseolina was not detected in living wheat tissues, it was recovered from wheat residue, suggesting that it may be facultatively saprophytic. These results suggest that cover cropping does not pose a risk for increasing disease caused by M. phaseolina and could be beneficial as conducive weed species, such as M. polymorpha, are suppressed.[Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Navigating Climate Change: Exploring the Dynamics Between Plant-Soil Microbiomes and Their Impact on Plant Growth and Productivity

Understanding the intricate interplay between plant and soil microbiomes and their effects on plant growth and productivity is vital in a rapidly changing climate. This review explores the interconnected impacts of climate change on plant-soil microbiomes and their profound effects on agricultural productivity. The ongoing rise in global temperatures, shifting precipitation patterns and extreme weather events significantly affect the composition and function of microbial communities in the rhizosphere. Changes in microbial diversity and activity due to rising temperatures impact nutrient cycling, microbial enzyme synthesis, soil health and pest and disease management. These changes also influence the dynamics of soil microbe communities and their capability to promote plant health. As the climate changes, plants' adaptive capacity and microbial partners become increasingly crucial for sustaining agriculture. Mitigating the adverse effects of climate change on plant growth and agricultural productivity requires a comprehensive understanding of the interconnected mechanisms driving these processes. It highlights various strategies for mitigating and adapting to environmental challenges, including soil management, stress-tolerant crops, cover cropping, sustainable land and water management, crop rotation, organic amendments and the development of climate-resilient crop varieties. It emphasises the need for further exploration of plant-soil microbiomes within the broader context of climate change. Promising mitigation strategies, including precision agriculture and targeted microbiome modifications, offer valuable pathways for future research and practical implementation of global food security and climate change.

Soybean nodulation shapes the rhizosphere microbiome to increase rapeseed yield

INTRODUCTION

Crop rotation, a crucial agricultural practice that enhances soil health and crop productivity, is widely used in agriculture worldwide. Soybeans play a crucial role in crop rotation owing to their nitrogen-fixing ability, which is facilitated by symbiotic bacteria in their root systems. The soybean-rapeseed rotation is an effective agricultural practice in the Yangtze River Basin of China. However, the mechanism underlying the effectiveness of this system remains unknown.

OBJECTIVES

The aim of this study was to decipher the mechanisms by which previous soybean cultivation enhances the growth of subsequent rapeseed.

METHODS

Soybeans with three distinct nodulation genotypes were rotated with rapeseed, and the impact of previous soybean cultivation on subsequent rapeseed growth was evaluated by examining the soybean root secretome and soil rhizosphere microbiome.

RESULTS

Soybean-rapeseed rotation significantly enhanced subsequent rapeseed growth and yield, especially when supernodulating soybean plants were used, which released the most nitrogen into the soil rhizosphere. The differences in soybean nodulation capability led to variations in root exudation, which in turn influenced the bacterial communities in the rhizosphere. Notably, the supernodulating soybean plants promoted Sphingomonadaceae family of bacteria growth by secreting oleic acid and cis-4-hydroxy-D-proline, and further attracted them through cis-4-hydroxy-D-proline. Furthermore, the exogenous application of Sphingomonadaceae bacteria, either alone or in combination with rhizobia, significantly enhanced the growth of rapeseed.

CONCLUSION

Our data definitively demonstrated the crucial role of previous soybean cultivation in enhancing the yield of rapeseed, with the assistance of Sphingomonadaceae bacteria and rhizobia. This study elucidates the role of soybean nodulation in rhizosphere bacterial dynamics, highlighting its importance in sustainable agricultural practices.

Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms

Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.

Harmonizing soil restoration and microbial diversity: Insights from a Two-Year field experiment with Sedum-Rice rotation systems

Phytoremediation coupled with agroproduction (PCA) model contributes to sustainable agriculture and environmental management. This study investigated the impact of continuous cropping early/late season rice (RR) and Sedum alfredii-rice rotation (SR) on soil physical and chemical properties, as well as their relationships with soil microbial community. In 2022, SR treatment significantly increased pH value and organic matter content by 7 % and 17 %, respectively, compared to the levels in 2020, while RR treatment showed no change. RR treatment resulted in a significant decrease in soil concentrations of Ca, Mg, and K by 18.42 %, 29.01 %, and 7.77 %, respectively. Furthermore, SR treatment saw reductions of 29.62 % in total Cd and 38.30 % in DTPA extractable Cd in the soil. Over the two years, both treatments notably influenced the diversity, structure, and network of the rhizosphere bacterial and fungal communities, which are crucial for nutrient cycling and plant health. Notably, SR treatment exhibited a more complex network compared to RR, suggesting a greater impact on the interconnected systems. Therefore, these findings highlight the potential of Sedum rotation system to rehabilitate contaminated soils while supporting agricultural practices, which is essential for food security and environmental sustainability. This research direction holds promise for future exploration and application in the fields of phytoremediation and agroecology.

Microbial Basis for Suppression of Soil-Borne Disease in Crop Rotation

The effect of crop rotation on soil-borne diseases is a representative case of plant-soil feedback in the sense that plant disease resistance is influenced by soils with different cultivation histories. This study examined the microbial mechanisms inducing the differences in the clubroot (caused by Plasmodiophora brassicae pathogen) damage of Chinese cabbage (Brassica rapa subsp. pekinensis) after the cultivation of different preceding crops. It addresses two key questions in crop rotation: changes in the soil bacterial community induced by the cultivation of different plants and the microbial mechanisms responsible for the disease-suppressive capacity of Chinese cabbage. Twenty preceding crops from different plant families showed significant differences in the disease damage, pathogen density, and bacterial community composition of the host plant. Structural equation modelling revealed that the relative abundance of four key bacterial orders in Chinese cabbage roots can explain 85% and 70% of the total variation in pathogen density and disease damage, respectively. Notably, the relative dominance of Bacillales and Rhizobiales, which have a trade-off relationship, exhibited predominant effects on pathogen density and disease damage. The disease-suppressive soil legacy effects of preceding crops are reflected in compositional changes in key bacterial orders, which are intensified by the bacterial community network.

Changes in the Yield Effect of the Preceding Crop in the US Corn Belt Under a Warming Climate

Crop rotation has been widely used to enhance crop yields and mitigate adverse climate impacts. The existing research predominantly focuses on the impacts of crop rotation under growing season (GS) climates, neglecting the influences of non-GS (NGS) climates on agroecosystems. This oversight limits our understanding of the comprehensive climatic impacts on crop rotation and, consequently, our ability to devise effective adaptation strategies in response to climate warming. In this study, we examine the impacts of both GS and NGS climate conditions on the yield effect of the preceding crop in corn-soybean rotation systems from 1999 to 2018 in the US Midwest. Using causal forest analysis, we estimate that crop rotation increases corn and soybean yields by 0.96 and 0.22 t/ha on average, respectively. We then employ statistical models to indicate that increasing temperatures and rainfall in the NGS reduce corn rotation benefits, while warming GS enhances rotation benefits for soybeans. By 2051-2070, we project that warming climates will reduce corn rotation benefits by 6.74% under Shared Socioeconomic Pathway (SSP) 1-2.6 and 17.18% under SSP 5-8.5. For soybeans, warming climates are expected to increase rotation benefits by 8.36% under SSP 1-2.6 and 13.83% under SSP 5-8.5. Despite these diverse climate impacts on both crops, increasing crop rotation could still improve county-average yields, as neither corn nor soybean was fully rotated. If we project that all continuous corn and continuous soybeans are rotated by 2051-2070, county-average corn yields will increase by 0.265 t/ha under SSP 1-2.6 and 0.164 t/ha under SSP 5-8.5, while county-average soybean yields will gain 0.064 t/ha under SSP 1-2.6 and 0.076 t/ha under SSP 5-8.5. These findings highlight the effectiveness of crop rotation in the face of warming NGS and GS in the future and can help evaluate opportunities for adaptation.

Analysis of the composition and function of rhizosphere microbial communities in plants with tobacco bacterial wilt disease and healthy plants

To explore the factors influencing the occurrence of bacterial wilt, the differences in the physicochemical properties, microbial community composition and function between rhizosphere soil of tobacco plants with bacterial wilt and healthy plants in the tobacco planting area of Fuzhou City, Jiangxi Province were analyzed and compared. The results showed that the rhizosphere soil of diseased tobacco exhibited significantly reduced levels of exchangeable potassium, water-soluble potassium, nitrate nitrogen, total nitrogen and pH, in comparison to the rhizosphere soil of healthy plants. Conversely, the available phosphorus content of the rhizosphere soil of diseased tobacco was significantly increased. The amount of Ralstonia solanacearum in soil was negatively correlated with pH, nitrate nitrogen and total nitrogen, and positively correlated with exchangeable potassium and water-soluble potassium. A total of 43 genera were significantly different between the two groups of rhizosphere soil, of which 24 genera were enriched in the rhizosphere of healthy plants, including Ideonella, Rhizophagus, Rhizobacter, Altererythrobacter and Ignavibacterium associated with plant disease resistance, Thermodesulfovibrio, Syntrophorhabdus, Syntrophus, Chlorobium, Hydrogenophaga and Limnohabitans associated with soil sulfur metabolism, as well as Ignavibacterium, Ideonella, Derxia and Azohydromonas associated with soil nitrogen cycling. Kyoto Encyclopedia of Genes and Genomes functional analysis of the unigenes obtained by metagenomic sequencing also showed that the differential unigenes were significantly enriched in the sulfur metabolism pathway. In addition, the rhizosphere soil of diseased tobacco plants exhibited a higher abundance of antibiotic-producing actinomycetes and an increased load of antibiotic resistance genes compared to that of healthy plants. In general, lower pH value, less content of nitrate nitrogen and total nitrogen, and more content of exchangeable potassium and water-soluble potassium could contribute to onset of bacterial wilt. Twenty-four genera, including Ideonella and Rhizophagus, may construct a healthy microecological network in the rhizosphere of tobacco plants. All these factors may interact with each other to control the development of bacterial wilt. This complicated interaction network needs to be explored further.IMPORTANCEPrevious studies have mainly focused on the differences in microbial species composition between healthy and diseased soils, but the differences in microbial community functions between two types of soil have not been well characterized. In this study, soil samples in diseased and healthy plant rhizospheres were collected for physicochemical property testing and metagenomic sequencing. We focused on analyzing the differences in physicochemical properties and microbial community functions between these soils, as well as the correlation between these factors and pathogen content. The results of this study provide a theoretical basis for further understanding the occurrence of tobacco bacterial wilt in the field.

Stratified Effects of Tillage and Crop Rotations on Soil Microbes in Carbon and Nitrogen Cycles at Different Soil Depths in Long-Term Corn, Soybean, and Wheat Cultivation

Understanding the soil bacterial communities involved in carbon (C) and nitrogen (N) cycling can inform beneficial tillage and crop rotation practices for sustainability and crop production. This study evaluated soil bacterial diversity, compositional structure, and functions associated with C-N cycling at two soil depths (0-15 cm and 15-30 cm) under long-term tillage (conventional tillage [CT] and no-till [NT]) and crop rotation (monocultures of corn, soybean, and wheat and corn-soybean-wheat rotation) systems. The soil microbial communities were characterized by metabarcoding the 16S rRNA gene V4-V5 regions using Illumina MiSeq. The results showed that long-term NT reduced the soil bacterial diversity at 15-30 cm compared to CT, while no significant differences were found at 0-15 cm. The bacterial communities differed significantly at the two soil depths under NT but not under CT. Notably, over 70% of the tillage-responding KEGG orthologs (KOs) associated with C fixation (primarily in the reductive citric acid cycle) were more abundant under NT than under CT at both depths. The tillage practices significantly affected bacteria involved in biological nitrogen (N2) fixation at the 0-15 cm soil depth, as well as bacteria involved in denitrification at both soil depths. The crop type and rotation regimes had limited effects on bacterial diversity and structure but significantly affected specific C-N-cycling genes. For instance, three KOs associated with the Calvin-Benson cycle for C fixation and four KOs related to various N-cycling processes were more abundant in the soil of wheat than in that of corn or soybean. These findings indicate that the long-term tillage practices had a greater influence than crop rotation on the soil bacterial communities, particularly in the C- and N-cycling processes. Integrated management practices that consider the combined effects of tillage, crop rotation, and crop types on soil bacterial functional groups are essential for sustainable agriculture.

Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations

BACKGROUND

Soil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, "sterile sentinels," for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method.

RESULTS

Compared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations.

CONCLUSIONS

Overall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.

Crop rotational diversity can mitigate climate-induced grain yield losses

Diversified crop rotations have been suggested to reduce grain yield losses from the adverse climatic conditions increasingly common under climate change. Nevertheless, the potential for climate change adaptation of different crop rotational diversity (CRD) remains undetermined. We quantified how climatic conditions affect small grain and maize yields under different CRDs in 32 long-term (10-63 years) field experiments across Europe and North America. Species-diverse and functionally rich rotations more than compensated yield losses from anomalous warm conditions, long and warm dry spells, as well as from anomalous wet (for small grains) or dry (for maize) conditions. Adding a single functional group or crop species to monocultures counteracted yield losses from substantial changes in climatic conditions. The benefits of a further increase in CRD are comparable with those of improved climatic conditions. For instance, the maize yield benefits of adding three crop species to monocultures under detrimental climatic conditions exceeded the average yield of monocultures by up to 553 kg/ha under non-detrimental climatic conditions. Increased crop functional richness improved yields under high temperature, irrespective of precipitation. Conversely, yield benefits peaked at between two and four crop species in the rotation, depending on climatic conditions and crop, and declined at higher species diversity. Thus, crop species diversity could be adjusted to maximize yield benefits. Diversifying rotations with functionally distinct crops is an adaptation of cropping systems to global warming and changes in precipitation.

The role of rhizosphere phages in soil health

While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.

Genome-Wide Association Studies on Chinese Wheat Cultivars Reveal a Novel Fusarium Crown Rot Resistance Quantitative Trait Locus on Chromosome 3BL

Fusarium crown rot (FCR), primarily caused by Fusarium pseudograminearum, has emerged as a new threat to wheat production and quality in North China. Genetic enhancement of wheat resistance to FCR remains the most effective approach for disease control. In this study, we phenotyped 435 Chinese wheat cultivars through FCR inoculation at the seedling stage in a greenhouse. Our findings revealed that only approximately 10.8% of the wheat germplasms displayed moderate or high resistance to FCR. A genome-wide association study (GWAS) using high-density 660K SNP led to the discovery of a novel quantitative trait locus on the long arm of chromosome 3B, designated as Qfcr.hebau-3BL. A total of 12 significantly associated SNPs were closely clustered within a 1.05 Mb physical interval. SNP-based molecular markers were developed to facilitate the practical application of Qfcr.hebau-3BL. Among the five candidate FCR resistance genes within the Qfcr.hebau-3BL, we focused on TraesCS3B02G307700, which encodes a protein kinase, due to its expression pattern. Functional validation revealed two transcripts, TaSTK1.1 and TaSTK1.2, with opposing roles in plant resistance to fungal disease. These findings provide insights into the genetic basis of FCR resistance in wheat and offer valuable resources for breeding resistant varieties.

Transplantation of soil from organic field confers disease suppressive ability to conducive soil

Organic agriculture is a sustainable method of farming, and confers disease-suppressing abilities to disease-conducive soils via specialized soil microbiomes. This study aimed at transforming a disease-conducive soil from a conventional field into disease-suppressive soil by inoculating soil from an organic field previously established as "disease-suppressive". The effectiveness of the transformed soil was established with the model plant wheat (Triticum aestivum) grown under natural conditions, with regard to its potential in inhibiting fungal phytopathogens, Rhizoctonia solani and Fusarium oxysporum. The conducive soil inoculated with the disease-suppressive soil performed better than the control conducive soil in terms of reduced disease severity in plants, improved soil nutrient content, increased activity of hydrolytic enzymes, and increased abundance of structural and functional microbial markers. The study demonstrates the efficacy of the soil microbiome under long-term organic agriculture in transforming disease-conducive soil into disease-suppressive soils. Such practises are simple and easy to implement, and could greatly improve the sustainability and crop yield in developing countries.

Long-Term Tillage and Crop Rotation Regimes Reshape Soil-Borne Oomycete Communities in Soybean, Corn, and Wheat Production Systems

Soil-borne oomycetes include devastating plant pathogens that cause substantial losses in the agricultural sector. To better manage this important group of pathogens, it is critical to understand how they respond to common agricultural practices, such as tillage and crop rotation. Here, a long-term field experiment was established using a split-plot design with tillage as the main plot factor (conventional tillage (CT) vs. no till (NT), two levels) and rotation as the subplot factor (monocultures of soybean, corn, or wheat, and corn-soybean-wheat rotation, four levels). Post-harvest soil oomycete communities were characterized over three consecutive years (2016-2018) by metabarcoding the Internal Transcribed Spacer 1 (ITS1) region. The community contained 292 amplicon sequence variants (ASVs) and was dominated by Globisporangium spp. (85.1% in abundance, 203 ASV) and Pythium spp. (10.4%, 51 ASV). NT decreased diversity and community compositional structure heterogeneity, while crop rotation only affected the community structure under CT. The interaction effects of tillage and rotation on most oomycetes species accentuated the complexity of managing these pathogens. Soil and crop health represented by soybean seedling vitality was lowest in soils under CT cultivating soybean or corn, while the grain yield of the three crops responded differently to tillage and crop rotation regimes.

A Microbiological Approach to Alleviate Soil Replant Syndrome in Peaches

Replant syndrome (RS) is a global problem characterized by reduced growth, production life, and yields of tree fruit/nut orchards. RS etiology is unclear, but repeated monoculture plantings are thought to develop a pathogenic soil microbiome. This study aimed to evaluate a biological approach that could reduce RS in peach (Prunus persica) orchards by developing a healthy soil bacteriome. Soil disinfection via autoclave followed by cover cropping and cover crop incorporation was found to distinctly alter the peach soil bacteriome but did not affect the RS etiology of RS-susceptible 'Lovell' peach seedlings. In contrast, non-autoclaved soil followed by cover cropping and incorporation altered the soil bacteriome to a lesser degree than autoclaving but induced significant peach growth. Non-autoclaved and autoclaved soil bacteriomes were compared to highlight bacterial taxa promoted by soil disinfection prior to growing peaches. Differential abundance shows a loss of potentially beneficial bacteria due to soil disinfection. The treatment with the highest peach biomass was non-autoclaved soil with a cover crop history of alfalfa, corn, and tomato. Beneficial bacterial species that were cultivated exclusively in the peach rhizosphere of non-autoclaved soils with a cover crop history were Paenibacillus castaneae and Bellilinea caldifistulae. In summary, the non-autoclaved soils show continuous enhancement of beneficial bacteria at each cropping phase, culminating in an enriched rhizosphere which may help alleviate RS in peaches.

Above- and belowground linkages during extreme moisture excess: leveraging knowledge from natural ecosystems to better understand implications for row-crop agroecosystems

Above- and belowground linkages are responsible for some of the most important ecosystem processes in unmanaged terrestrial systems including net primary production, decomposition, and carbon sequestration. Global change biology is currently altering above- and belowground interactions, reducing ecosystem services provided by natural systems. Less is known regarding how above- and belowground linkages impact climate resilience, especially in intentionally managed cropping systems. Waterlogged or flooded conditions will continue to increase across the Midwestern USA due to climate change. The objective of this paper is to explore what is currently known regarding above- and belowground linkages and how they impact biological, biochemical, and physiological processes in systems experiencing waterlogged conditions. We also identify key above- and belowground processes that are critical for climate resilience in Midwestern cropping systems by exploring various interactions that occur within unmanaged landscapes. Above- and belowground interactions that support plant growth and development, foster multi-trophic-level interactions, and stimulate balanced nutrient cycling are critical for crops experiencing waterlogged conditions. Moreover, incorporating ecological principles such as increasing plant diversity by incorporating crop rotations and adaptive management via delayed planting dates and adjustments in nutrient management will be critical for fostering climate resilience in row-crop agriculture moving forward.

The Golden Goal of Soil Management: Disease-Suppressive Soils

Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.

Diversifying and perennializing plants in agroecosystems alters retention of new C and N from crop residues

Managing soils to retain new plant inputs is key to moving toward a sustainable and regenerative agriculture. Management practices, like diversifying and perennializing agroecosystems, may affect the decomposer organisms that regulate how new residue is converted to persistent soil organic matter. Here we tested whether 12 years of diversifying/perennializing plants in agroecosystems through extended rotations or grassland restoration would decrease losses of new plant residue inputs and, thus, increase retention of carbon (C) and nitrogen (N) in soil. We tracked dual-labeled (¹³ C and ¹⁵ N), isotopically enriched wheat (Triticum aestivum) residue in situ for 2 years as it decomposed in three agroecosystems: maize-soybean (CS) rotation, maize-soybean-wheat plus red clover and cereal rye cover crops (CSW2), and spring fallow management with regeneration of natural grassland species (seven to 10 species; SF). We measured losses of wheat residue (C_wheat and N_wheat ) in leached soil solution and greenhouse gas fluxes, as well as how much was recovered in microbial biomass and bulk soil at 5-cm increments down to 20 cm. CSW2 and SF both had unique, significant effects on residue decomposition and retention dynamics that were clear only when using nuanced metrics that able to tease apart subtle differences. For example, SF retained a greater portion of C_wheat in 0-5 cm surface soils (155%, p = 0.035) and narrowed the C_wheat to N_wheat ratio (p < 0.030) compared to CS. CSW2 increased an index of carbon-retention efficiency, C_wheat retained in the mesocosm divided by total measured, from 0.18 to 0.27 (49%, p = 0.001), compared to CS. Overall, we found that diversifying and extending the duration of living plants in agroecosystems can lead to greater retention of new residue inputs in subtle ways that require further investigation to fully understand.

A new approach to characterising and predicting crop rotations using national-scale annual crop maps

Cropping decisions affect the nature, timing and intensity of agricultural management strategies. Specific crop rotations are associated with different environmental impacts, which can be beneficial or detrimental. The ability to map, characterise and accurately predict rotations enables targeting of mitigation measures where most needed and forecasting of potential environmental risks. Using six years of the national UKCEH Land Cover® plus: Crops maps (2015-2020), we extracted crop sequences for every agricultural field parcel in Great Britain (GB). Our aims were to first characterise spatial patterns in rotation properties over a national scale based on their length, type and structural diversity values, second, to test an approach to predicting the next crop in a rotation, using transition probability matrices, and third, to test these predictions at a range of spatial scales. Strict cyclical rotations only occupy 16 % of all agricultural land, whereas long-term grassland and complex-rotational agriculture each occupy over 40 %. Our rotation classifications display a variety of distinctive spatial patterns among rotation lengths, types and diversity values. Rotations are mostly 5 years in length, short mixed crops are the most abundant rotation type, and high structural diversity is concentrated in east Scotland. Predictions were most accurate when using the most local spatial approach (spatial scaling), 5-year rotations, and including long-term grassland. The prediction framework we built demonstrates that our crop predictions have an accuracy of 36-89 %, equivalent to classification accuracy of national crop and land cover mapping using earth observation, and we suggest this could be improved with additional contextual data. Our results emphasise that rotation complexity is multi-faceted, yet it can be mapped in different ways and forms the basis for further exploration in and beyond agronomy, ecology, and other disciplines.

The shift of soil microbial community induced by cropping sequence affect soil properties and crop yield

Rational cropping maintains high soil fertility and a healthy ecosystem. Soil microorganism is the controller of soil fertility. Meanwhile, soil microbial communities also respond to different cropping patterns. The mechanisms by which biotic and abiotic factors were affected by different cropping sequences remain unclear in the major grain-producing regions of northeastern China. To evaluate the effects of different cropping sequences under conventional fertilization practices on soil properties, microbial communities, and crop yield, six types of plant cropping systems were performed, including soybean monoculture, wheat-soybean rotation, wheat-maize-soybean rotation, soybean-maize-maize rotation, maize-soybean-soybean rotation and maize monoculture. Our results showed that compared with the single cropping system, soybean and maize crop rotation in different combinations or sequences can increase soil total organic carbon and nutrients, and promote soybean and maize yield, especially using soybean-maize-maize and maize-soybean-soybean planting system. The 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing showed that different cropping systems had different effects on bacterial and fungal communities. The bacterial and fungal communities of soybean monoculture were less diverse when compared to the other crop rotation planting system. Among the different cropping sequences, the number of observed bacterial species was greater in soybean-maize-maize planting setup and fungal species in maize-soybean-soybean planting setup. Some dominant and functional bacterial and fungal taxa in the rotation soils were observed. Network-based analysis suggests that bacterial phyla Acidobacteria and Actinobacteria while fungal phylum Ascomycota showed a positive correlation with other microbial communities. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) result showed the presence of various metabolic pathways. Besides, the soybean-maize-maize significantly increased the proportion of some beneficial microorganisms in the soil and reduced the soil-borne animal and plant pathogens. These results warrant further investigation into the mechanisms driving responses of beneficial microbial communities and their capacity on improving soil fertility during legume cropping. The present study extends our understanding of how different crop rotations effect soil parameters, microbial diversity, and metabolic functions, and reveals the importance of crop rotation sequences. These findings could be used to guide decision-making from the microbial perspective for annual crop planting and soil management approaches.

Legacy effects of fumigation on soil bacterial and fungal communities and their response to metam sodium application

BACKGROUND

Soil microorganisms are integral to maintaining soil health and crop productivity, but fumigation used to suppress soilborne diseases may affect soil microbiota. Currently, little is known about the legacy effects of soil fumigation on soil microbial communities and their response to fumigation at the production scale. Here, 16S rRNA gene and internal transcribed spacer amplicon sequencing was used to characterize the bacterial and fungal communities in soils from intensively managed crop fields with and without previous exposure to metam sodium (MS) fumigation. The effect of fumigation history, soil series, and rotation crop diversity on microbial community variation was estimated and the response of the soil microbiome to MS application in an open microcosm system was documented.

RESULTS

We found that previous MS fumigation reduced soil bacterial diversity but did not affect microbial richness and fungal diversity. Fumigation history, soil series, and rotation crop diversity were the main contributors to the variation in microbial β-diversity. Between fumigated and non-fumigated soils, predominant bacterial and fungal taxa were similar; however, their relative abundance varied with fumigation history. In particular, the abundance of Basidiomycete yeasts was decreased in fumigated soils. MS fumigation also altered soil bacterial and fungal co-occurrence network structure and associations. In microcosms, application of MS reduced soil microbial richness and bacterial diversity. Soil microbial β-diversity was also affected but microbial communities of the microcosm soils were always similar to that of the field soils used to establish the microcosms. MS application also induced changes in relative abundance of several predominant bacterial and fungal genera based on a soil's previous fumigation exposure.

CONCLUSIONS

The legacy effects of MS fumigation are more pronounced on soil bacterial diversity, β-diversity and networks. Repeated fumigant applications shift soil microbial compositions and may contribute to differential MS sensitivity among soil microorganisms. Following MS application, microbial richness and bacterial diversity decreases, but microbial β-diversity was similar to that of the field soils used to establish the microcosms in the short-term (< 6 weeks). The responses of soil microbiome to MS fumigation are context dependent and rely on abiotic, biotic, and agricultural management practices.

Soil bacterial community response to cover crop introduction in a wheat-based dryland cropping system

The incorporation of cover crops into cropping systems is important for enhancing soil health in agricultural systems. Soil microbes contribute to soil health by supplying key nutrients and providing protection against plant pests, diseases, and abiotic stress. While research has demonstrated the connection between cover crops and the soil microbiology, less is known regarding the impact of cover crops on the soil microbial community in semi-arid regions of the Northern Great Plains. Our objectives were to evaluate changes in the soil bacterial community composition and community networks in wheat grown after multi-species cover crops. Cover crops were compared to continuous cropping and crop/fallow systems and the effects of cover crop termination methods were also evaluated. Cover crops consisted of a cool season multispecies mix, mid-season multispecies mix, and a warm season multispecies mix, which were grown in rotation with winter wheat. A continuous cropping (wheat/barley) and wheat/fallow system were also included along with cover crop termination by grazing, herbicide application, and haying. Cover crop treatments and termination methods had no significant impact on microbial community alpha diversity. Cover crop termination methods also had no significant impact on microbial community beta diversity. Families belonging to the phyla Actinobacteria, Bacterioidota, and Proteobacteria were more abundant in the cool season cover crop treatment compared to the warm season cover crop treatment. Co-occurrence network analysis indicated that incorporation of cool season cover crops or mid-season mixes in a wheat-based cropping system led to greater complexity and connectivity within these microbial networks compared to the other treatments which suggests these communities may be more resilient to environmental disturbances.

Response of soil microecology to different cropping practice under Bupleurum chinense cultivation

The effects of cropping practices on the rhizosphere soil physical properties and microbial communities of Bupleurum chinense have not been studied in detail. The chemical properties and the microbiome of rhizosphere soil of B. chinense were assessed in the field trial with three cropping practices (continuous monocropping, Bupleurum-corn intercropping and Bupleurum-corn rotation). The results showed cropping practices changed the chemical properties of the rhizosphere soil and composition, structure and diversity of the rhizosphere microbial communities. Continuous monocropping of B. chinense not only decreased soil pH and the contents of NO3--N and available K, but also decreased the alpha diversity of bacteria and beneficial microorganisms. However, Bupleurum-corn rotation improved soil chemical properties and reduced the abundance of harmful microorganisms. Soil chemical properties, especially the contents of NH4+-N, soil organic matter (SOM) and available K, were the key factors affecting the structure and composition of microbial communities in the rhizosphere soil. These findings could provide a new basis for overcoming problems associated with continuous cropping and promote development of B. chinense planting industry by improving soil microbial communities.

Legacies at work: plant-soil-microbiome interactions underpinning agricultural sustainability

Agricultural intensification has had long-lasting negative legacies largely because of excessive inputs of agrochemicals (e.g., fertilizers) and simplification of cropping systems (e.g., continuous monocropping). Conventional agricultural management focuses on suppressing these negative legacies. However, there is now increasing attention for creating positive above- and belowground legacies through selecting crop species/genotypes, optimizing temporal and spatial crop combinations, improving nutrient inputs, developing intelligent fertilizers, and applying soil or microbiome inoculations. This can lead to enhanced yields and reduced pest and disease pressure in cropping systems, and can also mitigate greenhouse gas emissions and enhance carbon sequestration in soils. Strengthening positive legacies requires a deeper understanding of plant-soil-microbiome interactions and innovative crop, input, and soil management which can help to achieve agricultural sustainability.

Characterization of the Soil Bacterial Community from Selected Boxwood Gardens across the United States

In a recent study, we observed a rapid decline of the boxwood blight pathogen Calonectria pseudonaviculata (Cps) soil population in all surveyed gardens across the United States, and we speculated that these garden soils might be suppressive to Cps. This study aimed to characterize the soil bacterial community in these boxwood gardens. Soil samples were taken from one garden in California, Illinois, South Carolina, and Virginia and two in New York in early summer and late fall of 2017 and 2018. Soil DNA was extracted and its 16S rRNA amplicons were sequenced using the Nanopore MinION® platform. These garden soils were consistently dominated by Rhizobiales and Burkholderiales, regardless of garden location and sampling time. These two orders contain many species or strains capable of pathogen suppression and plant fitness improvement. Overall, 66 bacterial taxa were identified in this study that are known to have strains with biological control activity (BCA) against plant pathogens. Among the most abundant were Pseudomonas spp. and Bacillus spp., which may have contributed to the Cps decline in these garden soils. This study highlights the importance of soil microorganisms in plant health and provides a new perspective on garden disease management using the soil microbiome.

Functions and biosynthesis of plant signaling metabolites mediating plant-microbe interactions

Covering: 2015-2022Plants and microbes have coevolved since their appearance, and their interactions, to some extent, define plant health. A reasonable fraction of small molecules plants produced are involved in mediating plant-microbe interactions, yet their functions and biosynthesis remain fragmented. The identification of these compounds and their biosynthetic genes will open up avenues for plant fitness improvement by manipulating metabolite-mediated plant-microbe interactions. Herein, we integrate the current knowledge on their chemical structures, bioactivities, and biosynthesis with the view of providing a high-level overview on their biosynthetic origins and evolutionary trajectory, and pinpointing the yet unknown and key enzymatic steps in diverse biosynthetic pathways. We further discuss the theoretical basis and prospects for directing plant signaling metabolite biosynthesis for microbe-aided plant health improvement in the future.

Characteristics of Soil Fungal Communities in Soybean Rotations

Soybean continuous cropping (SC) leads to continuous cropping obstacles, and soil-borne fungal diseases occur frequently. Rotation can alleviate continuous cropping obstacles. However, the long-term effects of continuous cropping and rotation on the structure and function of the fungal community in soil are not clear. In this study, five cropping systems, SC, fallow (CK), fallow-soybean (FS), corn-soybean (CS), and wheat-soybean (WS), were implemented in the long-term continuous cropping area of soybean. After 13 years of planting, high-throughput sequencing was used to evaluate the structure and diversity of soil fungal communities and to study the relationship between fungal communities and soil environmental factors. The results showed that the abundance and diversity of fungal flora in SC soil were the highest. There were significant differences in the formation of soil fungal communities between soybean continuous cropping and the other treatments. There were 355 species of endemic fungi in SC soil. There were 231 and 120 endemic species in WS and CS, respectively. The relative abundance of the potential pathogens Lectera, Gibberella, and Fusarium in the SC treatment soil was significantly high, and the abundance of all potential pathogens in CK was significantly the lowest. The abundance of Lectera and Fusarium in CS was significantly the lowest. There was a positive correlation between potential pathogens in the soil. The relative abundance of potential pathogens in the soil was significantly positively correlated with the relative abundance of Ascomycetes and negatively correlated with the relative abundance of Basidiomycetes. Potential pathogenic genera had a significant negative correlation with soil OM, available Mn, K and soil pH and a significant positive correlation with the contents of soil available Cu, Fe, and Zn. In general, the fungal communities of SC, FS, WS, and CS were divided into one group, which was significantly different from CK. WS and CS were more similar in fungal community structure. The CK and CS treatments reduced the relative abundance of soil fungi and potential pathogens. Our study shows that SC and FS lead to selective stress on fungi and pathogenic fungi and lead to the development of fungal community abundance and diversity, while CK and CS can reduce this development, which is conducive to plant health.

Harnessing rhizobacteria to fulfil inter-linked nutrient dependency on soil and alleviate stresses in plants

Plant rhizo-microbiome comprises of complex microbial communities that colonizes at the interphase of plant roots and soil. Plant-growth-promoting rhizobacteria (PGPR) in the rhizosphere provides important ecosystem services ranging from release of essential nutrients for enhancing soil quality and improving plant health to imparting protection to plants against rising biotic and abiotic stresses. Hence, PGPR serve as restoring agents to rejuvenate soil health and mediate plant fitness in the facet of changing climate. Though, it is evident that nutrients availability in soil are managed through inter-linked mechanisms, how PGPR expediate these processes remain less recognized. Promising results of PGPR inoculation on plant growth are continually reported in controlled environmental conditions, however, their field application often fails due to competition with native microbiota and low colonization efficiency in roots. The development of highly efficient and smart bacterial synthetic communities by integrating bacterial ecological and genetic features provides better opportunities for successful inoculant formulations. This review provides an overview of the inter-play between nutrient availability and disease suppression governed by rhizobacteria in soil followed by the role of synthetic bacterial communities in developing efficient microbial inoculants. Moreover, an outlook on the beneficial activities of rhizobacteria in modifying soil characteristics to sustainably boost agroecosystem functioning is also provided.

Cover crop-driven shifts in soil microbial communities could modulate early tomato biomass via plant-soil feedbacks

Sustainable agricultural practices such as cover crops (CCs) and residue retention are increasingly applied to counteract detrimental consequences on natural resources. Since agriculture affects soil properties partly via microbial communities, it is critical to understand how these respond to different management practices. Our study analyzed five CC treatments (oat, rye, radish, rye-radish mixture and no-CC) and two crop residue managements (retention/R+ or removal/R-) in an 8-year diverse horticultural crop rotation trial from ON, Canada. CC effects were small but stronger than those of residue management. Radish-based CCs tended to be the most beneficial for both microbial abundance and richness, yet detrimental for fungal evenness. CC species, in particular radish, also shaped fungal and, to a lesser extent, prokaryotic community composition. Crop residues modulated CC effects on bacterial abundance and fungal evenness (i.e., more sensitive in R- than R+), as well as microbial taxa. Several microbial structure features (e.g., composition, taxa within Actinobacteria, Firmicutes and Ascomycota), some affected by CCs, were correlated with early biomass production of the following tomato crop. Our study suggests that, whereas mid-term CC effects were small, they need to be better understood as they could be influencing cash crop productivity via plant-soil feedbacks.

Genomics and Informatics, Conjoined Tools Vital for Understanding and Protecting Plant Health

Genomics' impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next-generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped in understanding how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.

Fungal Pathogens Associated with Crown and Root Rot of Wheat in Central, Eastern, and Southeastern Kazakhstan

Kazakhstan is the fourteenth largest wheat producer in the world. Despite this fact, there has not been a comprehensive survey of wheat root and crown rot. A quantitative survey was conducted for the purpose of establishing the distribution of fungi associated with root and crown rot on wheat (Triticum spp.). During the 2019 growing season, samples were taken from the affected plants’ roots and stem bases. A total of 1221 fungal isolates were acquired from 65 sites across the central (Karagandy region), eastern (East Kazakhstan region), and southeastern (Almaty region) parts of the country and identified using morphological and molecular tools. The internal transcribed spacer (ITS), translation elongation factor 1-alpha (EF1-α), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) sequences were successfully used to identify the species of fungal isolates. It was found that Bipolaris sorokiniana (44.80%) and Fusarium acuminatum (20.39%) were the most predominant fungal species isolated, which were present in 86.15 and 66.15% of the fields surveyed, respectively, followed by F. equiseti (10.16%), Curvularia spicifera (7.62%), F. culmorum (4.75%), F. oxysporum (4.10%), F. redolens (2.38%), Rhizoctonia solani AG2-1 (1.06%), Nigrospora oryzae (0.98%), C. inaequalis (0.90%), F. pseudograminearum (0.74%), F. flocciferum (0.74%), Macrophomina phaseolina (0.66%), F. cf. incarnatum (0.33%), Fusarium sp. (0.25%), and F. torulosum (0.16%). A total of 74 isolates representing 16 species were tested via inoculation tests on the susceptible Triticum aestivum cv. Seri 82 and the results revealed that F. culmorum and F. pseudograminearum, B. sorokiniana, Fusarium sp., R. solani, F. redolens, C. spicifera, C. inaequalis, and N. oryzae were virulent, whereas others were non-pathogenic. The findings of this investigation demonstrate the presence of a diverse spectrum of pathogenic fungal species relevant to wheat crown and root rot in Kazakhstan. To the best of our knowledge, this is the first report of F. pseudograminearum, Fusarium sp., C. spicifera, and C. inaequalis as pathogens on wheat in Kazakhstan.

Soil microbial communities following 20 years of fertilization and crop rotation practices in the Czech Republic

BACKGROUND

Although fertilization and crop rotation practices are commonly used worldwide in agriculture to maximize crop yields, their long-term effect on the structures of soil microorganisms is still poorly understood. This study investigated the long-term impact of fertilization and crop rotation on soil microbial diversity and the microbial community structure in four different locations with three soil types. Since 1996, manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and NPK (NPK; 330 kg N/ha) fertilizers were periodically applied to the soils classified as chernozem, luvisol and cambisol, which are among the most abundant or fertile soils used for agricultural purposes in the world. In these soils, potato (Solanum tuberosum L.), winter wheat (Triticum aestivum L.), and spring barley (Hordeum vulgare L.) were rotated every three years.

RESULTS

Soil chemistry, which was significantly associated with location, fertilization, crop rotation, and the interaction of fertilization and location, was the dominant driver of soil microbial communities, both prokaryotic and fungal. A direct effect of long-term crop rotation and fertilization on the structure of their communities was confirmed, although there was no evidence of their influence on microbial diversity. Fungal and bacterial communities responded differently to fertilization treatments; prokaryotic communities were only significantly different from the control soil (CF) in soils treated with MF and SF3x, while fungal communities differed across all treatments. Indicator genera were identified for different treatments. These taxa were either specific for their decomposition activities or fungal plant pathogens. Sequential rotation of the three crops restricted the growth of several of the indicator plant pathogens.

CONCLUSIONS

Long-term fertilization and crop rotation significantly altered microbial community structure in the soil. While fertilization affected soil microorganisms mainly through changes in nutrient profile, crop rotations lead to the attraction and repulsion of specific plant pathogens. Such changes in soil microbial communities need to be considered when planning soil management.

Effects of Four Cropping Patterns of Lilium brownii on Rhizosphere Microbiome Structure and Replant Disease

Replant disease caused by continuous cropping obstacles commonly occurs in a Lilium brownii consecutive monoculture. To reveal the mechanisms contributing to the continuous cropping obstacles of L. brownii, four cropping patterns (fallow, L. brownii-rice rotation, newly planted L. brownii, and 2-year L. brownii consecutive monoculture) were designed, and Illumina MiSeq (16S rDNA and ITS) was utilized to detect shifts in the microbial community in the rhizosphere. Our result showed that planting of L. brownii significantly reduced soil pH. Consecutive monoculture of L. brownii can significantly decrease the diversity and abundance of soil bacteria, but markedly increase the diversity and abundance of soil fungi. Under the four planting pattern treatments, the changes in soil pH were consistent with the changes in the Shannon diversity index of soil bacterial communities, whereas we observed a negative correlation between soil pH and Shannon diversity index for fungi. The relative abundance of Lactobacillales significantly increased in soils of L. brownii consecutive monoculture, while Acidobacteriales, Solibacterales, and Xanthomonadales increased in soils of L. brownii-rice rotation and newly planted L. brownii. Collectively, this work aimed to elucidate the relationship between the L. brownii planting patterns and soil microbiome, thereby providing a theoretical basis for screening new biological agents that may contribute to resolving continuous cropping obstacles of L. brownii.

The impact of different rotation regime on the soil bacterial and fungal communities in an intensively managed agricultural region

The continuous wheat-maize planting has led to the increase in epidemic frequency of wheat diseases under climate change. Analyzation of the soil microbial composition in different rotation crops is essential to select alternative rotation regime. This study investigated the bacterial and fungal community abundance and composition, and potential microbe-microbe interactions in three rotations, including wheat-maize → spring maize (WMFS), wheat-soybean (WS) and continuous wheat-maize (WM) planting. The results revealed that there were 110, 156, and 195 bacterial, and 17, 8, and 15 fungal operational taxonomic units respectively enriched by WMFS, WS, and WM. WM increased the relative abundance of Actinobacteria and α-Proteobacteria in wheat, and the relative abundance and copy number of genus Fusarium in maize. WMFS and WS could decrease the abundance of Fusarium in summer-crop across the growth stages and in wheat at elongation. WS also increased the copy number of ammonia-oxidizing bacteria in wheat at flowering and harvest. Network analysis revealed that WM resulted in simple and isolated wheat network with small modules dominating and none Nitrospirae and β-Proteobacteria in the main modules. WS formed interconnected and intricate wheat network with the maximum number of large modules and module connectors. Under WS, positive correlation between antagonistic Streptomyces (Actinobacteria) and genus Fusarium was found in wheat. Soil physicochemical properties explained the majority of the variation in bacterial and fungal β-diversity in wheat (P < 0.01). Rotation regime switching from WM to WMFS and WS may effectively damp the risk of wheat disease and maintain the wheat yield in intensive cereal production.

Site and land-use associations of soil bacteria and fungi define core and indicative taxa

Soil microbial diversity has major influences on ecosystem functions and services. However, due to its complexity and uneven distribution of abundant and rare taxa, quantification of soil microbial diversity remains challenging and thereby impeding its integration into long-term monitoring programs. Using metabarcoding, we analyzed soil bacterial and fungal communities at 30 long-term soil monitoring sites from the three land-use types arable land, permanent grassland, and forest with a yearly sampling between snowmelt and first fertilization over five years. Unlike soil microbial biomass and alpha-diversity, microbial community compositions and structures were site- and land-use-specific with CAP reclassification success rates of 100%. The temporally stable site core communities included 38.5% of bacterial and 33.1% of fungal OTUs covering 95.9% and 93.2% of relative abundances. We characterized bacterial and fungal core communities and their land-use associations at the family-level. In general, fungal families revealed stronger land-use associations as compared to bacteria. This is likely due to a stronger vegetation effect on fungal core taxa, while bacterial core taxa were stronger related to soil properties. The assessment of core communities can be used to form cultivation-independent reference lists of microbial taxa, which may facilitate the development of microbial indicators for soil quality and the use of soil microbiota for long-term soil biomonitoring.

Harnessing Chemical Ecology for Environment-Friendly Crop Protection

Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.

Response of soil microbiome structure and its network profiles to four soil amendments in monocropping strawberry greenhouse

With the constant surge of strawberry cultivation and human demand, widespread concern has been expressed about the severe soil and plant health problems caused by continuous strawberry cropping, particularly monocropping in greenhouses. Effective microorganisms (EM) and Bacillus subtilis (BS) have been extensively commercialized as biological control agents (BCAs) to promote plant growth and yield enhancement. However, their effects on soil microbes are obscure. To regulate the microbial community in continuous cropping strawberry soils, we developed four soil amendments based on these two BCAs by adding low and high contents of compost. The amplicon sequencing of bacterial and fungal ribosomal markers was applied to study the response of the soil microbiome structure. We noticed a sharp increase in bacterial diversity after adding EM-treated high compost and BS-treated low compost, while there was no significant change in fungal diversity among treatments. Through taxonomic classification and FUNGuild analysis, we found that the application of soil amendments resulted in a significant decline in the relative abundance of fungal plant pathogens (Rhizopus, Penicillium and Fusarium) in the soils; accordingly, the metabolic functions of a range of detrimental fungi were inhibited. Correlation analysis indicated that soil microbial community was indirectly driven by soil physicochemical properties. Co-occurrence networks revealed that soil amendments contributed to the connectivity of bacterial network, and EM-treated with high compost was the most complex and balanced. Collectively, EM-treated high compost and BS-treated low compost can well regulate the microbial community structure and thus maintain soil health.

Effects of Long-Term Bare Fallow During the Winter-Wheat Growth Season on the Soil Chemical Properties, Fungal Community Composition, and the Occurrence of Maize Fungal Diseases in North China

On the North China Plain, one of the most water-deficient regions in China, bare fallow has been implemented over a large-scale area to conserve water during the growth season of water-intensive winter wheat since 2015. However, the effects of this bare fallow on fungal community and the occurrence of crop diseases are poorly understood. Here we measured soil chemical properties, fungal community composition, and the occurrence of crop diseases after 15 years of long-term fallow (continuous maize or soybean) and non-fallow (maize-wheat rotation; soybean-wheat rotation) cropping systems. Bare fallow during the winter-wheat growth season significantly decreased soil organic matter, available nitrogen, and phosphorus. It also changed the composition of soil fungal communities, i.e., increased relative abundances of some potentially pathogenic species of Lectera, Fusarium, and Volutella but decreased beneficial Cladorrhium and Schizothecium. Meanwhile, the epidemic tendency of maize diseases changed correspondingly: the disease index of southern corn leaf blight and maize brown spot increased, but the incidence of stalk rot decreased compared with the non-fallow system. Soybean diseases were very mild regardless of the cropping system during the total experimental period. Network analysis demonstrated that the soil fungal diversity associated with maize diseases was affected by the decreased soil organic matter and available nitrogen and phosphorus. Our results suggest that bare fallow in the winter-wheat season affected the soil chemical properties, fungal community, and the occurrence of maize fungal diseases.

Role of soil in the regulation of human and plant pathogens: soils' contributions to people

Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a 'One Health' framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Crop rotation reduces the frequency of anaerobic soil bacteria in Red Latosol of Brazil

Crop diversity affects the processes of soil physical structuring and most likely provokes changes in the frequencies of soil microbial communities. The study was conducted for soil prokaryotic diversity sequencing 16S rDNA genes from a 25-year no-tillage experiment comprised of two crop systems: crop succession (Triticum aestivum-Glycine max) and rotation (Vicia sativa-Zea mays-Avena sativa-Glycine max-Triticum aestivum-Glycine max). The hypothesis was that a crop system with higher crop diversification (rotation) would affect the frequencies of prokaryotic taxa against a less diverse crop system (succession) altering the major soil functions guided by bacterial diversity. Soils in both crop systems were dominated by Proteobacteria (31%), Acidobacteria (23%), Actinobacteria (10%), and Gemmatimonadetes (7.2%), among other common copiotrophic soil bacteria. Crop systems did not affect the richness and diversity indexes of soil bacteria and soil archaea. However, the crop rotation system reduced only the frequencies of anaerobic metabolism bacteria Chloroacidobacteria, Holophagae, Spirochaetes, Euryarchaeota, and Crenarchaeota. It can be concluded that crop succession, a system that is poorer in root diversity over time, may have conditioned the soil to lower oxygen diffusion and built up ecological niches that suitable for anaerobic bacteria tolerating lower levels of oxygen. On the other hand, it appeared that crop rotation has restructured the soil over the years while enabling copiotrophic aerobic bacteria to dominate the soil ecosystem. The changes prompted by crop succession have implications for efficient soil organic matter decomposition, reduced greenhouse gas emissions, higher root activity, and overall soil productivity, which compromise to agriculture sustainability.

Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.

Genetics of Resistance to Common Root Rot (Spot Blotch), Fusarium Crown Rot, and Sharp Eyespot in Wheat

Due to soil changes, high density planting, and the use of straw-returning methods, wheat common root rot (spot blotch), Fusarium crown rot (FCR), and sharp eyespot (sheath blight) have become severe threats to global wheat production. Only a few wheat genotypes show moderate resistance to these root and crown rot fungal diseases, and the genetic determinants of wheat resistance to these devastating diseases are poorly understood. This review summarizes recent results of genetic studies of wheat resistance to common root rot, Fusarium crown rot, and sharp eyespot. Wheat germplasm with relatively higher resistance are highlighted and genetic loci controlling the resistance to each disease are summarized.

Long-term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions

Despite the importance of soil microorganisms for ecosystem services, long‐term surveys of their communities are largely missing. Using metabarcoding, we assessed temporal dynamics of soil bacterial and fungal communities in three land‐use types, i.e., arable land, permanent grassland, and forest, over five years. Soil microbial communities remained relatively stable and differences over time were smaller than those among sites. Temporal variability was highest in arable soils. Indications for consistent shifts in community structure over five years were only detected at one site for bacteria and at two sites for fungi, which provided further support for long‐term stability of soil microbial communities. A sliding window analysis was applied to assess the effect of OTU abundance on community structures. Partial communities with decreasing OTU abundances revealed a gradually decreasing structural similarity with entire communities. This contrasted with the steep decline of OTU abundances, as subsets of rare OTUs (<0.01%) revealed correlations of up to 0.97 and 0.81 with the entire bacterial and fungal communities. Finally, 23.4% of bacterial and 19.8% of fungal OTUs were identified as scarce, i.e., neither belonging to site‐cores nor correlating to environmental factors, while 67.3% of bacterial and 64.9% of fungal OTUs were identified as rare but not scarce. Our results demonstrate high stability of soil microbial communities in their abundant and rare fractions over five years. This provides a step towards defining site‐specific normal operating ranges of soil microbial communities, which is a prerequisite for detecting community shifts that may occur due to changing environmental conditions or anthropogenic activities.

Rhizosphere Microbiomes in a Historical Maize-Soybean Rotation System Respond to Host Species and Nitrogen Fertilization at the Genus and Subgenus Levels

Root-associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. In this study, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize (Zea mays L.) and soybean (Glycine max L.) in a long-term crop rotation study under conventional fertilization and low-N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere- and soil-colonizing microbial taxa. Time of sampling, host plant species, and N fertilization had major effects on microbiomes, while no effect of crop rotation was observed. Using variance partitioning as well as 16S sequence information, we further defined a set of 82 microbial genera and functional taxonomic groups at the subgenus level that show distinct responses to treatment factors. We identified taxa that are highly specific to either maize or soybean rhizospheres, as well as taxa that are sensitive to N fertilization in plant rhizospheres and bulk soil. This study provides insights to harness the full potential of soil microbes in maize and soybean agricultural systems through plant breeding and field management. IMPORTANCE Plant roots are colonized by large numbers of microbes, some of which may help the plant acquire nutrients and fight diseases. Our study contributes to a better understanding of root-colonizing microbes in the widespread and economically important maize-soybean crop rotation system. The long-term goal of this research is to optimize crop plant varieties and field management to create the best possible conditions for beneficial plant-microbe interactions to occur. These beneficial microbes may be harnessed to sustainably reduce dependency on pesticides and industrial fertilizer. We identify groups of microbes specific to the maize or to the soybean host and microbes that are sensitive to nitrogen fertilization. These microbes represent candidates that may be influenced through plant breeding or field management, and future research will be directed toward elucidating their roles in plant health and nitrogen usage.