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It is unclear how elevated CO2 (eCO2) and warming interactively influence soil N mineralization in the rhizosphere of rice (Oryza sativa L.), given that the N mineralization process in anaerobic paddy soils differs from that of aerobic upland soils. In this study, we conducted a rhizobox experiment in open top chambers and used 15N-13C dual-labeling to examine the impacts of eCO2 (700 ppm) and warming (2 °C above the ambient) on N mineralization and associated microbial processes in the rhizosphere of rice plants under anaerobic conditions. Compared to the control, the combination of eCO2 and warming increased rice N uptake by 50% in a no-added-N treatment and 32% under an N-added treatment, with the additional uptake mainly consisting of soil-derived N. Co-elevation of CO2 and temperature increased microbial biomass C and N and increased N mineralization by 41% and 23% in the no-added-N and N-added treatments, respectively. The absolute abundances of the N-mineralization genes chiA, pepA, pepN, and urea hydrolysis gene ureC in the rhizosphere increased by 22–30% under eCO2 and warming, corresponding to the additional N mineralization and photosynthetic C allocation into the soil. However, eCO2 plus warming did not increase the metabolic efficiency of N mineralization (mineralized N per unit microbial N). Our results suggest that the co-elevation of CO2 and temperature stimulated microbially mediated soil N mineralization in the rhizosphere of rice, posing a risk on the acceleration of soil organic matter decomposition.

Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.

We face major agricultural challenges that remain a threat for global food security. Soil microbes harbor enormous potentials to provide sustainable and economically favorable solutions that could introduce novel approaches to improve agricultural practices and, hence, crop productivity. In this review we give an overview regarding the current state-of-the-art of microbiome research by discussing new technologies and approaches. We also provide insights into fundamental microbiome research that aim to provide a deeper understanding of the dynamics within microbial communities, as well as their interactions with different plant hosts and the environment. We aim to connect all these approaches with potential applications and reflect how we can use microbial communities in modern agricultural systems to realize a more customized and sustainable use of valuable resources (e.g., soil).

Aims Continuous cropping of watermelon is known to result in the disruption of the rhizospheric bacteria and fungi that contribute to the occurrence of Fusarium wilt disease. However, the underlying changes in microbial composition and function as a response to mono-cropping are less studied. Methods In this study, differences in composition and potential function of the microbiome between healthy and diseased soils were investigated using MiSeq targeted sequencing and the functional GeoChip array, respectively. Results Twenty years of continuous watermelon monoculture was found to significantly alter the soil microbial communities by increasing bacterial diversity but decreasing fungal diversity. Compare to bacterial network, fungal co-occurrence networks were less robust and less connected in the monoculture diseased soil. Identified keystone species, belonging to the Proteobacteria, Bacteroidetesand Acidobacteria, were present in both the diseased and healthy soils. Key fungal species from the healthy soil belonged solely within the Ascomycete, while in the diseased soil Basidiomycota were dominant. As such, overall variations in the composition of the soil microbiome are accompanied by changes in the identities of the keystone species when comparing healthy versus diseased soils, further suggesting that soil function may also be altered. Relative abundances of genes associated with the degradation of hemicelluloses and chitin, the Calvin circle, ammonification, stress responses, iron uptake, and nitrogen fixation were significantly higher under long-term monoculture. Particularly, Fusarium spp. relative abundance was positively correlated with the relative abundances of genes involved in adherence, cellular metabolism, and immune evasion which may facilitate pathogen infection of plant roots. Conclusions In conclusion, these results highlight the significant compositional and functional differences in microbial communities between Fusarium wilt diseased soils and healthy soils under watermelon cultivation. This provides insight into the complex array of microorganisms in soils that suffer from Fusarium disease and illustrates potential directions towards the manipulation of the soil microbiome for suppression of this disease.

Conventional farming practices can lead to soil degradation and a decline in productivity. Regenerative agriculture (RA) is purported by advocates as a solution to these issues that focuses on soil health and carbon sequestration. The fundamental principles of RA are to keep the soil covered, minimise soil disturbance, preserve living roots in the soil year round, increase species diversity, integrate livestock, and limit or eliminate the use of synthetic compounds (such as herbicides and fertilisers). The overall objectives are to rejuvenate the soil and land and provide environmental, economic, and social benefits to the wider community. Despite the purported benefits of RA, a vast majority of growers are reluctant to adopt these practices due to a lack of empirical evidence on the claimed benefits and profitability. We examined the reported benefits and mechanisms associated with RA against available scientific data. The literature suggests that agricultural practices such as minimum tillage, residue retention, and cover cropping can improve soil carbon, crop yield, and soil health in certain climatic zones and soil types. Excessive use of synthetic chemicals can lead to biodiversity loss and ecosystem degradation. Combining livestock with cropping and agroforestry in the same landscape can increase soil carbon and provide several co-benefits. However, the benefits of RA practices can vary among different agroecosystems and may not necessarily be applicable across multiple agroecological regions. Our recommendation is to implement rigorous long-term farming system trials to compare conventional and RA practices in order to build knowledge on the benefits and mechanisms associated with RA on regional scales. This will provide growers and policy-makers with an evidence base from which to make informed decisions about adopting RA practices to realise their social and economic benefits and achieve resilience against climate change.

ObjectivesThe microbial community structure of the saccharifying starter, Nongxiangxing Daqu(Daqu), is a crucial factor in determining Baijiu’s quality. Lactic acid bacteria (LAB), are the dominant microorganisms in the Daqu. The present study investigated the effects of LAB on the microbial community structure and its contribution to microbial community function during the fermentation of Daqu.MethodsThe effect of LAB on the structure and function of the microbial community of Daqu was investigated using high-throughput sequencing technology combined with multivariate statistical analysis.ResultsLAB showed a significant stage-specific evolution pattern during Daqu fermentation. The LEfSe analysis and the random forest learning algorithm identified LAB as vital differential microorganisms during Daqu fermentation. The correlation co-occurrence network showed aggregation of LAB and Daqu microorganisms, indicating LAB’s significant position in influencing the microbial community structure, and suggests that LAB showed negative correlations with Bacillus, Saccharopolyspora, and Thermoactinomyces but positive correlations with Issatchenkia, Candida, Acetobacter, and Gluconobacter. The predicted genes of LAB enriched 20 functional pathways during Daqu fermentation, including Biosynthesis of amino acids, Alanine, aspartate and glutamate metabolism, Valine, leucine and isoleucine biosynthesis and Starch and sucrose metabolism, which suggested that LAB had the functions of polysaccharide metabolism and amino acid biosynthesis.ConclusionLAB are important in determining the composition and function of Daqu microorganisms, and LAB are closely related to the production of nitrogenous flavor substances in Daqu. The study provides a foundation for further exploring the function of LAB and the regulation of Daqu quality.

Global climate change is characterized by altered global atmospheric composition, including elevated CO 2 and O 3 , with important consequences on soil fungal communities. However, the function and community composition of soil fungi in response to elevated CO 2 together with elevated O 3 in paddy soils remain largely unknown. Here we used twelve open-top chamber facilities (OTCs) to evaluate the interactive effect of CO 2 (+ 200 ppm) and O 3 (+ 40 ppb) on the diversity, gene abundance, community structure, and functional composition of soil fungi during the growing seasons of two rice cultivars (Japonica, Wuyujing 3 vs. Nangeng 5055) in a Chinese paddy soil. Elevated CO 2 and O 3 showed no individual or combined effect on the gene abundance or relative abundance of soil fungi, but increased structural complexity of soil fungal communities, indicating that elevated CO 2 and/or O 3 promoted the competition of species-species interactions. When averaged both cultivars, elevated CO 2 showed no individual effect on the diversity or abundance of functional guilds of soil fungi. By contrast, elevated O 3 significantly reduced the relative abundance and diversity of symbiotrophic fungi by an average of 47.2% and 39.1%, respectively. Notably, elevated O 3 exerts stronger effects on the functional processes of fungal communities than elevated CO 2 . The structural equation model revealed that elevated CO 2 and/or O 3 indirectly affected the functional composition of soil fungi through community structure and diversity of soil fungi. Root C/N and soil environmental parameters were identified as the top direct predictors for the community structure of soil fungi. Furthermore, significant correlations were identified between saprotrophic fungi and root biomass, symbiotrophic fungi and root carbon, the pathotroph-symbiotroph and soil pH, as well as pathotroph-saprotroph-symbiotroph and soil microbial biomass carbon. These results suggest that climatic factors substantially affected the functional processes of soil fungal, and threatened soil function and food production, highlighting the detrimental impacts of high O 3 on the function composition of soil biota.

Microplastics, small particles that are released from plastics as they degrade, are ubiquitous and increasing in amount in most environments, including the soil. Here, we review the impacts of microplastics on the structure and activity of soil microbiomes and their key ecosystem functions. We then discuss how soil microbiomes regulate the environmental behavior of microplastics, such as enhancing pollutant adsorption and promoting degradation. Finally, we describe knowledge gaps and future priorities in understanding the ecological risks and potential mitigation strategies for microplastic pollution.

The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture.