The impact of living mulches established with three officinal plants (Alchemilla vulgaris, Fragaria vesca and Mentha x piperita) on the soil bacterial microbiome and activity, the nematodes population, and the nutrient status of an organic apple orchard was assessed. The composition and diversity of the bacterial communities were differentially modified by living mulches. The activity of the bacterial microbiome associated with F. vesca was higher and utilized more C sources in comparison to other treatments. The combined analysis of the core bacterial microbiome and metabolic activity pointed to a potential effect of F. vesca on different levels of the soil’s trophic network. The living mulches did not affect the overall number of nematodes, but in some cases, they modified the structure of the population: F. vesca induced the highest share of bacteria feeders and the lowest number of herbivores and fungal feeders. The living mulches modified the availability of some nutrients and the pH. Multivariate analysis of the whole dataset showed several potential inter-dependencies between the assessed parameters that are worthy of further study. In conclusion, the introduction of multifunctional living mulches based on officinal plants induced changes to the soil’s genetic and functional biodiversity and chemical properties. These modifications could deliver ecosystem services particularly relevant to organic apple orchards.

Healthy and fertile soils are the foundation of sustainable global agriculture, supporting both intensive and extensive crop cultivation, including orchards and vineyards across diverse agroecosystems. However, widespread use of synthetic fertilizers has degraded soil organic matter and overall quality, leading to significant environmental consequences and threats to ecosystem services. Challenges in accessing mineral fertilizers, along with growing concerns over environmental sustainability, have driven interest in alternative approaches such as compost, biofertilizers, biopesticides, and microbiome-based strategies to enhance soil fertility and reduce chemical inputs in agriculture. Compost derived from grapevine pruning waste shows promise in addressing agricultural challenges, but further research is needed to understand its effects on nutrient release dynamics and microbial activity. Inoculating compost with a fungal consortium presents an innovative strategy to enhance nutrient cycling and microbial interactions, addressing nutrient availability challenges. This study aimed to evaluate the impact of three fertilization methods on soil health: NPK (mineral fertilizer), PWC (pruning waste compost), and iPWC (pruning waste compost inoculated with fungal consortia). Conducted over 135 days in a controlled growth chamber, fifteen pots received equal macronutrient doses. Environmental parameters (humidity, temperature, light/dark cycles) were closely monitored. Throughout the experiment, release dynamics of key nutrients, soil enzyme activity, and microbial community responses were rigorously assessed. The results showed that compost inoculated with fungi significantly enhanced soil enzymes activities. Microbial community activity was higher in fungal and compost treatments, with greater functional diversity observed in the mineral fertilizer treatment. Compost released major minerals more slowly than chemical fertilizers, while enhancing the available fraction. These findings underscore compost’s potential, especially when supplemented with fungi, to improve soil health and promote sustainable agricultural practices and soil regeneration.

The assembly of rhizosphere microbial communities is essential for maintaining plant health, yet it is influenced by a wide range of biotic and abiotic factors. The key drivers shaping the composition of these communities, however, remain poorly understood. In this study, we analyzed 108 plant samples and evaluated root traits, plant growth characteristics, soil enzyme activities, rhizosphere metabolites, and soil chemical properties to identify the primary determinants of rhizosphere community assembly. Across 36 soil samples, we obtained 969,634 high-quality sequences, clustering into 6,284 ASVs predominantly classified into Proteobacteria (57.99%), Actinobacteria (30%), and Bacteroidetes (5.13%). Our findings revealed that rhizosphere metabolites accounted for more variance in microbial community composition compared to chemical properties (ANOVA, F = 1.53, p = 0.04), enzyme activities, or root traits (ANOVA, F = 1.04, p = 0.001). Seven small molecule metabolites, including glycerol, sorbitol, phytol, and alpha-ketoglutaric acid, were significantly correlated with βNTI, underscoring their role as critical drivers of microbial community assembly. The genus Rhizobium, significantly associated with βNTI (R = 0.25, p = 0.009), emerged as a keystone taxon shaping community structure. Soil culture experiments further validated that small molecule metabolites can modulate microbial community assembly. The ST treatment, enriched with these metabolites, produced 1,032,205 high-quality sequences and exhibited significant shifts in community composition (Adonis, p = 0.001, R = 0.463), with Rhizobium showing higher abundance compared to the control (CK). Variable selection (βNTI >2) drove phylogenetic turnover in ST, while stochastic processes (|βNTI| < 2) dominated in CK. This study provides quantitative insights into the role of rhizosphere metabolites in shaping microbial community assembly and highlights their potential for targeted modulation of rhizosphere microbiomes.

Beneficial rhizobacteria promote plant growth and protect plants against phytopathogens. Effective colonization on plant roots is critical for the rhizobacteria to exert beneficial activities. How bacteria migrate swiftly in the soil of semisolid or solid nature remains unclear. Here we report that sucrose, a disaccharide ubiquitously deployed by photosynthetic plants for fixed carbon transport and storage, and abundantly secreted from plant roots, promotes solid surface motility (SSM) and root colonization by Bacillus subtilis through a previously uncharacterized mechanism. Sucrose induces robust SSM by triggering a signaling cascade, first through extracellular synthesis of polymeric levan, which in turn stimulates strong production of surfactin and hyper-flagellation of the cells. B. subtilis poorly colonizes the roots of Arabidopsis thaliana mutants deficient in root-exudation of sucrose, while exogenously added sucrose selectively shapes the rhizomicrobiome associated with the tomato plant roots, promoting specifically bacilli and pseudomonad. We propose that sucrose activates a signaling cascade to trigger SSM and promote rhizosphere colonization by B. subtilis. Our findings also suggest a practicable approach to boost prevalence of beneficial Bacillus species in plant protection.

Soil health reflects the sustained capacity of soil to function as a vital living ecosystem, ensuring support for all forms of life. The evaluation of soil health relies heavily on physicochemical indicators. However, it remains unclear whether and how microbial traits are related to soil health in soil with long-term organic manure amendment. This study aims to examine how detrimental and beneficial microbial traits change with soil health based on physicochemical indicators. This research measures the effects of 9-year manure supplementation on soil health using multiomics techniques. We found that, compared to 100% chemical fertilizers, the soil health index increased by 5.2%, 19.3%, and 72.6% with 25%, 50%, and 100% organic fertilizer amendments, respectively. Correspondingly, the abundance of beneficial microorganisms, including Actinomadura, Actinoplanes, Aeromicrobium, Agromyces, Azospira, Cryobacterium, Dactylosporangium, Devosia, Hyphomicrobium, Kribbella, and Lentzea, increased progressively, while the abundance of the pathogenic fungus Fusarium decreased with the organic manure application rate. In addition, the application of organic manure significantly increased the concentrations of soil metabolites, such as sugars (raffinose, trehalose, maltose, and maltotriose) and lithocholic acid, which promoted plant growth and soil aggregation. Moreover, the abundances of pathogens and beneficial microorganisms and the concentrations of beneficial soil metabolites were significantly correlated with the soil health index based on physicochemical indicators. We conclude that organic fertilizer can enhance soil health by promoting the increase in beneficial microorganisms while suppressing detrimental microorganisms, which can serve as potential indicators for assessing soil health. In agricultural production, substituting 25–50% of chemical fertilizers with organic fertilizers significantly helps improve soil health and promotes crop growth.

In vineyard mulching research, using biodegradable liquid mulch represents a novel and environmentally conscious approach to mulching. In comparison, grapevine branch return has been identified as the most effective mulching method. The effects of in-row mulching with two materials, biodegradable liquid film (BLF) and grapevine branches (GBM), on soil properties and microbial communities in the vineyard were assessed using a one-way horizontal block test with tillage as a control. The results indicated that the application of mulching resulted in a reduction in soil bulk weight; an increase in soil moisture; an enhancement in soil organic matter; and a notable elevation in soil nutrients content compared to the control treatment. Both mulching techniques increased the abundance and diversity of soil microorganisms, strongly correlated with soil physicochemical properties. The correlation analysis demonstrated that total organic carbon (TOC); total nitrogen (TN); total potassium (TK); nitrate nitrogen (NN); and available phosphorus (AP) had the most significant impact on shaping the microbial community, exhibiting a positive correlation with microbial diversity. Additionally, soil nutrients were identified to exert a more pronounced influence on the composition of the bacterial community.

【目的】 探测不同覆盖处理对菠萝园土壤微生态环境的影响。【方法】 以未覆盖为对照（CK），比较研究了聚乙烯地膜（PM）、无纺布（NW）和可降解地膜（BF）覆盖下菠萝营养生长期土壤理化性状、酶活性以及细菌群落结构、代谢物的差异。【结果】 与CK相比，NW土壤中有效磷以及BF土壤中全氮含量显著提高；3种覆盖下土壤的过氧化氢酶和蔗糖酶活性显著降低，但PM土壤的蛋白酶、BF的酸性磷酸酶活性显著提高。与CK相比，PM土壤的放线菌数量减少；NW的细菌数量增多，放线菌减少；BF土壤的真菌和细菌数量增多，放线菌减少。16S测序表明3种覆盖的细菌菌群多样性均低于CK，其中BF的菌群丰度相对最高。与CK相比，PM、NW、BF土壤共筛选到17种显著差异代谢物，主要包括糖类、有机酸、含氮化合物和醇类代谢物，3种覆盖处理中BF土壤的糖类代谢物积累最高。CCA分析表明，pH影响土壤菌群结构发生分异，土壤养分、酶活性与细菌群落结构存在正相关。【结论】 3种覆盖处理中NW有利于维持营养生长期菠萝园土壤相对稳定的微生态环境。

Soil mulching is one of the common measures applied in organic agricultural production which could replace plastic films and protect the environment. In order to fully evaluate the effects of different straw mulching thicknesses on soil health, maize straw was mulched with the thicknesses of 0 cm (CK), 2 cm, 4 cm and 6 cm on soil surface to assess the effects on soil temperature (ST) and moisture (SM), soil pH, soil organic carbon (SOC), total nitrogen (TN), C/N, soil aggregates and soil bulk density (SBD) in a temperate organic vineyard. We found that straw mulching had a significant regulating effect, with soil moisture being elevated with increasing mulching thickness by 5.8%, 9.0% and 11.1% compared with CK. The soil SOC content increased by 3.0%, 2.4% and 2.3%. Although soil pH and C/N significantly (p < 0.05) increased, they fluctuated with increasing mulch thickness. Straw mulching also increased the content of >2 mm soil particle size and elevated the mean weight diameter (MWD) and geometric mean diameter (GMD). The increasing mulching thickness prolonged the effect on the stability of soil aggregates. The 4 cm maize straw mulching thickness has the best effect for ecologically and environmentally managing warm-temperate organic vineyards so it may have a great application prospect on a global scale.

为解决葡萄根系上浮和土壤酸化问题，探明葡萄园生草对葡萄根系生长和土壤营养状况的影响，以清耕为对照，在辽宁兴城地区葡萄园行内种植黑麦草（Lp）和紫花苜蓿（Ms），研究行内生草对葡萄不同根层根系长度和表面积、土壤有机质及矿质元素含量的影响。结果表明，黑麦草和紫花苜蓿均较清耕显著提高不同时期和不同土层的根系长度和根系表面积（P< 0.05），且其增幅为黑麦草 > 紫花苜蓿 > 清耕。黑麦草具有减轻葡萄园土壤酸化的效果，其土壤pH值6.22~7.04，高于清耕的6.14~6.39。黑麦草在坐果期、转色期和收获期的土壤有机质含量较清耕分别显著提高了24.71%，48.07%和44.44%（P< 0.05），而紫花苜蓿较对照分别提高了7.87%，29.88%和34.07%。黑麦草在坐果期、转色期和收获期时土壤中碱解氮含量较清耕分别显著提高了40.40%，51.46%，22.15%（P< 0.05），而紫花苜蓿较清耕分别提高了29.88%，28.03%，5.42%。黑麦草和紫花苜蓿较清耕均显著提高了各个时期的土壤有效磷含量（P< 0.05），钾元素含量明显升高，黑麦草处理的土壤全钾、全磷和有效磷含量最高，其次是紫花苜蓿，清耕最低。综上，行内种植黑麦草对增加葡萄根系长度和根系表面积、提高土壤有机质含量、减轻土壤酸化、增加必需营养元素含量等方面效果优于紫花苜蓿和清耕。

针对延怀盆地葡萄种植区长期受大风侵蚀，土壤沙化严重的问题，明确行间生草对葡萄园土壤理化性质的影响，探索北方埋土防寒区葡萄园行间生草技术。以怀来县为研究对象，于2017年在树龄为10 a的葡萄架下种植苔草和二月兰，以传统清耕为对照。种植3 a后采集土壤样品，分析土壤容重、持水量、团聚体含量、总碳、总氮、有机质、硝态氮、氨态氮以及有效态铁锰铜锌含量。结果表明：与传统清耕相比，种植3 a二月兰能显著增加0~20 cm表层土壤硝态氮含量，增加0~80 cm土层土壤有效磷、全氮含量，有效改善土壤物理性状；与传统清耕相比，种植3 a披针叶苔草能显著增加0~20 cm表层土壤有机质和全氮含量；二月兰与披针叶苔草连续种植3 a后均不同程度增加了葡萄园表层土壤各级团聚体中碳氮的含量。种植二月兰在提高0.125~0.250 mm粒级团聚体碳氮含量的效果最为明显；而苔草则表现为提高0.075~0.125 mm粒级团聚体碳氮含量的效果最为明显；2种行间生草方式对葡萄园沙化土壤团聚体结构的影响不同，种植3 a苔草显著增加>0.25 mm大团聚体含量，而种植3 a的二月兰因人为翻耕原因，导致<0.250 mm粒级团聚体显著增加。在延怀盆地葡萄行间种植草本植物能有效改善土壤理化性状，不同种类草本植物对土壤理化性状改善效果不同，因此在北方埋土防寒区选择适宜草种是推广该项技术的重要环节。

我国秸秆资源丰富但饲料化占比低,秸秆木质纤维素尤其是其中的木质素难以被动物体消化利用是影响秸秆饲料化进程的关键制约因素之一。生物降解木质素提升秸秆的营养价值是一种绿色、经济、可用于生产的促进秸秆饲料化方式。本文综述了秸秆木质素的化学成分及作用、木质素降解微生物及相关降解酶、木质素的生物发酵降解相关研究以及在动物养殖中的应用,以期为秸秆饲料化生产提供参考。

Composting is considered to be a primary treatment method for livestock manure and rice straw, and high degree of maturity is a prerequisite for safe land application of the composting products. In this study pilot-scale experiments were carried out to characterize the co-composting process of livestock manure with rice straw, as well as to establish a maturity evaluation index system for the composts obtained. Two pilot composting piles with different feedstocks were conducted for 3 months: (1) swine manure and rice straw (SM-RS); and (2) dairy manure and rice straw (DM-RS). During the composting process, parameters including temperature, moisture, pH, total organic carbon (TOC), organic matter (OM), different forms of nitrogen (total, ammonia and nitrate), and humification index (humic acid and fulvic acid) were monitored in addition to germination index (GI), plant growth index (PGI) and Solvita maturity index. OM loss followed the first-order kinetic model in both piles, and a slightly faster OM mineralization was achieved in the SM-RS pile. Also, the SM-RS pile exhibited slightly better performance than the DM-RS according to the evolutions of temperature, OM degradation, GI and PGI. The C/N ratio, GI and PGI could be included in the maturity evaluation index system in which GI>120% and PGI>1.00 signal mature co-composts.Copyright © 2013 Elsevier Ltd. All rights reserved.

Wood is the main renewable material on Earth and is largely used as building material and in paper-pulp manufacturing. This review describes the composition of lignocellulosic materials, the different processes by which fungi are able to alter wood, including decay patterns caused by white, brown, and soft-rot fungi, and fungal staining of wood. The chemical, enzymatic, and molecular aspects of the fungal attack of lignin, which represents the key step in wood decay, are also discussed. Modern analytical techniques to investigate fungal degradation and modification of the lignin polymer are reviewed, as are the different oxidative enzymes (oxidoreductases) involved in lignin degradation. These include laccases, high redox potential ligninolytic peroxidases (lignin peroxidase, manganese peroxidase, and versatile peroxidase), and oxidases. Special emphasis is given to the reactions catalyzed, their synergistic action on lignin, and the structural bases for their unique catalytic properties. Broadening our knowledge of lignocellulose biodegradation processes should contribute to better control of wood-decaying fungi, as well as to the development of new biocatalysts of industrial interest based on these organisms and their enzymes.

Studying changes in soil humus composition and humic acid (HA) structural characteristics caused by agronomic practices provide insights into the pathways of soil organic carbon (C) stabilisation dynamics. This five-year field study evaluated the effects of straw returning modes on humus composition and HA structure. Treatments included (i) corn straw returned on the soil surface (NTS), (ii) corn straw incorporated into soil within 0–10 cm (MTS), (iii) corn straw incorporated into soil within 0–20 cm (CTS) and (iv) no corn straw applied (CT). Soil HA was characterised by Fourier transform infrared (FTIR) and fluorescence spectroscopies. The results demonstrated that corn straw returning improved humus C fractions in this order NTS &amp;gt; MTS &amp;gt; CTS &amp;gt; CT in 0–20 cm depth. The FTIR and fluorescence results demonstrated that corn straw returning enhanced aliphatic, hydroxyl, methoxyl and carboxyl groups and simplified HA molecular structure, indicating regenerated and newly formed HA. Among all treatments, NTS was more conducive in simplifying HA molecular structure and enhancing aliphatic and hydrophobic C. Hydrophobicity in aliphatic C is the driving force in the stabilisation of soil C, which is important for sustainable agriculture. Therefore, we conclude that NTS is the better practice to turn arable lands into a sink for C.

Different mulches have variable effects on soil physicochemical characteristics, bacterial and fungal communities and ecosystem functions. However, the information about soil microbial diversity, community structure and ecosystem function in tea plantation under different mulching patterns was limited. In this study, we investigated bacterial and fungal communities of tea plantation soils under polyethylene film and peanut hull mulching using high-throughput 16S rRNA and ITS rDNA gene Illumina sequencing.The results showed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria and Chloroflexi, and the dominant fungal phyla were Ascomycota, Mortierellomycota and Basidiomycota in all samples, but different mulching patterns affected the distribution of microbial communities. At the phylum level, the relative abundance of Nitrospirae in peanut hull mulching soils (3.24%) was significantly higher than that in polyethylene film mulching soils (1.21%) in bacterial communities, and the relative abundances of Mortierellomycota and Basidiomycota in peanut hull mulching soils (33.72, 21.93%) was significantly higher than that in polyethylene film mulching soils (14.88, 6.53%) in fungal communities. Peanut hull mulching increased the diversity of fungal communities in 0-20 cm soils and the diversity of bacterial communities in 20-40 cm soils. At the microbial functional level, there was an enrichment of bacterial functional features, including amino acid transport and metabolism and energy production and conversion, and there was an enrichment of fungal functional features, including undefined saprotrophs, plant pathogens and soils aprotrophs.Unique distributions of bacterial and fungal communities were observed in soils under organic mulching. Thus, we believe that the organic mulching has a positive regulatory effect on the soil bacterial and fungal communities and ecosystem functions, and so, is more suitable for tea plantation.

An active and diverse soil biota is important for maintaining crop productivity and quality, and preservation of these traits is a major goal of sustainable farming. This study aimed at unravelling the impact of different management practices on soil fungal and bacterial biodiversity in vineyards as a model for permanent crops. Species diversity was assessed using an amplicon sequencing approach in a long-term field experiment in the Rheingau wine region of Germany where integrated, organic and biodynamic management practices had been in place for 10 years. Fungal community composition under integrated management differed significantly from organic and biodynamic management, whereas fungal species richness remained unaffected. Soil under integrated management had a significantly reduced bacterial species richness compared to organic, but community composition was similar to organically and biodynamically managed soils. Highest fungal richness was obtained under cover crop between rows in topsoil, arising from cover cropping and organic carbon supply.

The aim of this work was to investigate the effects of biodynamic management with and without the addition of green manure, in comparison with organic management, on the microbiota in vineyards soil.High throughput sequencing was used to compare the taxonomic structure of the soil bacterial and fungal communities from vineyards managed with different methods (organic, biodynamic or biodynamic with green manure). Our results showed that microbial communities associated with biodynamic and organic farming systems were very similar, while green manure was the greatest source of soil microbial biodiversity and significantly changed microbial richness and community composition compared with other soils. Green manure also significantly enriched bacterial taxa involved in the soil nitrogen cycle (e.g. Microvirga sp., Pontibacter sp. and Nitrospira sp.).Our results showed that the diversity and composition of the microbial communities associated with biodynamic and organic farming systems were similar, indicating that the use of biodynamic preparations 500 and 501 did not cause any significant detectable changes to the soil microbial community in the short term, while the effects of green manure were significant in soil microbiota.The microbiological richness and structure of soil are used as a sensitive indicator of soil quality. The extension of organic/biodynamic farming, associated with green manure application, could contribute to increase the abundance of functional groups of biological and agronomical relevance and maintaining microbial biodiversity in vineyard soils.© 2017 The Society for Applied Microbiology.

The microbiome of a vineyard may play a critical role in fruit development, and consequently, may impact quality properties of grape and wine. Vineyard management approaches that have directly manipulated the microbiome of grape clusters have been studied, but little is known about how vineyard management practices that impact the soil microbial pool can influence this dynamic. We examined three under-vine soil management practices: 1) herbicide application, 2) soil cultivation (vegetation removal), and 3) natural vegetation (no vegetation removal) in a Riesling vineyard in New York over a three-year period. The microbiomes associated with soil and grapes were profiled using high-throughput sequencing of the bacterial 16 S rRNA gene and fungal ITS regions. Our results showed that soil bacterial composition under natural vegetation differs from that seen in glyphosate-maintained bare soil. Soil fungal composition under the natural vegetation treatment was distinct from other treatments. Although our study revealed soil microbiome shifts based on under-vine management, there were no corresponding changes in fruit-associated microbial composition. These results suggested that other vineyard management practices or environmental factors are more influential in shaping the grape-associated microbiome.

The soil microbiome governs biogeochemical cycling of macronutrients, micronutrients and other elements vital for the growth of plants and animal life. Understanding and predicting the impact of climate change on soil microbiomes and the ecosystem services they provide present a grand challenge and major opportunity as we direct our research efforts towards one of the most pressing problems facing our planet. In this Review, we explore the current state of knowledge about the impacts of climate change on soil microorganisms in different climate-sensitive soil ecosystems, as well as potential ways that soil microorganisms can be harnessed to help mitigate the negative consequences of climate change.

Microbial activity in forest soils is driven by the dynamics of ecosystem processes, largely dependent on trees as the major primary producers. Diurnal variation of root activity, seasonality of photosynthate production or recalcitrance of decomposing plant biomass all affect microbial abundance, composition of their communities and activity. Due to low N content, fungi appear to be the major decomposers of complex plant biomass: litter and deadwood and to largely shape associated bacterial communities and their activity. On the other hand, bacteria are important in decomposition of fungal mycelia and N-cycle processes including N-fixation. Microbial activity is also affected in the short term by climatic events and in the long-term by ecosystem development after disturbances.Copyright © 2017 Elsevier Ltd. All rights reserved.

Advances in our understanding of the decomposition processes in forest ecosystems over the past three decades have demonstrated the importance of lignin as a regulating factor in the decomposition of leaf litter. Consequently, increasingly more attention is being focused on the ecology of fungi associated with lignin decomposition. The aim of this review is to provide a critical summary of the ecology of ligninolytic fungi inhabiting leaf litter and forest floor materials. The review focuses on the following aspects of ligninolytic fungi: the taxonomic and functional diversity of ligninolytic fungi, the outcomes of interactions between ligninolytic fungi and other organisms, the activity and abundance of ligninolytic fungi measured by the production of bleached leaves and humus, the activity of ligninolytic enzymes in soil environments, the substratum and seral succession, spatial and temporal patterns in both mycelial abundance and species distribution, and the effect of environmental factors such as nitrogen deposition and global environmental changes on ligninolytic fungi. This review integrates the ecology, diversity, and activity of ligninolytic fungi into the context of an ecosystem in order to provide an understanding of the roles of ligninolytic fungi in decomposition processes.

The colonization of land by plants appears to have coincided with the appearance of mycorrhiza-like fungi. Over evolutionary time, fungi have maintained their prominent role in the formation of mycorrhizal associations. In addition, however, they have been able to occupy other terrestrial niches of which the decomposition of recalcitrant organic matter is perhaps the most remarkable. This implies that, in contrast to that of aquatic organic matter decomposition, bacteria have not been able to monopolize decomposition processes in terrestrial ecosystems. The emergence of fungi in terrestrial ecosystems must have had a strong impact on the evolution of terrestrial bacteria. On the one hand, potential decomposition niches, e.g. lignin degradation, have been lost for bacteria, whereas on the other hand the presence of fungi has itself created new bacterial niches. Confrontation between bacteria and fungi is ongoing, and from studying contemporary interactions, we can learn about the impact that fungi presently have, and have had in the past, on the ecology and evolution of terrestrial bacteria. In the first part of this review, the focus is on niche differentiation between soil bacteria and fungi involved in the decomposition of plant-derived organic matter. Bacteria and fungi are seen to compete for simple plant-derived substrates and have developed antagonistic strategies. For more recalcitrant organic substrates, e.g. cellulose and lignin, both competitive and mutualistic strategies appear to have evolved. In the second part of the review, bacterial niches with respect to the utilization of fungal-derived substrates are considered. Here, several lines of development can be recognized, ranging from mutualistic exudate-consuming bacteria that are associated with fungal surfaces to endosymbiotic and mycophagous bacteria. In some cases, there are indications of fungal specific selection in fungus-associated bacteria, and possible mechanisms for such selection are discussed.

为探明豆/禾牧草连续间作下的根系生长特性、碳氮代谢特性及二者相互耦联机制的长期效应，通过田间框栽土培试验，以紫花苜蓿单作和燕麦单作为参照，对紫花苜蓿/燕麦间作种植后第2年、第3年（高产期）连续2年的根系特征、碳氮代谢特性及其相互协调关系开展研究。结果表明：燕麦的生物量表现为间作显著高于单作（P&lt;0.05）；燕麦的根表面积和根平均直径表现为间作显著高于单作（P&lt;0.05）；燕麦的蒸腾速率（T_r）、净光合速率（P_n）、气孔导度（G_s）、核酮糖-1，5-二磷酸羧化酶（RuBPCase）活性、4个氮代谢酶活性和碳水化合物积累量表现为间作显著高于单作（P&lt;0.05），而紫花苜蓿与燕麦表现相反。通过相关性分析发现，生物量与光合气体交换参数、氮代谢酶活性、根系特性呈正相关；根表面积、根平均直径与T_r、P_n、G_s、硝酸还原酶（NR）活性、氮积累量、蛋白总量呈显著正相关（P&lt;0.05）；根体积、根表面积、根平均直径与亚硝酸还原酶（NiR）活性、谷氨酸合酶（GOGAT）活性呈极显著正相关（P&lt;0.01）。由此可知，紫花苜蓿与燕麦间作更有利于燕麦优化其根系形态，同时也会显著提高燕麦净光合速率和蒸腾速率，增强燕麦RuBPCase、NR和谷氨酰胺合成酶（GS）等碳、氮代谢酶活性，进而促进其体内碳水化合物及蛋白质积累以改善燕麦生物量和品质，连续间作减弱了系统内燕麦对紫花苜蓿根表面积和根体积的抑制，拓展了紫花苜蓿总根长，但整体而言，间作抑制了紫花苜蓿根系生长和碳、氮代谢水平，不利于其代谢产物及生物量的积累；且总根长、根表面积和根体积对碳、氮代谢起显著促进作用，紫花苜蓿/燕麦间作体系内根系及碳、氮代谢的协调一致可有效提高体系内生物量和蛋白总量。

The planting of mangroves is extensively used to control the invasive plant Spartina alterniflora in coastal wetlands. Different plant species release diverse sets of small organic compounds that affect rhizosphere conditions and support high levels of microbial activity. The root-associated microbial community is crucial for plant health and soil nutrient cycling, and for maintaining the stability of the wetland ecosystem.

Soil organic matter (SOM) has a critical role in regulating soil phosphorus (P) dynamics and producing phytoavailable P. However, soil P dynamics are often explained mainly by the effects of soil pH, clay contents, and elemental compositions, such as calcium, iron, and aluminum. Therefore, a better understanding of the mechanisms of how SOM influences phytoavailable P in soils is required for establishing effective agricultural management for soil health and enhancement of soil fertility, especially P-use efficiency. In this review, the following abiotic and biotic mechanisms are discussed; (1) competitive sorption between SOM with P for positively charged adsorption sites of clays and metal oxides (abiotic reaction), (2) competitive complexations between SOM with P for cations (abiotic reaction), (3) competitive complexations between incorporation of P by binary complexations of SOM and bridging cations with the formation of stable P minerals (abiotic reaction), (4) enhanced activities of enzymes, which affects soil P dynamics (biotic reaction), (5) mineralization/immobilization of P during the decay of SOM (biotic reaction), and (6) solubilization of inorganic P mediated by organic acids released by microbes (biotic reaction).© The Author(s) 2023.

Organic agriculture is becoming an increasingly popular direction in modern agriculture. At the same time, some researchers and practitioners still have doubts about the ability of this technology to maintain the balance of nutrients in the soil. The article is a contribution to the study of the influence of long-term organic farming on agrochemical soil parameters. The aim of the study was to study the influence of organic farming technology on the content of humus, mobile forms of potassium and mobile forms of phosphorus in the soil of the most important components for fertility – humus, mobile forms of potassium and mobile forms of phosphorus in the non-carbonate chernozems of Western Siberia. The chernozems of Western Siberia are characterized by a high content of humus and nutrients, have optimal properties for agricultural crops. A statistically processed comparison of the quantitative content of humus, mobile forms of potassium and mobile forms of phosphorus in fields with long-term use of organic farming technology, and in similar fields where this technology was not used, was carried out. The article includes a brief geographical, geological, climatic characteristics of the place of the experiment, a description of the applied agricultural technologies and fertilizers. As a result, it was found that the use of organic farming technology has a positive effect on the state of soils, which is confirmed by an increase in the content of humus, mobile forms of potassium and mobile forms of phosphorus.

Plant health in natural environments depends on interactions with complex and dynamic communities comprising macro- and microorganisms. While many studies have provided insights into the composition of rhizosphere microbiomes (rhizobiomes), little is known about whether plants shape their rhizobiomes. Here, we discuss physiological factors of plants that may govern plant-microbe interactions, focusing on root physiology and the role of root exudates. Given that only a few plant transport proteins are known to be involved in root metabolite export, we suggest novel families putatively involved in this process. Finally, building off of the features discussed in this review, and in analogy to well-known symbioses, we elaborate on a possible sequence of events governing rhizobiome assembly.Copyright © 2017 Elsevier Ltd. All rights reserved.

Long-term carbon (C) stabilisation in tropical and subtropical soils under no-tillage (NT) rests on the formation of mineral–organic associations (MOAs) that can be enriched with microbial metabolites. In this work, we assessed the role of long-term tillage and cropping systems and mineral N fertilisation in enriching MOAs with microbial metabolites in a subtropical soil. For this purpose, we sampled a sandy clay loam Acrisol up to 1 m depth involved in an ongoing 30-year-old experiment under two different tillage systems (conventional tillage and NT) in the presence and absence of legume cover crops and mineral nitrogen (N) fertilisation. The soil samples were subjected to particle size fractionation and n-alkane analysis. The NT and the presence of legume cover crops in the surface soil layer (0-5 cm) increased the abundance of plant-derived lipids (i.e. compounds with n-alkane chains of 25-33 C atoms) in the whole soil. Microbial-derived lipids (i.e. compounds with shorter n-alkane chains (15-24 C atoms)) were more abundant in the clay fraction of the surface (0-5 cm) and sub-surface soil layers (20-30 and 75-100 cm) in NT soil receiving high-quality residues of legume cover crops. However, N fertilisation decreased the abundance of microbial-derived lipids in the clay fraction of the 0-5 and 20-30 cm soil layers. Our findings highlight the role of N-rich residues of legume cover crops, but not of mineral N fertilisation, in the long-term stabilisation of C in MOAs in NT soils through the action of microbial residues.

Knowledge of the impacts of no-tillage and cover cropping on carbon accumulation and stabilisation in highly weathered agricultural soils of subtropical regions is scant. We hypothesised that implementation of no-tillage coupled with high-quality legume residues in highly weathered agricultural soils would result in high carbon accumulation rates, mainly as microbe- and plant-derived materials in fine mineral–organic complexes.

Interplanting crops is the best method to grow crops synergistically for better utilization of land and agro-resources. Grape (Vitis vinifera) and potato (Solanum tuberosum L.) have highly efficient agricultural planting systems in China, however, how soil physicochemical properties and soil microbial communities and metabolites affect the output of grape-potato interplanting remained unknown. In this study, we employed three planting patterns (CK: grape monocropping; YY: grape interplanted with potato (variety ‘Favorita’); LS: grape interplanted with potato (variety ‘Longshu7’)) at two experimental sites i.e., the Huizhou (2022) site and the Qingyuan site (2023). The grape variety for all planting patterns was ‘Sunshine Rose’. Soil samples (top 0-20 cm) at both sites were collected to observe the diversity of bacterial communities and soil metabolites. Our findings revealed that, compared with monocropping, the interplanted systems resulted in higher concentrations of total nitrogen, available phosphorus, and available potassium and enhanced the activities of acid phosphatase, urease, and protease. The potato root exudates also altered the relative abundance of Bacillus, Kaistobacter, and Streptomyces in the rhizosphere. Among the soil metabolites, lipids and organic acids showed the most significant changes. Notably, 13-L-hydroperoxylinoleic acid is the key differentially abundant metabolite involved in the regulation of linoleic acid metabolism pathways. The association analyses of the metabolome, microbiome, and soil physicochemical properties revealed that the interactions of microbes and metabolites resulted in differences in the soil nutrient content, whereas the interactions of 13-L-hydroperoxylinoleic acid and Firmicutes improved the soil nutrient levels and bacterial composition in the interplanting systems. In summary, our findings demonstrated that intercropping grapes with potato ‘Favorita’ was better with respect to improving soil nutrients, soil enzyme activity, the diversity of soil bacteria, and soil metabolites without causing adverse impacts on grape yield. Overall, this study explained the physiological mechanisms by which soil microorganisms and metabolites promote potato growth in grape interplanting and provided new perspectives for the utilization of soil resources in vineyards.

Biochar and green manure have been widely applied in agricultural production and are important means to achieve sustainable agriculture. However, there is limited research systematically and comprehensively exploring the response of soil microbiota and the changes in soil metabolomics after the addition of two different carbon source amendments to the soil, and the differential mechanisms of soil metabolomics between them remain unclear. In this study, a long-term field experiment (initiated in 2019) was conducted to investigate the effects of biochar and green manure application on soil nutrients and soil functions driven by soil microbes. Compared to the pure fertilizer treatment, biochar increased soil total carbon by 14.54% to 27.04% and soil available potassium by 4.67% to 27.46%. Ryegrass significantly increased soil available phosphorus and organic matter. Under different fertilization regimes, the ecological niches of soil microbes changed significantly. Network analysis revealed that long-term ryegrass returning reduced the complexity of soil microbial networks. Ryegrass and biochar increased dispersal limitation in fungal assemblages (reaching 93.33% and 86.67%, respectively), with biochar particularly enhancing variable selection in bacterial assemblages (accounting for 53.33%). Variation partitioning analysis based on redundancy analysis indicated that humic substances had the highest explanatory power for microbial community variation, with humic substances explaining 38.49% of bacteria and 52.19% of fungi variation. The ryegrass treatment mainly changed the abundance of carbohydrates (CH), amines (AM), c (AH), and lipids (LP), while the BC treatment mainly altered the abundance of organic acids (AC), amines (AM), and carbohydrates (CH). Meanwhile, both treatments significantly reduced the bisphenol A, one of the soil pollutants. Ryegrass incorporation significantly increased the abundance of genes related to soil C, N, P, and S cycling, especially genes involved in carbon decomposition, while biochar significantly enhanced the abundance of nitrogen fixation genes nifH and Hao in soil. Random forest model results indicated that carbohydrates, alcohols, aromatics (AR), and ester (ES) were the main categories of metabolites in soil influenced by differential microbes, and Finegoldia served as a common important metabolic driving species. In summary, this study reveals the processes of soil function, microbial community succession, and metabolism driven by ryegrass and biochar, providing important insights for optimizing soil management and improving soil quality.

Maintaining soil health is fundamental to sustaining agricultural productivity, however, the intricate role of soil microbial diversity in this process is not fully understood. Current research acknowledges that soil microorganisms including bacteria, fungi, and archaea are pivotal in driving essential soil functions such as nutrient cycling, organic matter decomposition, and disease suppression. However, the impacts of global environmental changes and intensive agricultural practices on the diversity of these microorganisms remain a critical gap in the literature. This gap is significant because a decline in microbial diversity could severely compromise soil health, and consequently crop productivity. Here, we provide a comprehensive review of the factors influencing soil microbial diversity and examine their implications for crop performance. We assess both natural factors such as soil pH, moisture, temperature, and vegetation type as well as human-induced factors including tillage systems and fertilizer application. The review synthesizes recent findings on how these factors shape microbial communities and their functional roles in nutrient cycling, soil structure formation, and disease suppression. Our analysis highlights the mechanisms by which microbial diversity enhances plant growth and yield, addressing the gap in understanding the direct links between microbial diversity and agricultural outcomes. Our findings underscore the urgent need for sustainable agricultural practices that protect and enhance microbial diversity to safeguard long-term soil fertility and crop productivity. By addressing the challenges in manipulating soil microbial communities and integrating microbial ecology with crop management practices, this research advances our ability to sustain agricultural systems in the face of global environmental changes.

The rapid development of nanotechnology makes the environmental impact assessment a necessity to ensure the sustainable use of engineered nanomaterials. Here, silver nanoparticles (AgNPs) at 100 mg/kg were added to soils in the absence or presence of cucumber () plants for 60 days. The response of the soil microbial community and associated soil metabolites was investigated by 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics, respectively. The results show that AgNP exposure significantly increased the soil pH in both unplanted and cucumber-planted soils. The soil bacterial community structure was altered upon Ag exposure in both soils. Several functionally significant bacterial groups, which are associated with carbon, nitrogen, and phosphorus cycling, were compromised by AgNPs in both unplanted and cucumber-planted soils. Generally, plants played a limited role in mediating the impact of AgNPs on the bacterial community. Soil metabolomic analysis showed that AgNPs altered the metabolite profile in both unplanted and cucumber-planted soils. The significantly changed metabolites are involved in sugar and amino acid-related metabolic pathways, indicating the perturbation of C and N metabolism, which is consistent with the bacterial community structure results. In addition, several fatty acids were significantly decreased upon exposure to AgNPs in both unplanted and cucumber-planted soils, suggesting the possible oxidative stress imposed on microbial cell membranes. These results provide valuable information for understanding the biological and biochemical impact of AgNP exposure on both plant species and on soil microbial communities; such understanding is needed to understand the risk posed by these materials in the environment.

Soil communities are diverse taxonomically and functionally. This ecosystem experiences highly complex networks of interactions, but may also present functionally independent entities. Plant roots, a metabolically active hotspot in the soil, take an essential part in below-ground interactions. While plants are known to release an extremely high portion of the fixated carbon to the soil, less information is known about the composition and role of C-containing compounds in the rhizosphere, in particular those involved in chemical communication. Specialized metabolites (or secondary metabolites) produced by plants and their associated microbes have a critical role in various biological activities that modulate the behavior of neighboring organisms. Thus, elucidating the chemical composition and function of specialized metabolites in the rhizosphere is a key element in understanding interactions in this below-ground environment. Here, we review key classes of specialized metabolites that occur as mostly non-volatile compounds in root exudates or are emitted as volatile organic compounds (VOCs). The role of these metabolites in below-ground interactions and response to nutrient deficiency, as well as their tissue and cell type-specific biosynthesis and release are discussed in detail.© 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

In conventional tea plantations, a large amount of pruned material returns to the soil surface, putting a high quantity of polyphenols into the soil. The accumulation of active allelochemicals in the tea rhizosphere and subsequent shift in beneficial microbes may be the cause of acidification, soil sickness, and regeneration problem, which may be attributed to hindrance of plant growth, development, and low yield in long-term monoculture tea plantation. However, the role of pruning leaf litter in soil sickness under consecutive tea monoculture is unclear. Here, we investigated soil samples taken from conventional tea gardens of different ages (2, 15, and 30 years) and under the effect of regular pruning. Different approaches including liquid chromatography-mass spectrometry (LC-MS) analysis of the leaf litter, metagenomic study of root-associated bacterial communities, and interaction of polyphenols with selected bacteria were applied to understand the effect of leaf litter-derived polyphenols on the composition and structure of the tea rhizosphere microbial community. Our results indicated that each pruning practice returns a large amount of leaf litter to each tea garden. LC-MS results showed that leaf litter leads to the accumulation of various allelochemicals in the tea rhizosphere, including,,,, and with increasing age of the tea plantation. Meanwhile, in the tea garden grown consecutively for 30 years (30-Y), the phenol oxidase and peroxidase activities increased significantly. Pyrosequencing identified and as the dominant genera, while plant growth-promoting bacteria, especially,, and, were significantly reduced in the long-term tea plantation. The qPCR results of 30-Y soil confirmed that the copy numbers of bacterial genes per gram of the rhizosphere soil were significantly reduced, while that of increased significantly. study showed that the growth of catechin-degrading bacteria (e.g., ) increased and plant-promoting bacteria (e.g., ) decreased significantly with increasing concentration of these allelochemicals. Furthermore, interaction showed a 0.36-fold decrease in the pH of the broth after 72 h with the catechin degradation. In summary, the increase of and in the 30-Y garden was found to be associated with the accumulation of catechin substrates. In response to the long-term monoculture of tea, the variable soil pH along with the litter distribution negatively affect the population of plant growth-promoting bacteria (e.g.,,, and ). Current research suggests that the removal of pruned branches from tea gardens can prevent soil sickness and may lead to sustainable tea production.Copyright © 2020 Arafat, Ud Din, Tayyab, Jiang, Chen, Cai, Zhao, Lin, Lin and Lin.

Choline is abundant in association with eukaryotes and plays roles in osmoprotection, thermoprotection, and membrane biosynthesis in many bacteria. Aerobic catabolism of choline is widespread among soil proteobacteria, particularly those associated with eukaryotes. Catabolism of choline as a carbon, nitrogen, and/or energy source may play important roles in association with eukaryotes, including pathogenesis, symbioses, and nutrient cycling. We sought to generate choline analogues to study bacterial choline catabolismin vitroandin situ. Here we report the characterization of a choline analogue, propargylcholine, which inhibits choline catabolism at the level of Dgc enzyme-catalyzed dimethylglycine demethylation inPseudomonas aeruginosa. We used genetic analyses and13C nuclear magnetic resonance to demonstrate that propargylcholine is catabolized to its inhibitory form, propargylmethylglycine. Chemically synthesized propargylmethylglycine was also an inhibitor of growth on choline. Bioinformatic analysis suggests that there are genes encoding DgcA homologues in a variety of proteobacteria. We examined the broader utility of propargylcholine and propargylmethylglycine by assessing growth of other members of the proteobacteria that are known to grow on choline and possess putative DgcA homologues. Propargylcholine showed utility as a growth inhibitor inP. aeruginosabut did not inhibit growth in other proteobacteria tested. In contrast, propargylmethylglycine was able to inhibit choline-dependent growth in all tested proteobacteria, includingPseudomonas mendocina,Pseudomonas fluorescens,Pseudomonas putida,Burkholderia cepacia,Burkholderia ambifaria, andSinorhizobium meliloti. We predict that chemical inhibitors of choline catabolism will be useful for studying this pathway in clinical and environmental isolates and could be a useful tool to study proteobacterial choline catabolismin situ.

The Lands Pathway is a fundamental biochemical process named for its discovery by William EM Lands and revealed in a series of seminal papers published in the Journal of Biological Chemistry between 1958-65. It describes the selective placement in phospholipids of acyl chains, by phospholipid acyltransferases. This pathway has formed a core component of our knowledge of phospholipid and also diglyceride metabolism in mammalian tissues for over 60 years now. Our understanding of how the Lands pathways are enzymatically mediated via large families of related gene products that display both substrate and tissue specificity has grown exponentially since. Recent studies building on this are starting to reveal key roles for the Lands pathway in specific scenarios, in particular inflammation, immunity and inflammation. This review will cover the Lands cycle from historical perspectives first, then present new information on how this important cycle forms a central regulatory node connecting fatty acyl and phospholipid metabolism and how its altered regulation may present new opportunities for therapeutic intervention in human disease.© 2022 The Author(s).