Correlation of bacterial community with phosphorus fraction drives discovery of Actinobacteria involved soil phosphorus transformation during the trichlorfon degradation

Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health

Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.

Alterations in bacterial structure and function in seawater due to Mytilus coruscus farming: implications for sustainable aquaculture management

Microorganisms are essential for maintaining the ecological balance and supporting the health of aquatic animals in aquaculture environments. This study utilized high-throughput sequencing technology to analyze the diversity, composition, co-occurrence networks, assembly mechanisms, and functional predictions of bacterial communities in seawater from both Mytilus coruscus aquaculture areas (AA) and non-aquaculture areas (NAA) across different seasons. The results indicated that the number of operational taxonomic units (OTUs) in the AA group was higher than the NAA group, while the Simpson index was significantly lower in the bottom water (p < 0.05). Additionally, the β-diversity (Bray-Curtis distance and βMNTD) was significantly reduced in the AA group compared to the NAA group (p < 0.05). M. coruscus farming influenced the relative abundance of certain genera, including Pseudoalteromonas, HIMB11, and Clade Ia, with the AA group exhibiting a greater number of specialist species. Co-occurrence network analysis revealed that the bacterial network in the NAA group had a higher number of nodes, edges, and modularity, whereas the AA group displayed greater closeness centrality and betweenness centrality. Following the removal of 80% of the nodes, the natural connectivity of the surface water in the AA group declined more rapidly than in the NAA group. Homogeneous selection was the primary assembly mechanism of bacterial communities in the AA group, while diffusion limitation was predominant in the NAA group. FAPROTAX functional predictions indicated the higher relative abundance of functions associated with organic matter degradation and nitrogen cycling in the AA group. These findings suggest that M. coruscus farming activities significantly alter the structure and function of bacterial communities in seawater, providing valuable data to support sustainable aquaculture for M. coruscus and optimize fisheries' carbon sink management strategies.

Phosphorus resource partitioning underpins diversity patterns and assembly processes of microbial communities in plateau karst lakes

Eutrophication triggered by internal phosphorus (P) poses a substantial threat to the biodiversity of organisms in freshwater ecosystems. However, little is known about the linkages between P resource partitioning and microbial succession, especially in karst sediments. Here, we studied the diversity patterns and assembly processes of bacterial and archaeal communities in sediment cores from two historically hyper-eutrophicated karst lakes, Hongfeng Lake and Aha Lake, and investigated the relative contribution of P fractions to them. Our null and neutral models consistently indicated that bacterial and archaeal community assembly was judged to be deterministic rather than stochastic. We found a monotonically decreasing pattern for bacterial Shannon diversity toward deep sediments in Aha Lake, but U- or hump-shaped patterns for archaea in Hongfeng and Aha Lakes. Intriguingly, the community dissimilarity Bray-Curtis of bacteria and archaea consistently increased with increasing depth distance, with slopes of 0.0080 and 0.0069 in Hongfeng Lake and 0.0078 and 0.0087 in Aha Lake, respectively. Such cross-taxon congruence was well-supported by equivalent ecological processes (i.e., environmental selection). For bacteria and archaea, Shannon diversity was primarily affected by the total P (TP) fractions such as the loosely adsorbed TP or calcium-bound TP and sediment TP. Their community composition was significantly (P < 0.05) affected by calcium-bound inorganic P (Pi), loosely adsorbed Pi and reductant-soluble Pi. Although sediment properties were important, bacterial and archaeal diversity or community composition were well-explained by the Pi fractions, with high direct or indirect effects. In particular, Pi fractions exhibited stronger effects on bacterial and archaeal characteristics than organic P fractions. Taken together, our study provides novel insights into the ecological importance of P resource partitioning to microbial succession, which has crucial implications for disentangling the biogeochemical processes of P cycling in aquatic ecosystems.

NaIO4/air-initiated phosphorylation of alcohols with H-phosphine oxides for the construction of P(O)-O bonds in water

A facile and efficient protocol for P(O)-O bond formation was discovered through NaIO4/air-initiated phosphorylation of alcohols with H-phosphine oxides in water. This reaction showed good functional group tolerance and a broad substrate scope, providing an alternative method for constructing P(O)-O bonds. Mechanistic studies suggested that a phosphoryl radical-involving process from H-phosphine oxides facilitated the phosphorylation of alcohols under air.

Root-knot nematode infections and soil characteristics significantly affected microbial community composition and assembly of tobacco soil microbiota: a large-scale comparison in tobacco-growing areas

Introduction

Tobacco root-knot nematode (RKN) is a highly destructive soil-borne disease worldwide. However, there is a lack of research on the relationship between RKN and tobacco root microbial community composition under large-scale geographical conditions in China.

Methods

In this study, we collected 65 samples from 28 main tobacco-growing areas across 10 provinces in China and conducted 16S rDNA sequencing to investigate the dynamic microbial changes in tobacco soil infected by RKN compared to healthy tobacco soil. Based on the analysis of rhizosphere soil bacterial communities, changes after RKN infection, and soil environmental factors.

Results

We found the 28 tobacco-growing areas could be divided into two distinct groups with different microbial compositions and varying responses to RKN infection. In group1 of the provinces of Anhui, Henan, Shanxi, and Heilongjiang, Vicinamibacteria dominated the bacterial community, while Acidobacteriae was present in low abundance. In contrast, group2 of the other six provinces (Yunnan, Guizhou, Chongqing, Guangxi, Hubei, and Shandong) exhibited an opposite pattern. After infected by RKN, the genera Chitinophaga increased significant in group 1, while the genera Rhodococcus in group 2 exhibited a substantial increase. Alpha-diversity analysis revealed that RKN-infected tobacco exhibited a richer and more diverse rhizosphere soil bacterial community compared to healthy tobacco in most growing areas. A total of 12 kinds of soil environmental factors were measured in healthy and RKN-infected tobacco soil, and based on the co-occurrence and correlation analysis between environmental factors and microbial species, the pH level, calcium (Ca), magnesium (Mg), phosphorus (P), iron (Fe), and sodium (Na) were identified as key environmental factors influencing the population composition of rhizosphere microorganisms during RKN infection. We observed that RKN infection further increased the pH in weakly alkaline group 1 soil, while weakly acidic group 2 soil experienced a further decrease in pH. Furthermore, we identified three genera as potential biocontrol or plant growth-promoting bacteria for tobacco.

Discussion

These findings provide valuable reference data for managing RKN disease in different tobacco-growing areas and contribute to the exploration of new and effective biological control methods.

Slow release of attapulgite based nano-enabled glyphosate improves soil phosphatase activity, organic P-pool and proliferation of dominant bacterial community

Glyphosate (Glp) was encapsulated onto the dopamine-modified attapulgite to develop an attapulgite-based nano-enabled Glp (DGlp) in this study with comparable weed control effects to pure Glp and commercial Glp solutions. Within 24 hours, the active Glp molecule was slowly released from DGlp at a maximum remaining rate of over 90%, and then degraded similarly to Glp solution in soil. The addition of DGlp improved soil available phosphorus (P) contents, phosphatase activity, and enzyme extractable P fraction. However, compared to Glp solution, DGlp addition had no effect on the transformation of soil inorganic P fractions. The 16S rRNA sequencing and co-occurrence network results revealed that DGlp had no significant effect on the soil bacterial diversity but diminished the complexity of soil bacterial network. According to the Mantel test, DGlp addition stimulated soil phosphatase activity and proliferation of dominant bacterial taxa (Proteobacteria and Firmicutes) capable of degrading Glp. Proteobacteria and Firmicutes that had been extensively recruited and enriched for their phosphatase activities may have mobilized reactive enzyme-P, significantly enhancing the transformation of reactive organic P and P-pool in soil. These results contributed to our understanding of the ecotoxicity and environmental impacts of nano-enabled Glp prior to its successful and sustainable application in agriculture.

Co-existing antibiotics alter the enantioselective dissipation characteristics of zoxamide and drive combined impact on soil microenvironment

Co-existence of antibiotics (ABX) in soil may expand the environmental harm of pesticide pollution. Our study investigated the combined effects of five antibiotics chlortetracycline (CTC), oxytetracycline (OTC), tetracycline (TC), sulfamethoxazole (SMX), enrofloxacin (ENR) on enantioselective fate of zoxamide (ZXM) and soil health. The results showed that S-(+)-ZXM preferentially dissipated in soil. ABX prolonged dissipation half-life and reduced enantioselectivity of ZXM. Soil was detected to be more acidic after long-term treatment of ZXM and ABX. Lowest soil available N, P, K were found in ZXM + SMX, ZXM + OTC and ZXM + SMX groups at 80 days, respectively. ABX had demonstrated effective promotion of catalase (S-CAT), urease (S-UE) and negative impact on dehydrogenase (S-DHA), sucrase (S-SC) activities. Bacteria Lysobacter, Sphingomonas and fungus Mortierella were identified as the most dominant genera, which possessed as potential microbial resources for removal of composite pollution from ZXM and ABX. SMX and TC, SMX, ENR, respectively, contributed to the alteration of bacteria and fungi community abundance. Soil acidity, available N and enzyme activity showed stronger correlations with bacteria and fungi compared to other environmental factors. Our findings highlighted the interactions between ZXM and ABX from the perspective of soil microenvironment changes. Moreover, a theoretical basis for the mechanism was actively provided.

A colorimetric analytical method based on a TCPP-CuCo2O4-like peroxidase for the detection of trichlorfon

In this work, a highly sensitive colorimetric sensing platform was designed for the detection of trichlorfon based on inhibiting thiocholine (TCh)-induced redox reaction. 5,10,15,20-Tetracarboxyphenylporphyrin (TCPP) functionalized CuCo2O4 (TCPP-CuCo2O4) was synthesized to construct a colorimetric sensing platform for trichlorfon. In the presence of H2O2, TCPP-CuCo2O4 can oxidize colorless 3,3',5,5'-tetramethylbenzidine (TMB) into blue ox-TMB, accompanied by a strong absorption peak at 652 nm, while acetylcholinesterase (AChE) can specifically hydrolyze acetylthiocholine (ATCh) into TCh, which can reduce ox-TMB back into colorless TMB, resulting in a lower absorbance at 652 nm. Trichlorfon can irreversibly inhibit the activity of AChE and thus recover the absorption peak. Under the optimized conditions, detection of trichlorfon has a wide linear range of 40-4000 ng mL-1 with a linear correlation coefficient of 0.9904. The proposed method can be applied to the detection of trichlorfon in vegetables and has good application prospects.

Dynamics of dominant rhizospheric microbial communities responsible for trichlorfon absorption and translocation in maize seedlings

In this study, the available phosphorus (AP) and TCF concentrations in soils and maize (Zea mays) seedling tissues were measured in response to escalating TCF concentrations during 216 hr of culture. Maize seedlings growth considerably enhanced soil TCF degradation, reaching the highest of 73.2% and 87.4% at 216 hr in 50 and 200 mg/kg TCF treatments, respectively, and increased AP contents in all the seedling tissues. Soil TCF was majorly accumulated in seedling roots, reaching maximum concentration of 0.017 and 0.076 mg/kg in TCF-50 and TCF-200, respectively. The hydrophilicity of TCF might hinder its translocation to the aboveground shoot and leaf. Using bacterial 16 S rRNA gene sequencing, we found that TCF addition drastically lessened bacterial community interactions and hindered the complexity of their biotic networks in rhizosphere than in bulk soils, leading to the homogeneity of bacterial communities that were resistant or prone to TCF biodegradation. Mantel test and redundancy analysis suggested a significant enrichment of dominant species Massilia belonging to Proteobacteria phyla, which in turn affecting TCF translocation and accumulation in maize seedling tissues. This study provided new insight into the biogeochemical fate of TCF in maize seedling and the responsible rhizobacterial community in soil TCF absorption and translocation.

Penicillium oxalicum augments soil lead immobilization by affecting indigenous microbial community structure and inorganic phosphate solubilization potential during microbial-induced phosphate precipitation

Phosphate-solubilizing microorganisms (PSMs) are critically important for increasing soil phosphate (P) and decreasing lead (Pb) bioavailability during microbial-induced phosphate precipitation (MIPP). However, their relative contributions to the indigenous soil microbial communities and P-cycling genes during the MIPP process remain unclear. In this study, inoculation of the PSM P. oxalicum in hydroxyapatite-cultured and Pb-contaminated soil increased soil phosphatase activities, available P (AP) concentrations and reduced available Pb levels. Metagenomics revealed a 3.9-44.0% increase in the abundance of P-cycling genes by P. oxalicum inoculation. No P-cycling genes were assigned to Penicillium. While P. oxalicum increased the complexity of microbial community co-occurrence networks, and improved the directly interrelationships between Penicillium and genera containing P-cycling gene. These results suggesting that P. oxalicum obviously positively affected the regulation of indigenous P-cycling functional communities during the MIPP process. Inorganic P solubilization genes (gcd, ppa, and ppx) have been shown to affect soil AP, suggesting that inorganic P solubilization is the major driver of Pb immobilization improvement following P. oxalicum inoculation. These results enhance our understanding of the significant ecological role of PSMs in governing soil P-cycling and alleviating Pb²⁺ biotoxicity during the MIPP process.

Biochar addition regulates soil phosphorus fractions and improves release of available phosphorus under freezing-thawing cycles

Currently, the shortage of phosphorus resources is becoming more and more serious. In general, phosphorus fertilizer is poorly utilized in soil and tends to gradually accumulate. Freezing-thawing cycles (FT) are seasonal phenomenon occurring in high latitudes and altitudes regions, which have obvious influence on the form of phosphorus in soil. This study investigates the effect of biochar on soil physicochemical properties, phosphorus form and availability under FT and thermostatic incubation (TH) condition. Compared with treatment without biochar, 4 % biochar addition increased the soil pH value, electrical conductivity, organic matter and Olsen-P of soil by a maximum of 0.76, 285.55 μS/cm, 28.60 g/kg and 139.27 mg/kg, respectively. Moreover, according to Hedley-P classification results, under FT condition, the content of labile phosphorus pool is always higher than those under TH. FT may promote the conversion of phosphorus from other fractions to labile phosphorus pool. Redundancy analysis results show that biochar addition and FT can not only directly change the soil phosphorus pool, but also alter the soil physicochemical properties and microbial community, which further affect the adsorption and mineralization of phosphorus in soil. The results of this study will be devoted to understanding the changes in soil phosphorus fractions under the effects of biochar addition and FT, providing references for agricultural production in areas where FT occur.