Metagenomic insights into nitrogen and phosphorus cycling at the soil aggregate scale driven by organic material amendments

Macrogenomics reveal the effects of inter-cropping perilla on kiwifruit: impact on inter-root soil microbiota and gene expression of carbon, nitrogen, and phosphorus cycles in kiwifruit

Intercropping systems can improve soil fertility and health, however, soil microbial communities and functional genes related to carbon, nitrogen and phosphorus cycling under the intercropping system of mesquite and perilla have not been studied. Therefore, in the present study, different planting densities and varieties of Perilla frutescens (L.) Britt and kiwifruit were used for intercropping, and changes in soil microbial communities and carbon, nitrogen, and phosphorus cycling genes in kiwifruit inter-roots under inter-cropping conditions were investigated by macro-genome sequencing technology. The results showed that intercropping with Perill caused a decrease in most soil nutrients, soil enzyme activities, and had a significant impact on the microbial (bacteria and fungi) diversity. Inter-cropping increased the relative abundance of the dominant bacterial phylum "Proteobacteria" and "Actinobacteria" by 47 and 57%, respectively, but decreased the relative abundance of the dominant fungal phylum "Chordata" and "Streptophyta" by 11 and 20%, respectively, in the inter-root soil of kiwifruit, and had a significant impact on the microbial (bacteria and fungi) diversity. In addition, inter-cropping could greatly increase the inter-root soil carbon sequestration (PccA, korA/B/C/D, fhs, and rbcl/s), carbon degradation (abfD), organic nitrogen mineralization (GDH2), denitrification (napA/B, nirB, norB), organic phosphorus mineralization (phop, phn), and inorganic phosphorus solubilization (gcd, ppk) gene abundance. The gene co-occurrence network indicated that soil korB, nirB, and gnd key functional genes for carbon, nitrogen, and phosphorus cycling in kiwifruit inter-root soils and their expression was up-regulated in the inter-cropping group. Structural equation (SEM) further showed that soil total nitrogen, organic matter, total carbon and acid phosphatase had significant effects on microbial diversity (p < 0.05) and soil carbon cycling gene korB and phosphorus cycling gene purH (p < 0.001), while korB and purH had positive effects on kiwifruit quality. In conclusion, intercropping perilla in kiwifruit orchards changed the structure of bacterial and fungal communities in the inter-root soil of kiwifruit, but I believe that intercropping perilla stimulates carbon degradation, leading to carbon emission and serious loss of soil nutrients, and that prolonged intercropping may adversely affect the quality of kiwifruit, and thus its limitations should be noted in future studies.

Impacts of fertilization methods on Salvia miltiorrhiza quality and characteristics of the epiphytic microbial community

Plant epiphytic microorganisms have established a unique symbiotic relationship with plants, which has a significant impact on their growth, immune defense, and environmental adaptation. However, the impact of fertilization methods on the epiphytic microbial community and their correlation with the yield and quality of medicinal plant was still unclear. In current study, we conducted a field fertilization experiment and analyzed the composition of epiphytic bacterial and fungal communities employing high throughput sequencing data in different organs (roots, stems, and leaves) of Salvia miltiorrhiza, as well as their correlation with plant growth. The results showed that fertilization significantly affected the active ingredients and hormone content, soil physicochemical properties, and the composition of epiphytic microbial communities. After fertilization, the plant surface was enriched with a core microbial community mainly composed of bacteria from Firmicutes, Proteobacteria, and Actinobacteria, as well as fungi from Zygomycota and Ascomycota. Additionally, plant growth hormones were the principal factors leading to alterations in the epiphytic microbial community of S. miltiorrhiza. Thus, the most effective method of fertilization involved the application of base fertilizer in combination with foliar fertilizer. This study provides a new perspective for studying the correlation between microbial community function and the quality of S. miltiorrhiza, and also provides a theoretical basis for the cultivation and sustainable development of high-quality medicinal plants.

Comparison and analysis of soil microbial communities in organic and conventional paddy fields by farming season

Interest in soil health and biodiversity conservation has become increasingly important. Consequently, studies comparing the chemical and biological characteristics of organic and traditional paddy soils have been increasing. Soil microorganisms are essential in nutrient cycling; however, their diversity is challenging to ascertain because of their environmental sensitivity and complex interactions. Particularly, in domestic rice cultivation, the soil undergoes multiple irrigation and drainage processes during crop growth, providing a diverse ecological environment for soil microorganisms. The objective of this study is to compare the microbial community and diversity between paddy soils in two agricultural systems. We selected organic and conventional paddy fields in Yangpyeong, Gyeonggi Province, and collected monthly samples from August to November 2022 for analysis. Bacteria and fungi were amplified from the 16S rRNA V3V4 region, ITS 3-4 region respectively, For the comparison of microbial diversity, Alpha diversity indices (Chao1, Shannon, Gini-Simpson indices) were analyzed. The results indicated genus-level differences in microbial communities, with the genera Mucor and Sirastachys exclusively present in organic paddy soils, while the genus Ustilaginoidea was exclusively found in conventional paddy soils. Among them, Ustilaginoidea is reported to be a fungus causing false smut disease, causing damage to crop growth and quality. Additionally, the comparison of microbial diversity between the two farming showed no significant differences (p>0.05). In conclusion, When the microbial communities present in both farming systems were examined, organic farming appeared to be more advantageous than conventional farming regarding crop disease and health. This study provides essential soil chemical and microbiological data for understanding the fundamental characteristics of paddy soils in South Korea.

Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem

Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY-NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.

Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2

Introduction

At present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.

Methods

The composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.

Results

First, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.

Discussion

Overall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.

The effect of intercropping leguminous green manure on theanine accumulation in the tea plant: A metagenomic analysis

Intercropping is a widely recognised technique that contributes to agricultural sustainability. While intercropping leguminous green manure offers advantages for soil health and tea plants growth, the impact on the accumulation of theanine and soil nitrogen cycle are largely unknown. The levels of theanine, epigallocatechin gallate and soluble sugar in tea leaves increased by 52.87% and 40.98%, 22.80% and 6.17%, 22.22% and 29.04% in intercropping with soybean-Chinese milk vetch rotation and soybean alone, respectively. Additionally, intercropping significantly increased soil amino acidnitrogen content, enhanced extracellular enzyme activities, particularly β-glucosidase and N-acetyl-glucosaminidase, as well as soil multifunctionality. Metagenomics analysis revealed that intercropping positively influenced the relative abundances of several potentially beneficial microorganisms, including Burkholderia, Mycolicibacterium and Paraburkholderia. Intercropping resulted in lower expression levels of nitrification genes, reducing soil mineral nitrogen loss and N2 O emissions. The expression of nrfA/H significantly increased in intercropping with soybean-Chinese milk vetch rotation. Structural equation model analysis demonstrated that the accumulation of theanine in tea leaves was directly influenced by the number of intercropping leguminous green manure species, soil ammonium nitrogen and amino acid nitrogen. In summary, the intercropping strategy, particularly intercropping with soybean-Chinese milk vetch rotation, could be a novel way for theanine accumulation.

Metagenomic analysis of the microbial communities and associated network of nitrogen metabolism genes in the Ryukyu limestone aquifer

While microbial biogeochemical activities such as those involving denitrification and sulfate reduction have been considered to play important roles in material cycling in various aquatic ecosystems, our current understanding of the microbial community in groundwater ecosystems is remarkably insufficient. To assess the groundwater in the Ryukyu limestone aquifer of Okinawa Island, which is located in the southernmost region of Japan, we performed metagenomic analysis on the microbial communities at the three sites and screened for functional genes associated with nitrogen metabolism. 16S rRNA amplicon analysis showed that bacteria accounted for 94-98% of the microbial communities, which included archaea at all three sites. The bacterial communities associated with nitrogen metabolism shifted by month at each site, indicating that this metabolism was accomplished by the bacterial community as a whole. Interestingly, site 3 contained much higher levels of the denitrification genes such as narG and napA than the other two sites. This site was thought to have undergone denitrification that was driven by high quantities of dissolved organic carbon (DOC). In contrast, site 2 was characterized by a high nitrate-nitrogen (NO3-N) content and a low amount of DOC, and this site yielded a moderate amount of denitrification genes. Site 1 showed markedly low amounts of all nitrogen metabolism genes. Overall, nitrogen metabolism in the Ryukyu limestone aquifer was found to change based on environmental factors.

Granular bacterial inoculant alters the rhizosphere microbiome and soil aggregate fractionation to affect phosphorus fractions and maize growth

The constraint of phosphorus (P) fixation on crop production in alkaline calcareous soils can be alleviated by applying bioinoculants. However, the impact of bacterial inoculants on this process remains inadequately understood. Here, a field study was conducted to investigate the effect of a high-concentration, cost-effective, and slow-release granular bacterial inoculant (GBI) on maize (Zea mays L.) plant growth. Additionally, we explored the effects of GBI on rhizosphere soil aggregate physicochemical properties, rhizosphere soil P fraction, and microbial communities within aggregates. The outcomes showed a considerable improvement in plant growth and P uptake upon application of the GBI. The application of GBI significantly enhanced the AP, phoD gene abundance, alkaline phosphatase activity, inorganic P fractions, and organic P fractions in large macroaggregates. Furthermore, GBI impacted soil aggregate fractionation, leading to substantial alterations in the composition of fungal and bacterial communities. Notably, key microbial taxa involved in P-cycling, such as Saccharimonadales and Mortierella, exhibited enrichment in the rhizosphere soil of plants treated with GBI. Overall, our study provides valuable insight into the impact of GBI application on microbial distributions and P fractions within aggregates of alkaline calcareous soils, crucial for fostering healthy root development and optimal crop growth potential. Subsequent research endeavors should delve into exploring the effects of diverse GBIs and specific aggregate types on P fraction and community composition across various soil profiles.

Genome-Resolved Metagenomics and Denitrifying Strain Isolation Reveal New Insights into Microbial Denitrification in the Deep Vadose Zone

The heavy use of nitrogen fertilizer in intensive agricultural areas often leads to nitrate accumulation in subsurface soil and nitrate contamination in groundwater, which poses a serious risk to public health. Denitrifying microorganisms in the subsoil convert nitrate to gaseous forms of nitrogen, thereby mitigating the leaching of nitrate into groundwater. Here, we investigated denitrifying microorganisms in the deep vadose zone of a typical intensive agricultural area in China through microcosm enrichment, genome-resolved metagenomic analysis, and denitrifying bacteria isolation. A total of 1000 metagenome-assembled genomes (MAGs) were reconstructed, resulting in 98 high-quality, dereplicated MAGs that contained denitrification genes. Among them, 32 MAGs could not be taxonomically classified at the genus or species level, indicating that a broader spectrum of taxonomic groups is involved in subsoil denitrification than previously recognized. A denitrifier isolate library was constructed by using a strategy combining high-throughput and conventional cultivation techniques. Assessment of the denitrification characteristics of both the MAGs and isolates demonstrated the dominance of truncated denitrification. Functional screening revealed the highest denitrification activity in two complete denitrifiers belonging to the genus Pseudomonas. These findings greatly expand the current knowledge of the composition and function of denitrifying microorganisms in subsoils. The constructed isolate library provided the first pool of subsoil-denitrifying microorganisms that could facilitate the development of microbe-based technologies for nitrate attenuation in groundwater.

Mechanisms underlying soil microbial regulation of available phosphorus in a temperate forest exposed to long-term nitrogen addition

With exogenous nitrogen (N) input into soil, phosphorus (P) could become a limiting nutrient for plant growth. Soil microbes play a crucial role in regulating soil P cycle and availability. P functional genes, further, regulate soil P availability. It is unclear how the addition of N in different chemical forms and rates influences the composition of soil microbes associated with P cycling and the abundance of P functional genes. A long-term experiment of N addition in three chemical forms with two levels in a temperate forest was performed to reveal the influences and the underlying mechanisms. We found that both chemical N forms and N rates selected for different P-solubilizing microbes. Ammonia form-N increased the abundances of P-solubilizing bacteria at low and high rates. Continuous N deposition included a significant decrease in soil pH and inhibited the viability and activity of bacterial communities in soil, especially the P-solubilizing bacteria. Thus, it restricted inorganic P mobilization and led to a decrease in soil available P. In addition, ammonium-N enhanced the relative abundance of most of the functional genes related to organic P mineralization, while nitrate-N presented a decrease trend. Ammonium-N significantly decreased most of the functional genes relevant to P transportation, whereas the other chemical N forms did not change them. Although N-addition consistently decreased the functional genes relevant to inorganic P solubilization, two of them (ppx and ppa) were the exceptions and showed an increase trend. N addition also decreased soil pH and altered soil properties, and indirectly contributed to the changes in community composition of P-solubilizing microbes and the abundances of multiple P functional genes. Our results provide a mechanistic explanation for the regulation of microbes on N-induced available P limitation via tuning the compositions of P-solubilizing microbes and the abundances of multiple P functional genes.

Soil aggregate-driven changes in nutrient redistribution and microbial communities after 10-year organic fertilization

Research studies on nutrient content and microbial communities after the application of organic manure have been reported, while available information about multi-interaction mechanisms of nutrient stoichiometry and microbial succession in soil aggregates remains limited. This work conducted a 10-year field experiment amended with cow manure (1.5 t/ha), during which the application of organic manure stimulated the fragmentation of soil macro-aggregates (>5 mm) and the agglomeration of soil micro-aggregates (<0.25 mm). Hence, the proportion of medium-size aggregates (0.25-5 mm) was increased in bulk soil, and there was an insignificant difference in the stability of soil aggregates. Meanwhile, the application of organic manure increased soil organic carbon (SOC), total nitrogen (TN) and phosphorus (TP) in all soil aggregate fractions. SOC, TN and TP were higher in micro-aggregates (<0.25 mm) after the application of organic manure, thus the dominating phylum of bacteria and fungi was more abundance in micro-aggregates due to the increase in nutrient level. During the organic fertilization process, fungal communities significantly changed because the variation of carbon-to-nitrogen ratio (C:N) in soil aggregates. Cultivated farmland in Northeast China showed a considerable capacity to sequestrate SOC during the organic fertilization process, but nitrogen may be a primary macro-element limiting soil productivity. Theoretically, organic manure amended with nitrogen fertilizer could be an effective measure to maintain microbial diversity and crop productivity in agro-ecosystems in Northeast China.

Cadmium-tolerant Bacillus cereus 2-7 alleviates the phytotoxicity of cadmium exposure in banana plantlets

Bananas are the world's important fruit and staple crop in the developing countries. Cadmium (Cd) contamination in soils results in the decrease of crop yield and food safety. Bioremediation is an environmental-friendly and effective measure using Cd-tolerant plant growth promoting rhizobacteria (PGPR). In our study, a Cd-resistant PGPR Bacillus cereus 2-7 was isolated and identified from a discarded gold mine. It could produce multiple plant growth promoting biomolecules such as siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC)-deaminase and phosphatase. The extracellular accumulation was a main manner of Cd removal. Surplus Cd induced the expression of Cd resistance/transport genes of B. cereus 2-7 to maintain the intracellular Cd homeostasis. The pot experiment showed that Cd contents decreased by 50.31 % in soil, 45.43 % in roots, 56.42 % in stems and 79.69 % in leaves after the strain 2-7 inoculation for 40 d. Bacterial inoculation alleviated the Cd-induced oxidative stress to banana plantlets, supporting by the increase of chlorophyll contents, plant height and total protein contents. The Cd remediation mechanism revealed that B. cereus 2-7 could remodel the rhizosphere bacterial community structure and improve soil enzyme activities to enhance the immobilization of Cd. Our study provides a Cd-bioremediation strategy using Cd-resistant PGPR in tropical and subtropical area.

Organic amendment-mediated reclamation and build-up of soil microbial diversity in salt-affected soils: fostering soil biota for shaping rhizosphere to enhance soil health and crop productivity

Soil salinization is a serious environmental problem that affects agricultural productivity and sustainability worldwide. Organic amendments have been considered a practical approach for reclaiming salt-affected soils. In addition to improving soil physical and chemical properties, organic amendments have been found to promote the build-up of new halotolerant bacterial species and microbial diversity, which plays a critical role in maintaining soil health, carbon dynamics, crop productivity, and ecosystem functioning. Many reported studies have indicated the development of soil microbial diversity in organic amendments amended soil. But they have reported only the development of microbial diversity and their identification. This review article provides a comprehensive summary of the current knowledge on the use of different organic amendments for the reclamation of salt-affected soils, focusing on their effects on soil properties, microbial processes and species, development of soil microbial diversity, and microbial processes to tolerate salinity levels and their strategies to cope with it. It also discusses the factors affecting the microbial species developments, adaptation and survival, and carbon dynamics. This review is based on the concept of whether addition of specific organic amendment can promote specific halotolerant microbe species, and if it is, then which amendment is responsible for each microbial species' development and factors responsible for their survival in saline environments.

Long-term application of nitrogen and phosphorus fertilizers changes the process of community construction by affecting keystone species of crop rhizosphere microorganisms

Keystone species of microbial communities play a very important role in community structure and ecosystem function; however, the effect of long-term nitrogen (N) and phosphorus (P) fertilizers on key taxa and the mechanisms of community construction of rhizosphere microbial communities remain unclear. In this study, the effect of nine fertilization treatments (N0P0, N0P1, N0P2, N1P0, N1P1, N1P2, N2P0, N2P1, and N2P2) on soil microbial community diversity, keystone species, and construction methods in the crop rhizosphere were studied in a loess hilly area after 26 years of fertilization. The results showed that fertilization significantly increased the nutrient contents of the rhizospheric soil and root system and significantly affected microbial community composition (based on the Bray-Curtis distance) and community construction process (β-nearest taxon index: βNTI). The decrease in the abundance of oligotrophic bacteria (from phyla Acidobacteriota and Chloroflexi) in the keystone species of bacterial communities shifted the community construction process from homogenizing dispersal to variable selection process and was significantly regulated by soil factors (total P and carbon-N ratio). However, the decrease in the abundance of keystone species (from phylum Basidiomycota) in the fungal communities did not have a significant effect on community construction, which was mainly affected by root characteristics (root N content and soluble sugar). This study found that long-term N and P fertilization changed the keystone species composition of bacterial communities by affecting the nutrient content of the rhizospheric soil, such as total P, so that the construction mode of communities changed from a stochastic to a deterministic process, and the N2 fertilization, especially the N1P2 treatment was better for increasing network stability (modularity and clustering coefficient).

Organic amendments improve salinity-induced osmotic and oxidative stress tolerance in Okra (Abelmoschus esculentus (L.)Moench)

AIMS

Salinity adversely affects okra [Abelmoschus esculentus (L.) Moench] plants by inducing osmotic and oxidative stresses. This study was designed to enhance salinity-induced osmotic and oxidative stress tolerance in okra plants by applying organic amendments.

METHODS

The effects of different organic amendments (municipal solid waste compost, farmyard manure (FYM) and press mud) on osmotic potential, water use efficiency, activities of antioxidant enzymes, total soluble sugar, total soluble proline, total soluble protein and malondialdehyde (MDA) contents of okra plants grown under saline conditions (50 mM sodium chloride) were evaluated in a pot experiment. The organic amendments were applied each at the rate of 5% and 10% per pot or in various combinations (compost + FYM, FYM + press mud and compost + press mud each at the rate of 2.5% and 5% per pot).

RESULTS

As compared to control, high total soluble sugar (60.41), total soluble proline (33.88%) and MDA (51%) contents and increased activities of antioxidant enzymes [superoxide dismutase (83.54%), catalase (78.61%), peroxidase (53.57%] in salinity-stressed okra plants, were indicative of oxidative stress. Salinity significantly reduced the osmotic potential (41.78%) and water use efficiency (4.75%) of okra plants compared to control. Under saline conditions, 5% (farmyard manure + press mud) was the most effective treatment, which significantly improved osmotic potential (27.05%), total soluble sugar (4.20%), total soluble protein (73.62%) and total soluble proline (23.20%) contents and superoxide dismutase activity (32.41%), compared to saline soil. Application of 2.5% (FYM + press mud), 5% press mud, and 10% compost significantly reduced MDA content (27%) and improved activities of catalase (38.64%) and peroxidase (48.29%), respectively, compared to saline soil, thus facilitated to alleviate oxidative stress in okra plants.

CONCLUSIONS

Using organic amendments (municipal solid waste compost, farmyard manure and press mud) was a cost-effective approach to improve salinity-induced osmotic and oxidative stress tolerance in okra plants.

Effects of straw and plastic film mulching on microbial functional genes involved in soil nitrogen cycling

Introduction

Microorganisms regulate soil nitrogen (N) cycling in cropping systems. However, how soil microbial functional genes involved in soil N cycling respond to mulching practices is not well known.

Methods

We collected soil samples from a spring maize field mulched with crop straw (SM) and plastic film (FM) for 10-year and with no mulching (CK) in the Loess Plateau. Microbial functional genes involved in soil N cycling were quantified using metagenomic sequencing. We collected soil samples from a spring maize field mulched with crop straw (SM) and plastic film (FM) for 10-year and with no mulching (CK) in the Loess Plateau. Microbial functional genes involved in soil N cycling were quantified using metagenomic sequencing.

Results

Compared to that in CK, the total abundance of genes involved in soil N cycling increased in SM but had no significant changes in FM. Specifically, SM increased the abundances of functional genes that involved in dissimilatory nitrate reduction to ammonium (nirB, napA, and nrfA), while FM decreased the abundances of functional genes that involved in ammonification (ureC and ureA) in comparison with CK. Other genes involved in assimilatory nitrate reduction, denitrification, and ammonia assimilation, however, were not significantly changed with mulching practices. The nirB and napA were derived from Proteobacteria (mainly Sorangium), and the ureC was derived from Actinobacteria (mainly Streptomyces). Mental test showed that the abundance of functional genes that involved in dissimilatory nitrate reduction was positively correlated with the contents of soil microbial biomass N, potential N mineralization, particulate organic N, and C fractions, while ammonification related gene abundance was positively correlated with soil pH, microbial biomass C and N, and mineral N contents.

Discussion

Overall, this study showed that SM could improve soil N availability and promote the soil N cycling by increasing the abundance of functional genes that involved in DNRA, while FM reduced the abundance of functional genes that involved in ammonification and inhibited soil N cycling.

Dynamic Responses of Rhizosphere Microorganisms to Biogas Slurry Combined with Chemical Fertilizer Application during the Whole Life Cycle of Rice Growth

Biogas slurry combined with chemical fertilizer (BCF) is widely used as a fertilizer in paddy fields and rhizosphere microorganisms are key players in plant growth and reproduction. However, the dynamic responses of rhizosphere microorganisms of field-grown rice to BCF application still remain largely unknown. In this study, a field experiment was conducted in two proximate paddy fields in Chongming Island to study the impacts of BCF on the changes in rhizosphere microorganisms during the whole rice growth, including seedling, tillering, booting, and grain-filling stages, with solely chemical fertilizer (CF) treatment as control. The results showed BCF could increase the N-, P-, and C- levels in paddy water as well as the rhizosphere microbial abundance and diversity compared with control. In particular, the phosphate-solubilizing- and cellulose-decomposing-bacteria (e.g., Bacillus) and fungi (e.g., Mortierella) were more abundant in the rhizosphere of BCF than those of CF. Moreover, these microbes increased markedly at the booting and grain-filling stages in BCF, which could promote rice to obtain available nutrients (P and C). It was noted that denitrifying-like bacteria (e.g., Steroidobacteraceae) decreased and dissimilatory nitrate reduction to ammonia-related bacteria (e.g., Geobacter, Anaeromyxobacter, and Ignavibacterium) increased at the booting and filling stages, which could promote N-availability. TP in paddy water of BCF was most correlated to the bacteria, while COD was the most critical regulator for the fungi. Furthermore, correlation network analysis showed nutrient-cycling-related microorganisms were more closely interconnected in BCF than those in CF. These findings showed the application of biogas slurry plus chemical fertilizer could regulate rhizosphere microorganisms towards a beneficial fertilizer use for rice growth.

Distinct influence of conventional and biodegradable microplastics on microbe-driving nitrogen cycling processes in soils and plastispheres as evaluated by metagenomic analysis

Plastic mulching is one of the large contributors to microplastic (MP) accumulation in agricultural landscapes. However, the effects of conventional (PE-MPs) and biodegradable MPs (BMPs) on microbial functional and genomic information encoding nitrogen (N) cycling have yet to be addressed. Here, a soil microcosmic experiment was conducted by adding PE-MPs and BMPs to a Mollisol at dosage of 5% (w/w) followed by incubation for 90 days. The soils and MPs were examined by metagenomics and genome binning methods. The results revealed that BMPs harbored rougher surfaces and induced stronger alterations in microbial functional and taxonomic profiles in the soil and plastisphere than PE-MPs. In comparison to their respective soils, the plastispheres of PE-MPs and BMPs stimulated the processes of N fixation, N degradation and assimilatory nitrate reduction (ANRA) and reduced the gene abundances encoding nitrification and denitrification, in which BMPs induced stronger influences than PE-MPs. Ramlibacter mainly drove the differences in N cycling processes between the soils containing two types of MPs and was further enriched in the BMP plastisphere. Three high-quality genomes were identified as Ramlibacter stains with higher abundances in the plastisphere of BMP than that of PE-MP. These Ramlibacter strains had the metabolic capacities of N fixation, N degradation, ANRA and ammonium transport, which were potentially attributed to their biosynthesis and the accumulation of soil NH₄⁺-N. Taken together, our results highlight the genetic mechanisms of soil N bioavailability in the presence of biodegradable MPs, which have important implications for maintaining sustainable agriculture and controlling microplastic risk.

N/S element transformation modulating lithospheric microbial communities by single-species manipulation

BACKGROUND

The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation.

RESULTS

Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil.

CONCLUSIONS

The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.

Microbial communities and sediment nitrogen cycle in a coastal eutrophic lake with salinity and nutrients shifted by seawater intrusion

Coastal waters are often influenced by seawater intrusion and terrestrial emissions because of its special location. In this study, the dynamics of microbial community with the role of nitrogen cycle in sediment in a coastal eutrophic lake were studied under a warm season. The water salinity gradually increased from 0.9‰ in June to 4.2‰ in July and 10.5‰ in August because of seawater invasion. Bacterial diversity of surface water was positively related with salinity and nutrients of total nitrogen (TN) as well as total phosphorus (TP), but eukaryotic diversity had no relationship with salinity. In surface water, algae belonging to Cyanobacteria and Chlorophyta were dominant phyla in June with the relative abundances of >60%, but Proteobacteria became the largest bacterial phylum in August. The variation of these predominant microbes had strong relationship with salinity and TN. In sediment, the bacterial and eukaryotic diversity was greater than that of water, and a significantly different microbial community was observed with dominant bacterial phyla Proteobacteria and Chloroflexi, and dominant eukaryotic phyla Bacillariophyta, Arthropoda, and Chlorophyta. Proteobacteria was the only enhanced phylum in the sediment with the highest relative abundance of 54.62% ± 8.34% due to seawater invasion. Denitrifying genera (29.60%-41.81%) were dominant in surface sediment, then followed by microbes related to nitrogen fixation (24.09%-28.87%), assimilatory nitrogen reduction (13.54%-19.17%), dissimilatory nitrite reduction to ammonium (DNRA, 6.49%-10.51%) and ammonification (3.07%-3.71%). Higher salinity caused by seawater invasion enhanced the accumulation of genes involved in dentrificaiton, DNRA and ammonification, but decreased genes related to nitrogen fixation and assimilatory nitrogen reduction. Significant variation of dominant genes of narG, nirS, nrfA, ureC, nifA and nirB mainly caused by the changes in Proteobacteria and Chloroflexi. The discovery of this study would be helpful to understand the variation of microbial community and nitrogen cycle in coastal lake under seawater intrusion.

Tritium and Carbon-14 Contamination Reshaping the Microbial Community Structure, Metabolic Network, and Element Cycle in the Seawater Environment

The potential ecological risks caused by entering radioactive wastewater containing tritium and carbon-14 into the sea require careful evaluation. This study simulated seawater's tritium and carbon-14 pollution and analyzed the effects on the seawater and sediment microenvironments. Tritium and carbon-14 pollution primarily altered nitrogen and phosphorus metabolism in the seawater environment. Analysis by 16S rRNA sequencing showed changes in the relative abundance of microorganisms involved in carbon, nitrogen, and phosphorus metabolism and organic matter degradation in response to tritium and carbon-14 exposure. Metabonomics and metagenomic analysis showed that tritium and carbon-14 exposure interfered with gene expression involving nucleotide and amino acid metabolites, in agreement with the results seen for microbial community structure. Tritium and carbon-14 exposure also modulated the abundance of functional genes involved in carbohydrate, phosphorus, sulfur, and nitrogen metabolic pathways in sediments. Tritium and carbon-14 pollution in seawater adversely affected microbial diversity, metabolic processes, and the abundance of nutrient-cycling genes. These results provide valuable information for further evaluating the risks of tritium and carbon-14 in marine environments.

Starting-up performances and microbial community shifts in the coupling process (SAPD-A) with sulfide autotrophic partial denitrification (SAPD) and anammox treating nitrate and ammonium contained wastewater

A novel coupling process (SAPD-A) with sulfide autotrophic partial denitrification (SAPD) (NO₃^--N→NO₂^--N) and anaerobic ammonium oxidation (Anammox) was developed using anaerobic sequencing batch reactor (ASBR) in this work. The integrated process comprised two stages. Firstly, the starting-up of SAPD process succeeded by gradually increasing the influent nitrate and sulfide in 95 days. The average nitrate removal efficiency (NRE) and NO₂^--N accumulation rates were 71.24% ± 0.21% and 46.44% ± 0.53% at SAPD process (days 75-95). Then, successful coupling process (SAPD-A) was implemented in two stages (stage I and stage II of SAPD-A). In stage I, it is feasible to promote the successful construction of SAPD-A process by elevating influent ammonium only based on SAPD system, making the NRE increased from 44.45% ± 0.46% (day 95) to 64.62% ± 0.12% at the end of stage I in SAPD-A system (day 126). Meanwhile, the ammonium nitrogen removal efficiency (ARE) and total nitrogen removal efficiency (TN-RE) also rose up to 42.46% ± 2.02% and 63.28% ± 0.54% respectively. Furthermore, the average ARE, NRE and TN-RE during the stage II in the bioreactor could reach 65.17% ± 1.45%, 74.50% ± 0.81% and 77.81% ± 0.37% by loading some biofilters (with of approximate 10% of the volume of the bioreactor) attached anaerobic ammonium oxidation bacteria (AnAOB). High-throughput sequencing results showed that the dominant genera concerning nitrogen removal were norank_f_norank_o_Fimbriimonadates (with the abundance of 2.88-8.54%), norank_ o_ norank _ c_ OM190 (2.48-4.41%), norank_f_norank_o_norank_c_WWE3 (11.01-17.69%), subgroup_10 (1.97-3.81%), Limnobacter（2.17-3.49%）, norank_f_n orank_ o_norank_ c_OLB14 (2.03-5.23%), norank-f-PHOS-HE36 (2.18-5.5%), Ellin6067 (1.34-2.24%) and Candidatus_ Brocadia (1.95-2.42%) during the whole starting-up period of coupling SAPD-A process. Batch experiments revealed that the sulfide was fully oxidized within 2 h, with the maximum reaction rate of 38.30 ± 1.53 mg (L h)^-1 in the first 1 h. Simultaneously, the concentration of nitrate sharply decreased from 53.08 ± 0.23 mg L^-1 to 24.16 ± 0.42 mg L^-1 with the reaction rate of 66.41 ± 2.12 mg (L h)^-1 in 0.5 h. Also, the ammonium concentration significantly declined from 47.88 ± 0.34 mg L^-1 to 10.98 ± 0.39 mg L^-1 in 8 h. Anammox process was responsible for the dominant nitrogen removal in the coupling SAPD-A system.

Mock community as an in situ positive control for amplicon sequencing of microbiotas from the same ecosystem

Metataxonomy has become the standard for characterizing the diversity and composition of microbial communities associated with multicellular organisms and their environment. Currently available protocols for metataxonomy assume a uniform DNA extraction, amplification and sequencing efficiency for all sample types and taxa. It has been suggested that the addition of a mock community (MC) to biological samples before the DNA extraction step could aid identification of technical biases during processing and support direct comparisons of microbiota composition, but the impact of MC on diversity estimates of samples is unknown. Here, large and small aliquots of pulverized bovine fecal samples were extracted with no, low or high doses of MC, characterized using standard Illumina technology for metataxonomics, and analysed with custom bioinformatic pipelines. We demonstrated that sample diversity estimates were distorted only if MC dose was high compared to sample mass (i.e. when MC > 10% of sample reads). We also showed that MC was an informative in situ positive control, permitting an estimation of the sample 16S copy number, and detecting sample outliers. We tested this approach on a range of sample types from a terrestrial ecosystem, including rhizosphere soil, whole invertebrates, and wild vertebrate fecal samples, and discuss possible clinical applications.

Diversity, distribution and organic substrates preferences of microbial communities of a low anthropic activity cave in North-Western Romania

Introduction

Karst caves are characterized by relatively constant temperature, lack of light, high humidity, and low nutrients availability. The diversity and functionality of the microorganisms dwelling in caves micro-habitats are yet underexplored. Therefore, in-depth investigations of these ecosystems aid in enlarging our understanding of the microbial interactions and microbially driven biogeochemical cycles. Here, we aimed at evaluating the diversity, abundance, distribution, and organic substrate preferences of microbial communities from Peștera cu Apă din Valea Leșului (Leșu Cave) located in the Apuseni Mountains (North-Western Romania).

Materials and Methods

To achieve this goal, we employed 16S rRNA gene amplicon sequencing and community-level physiological profiling (CLPP) paralleled by the assessment of environmental parameters of cave sediments and water.

Results and Discussion

Pseudomonadota (synonym Proteobacteria) was the most prevalent phylum detected across all samples whereas the abundance detected at order level varied among sites and between water and sediment samples. Despite the general similarity at the phylum-level in Leșu Cave across the sampled area, the results obtained in this study suggest that specific sites drive bacterial community at the order-level, perhaps sustaining the enrichment of unique bacterial populations due to microenvironmental conditions. For most of the dominant orders the distribution pattern showed a positive correlation with C-sources such as putrescine, γ-amino butyric acid, and D-malic acid, while particular cases were positively correlated with polymers (Tween 40, Tween 80 and α-cyclodextrin), carbohydrates (α-D-lactose, i-erythritol, D-mannitol) and most of the carboxylic and ketonic acids. Physicochemical analysis reveals that sediments are geochemically distinct, with increased concentration of Ca, Fe, Al, Mg, Na and K, whereas water showed low nitrate concentration. Our PCA indicated the clustering of different dominant orders with Mg, As, P, Fe, and Cr. This information serves as a starting point for further studies in elucidating the links between the taxonomic and functional diversity of subterranean microbial communities.

Feedstock-dependent abundance of functional genes related to nitrogen transformation controlled nitrogen loss in composting

The objective of this work was to explore how selection of feedstock affects nitrogen cycle genes during composting, which eventually determines the nitrogen loss. Four composting mixes (CM: chicken manure; SM: sheep manure; MM_1/3: mixed manure with CM: SM = 1:3 w/w, MM_3/1: CM: SM = 3:1 w/w) were investigated. Results showed that adding 25 % and 75 % SM to CM reduced 26.5 % and 57.9 % nitrogen loss, respectively. CM contained more ammonification genes and nrfA gene, while SM had more denitrification genes. Nitrogen fixation genes in CM were slightly higher than that in SM at the initial stage, but they sharply dropped off as the composting entered the high temperature stage. MM_1/3 showed significantly reduced ammonification genes than CM, and increased nitrogen fixation and NH₄⁺ assimilation genes. Therefore, adding SM to CM could change the abundance of genes and enzymes related to nitrogen cycle to reduce nitrogen loss.

Fertilizing-induced changes in the nitrifying microbiota associated with soil nitrification and crop yield

Ammonia oxidizing archaea (AOA) and bacteria (AOB), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira (CMX) play pivotal roles in global nitrogen-cycling network. Despite its importance, the driving forces for niche specialization of these nitrifiers, as well as their relative contributions to nitrification and crop yield have not been fully understood. Here, we investigated the niche specialization and environmental prevalence of nitrifying communities, and their importance for the nitrification rate and crop yield across a gradient of nitrogen inputs in a two-decade old field experiment. The results of ¹⁵N-tracer and quantitative PCR revealed that AOB and NOB jointly determined the gross nitrification rates across mineral fertilizer treatments, whereas AOA and AOB contributed more than other nitrifiers to nitrification under with organic fertilizer amendments. Linear regression model revealed that crop yield could be linked with AOB and NOB under inorganic farming but closely associated with CMX under organic management. Amplicon sequencing of these functional genes further demonstrated that mineral and organic fertilizers have distinct influences on the β-diversity and niche breadth of these nitrifying communities, indicating that fertilization triggered niche specialization of nitrifying guilds in agricultural soils. Notably, organic fertilization enhanced the network complexity of these nitrifiers by harboring keystone taxa. Random forest analysis provide robustly evidence for the hypothesis that abundance of functional genes contributed more than a- and β-diversity of these nitrifiers for driving nitrification rates and crop yields. Collectively, these findings provide the empirical evidence for the environmental adaptation and niche specialization of nitrifying communities, and their contributions in nitrification and crop yield when confronted with long-term nitrogen inputs.

Effects of Fermented Seaweed Fertilizer Treatment on Paddy Amino Acid Content and Rhizosphere Microbiome Community

Seaweed has often been reported on for it potential bioresources for fertilizers to improve crop productivity and reduce the use of chemical fertilizers (CF). However, little is known about the nutritional status of the crop grown with the implementation of seaweed fertilizers (SF). In this study, the amino acid content of rice produced by SF implementation was evaluated. Furthermore, the rhizosphere bacterial community was also investigated. The paddy seedlings were divided into five groups, control (C0), chemical fertilizer (CF), seaweed fertilizer (SF), chemical and seaweed fertilizer combination 25:75 (CFSF1), and chemical and fertilizer combination 50:50 (CFSF2). The CFSF2 group shown significantly better growth characteristics compared to other groups. Based on the concentration of macronutrients (N, P, K) in paddy leaf, CFSF2 also shown the best results. This also correlates with the abundant amino acid composition in CFSF2 in almost all tested amino acids, namely, serine, phenylalanine, isoleucine, valine, glycine, tyrosine, proline, threonine, histidine, and arginine. Interestingly, beneficial bacteria Rhizobiales were significantly higher in CFSF2-treated soil (58%) compared to CF (29%). Another important group, Vicinamibacterales, was also significantly higher in CFSF2 (58%) compared to CF (7%). Hence, these potentially contributed to the high rice amino acid content and yield in the CFSF2-treated paddy. However, further field-scale studies are needed to confirm the bioindustrial application of seaweed in agricultural systems.

Remediation of organic amendments on soil salinization: Focusing on the relationship between soil salts and microbial communities

Soil salinization has emerged as a major factor with an adverse influence on agricultural green development worldwide. It is necessary to develop high-efficiency and ecologically beneficial management measures for alleviating soil salinization. The experiment of application for cow manure (CM), biochar (BC), and bio-organic fertilizer (BIO) in soil with light salinity was conducted to investigate the remediation of organic materials on soil salinization with melon (Cucumis melo L.) by reducing the availability of saline ions and shifting the soil microbial community. Results showed that BC treatment significantly decreased the EC values of the soil and soil solution by 19.23% and 27.02% and the concentrations of Na⁺, K⁺, and Cl^- by 13.28%, 13.08%, and 15.21%, respectively, followed by CM and BIO treatments. High-throughput sequencing identified that organic amendments significantly improved the richness of the soil bacterial community and increased the relative abundances of Acidobacteria and Firmicutes by 33.11% and 111.2%, respectively, and the beneficial salt-tolerant bacterial genera Flavobacterium, Bacillus and Arthrobacter by 32.04%, 38.92% and 35.67%, respectively. Additionally, soil Na⁺, Ca²⁺, K⁺ and Cl^- were significantly negatively correlated with Acidobacteria and Flavobacterium and were also the most important factors driving the changes in the structure of the soil bacterial communities. The bacterial networks were more complex in the organic amendments treatments than in CK, reflecting through more nodes and links and a higher average clustering coefficient, density and modularity. This study provided a comprehensive understanding of the application of organic amendments in alleviating soil salinization and improving soil bacterial and fungal communities and provides scientific support for agriculture green development.

The ecological clusters of soil organisms drive the ecosystem multifunctionality under long-term fertilization

Long-term fertilization is known to impact the biodiversity and community structures of soil organisms, which are responsible for multiple soil ecosystem functions (multifunctionality). However the relationship between the alterations of soil organisms and ecosystem multifunctionality remains unclear, especially in the case of long-term fertilization. To explore the contribution of soil organismal biodiversity and community structures to ecosystem multifunctionality, we took soil samples from a nearly 25-year field fertilization experiment. Organic matter significantly improved the soil ecosystem multifunctionality. Ecosystem multifunctionality was found to be closely linked to the biodiversity and communities of soil organisms within the major ecological clustering of soil organisms (Module 1) according to the trophic co-occurrence network, rather than the entire community of soil organisms. This indicated that ecological clusters of soil organisms within the network were critical in maintaining soil ecosystem multifunctionality. The application of organic fertilization could enrich specialized soil organisms and increase interactions of soil organisms in the ecological cluster. As a result, our findings emphasize the role of ecological clusters in the soil organismal co-occurrence network in controlling soil multifunctionality after long-term fertilization, presenting a novel perspective on the link between soil biodiversity and ecosystem multifunctionality.

Accumulation, regional distribution, and environmental effects of Sb in the largest Hg-Sb mine area in Qinling Orogen, China

In this study, knowledge gaps on Sb concentration in rocks, ores, tailings, soil, river water, sediments, and crops of mine areas were identified and discussed in terms of contamination levels, spatial distribution, and environmental effects. Accordingly, Xunyang Hg-Sb mine, the largest Hg-Sb deposit in China as research region in this study, field sampling and laboratory analysis were conducted. The results showed elevated concentrations of Sb in the soil, sediment, and river water. The X-ray diffraction analysis indicated that the main minerals of the rocks were quartz, dolomite, calcite, and margarite. Based on the TESCAN integrated mineral analyzer analysis, the main ore minerals in the Gongguan mine were dolomite (93.97%), cinnabar (2.50%), stibnite (2.48%), calcite (0.38%), and quartz (0.38%). The μ-XRF analysis indicated that Sb distribution was similar to those of S and O, instead of those of Hg and As. The clear spatial variation of Sb concentration in environmental media, mines, tailings, and settling ponds affected Sb accumulation. Actinobacteriota, Proteobacteria, Acidobacteriota, and Chloroflexi were the dominant phyla in the soil. Patescibacteria, Proteobacteria, and Bdellovibrionota were negatively correlated with Sb in the soil (p < 0.05). Exposure to Sb through maize grain and cabbage consumption poses serious non-carcinogenic health risk for residents. This work provides a scientific basis for the environmental quality assessment of Sb mine areas and development of applicable guidelines.

Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes

Enhancing soil phosphate solubilization is a promising strategy for agricultural sustainability, while little is known about the mechanisms of how microorganisms cope with differing phosphorus availability. Using a combination of genome-resolved metagenomics and amplicon sequencing, we investigated the microbial mechanisms involved in phosphorus cycling under three agricultural treatments in a wheat-maize rotation system and two natural reforestation treatments. Available soil phosphorus was the key factor shaping bacterial and fungal community composition and function across our agricultural and reforestation sites. Membrane-bound quinoprotein glucose dehydrogenase (PQQGDH) and exopolyphosphatases (PPX) governed microbial phosphate solubilization in agroecosystems. In contrast, genes encoding glycerol-3-phosphate transporters (ugpB, ugpC, and ugpQ) displayed a significantly greater abundance in the reforestation soils. The gcd gene encoding PQQGDH was found to be the best determinant for bioavailable soil phosphorus. Metagenome-assembled genomes (MAGs) affiliated with Cyclobacteriaceae and Vicinamibacterales were obtained from agricultural soils. Their MAGs harbored not only gcd but also the pit gene encoding low-affinity phosphate transporters. MAGs obtained from reforestation soils were affiliated with Microtrichales and Burkholderiales. These contain ugp genes but no gcd, and thereby are indicative of a phosphate transporter strategy. Our study demonstrates that knowledge of distinct microbial phosphorus acquisition strategies between agricultural and reforestation soils could help in linking microbial processes with phosphorus cycling.

IMPORTANCE The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity. In this study, we combined functional metagenomics and amplicon sequencing to analyze microbial phosphorus cycling processes in natural reforestation and agricultural soils. We found that the phosphorus acquisition strategies significantly differed between these two ecosystems. A microbial phosphorus solubilization strategy dominated in the agricultural soils, while a microbial phosphate transporter strategy was observed in the reforestation soils. We further identified microbial taxa that contributed to enhanced phosphate solubilization in the agroecosystem. These microbes are predicted to be beneficial for the increase in phosphate bioavailability through agricultural practices.