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

Arbuscular mycorrhizal fungi promote functional gene regulation of phosphorus cycling in rhizosphere microorganisms of Iris tectorum under Cr stress

The mutualistic symbiotic system formed by clumping arbuscular mycorrhizal fungi (AMF) and plants can remediate heavy metal-contaminated soils. However, the specific mechanisms underlying the interaction between AMF and inter-root microbial communities, particularly their impact on organic phosphorus (P) cycling, remain unclear. This study investigated the gene regulation processes involved in inter-root soil phosphorus cycling in wetland plants, specifically Iris tectorum, following inoculation with AMF under varying concentrations of chromium (Cr) stress. Through macro-genome sequencing, we analyzed the composition and structure of the inter-root soil microbial community associated with Iris tectorum under greenhouse pot conditions. The results demonstrated significant changes in the diversity and composition of the inter-root soil microbial community following AMF inoculation, with Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Bacteroidetes being the dominant taxa. Under Cr stress, species and gene co-occurrence network analysis revealed that AMF promoted the transformation process of organic phosphorus mineralization and facilitated inorganic phosphorus uptake. Additionally, network analysis of functional genes indicated strong aggregation of (pstS, pstA, pstC, TC.PIT, phoR, pp-gppA) genes, which collectively enhanced phosphorus uptake by plants. These findings shed light on the inter-root soil phosphorus cycling process during the co-remediation of Cr-contaminated soil by AMF-Iris tectorum symbiosis, providing valuable theoretical support for the application of AMF-wetland plant symbiosis systems to remediate heavy metal-contaminated soil.

Contrasting fertilization and phenological stages shape microbial-mediated phosphorus cycling in a maize agroecosystem

Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome. We investigated the effects of these treatments on the relative abundance of bacterial and archaeal genes and proteins related to organic P mineralization, inorganic P solubilization, and the P starvation response regulation through a multi-omic approach. Moreover, we explored the impact of maize phenology by collecting samples at germination and flowering stages. Our findings suggest that the phenological stage has a notable impact on the abundance of P cycle genes within bacterial and archaeal communities, particularly regarding the solubilization of inorganic P. Furthermore, significant variations were observed in the relative abundance of genes associated with different P cycles in response to various fertilizer treatments. Sludge and struvite application improved P availability, which was related to an increase in the relative abundance of Sphingomonas (Proteobacteria) and Luteitalea (Acidobacteria) respectively, and genes related to inorganic P solubilization. Furthermore, we observed a substantial taxonomic clustering of functional processes associated with the P cycle. Among the dominant bacterial populations containing P-related genes, those microbes possessing genes linked to the solubilization of inorganic P typically did not harbor genes associated with the mineralization of organic P. This phenomenon was particularly evident among members of Actinobacteria. Overall, we reveal important shifts in bacterial and archaeal communities and associated molecular processes, stressing the intricate interplay between fertilization, phenology, and P cycling in agroecosystems.

Priestia aryabhattai Improves Soil Environment and Promotes Alfalfa Growth by Enhancing Rhizosphere Microbial Carbon Sequestration Capacity Under Greenhouse Conditions

Plant Growth-Promoting Rhizobacteria (PGPR) are gaining increasing attention, but their interactions with indigenous rhizosphere microbiomes remain unclear. To address this issue, we isolated a strain of Priestia aryabhattai with a growth-promoting effect. Under greenhouse conditions, its growth-promoting effect on alfalfa was evaluated, and amplicon sequencing was used to analyze changes in the rhizosphere microbial community to explore the growth promotion mechanism. Our study shows that inoculation with Priestia aryabhattai increases the α-diversity index of the alfalfa rhizosphere microbiome and enhances the abundance of beneficial bacterial genera. This is likely because inoculation with Priestia aryabhattai increased the abundance of carbon-sequestering genera, particularly Gemmatimonas, thereby improving the soil environment. The increased abundance of beneficial bacteria stimulates root development in alfalfa and enhances nutrient uptake, particularly phosphorus, which in turn boosts photosynthesis and promotes alfalfa growth. In summary, Priestia aryabhattai improves soil environment and promotes alfalfa growth by enhancing the carbon sequestration capacity of the rhizosphere microbial community. This work provides theoretical support and insight for the development of PGPR inoculants and for further research on their mechanisms.

Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era

BACKGROUND

The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics.

RESULTS

Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria.

CONCLUSION

This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.

Effects of biochar and compost on the abundant and rare microbial communities assembly and multifunctionality in pesticide-contaminated soil under freeze‒thaw cycles

Biochar and compost are effective ways to improve soil quality and reduce pesticide pollution. However, the effects of them on the abundant and rare microbial communities in freeze‒thaw soil need to be further clarified. Therefore, this study took biochar, compost, and their combination as examples to explore their effects on the abundant and rare microbial communities and multifunctionality in glyphosate, imidacloprid and pyraclostrobin contaminated soil under freeze‒thaw cycles. We found that freeze‒thaw cycles enhanced the functional groups and surface aromaticity of biochar and compost, thereby improving the adsorption capacity. Biochar and compost reduced the concentration and half-life of three pesticides and enhanced the degradation function of rare taxa in soil. Biochar and compost improved the structure composition and co-occurrence relationship of abundant and rare taxa. Meanwhile, the assembly processes of abundant and rare sub-communities were mainly driven by stochastic processes and the Combined treatment promoted the transition from dispersal limitation to homogenizing dispersal and homogeneous selection. Moreover, the Combined treatment significantly improved the multifunctionality before and after freezing and thawing by increasing the diversity of rare taxa and assembly processes. The results provide new insights for farmland soil remediation in seasonal frozen areas, especially the soil functional cycle of abundant and rare microorganisms.

Monitoring of indicators and bacterial succession in organic-amended technosols for the restoration of semiarid ecosystems

Restoration of mining sites is essential to ensure ecosystem services and biodiversity. One restoration strategy employed in arid and semi-arid zones is the use of organic amendments to establishment technosols. However, it is necessary to monitor the restoration progress in order to select appropriate amendments. This study monitored the effects of compost gardening, greenhouse horticulture and stabilized sewage sludge, and their blends. We focused on soil physical and chemical indicators and bacterial community structure and diversity during the 30 months after application. Organic amendments increased total organic carbon and nitrogen within six months, staying elevated compared to natural soils over 30 months. Electrical conductivity rose then stabilized, the pH slightly decreased but stayed alkaline, and water holding capacity improved in treated technosols. Bacterial diversity increased in amended technosols compared to control. Alpha diversity varied with treatment and time, peaking at 18 months. Technosols with plant compost showed reduced bacterial richness at 30 months, while those with sewage sludge and its mixtures maintained it. The bacterial community analysis showed significant differences among treatments and times, highlighting dominant phyla like Proteobacteria and Bacteroidetes. PCoA analysis showed clear separation of bacterial communities from treated, natural, and control soils, with notable differences between plant and sludge treatments. Soil variables such as TOC, TN, EC and water holding capacity explained >82 % of the variation in bacterial communities. Eighty-three indicator taxa were identified that explained the differences between the microbial communities of treated and untreated soils, highlighting the importance of taxa such as Pelagibacterium spp., Roseivirga spp. and Cellvibrio spp. in preserving soil health. In short, organic amendments improve soil properties and promote the diversity and stability of beneficial microbial communities in semi-arid mined soils, underlining their crucial role in the restoration and long-term maintenance of degraded soils.

Characteristics and driving forces of the soil microbial community during 35 years of natural restoration in abandoned areas of the Daxin manganese mine, China

The restoration of mining wastelands, particularly in karst regions contaminated by heavy metals, is an environmental challenge in need of urgent attention. Soil microbes play a vital role in nutrient cycling and ecosystem recovery, yet the long-term evolution of soil microbial communities in such settings remains poorly understood. This study explored the dynamics and influencing factors of soil microbial communities during 35 years of natural restoration in abandoned manganese (Mn) mine areas in Guangxi Province, China. The results revealed that the concentrations of Mn, Cd, Zn, and Cu were significantly (p < 0.05) reduced by 80.4-85.3%, 55.3-70.0%, 21.0-38.1%, and 29.4-49.4%, respectively, in the mid-late restoration periods (R19 and R35) compared with R1. The α diversities of the bacterial and fungal communities significantly increased in the middle-late restoration periods (R19 and R35), indicating increased microbial diversity as restoration progressed. The bacterial community structure exhibited more pronounced changes than did the fungal community structure, with significant shifts observed in dominant phyla such as Proteobacteria, Actinobacteria, Acidobacteriota, and Ascomycota. Notably, the relative abundances of Rhizobiales, Burkholderiales, and Hypocreales increased gradually with succession. Co-occurrence network analysis revealed that bacterial interactions became stronger over time, whereas interactions between bacteria and fungi weakened. Mantel tests and partial least squares path modeling (PLS‒PM) identified soil pH, heavy metals (Mn, Cd, Zn, and Cu), and nutrients (SOM and TN) as key drivers shaping the microbial community composition. These factors were more strongly correlated with bacterial communities than with fungal communities, underscoring the different responses of microbial groups to environmental changes during natural restoration. These findings enhance our understanding of the ecological processes governing microbial community succession in heavy metal-contaminated soils undergoing natural restoration.

Plant-microbe interactions in the rhizosphere for smarter and more sustainable crop fertilization: the case of PGPR-based biofertilizers

Biofertilizers based on plant growth promoting rhizobacteria (PGPR) are nowadays gaining increasingly attention as a modern tool for a more sustainable agriculture due to their ability in ameliorating root nutrient acquisition. For many years, most research was focused on the screening and characterization of PGPR functioning as nitrogen (N) or phosphorus (P) biofertilizers. However, with the increasing demand for food using far fewer chemical inputs, new investigations have been carried out to explore the potential use of such bacteria also as potassium (K), sulfur (S), zinc (Zn), or iron (Fe) biofertilizers. In this review, we update the use of PGPR as biofertilizers for a smarter and more sustainable crop production and deliberate the prospects of using microbiome engineering-based methods as potential tools to shed new light on the improvement of plant mineral nutrition. The current era of omics revolution has enabled the design of synthetic microbial communities (named SynComs), which are emerging as a promising tool that can allow the formulation of biofertilizers based on PGPR strains displaying multifarious and synergistic traits, thus leading to an increasingly efficient root acquisition of more than a single essential nutrient at the same time. Additionally, host-mediated microbiome engineering (HMME) leverages advanced omics techniques to reintroduce alleles coding for beneficial compounds, reinforcing positive plant-microbiome interactions and creating plants capable of producing their own biofertilizers. We also discusses the current use of PGPR-based biofertilizers and point out possible avenues of research for the future development of more efficient biofertilizers for a smarter and more precise crop fertilization. Furthermore, concerns have been raised about the effectiveness of PGPR-based biofertilizers in real field conditions, as their success in controlled experiments often contrasts with inconsistent field results. This discrepancy highlights the need for standardized protocols to ensure consistent application and reliable outcomes.

Prospects of phosphate solubilizing microorganisms in sustainable agriculture

Phosphorus (P), an essential macronutrient for various plant processes, is generally a limiting soil component for crop growth and yields. Organic and inorganic types of P are copious in soils, but their phyto-availability is limited as it is present largely in insoluble forms. Although phosphate fertilizers are applied in P-deficit soils, their undue use negatively impacts soil quality and the environment. Moreover, many P fertilizers are lost because of adsorption and fixation mechanisms, further reducing fertilizer efficiencies. The application of phosphate-solubilizing microorganisms (PSMs) is an environmentally friendly, low-budget, and biologically efficient method for sustainable agriculture without causing environmental hazards. These beneficial microorganisms are widely distributed in the rhizosphere and can hydrolyze inorganic and organic insoluble P substances to soluble P forms which are directly assimilated by plants. The present review summarizes and discusses our existing understanding related to various forms and sources of P in soils, the importance and P utilization by plants and microbes,, the diversification of PSMs along with mixed consortia of diverse PSMs including endophytic PSMs, the mechanism of P solubilization, and lastly constraints being faced in terms of production and adoption of PSMs on large scale have also been discussed.

Single-cell exploration of active phosphate-solubilizing bacteria across diverse soil matrices for sustainable phosphorus management

Phosphate-solubilizing bacteria (PSB) are crucial for enhancing phosphorus bioavailability and regulating phosphorus transformation processes. However, the in situ phosphorus-solubilizing activity and the link between phenotypes and genotypes for PSB remain unidentified. Here we employed single-cell Raman spectroscopy combined with heavy water to discern and quantify soil active PSB. Our results reveal that PSB abundance and in situ activity differed significantly between soil types and fertilization treatments. Inorganic fertilizer input was the key driver for active PSB distribution. Targeted single-cell sorting and metagenomic sequencing of active PSB uncovered several low-abundance genera that are easily overlooked within bulk soil microbiota. We elucidate the underlying functional genes and metabolic pathway, and the interplay between phosphorus and carbon cycling involved in high phosphorus solubilization activity. Our study provides a single-cell approach to exploring PSB from native environments, enabling the development of a microbial solution for the efficient agronomic use of phosphorus and mitigating the phosphorus crisis.

The phosphate-solubilising fungi in sustainable agriculture: unleashing the potential of fungal biofertilisers for plant growth

Phosphate-solubilising fungi (PSF) are beneficial microorganisms that play a pivotal role in plant growth by increasing the availability of phosphorus (P) in soil. Although phosphorus is an essential nutrient for plants, it often becomes inaccessible as it binds into insoluble forms. PSF effectively facilitate the release of this bound phosphorus through diverse mechanisms. Numerous fungal species demonstrate the ability to solubilise various types of phosphate compounds. Among the commonly researched PSF are Penicillium, Aspergillus, Rhizopus, Fusarium, Trichoderma, and Sclerotium. Moreover, yeasts such as Saccharomyces cerevisiae can potentially be leveraged as PSF. PSF secrete organic acids that chelate phosphate ions, thereby increasing their solubility in the soil. Moreover, PSF contribute to the decomposition of organic phosphorus compounds in soil by employing enzymes such as phosphatases, phytases, and phosphonatases. Furthermore, PSF can interact with other soil microorganisms, including nitrogen-fixing bacteria and arbuscular mycorrhizal fungi (AM-fungi), fostering synergistic effects that further enhance plant growth and nutrient absorption. The utilisation of PSF as biofertilisers offers numerous advantages over chemical fertilisers, including environmental friendliness, cost-effectiveness, and enhanced fertiliser utilisation efficiency. Furthermore, PSF can prove beneficial in challenging environments characterised by high phosphate sorption. Hence, this review serves as an updated study aimed at broadening the understanding of PSF and its potential applications in P solubilisation. This review also focuses on the diversity of PSF, the mechanisms underlying solubilisation, ecological roles of PSF in soil microbiome, and the benefits of sustainable agriculture. By delving into the ecological roles of PSF and their potential as biofertilisers, this study contributes to a deeper understanding of sustainable agriculture practices and addresses challenges in phosphate-scarce environments.

Soil phosphorus cycling microbial functional genes of monoculture and mixed plantations of native tree species in subtropical China

Background

Transforming coniferous plantation into broadleaved or mixed broadleaved-coniferous plantations is the tendency of forest management strategies in subtropical China. However, the effects of this conversion on soil phosphorus (P) cycling microbial functional genes are still unknown.

Methods

Soil samples were collected from 0-20, 20-40, and 40-60 cm (topsoil, middle layer, and subsoil, respectively) under coniferous Pinus massoniana (PM), broadleaved Erythrophleum fordii (EF), and their mixed (PM/EF) plantation in subtropical China. Used metagenomic sequencing to examine the alterations of relative abundances and molecular ecological network structure of soil P-cycling functional genes after the conversion of plantations.

Results

The composition of P-cycling genes in the topsoil of PM stand was significantly different from that of PM/EF and EF stands (p < 0.05), and total phosphorus (TP) was the main factor causing this difference. After transforming PM plantation into EF plantation, the relative abundances of P solubilization and mineralization genes significantly increased in the topsoil and middle layer with the decrease of soil TP content. The abundances of P-starvation response regulation genes also significantly increased in the subsoil (p < 0.05), which may have been influenced by soil organic carbon (SOC). The dominant genes in all soil layers under three plantations were phoR, glpP, gcd, ppk, and ppx. Transforming PM into EF plantation apparently increased gcd abundance in the topsoil (p < 0.05), with TP and NO3 --N being the main influencing factors. After transforming PM into PM/EF plantations, the molecular ecological network structure of P-cycling genes was more complex; moreover, the key genes in the network were modified with the transformation of PM plantation.

Conclusion

Transforming PM into EF plantation mainly improved the phosphate solubilizing potential of microorganisms at topsoil, while transforming PM into PM/EF plantation may have enhanced structural stability of microbial P-cycling genes react to environmental changes.

Differential Mechanisms of Microbial As(III) and Sb(III) Oxidation and Their Contribution to Tailings Reclamation

Mine tailings are extremely oligotrophic environments frequently contaminated with elevated As and Sb, making As(III) and Sb(III) oxidation potentially important energy sources for the tailing microbiome. Although they have been proposed to share similar metabolic pathways, a systemic comparison of the As(III) and Sb(III) oxidation mechanisms and energy utilization efficiencies requires further elucidation. In this study, we employed a combination of physicochemical, molecular, and bioinformatic analyses to compare the kinetic and genetic mechanisms of As(III) and Sb(III) oxidation as well as their respective energy efficiencies for fueling the key nutrient acquisition metabolisms. Thiobacillus and Rhizobium spp. were identified as functional populations for both As(III) and Sb(III) oxidation in mine tailings by DNA-stable isotope probing. However, these microorganisms mediated As(III) and Sb(III) oxidation via different metabolic pathways, resulting in preferential oxidation of Sb(III) over As(III). Notably, both As(III) and Sb(III) oxidation can facilitate nitrogen fixation and phosphate solubilization in mine tailings, with Sb(III) oxidation being more efficient in powering these processes. Thus, this study provided novel insights into the microbial As(III) and Sb(III) oxidation mechanisms and their respective nutrient acquisition efficiencies, which may be critical for the reclamation of mine tailings.

Endosaccharibacter trunci gen. nov., sp. nov. and Rhizosaccharibacter radicis gen. nov., sp. nov., two novel bacteria of the family Acetobacteraceae isolated from sugarcane

Two novel endophytic bacterial strains, designated KSS8T and KSS12T, were isolated from the stems and roots of sugarcane, respectively, collected in Nakhon Ratchasima, Thailand. They were Gram-stain-negative, aerobic, and rod-shaped. The strain KSS8T was a motile bacterium with a subpolar flagellum, while the strain KSS12T was non-motile. Strains KSS8T and KSS12T were closely related to Lichenicola cladoniae PAMC 26569T (97.3 and 95.6 %, respectively) and Lichenicoccus roseus KEBCLARHB70RT (97.2 and 95.8 %, respectively) based on the similarity on their 16S rRNA gene sequence. This similarity corresponded to their phylogenomic positions within the evolutionary radiation of the family Acetobacteraceae. The average nucleotide identities and digital DNA-DNA hybridization values between the genome sequences of the two strains and other genera were significantly lower than the defined threshold values of 95-96 % and 70 %, respectively, which are used for the delineation of prokaryotic species. Both strains contained summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, C19:0 cyclo ω8c, C18:0, and C18:1 2OH as the predominant cellular fatty acids, but C18:3 ω6c (6, 9, 12) were found only in strain KSS12T. Based on phenotypic, chemotaxonomic, phylogenetic, and genomic analyses, these strains clearly represented two novel genera within the family Acetobacteraceae, for which the name Endosaccharibacter gen. nov., with the type species Endosaccharibacter trunci sp. nov. (type strain, KSS8T = TBRC 14669T = NBRC 115232T = KCTC 92115T = LMG 32414T) and the name Rhizosacchari bacter gen. nov., with the type species Rhizosaccharibacter radicis sp. nov. (type strain, KSS12T = TBRC 13066T = NBRC 114898T = KCTC 82433T = LMG 32137T) are proposed.

Different microbial functional traits drive bulk and rhizosphere soil phosphorus mobilization in an alpine meadow after nitrogen input

Enhanced nitrogen (N) input is expected to influence the soil phosphorus (P) cycling through biotic and abiotic factors. Among these factors, soil microorganisms play a vital role in regulating soil P availability. However, the divergent contribution of functional microorganisms to soil P availability in the rhizosphere and bulk soil under N addition remains unclear. We conducted an N addition experiment with four N input rates (0, 5, 10, and 15 g N m-2 year-1) in an alpine meadow over three years. Metagenomics was employed to investigate the functional microbial traits in the rhizosphere and bulk soil. We showed that N addition had positive effects on microbial functional traits related to P-cycling in the bulk and rhizosphere soil. Specifically, high N addition significantly increased the abundance of most microbial genes in the bulk soil but only enhanced the abundance of five genes in the rhizosphere soil. The soil compartment, rather than the N addition treatment, was the dominant factor explaining the changes in the diversity and network of functional microorganisms. Furthermore, the abundance of functional microbial genes had a profound effect on soil available P, particularly in bulk soil P availability driven by the ppa and ppx genes, as well as rhizosphere soil P availability driven by the ugpE gene. Our results highlight that N addition stimulates the microbial potential for soil P mobilization in alpine meadows. Distinct microbial genes play vital roles in soil P availability in bulk and rhizosphere soil respectively. This indicates the necessity for models to further our knowledge of P mobilization processes from the bulk soil to the rhizosphere soil, allowing for more precise predictions of the effects of N enrichment on soil P cycling.

Isolation, molecular identification, and genomic analysis of Mangrovibacter phragmitis strain ASIOC01 from activated sludge harboring the bioremediation prowess of glycerol and organic pollutants in high-salinity

The physiological and genotypic characteristics of Mangrovibacter (MGB) remain largely unexplored, including their distribution and abundance within ecosystems. M. phragmitis (MPH) ASIOC01 was successfully isolated from activated sludge (AS), which was pre-enriched by adding 1,3-dichloro-2-propanol and 3-chloro-1,2-propanediol as carbon sources. The new isolate, MPH ASIOC01, exhibited resilience in a medium containing sodium chloride concentration up to 11% (with optimal growth observed at 3%) and effectively utilizing glycerol as their sole carbon source. However, species delimitation of MGBs remains challenging due to high 16S rRNA sequence similarity (greater than 99% ANI) among different MGBs. In contrast, among the housekeeping gene discrepancies, the tryptophan synthase beta chain gene can serve as a robust marker for fast species delimitation among MGBs. Furthermore, the complete genome of MPH ASIOC01 was fully sequenced and circlized as a single contig using the PacBio HiFi sequencing method. Comparative genomics revealed genes potentially associated with various phenotypic features of MGBs, such as nitrogen-fixing, phosphate-solubilizing, cellulose-digesting, Cr-reducing, and salt tolerance. Computational analysis suggested that MPH ASIOC01 may have undergone horizontal gene transfer events, possibly contributing unique traits such as antibiotic resistance. Finally, our findings also disclosed that the introduction of MPH ASIOC01 into AS can assist in the remediation of wastewater chemical oxygen demand, which was evaluated using gas chromatograph-mass spectrometry. To the best of our knowledge, this study offers the most comprehensive understanding of the phenotypic and genotypic features of MGBs to date.

Strawberry Yield Improvement by Hydrogen-Based Irrigation Is Functionally Linked to Altered Rhizosphere Microbial Communities

Molecular hydrogen (H2) is crucial for agricultural microbial systems. However, the mechanisms underlying its influence on crop yields is yet to be fully elucidated. This study observed that H2-based irrigation significantly increased strawberry (Fragaria × ananassa Duch.) yield with/without nutrient fertilization. The reduction in soil available nitrogen (N), phosphorus (P), potassium (K), and organic matter was consistent with the increased expression levels of N/P/K-absorption-related genes in root tissues at the fruiting stage. Metagenomics profiling showed the alterations in rhizosphere microbial community composition achieved by H2, particularly under the conditions without fertilizers. These included the enrichment of plant-growth-promoting rhizobacteria, such as Burkholderia, Pseudomonas, and Cupriavidus genera. Rhizobacteria with the capability to oxidize H2 (group 2a [NiFe] hydrogenase) were also enriched. Consistently, genes related to soil carbon (C) fixation (i.e., rbcL, porD, frdAB, etc.), dissimilar nitrate reduction (i.e., napAB and nrfAH), and P solublization, mineralization, and transportation (i.e., ppx-gppA, appA, and ugpABCE) exhibited higher abundance. Contrary tendencies were observed in the soil C degradation and N denitrification genes. Together, these results clearly indicate that microbe-mediated soil C, N, and P cycles might be functionally altered by H2, thus increasing plant nutrient uptake capacity and horticultural crop yield.

Metabarcoding analysis reveals an interaction among distinct groups of bacteria associated with three different varietals of grapes used for wine production in Brazil

Grapes are globally popular with wine production being one of the most well-known uses of grapes worldwide. Brazil has a growing wine industry, and the Serra Gaúcha region is a significant contributor to the country's wine production. Nonetheless, other states are increasing their relevance in this segment. Environmental factors and the soil microbiome (bacteria and fungi) heavily influence grape quality, shaping the crucial "terroir" for wines. Here, soil quality was assessed through nutrient analysis and bacteria microbial diversity, which could significantly impact grape health and final wine attributes. Soil samples from São Paulo's vineyards, focusing on Syrah, Malbec, and Cabernet Sauvignon, underwent chemical and microbial analysis via 16S rRNA metabarcoding and highlighted significant differences in soil composition between vineyards. Statistical analyses including PCA and CAP showcased region-based separation and intricate associations between microbiota, region, and grape variety. Correlation analysis pinpointed microbial genera linked to specific soil nutrients. Random Forest analysis identified abundant bacterial genera per grape variety and the Network analysis revealed varied co-occurrence patterns, with Cabernet Sauvignon exhibiting complex microbial interactions. This study unveils complex relationships between soil microbiota, nutrients, and diverse grape varieties in distinct vineyard regions. Understanding how these specific microorganisms are associated with grapes can improve vineyard management, grape quality, and wine production. It can also potentially optimize soil health, bolster grapevine resilience against pests and diseases, and contribute to the unique character of wines known as terroir.

Root-mediated acidification, phosphatase activity and the phosphorus-cycling microbial community enhance phosphorus mobilization in the rhizosphere of wetland plants

Rhizoremediation of wetland plants is an environmentally friendly strategy for sediment phosphorous (P) removal, the basic underlying principle of which is the complex interactions between roots and microorganisms. This study investigated the immobilization and mobilization mechanisms of P in the rhizosphere of wetland plants using high-resolution spatial visualization techniques and metagenomic sequencing. Two-dimensional visualization of the spatial distribution of P, iron (Fe) and manganese (Mn) indicated that the sequestration of Fe-oxides rather than Mn-oxides caused the depletion of labile P, resulting in an increase in the Fe-adsorbed P fraction. Plants altered the rhizospheric environments and P-cycling microbial community to mobilize low-availability P from sediments. Mineral P solubilization and organic P mineralization were enhanced by local acidification and increased phosphatase activity, respectively. Microbial P mobilization also increased with increasing relative abundances of P solubilization and mineralization genes (gcd and phnW) and decreasing P transportation genes (ugpA, ugpB, and pit) genes in the rhizosphere. These processes led to the remobilization of 10.04 % of inorganic P, and 15.23 % of organic P, in the rhizosphere during the incubation period. However, the resupply of P via the above processes did not compensate for the depletion of rhizospheric P via root uptake and mineral sequestration. Our results provide novel insights into the mechanisms of rhizospheric P cycling, which will help to inform future phytoremediation strategies.

Soil microbial functional profiles of P-cycling reveal drought-induced constraints on P-transformation in a hyper-arid desert ecosystem

Soil water conditions are known to influence soil nutrient availability, but the specific impact of different conditions on soil phosphorus (P) availability through the modulation of P-cycling functional microbial communities in hyper-arid desert ecosystems remains largely unexplored. To address this knowledge gap, we conducted a 3-year pot experiment using a typical desert plant species (Alhagi sparsifolia Shap.) subjected to two water supply levels (25 %-35 % and 65 %-75 % of maximum field capacity, MFC) and four P-supply levels (0, 1, 3, and 5 g P m-2 y-1). Our investigation focused on the soil Hedley-P pool and the four major microbial groups involved in the critical phases of soil microbial P-cycling. The results revealed that the drought (25 %-35 % MFC) and no P-supply treatments reduced soil resin-P and NaHCO3-Pi concentrations by 87.03 % and 93.22 %, respectively, compared to the well-watered (65 %-75 % MFC) and high P-supply (5 g P m-2 y-1) treatments. However, the P-supply treatment resulted in a 12 %-22 % decrease in the soil NH4+-N concentration preferred by microbes compared to the no P-supply treatment. Moreover, the abundance of genes engaged in microbial P-cycling (e.g. gcd and phoD) increased under the drought and no P-supply treatments (p < 0.05), suggesting that increased NH4+-N accumulation under these conditions may stimulate P-solubilizing microbes, thereby promoting the microbial community's investment in resources to enhance the P-cycling potential. Furthermore, the communities of Steroidobacter cummioxidans, Mesorhizobium alhagi, Devosia geojensis, and Ensifer sojae, associated with the major P-cycling genes, were enriched in drought and no or low-P soils. Overall, the drought and no or low-P treatments stimulated microbial communities and gene abundances involved in P-cycling. However, this increase was insufficient to maintain soil P-bioavailability. These findings shed light on the responses and feedback of microbial-mediated P-cycling behaviors in desert ecosystems under three-year drought and soil P-deficiency.

Modifying humus-phosphorus-arsenic interactions in sludge composting: The strengthening of phosphorus availability and arsenic efflux detoxification mechanisms

Arsenic (As) in sewage sludge poses a significant threat to environmental and human health, which has attracted widespread attention. This study investigated the value of adding sodium percarbonate (SP) on phosphorus (P) availability and As efflux detoxification through HS-P-As interactions. Due to the unique structure of humus (HS) and the similar chemical properties of P and As, the conditions for HS-P-As interaction are provided. This study discussed the content, morphology and microbial communities of HS, P and As by using metagenomic and correlation analysis. The results showed that the humification index in the experiment group (SPC) was 2.34 times higher than that in the control group (CK). The available phosphorus (AP) content of SPC increased from 71.09 mg/kg to 126.14 mg/kg, and SPC was 1.11 times that of CK. The relative abundance of ACR3/ArsB increased. Pst, Actinomyces and Bacillus commonly participated in P and As conversion. The correlation analysis revealed that the humification process was enhanced, the AP was strengthened, and the As was efflux detoxified after SP amendment. All in all, this study elucidated the key mechanism of HS-P-As interaction and put forward a new strategy for sewage sludge resource utilization and detoxification.

Soil prokaryotic and fungal biome structures associated with crop disease status across the Japan Archipelago

Archaea, bacteria, and fungi in the soil are increasingly recognized as determinants of agricultural productivity and sustainability. A crucial step for exploring soil microbiomes with important ecosystem functions is to perform statistical analyses on the potential relationship between microbiome structure and functions based on comparisons of hundreds or thousands of environmental samples collected across broad geographic ranges. In this study, we integrated agricultural field metadata with microbial community analyses by targeting 2,903 bulk soil samples collected along a latitudinal gradient from cool-temperate to subtropical regions in Japan (26.1-42.8 °N). The data involving 632 archaeal, 26,868 bacterial, and 4,889 fungal operational taxonomic units detected across the fields of 19 crop plant species allowed us to conduct statistical analyses (permutational analyses of variance, generalized linear mixed models, randomization analyses, and network analyses) on the relationship among edaphic factors, microbiome compositions, and crop disease prevalence. We then examined whether the diverse microbes form species sets varying in potential ecological impacts on crop plants. A network analysis suggested that the observed prokaryotes and fungi were classified into several species sets (network modules), which differed substantially in association with crop disease prevalence. Within the network of microbe-to-microbe coexistence, ecologically diverse microbes, such as an ammonium-oxidizing archaeon, an antibiotics-producing bacterium, and a potentially mycoparasitic fungus, were inferred to play key roles in shifts between crop-disease-promotive and crop-disease-suppressive states of soil microbiomes. The bird's-eye view of soil microbiome structure will provide a basis for designing and managing agroecosystems with high disease-suppressive functions.IMPORTANCEUnderstanding how microbiome structure and functions are organized in soil ecosystems is one of the major challenges in both basic ecology and applied microbiology. Given the ongoing worldwide degradation of agroecosystems, building frameworks for exploring structural diversity and functional profiles of soil microbiomes is an essential task. Our study provides an overview of cropland microbiome states in light of potential crop-disease-suppressive functions. The large data set allowed us to explore highly functional species sets that may be stably managed in agroecosystems. Furthermore, an analysis of network architecture highlighted species that are potentially used to cause shifts from disease-prevalent states of agroecosystems to disease-suppressive states. By extending the approach of comparative analyses toward broader geographic ranges and diverse agricultural practices, agroecosystem with maximized biological functions will be further explored.

Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland

The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.

Soil phosphorus transformation and plant uptake driven by phosphate-solubilizing microorganisms

Phosphorus (P) is an important nutrient for plants, and a lack of available P greatly limits plant growth and development. Phosphate-solubilizing microorganisms (PSMs) significantly enhance the ability of plants to absorb and utilize P, which is important for improving plant nutrient turnover and yield. This article summarizes and analyzes how PSMs promote the absorption and utilization of P nutrients by plants from four perspectives: the types and functions of PSMs, phosphate-solubilizing mechanisms, main functional genes, and the impact of complex inoculation of PSMs on plant P acquisition. This article reviews the physiological and molecular mechanisms of phosphorus solubilization and growth promotion by PSMs, with a focus on analyzing the impact of PSMs on soil microbial communities and its interaction with root exudates. In order to better understand the ability of PSMs and their role in soil P transformation and to provide prospects for research on PSMs promoting plant P absorption. PSMs mainly activate insoluble P through the secretion of organic acids, phosphatase production, and mycorrhizal symbiosis, mycorrhizal symbiosis indirectly activates P via carbon exchange. PSMs can secrete organic acids and produce phosphatase, which plays a crucial role in soil P cycling, and related genes are involved in regulating the P-solubilization ability. This article reviews the mechanisms by which microorganisms promote plant uptake of soil P, which is of great significance for a deeper understanding of PSM-mediated soil P cycling, plant P uptake and utilization, and for improving the efficiency of P utilization in agriculture.

Enhancing phosphate-solubilising microbial communities through artificial selection

Microbial communities, acting as key drivers of ecosystem processes, harbour immense potential for sustainable agriculture practices. Phosphate-solubilising microorganisms, for example, can partially replace conventional phosphate fertilisers, which rely on finite resources. However, understanding the mechanisms and engineering efficient communities poses a significant challenge. In this study, we employ two artificial selection methods, environmental perturbation, and propagation, to construct phosphate-solubilising microbial communities. To assess trait transferability, we investigate the community performance in different media and a hydroponic system with Chrysanthemum indicum. Our findings reveal a distinct subset of phosphate-solubilising bacteria primarily dominated by Klebsiella and Enterobacterales. The propagated communities consistently demonstrate elevated levels of phosphate solubilisation, surpassing the starting soil community by 24.2% in activity. The increased activity of propagated communities remains consistent upon introduction into the hydroponic system. This study shows the efficacy of community-level artificial selection, particularly through propagation, as a tool for successfully modifying microbial communities to enhance phosphate solubilisation.

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.

Root colonization by beneficial rhizobacteria

Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.

Differential impacts of sewage sludge and biochar on phosphorus-related processes: An imaging study of the rhizosphere

Recycling of phosphorus (P) from waste streams in agriculture is essential to reduce the negative environmental effects of surplus P and the unsustainable mining of geological P resources. Sewage sludge (SS) is an important P source; however, several issues are associated with the handling and application of SS in agriculture. Thus, post-treatments such as pyrolysis of SS into biochar (BC) could address some of these issues. Here we elucidate how patches of SS in soil interact with the living roots of wheat and affect important P-related rhizosphere processes compared to their BC counterparts. Wheat plants were grown in rhizoboxes with sandy loam soil, and 1 cm Ø patches with either SS or BC placed 10 cm below the seed. A negative control (CK) was included. Planar optode pH sensors were used to visualize spatiotemporal pH changes during 40 days of plant growth, diffusive gradients in thin films (DGT) were applied to map labile P, and zymography was used to visualize the spatial distribution of acid (ACP) and alkaline (ALP) phosphatase activity. In addition, bulk soil measurements of available P, pH, and ACP activity were conducted. Finally, the relative abundance of bacterial P-cycling genes (phoD, phoX, phnK) was determined in the patch area rhizosphere. Labile P was only observed in the area of the SS patches, and SS further triggered root proliferation and increased the activity of ACP and ALP in interaction with the roots. In contrast, BC seemed to be inert, had no visible effect on root growth, and even reduced ACP and ALP activity in the patch area. Furthermore, there was a lower relative abundance of phoD and phnK genes in the BC rhizosphere compared to the CK. Hence, optimization of BC properties is needed to increase the short-term efficiency of BC from SS as a P fertilizer.

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.

Understanding how various forms of phosphorus stress affect microbiome functions and boost plant disease resistance: Insights from metagenomic analysis

The plant's response to phosphorus (P) starvation suppresses its immunity and regulates rhizosphere microbial colonization. However, the impact of various P forms on plant disease resistance and microbial composition remains underreported. This paper examines the soybean rhizosphere microbiome facing co-stress from Fusarium oxysporum and diverse P forms. Macrogenomic analysis evaluates whether P addition enhances plant disease resistance and rhizosphere microbial function, and if such effects relate to P forms. Results show that different P forms mitigate F. oxysporum-induced plant inhibition by promoting P turnover. P forms predominantly affect microbial composition, followed by soil and plant properties. In soybean, the phosphate transport strategy (ugpA/Q) was selected to maintain high P to enhance immunity in the KH2PO4 treatment, while organo-P mineralization (phnH/F/W/G) was selected for superphosphate treatment. The Frankiales, a P-turnover microorganism, copiotrophic microorganisms, and indicator bacteria of plant properties, initially increase after F. oxysporum inoculation and then decrease post P addition, regardless of P forms. Additionally, the rhizosphere microbial community's metabolic activities and compounds significantly aid soybean defense against F. oxysporum, with functional types depending on P forms. Therefore, these findings establish a novel approach to enhance host defense against soil-borne diseases through P nutrition regulation to mediate host-driven metabolic activities of microbial communities.

Harnessing biological nitrogen fixation in plant leaves

The importance of biological nitrogen fixation (BNF) in securing food production for the growing world population with minimal environmental cost has been increasingly acknowledged. Leaf surfaces are one of the biggest microbial habitats on Earth, harboring diverse free-living N2-fixers. These microbes inhabit the epiphytic and endophytic phyllosphere and contribute significantly to plant N supply and growth. Here, we summarize the contribution of phyllosphere-BNF to global N cycling, evaluate the diversity of leaf-associated N2-fixers across plant hosts and ecosystems, illustrate the ecological adaptation of N2-fixers to the phyllosphere, and identify the environmental factors driving BNF. Finally, we discuss potential BNF engineering strategies to improve the nitrogen uptake in plant leaves and thus sustainable food production.

Phosphate-solubilizing bacteria: Their agroecological function and optimistic application for enhancing agro-productivity

Phosphorus (P) is a limiting nutrient in the soil-plant nutrient cycling. Although the exogenous application of chemical P fertilizers can satisfy crop P requirements during critical growth phases. While excessive P fertilizers use results in low phosphorus acquisition efficiency (PAE), it has serious environmental consequences and hastens the depletion of P mineral reserves. Phosphate-solubilizing bacteria (PSB) have the potential to make insoluble phosphate available to plants through solubilization and mineralization, increasing crop yields while maintaining environmental sustainability. Existing reviews mainly focus on the beneficial effects of PSB on crop performance and related mechanisms, while few of them elucidate the action mechanisms of PSB in soil-microbe-plant interactions for crop cultivation with high yield efficiency. Hence, this study provides a comprehensive review of the physicochemical and molecular mechanisms (e.g., root exudates, extracellular polysaccharides, organic acids, phosphatases, and phosphate-specific transport systems) of PSB to facilitate the P cycle in the soil-plant systems. Further, the potential of commercial applications of PSB (e.g., genetic engineering, seed priming and coating) are also discussed in order to highlight their contribution to sustainable agriculture. Finally, existing challenges and future prospects in agricultural applications are proposed. In conclusion, we firmly believe that PSB represent a highly significant biotechnological tool for enhancing agricultural productivity and offers a wide range of extensive potential applications.

Stimulation of primed carbon under climate change corresponds with phosphorus mineralization in the rhizosphere of soybean

Elevated CO2 and temperature likely alter photosynthetic carbon inputs to soils, which may stimulate soil microbial activity to accelerate the decomposition of soil organic carbon (SOC), liberating more phosphorus (P) into the soil solution. However, this hypothesis on the association of SOC decomposition and P transformation in the plant rhizosphere requires robust soil biochemical evidence, which is critical to nutrient management for the mitigation of soil quality against climate change. This study investigated the microbial functional genes relevant to P mineralization together with priming processes of SOC in the rhizosphere of soybean grown under climate change. Soybean plants were grown under elevated CO2 (eCO2, 700 ppm) combined with warming (+ 2 °C above ambient temperature) in open-top chambers. Photosynthetic carbon flow in the plant-soil continuum was traced with 13CO2 labeling. The eCO2 plus warming treatment increased the primed carbon (C) by 43 % but decreased the NaHCO3-extratable organic P by 33 %. Furthermore, NaHCO3-Po was negatively correlated with phosphatase activity and microbial biomass C. Elevated CO2 increased the abundances of C degradation genes, such as abfA and ManB, and P mineralization genes, such as gcd, phoC and phnK. The results suggested that increased photosynthetic carbon inputs to the rhizosphere of plants under eCO2 plus warming stimulated the microbial population and metabolic functions of both SOC and organic P mineralization. There is a positive relationship between the rhizosphere priming effect and P mineralization. The response of microorganisms to plant-C flow is decisive for coupled C and P cycles, which are likely accelerated under climate change.

Impacts of Oak Mulch Amendments on Rhizosphere Microbiome of Citrus Trees Grown in Florida Flatwood Soils

Rhizosphere interactions are an understudied component of citrus production. This is even more important in Florida flatwood soils, which pose significant challenges in achieving sustainable and effective fruit production due to low natural fertility and organic matter. Citrus growers apply soil amendments, including oak mulch, to ameliorate their soil conditions. Thus, the aim of this research was to evaluate the effects of oak mulch on citrus nutrient uptake, soil characteristics, and rhizosphere composition. The plant material consisted of 'Valencia' sweet orange (Citrus × sinensis) trees grafted on 'US-812' (C. reticulata × C. trifoliata) rootstock. The experiment consisted of two treatments, which included trees treated with oak mulch (300 kg of mulch per plot) and a control. The soil and leaf nutrient contents, soil pH, cation exchange capacity, moisture, temperature, and rhizosphere bacterial compositions were examined over the course of one year (spring and fall 2021). During the spring samplings, the citrus trees treated with oak mulch resulted in significantly greater soil Zn and Mn contents, greater soil moisture, and greater rhizosphere bacterial diversity compared to the control, while during the fall samplings, only a greater soil moisture content was observed in the treated trees. The soil Zn and Mn content detected during the spring samplings correlated with the significant increases in the diversity of the rhizosphere bacterial community composition. Similarly, the reduced rates of leaching and evaporation (at the soil surface) of oak mulch applied to Florida sandy soils likely played a large role in the significant increase in moisture and nutrient retention.

Effects of different remediation methods on phosphorus transformation and availability

The effects of different heavy metal pollution remediation methods on soil nutrient transformation and soil health remain unclear. In this study, the effects of phytoextraction (PE) and passivation remediation (PR) on Cd-polluted soil phosphorus transformation and availability were compared by pot experiment. The results showed that PE significantly reduced the concentrations of total and available Cd (both H2O-Cd and DTPA-Cd) in soil, PR also decreased available Cd content but had no significant effect on total Cd content. PE slightly increased soil pH and NH4+-N content, while PR significantly increased soil pH, NO3--N and AK content. PE promoted the conversion of stable P (including HCl-Pi and residual-Pt), and increased the content of labile P (including H2O-Pi, NaHCO3-Pi and NaHCO3-Po) and the proportion of moderately labile P (including NaOH-Pi and NaOH-Po), while PR showed the opposite trend. PE showed a higher soil phoC gene abundance and acid phosphatase (ACP) activity, while PR showed a higher phoD gene copies and alkaline phosphatase (ALP) activity. Soil bacteria and phoD-harboring bacteria community was significantly affected by remediation methods and soil types. Compared with PR, PE reduced phoD-harboring bacterial diversity but significantly increased the abundance of genera associated with P dissolution (Streptomyces) and P conversion (Bradyrhizobium and Frankia), both of which were significantly positively correlated with labile P or moderately labile P. In general, compared with PR, PE can effectively remove soil Cd pollution, while maintaining a higher content of labile P and a higher proportion of moderately labile P, which can be considered as a green and sustainable remediation strategy conducive to soil quality.

Manure-derived hydrochar superior to manure: Reducing non-point pollution risk by altering nitrogen and phosphorus fugacity in the soil-water system

Hydrothermal carbonization (HTC) technology is an emerging technology for the disposal of manure-based wet wastes. However, the effects of manure-derived hydrochar inputs to agricultural soils on nitrogen (N) and phosphorus (P) morphology and conversion in soil-water systems remain largely unexplored. In this study, pig and cattle manure (PM and CM), and their derived hydrochar (PCs and CCs) were applied to agricultural soils, with changes in nutrient morphology and enzyme activities related to N and P transformation in the soil-water systems observed through flooded incubation experiments. The results showed that floodwater ammonia N concentrations were reduced by 12.9-29.6% for PCs relative to PM, and 21.6-36.9% for CCs relative to CM, respectively. Moreover, floodwater total P concentrations of PCs and CCs were reduced by 11.7-20.7% relative to PM and CM. Soil enzyme activities closely related to N and P transformations in the soil-water system responded differently to manure and manure-derived hydrochar application. Compared to manure, the application of manure-derived hydrochar inhibited soil urease and acid phosphatase activity by up to 59.4% and 20.3%, respectively, whereas it had significant promotion effects on soil nitrate reductase (∼69.7%) and soil nitrite reductase (∼64.0%). The products of manure after HTC treatments have the characteristics of organic fertilizers, and the fertilization effects of PCs are more prominent than CCs, which are subject to further verification in field trials. Our findings improve the current understanding of manure-derived organic matter affecting N and P conversions in soil-water systems and the risk for non-point source pollution.

Enhanced biological phosphorus removal by high concentration powder carrier bio-fluidized bed (HPB): Phosphorus distribution, cyclone separation, and metagenomics

This study provides a comparative investigation of phosphorus removal between anaerobic-anoxic-oxic (AAO) and high-concentration powder carrier bio-fluidized bed (HPB) in the same full-scale wastewater treatment plant. The results showed that the total phosphorus removal of HPB was 71.45%-96.71%. Compared with AAO, the total phosphorus removal of HPB can be increased by a maximum of 15.73%. The mechanisms of enhanced phosphorus removal by HPB include the followings. Biological phosphorus removal was significant. The anaerobic phosphorus release capacity of HPB was enhanced and polyphosphate (Poly-P) in the excess sludge of HPB was 1.5 times higher than that of AAO. The relative abundance of Candidatus Accumulibacter was 5 times higher than that of AAO, and oxidative phosphorylation and butanoate metabolism were enhanced. The analysis of phosphorus distribution showed that cyclone separation increased the chemical phosphorus precipitation (Chem-P) in the excess sludge by 16.96% to avoid accumulation in the biochemical tank. The phosphorus adsorbed by extracellular polymeric substance (EPS) in the recycled sludge was stripped, and the EPS bound-P in the excess sludge increased by 1.5 times. This study demonstrated the feasibility of HPB to improve the phosphorus removal efficiency for domestic wastewater.

Artificial mixed microbial system for polycyclic aromatic hydrocarbons degradation

Polycyclic aromatic hydrocarbons (PAHs) are environmental pollutants with major risks to human health. Biological degradation is environmentally friendly and the most appealing remediation method for a wide range of persistent pollutants. Meanwhile, due to the large microbial strain collection and multiple metabolic pathways, PAH degradation via an artificial mixed microbial system (MMS) has emerged and is regarded as a promising bioremediation approach. The artificial MMS construction by simplifying the community structure, clarifying the labor division, and streamlining the metabolic flux has shown tremendous efficiency. This review describes the construction principles, influencing factors, and enhancement strategies of artificial MMS for PAH degradation. In addition, we identify the challenges and future opportunities for the development of MMS toward new or upgraded high-performance applications.

Deciphering endemic rhizosphere microbiome community's structure towards the host-derived heavy metals tolerance and plant growth promotion functions in serpentine geo-ecosystem

Environmental microbes in rhizosphere soil and surrounding plants have the potential to alter ecosystem functions. We investigated the microbial communities inhabiting the rhizosphere soils of both serpentine and non-serpentine rhizosphere zones to evaluate their heavy metal tolerance and ability to promote plant growth, utilizing 16S rRNA metabarcoding. The Biolog-EcoPlate technique was employed to determine how abiotic stress factors affect carbon utilization capacity by rhizospheric microbial communities in the serpentine geo-ecosystem. The phyla Proteobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae colonized in the roots of Miscanthus sp., Biden sp., and Oryza sp. showed noticeable differences in different rhizosphere zones. The PICRUSt2-based analysis identified chromium/iron resistance genes (ceuE, chrA) and arsenic resistance genes (arsR, acr3, arsC) abundant in all the studied rhizosphere soils. Notably, nickel resistance genes (nikA, nikD, nikE, and nikR) from Arthrobacter, Microbacterium, and Streptomyces strongly correlate with functions related to solubilization of nickel and an increase in siderophore and IAA production. The abundance of Arthrobacter, Clostridium, Geobacter, Dechloromonas, Pseudomonas, and Flavobacterium was positively correlated with chromium and nickel but negatively correlated with the calcium/magnesium ratio. Our results contribute to a better understanding of the functions of plant-tolerant PGPR interaction in the heavy metal-contaminated rhizosphere and eco-physiological responses from long-term biological weathering.

Effects of nitrogen deposition on carbon and nutrient cycling along a natural soil acidity gradient as revealed by metagenomics

Nitrogen (N) deposition and soil acidification are environmental challenges affecting ecosystem functioning, health, and biodiversity, but their effects on functional genes are poorly understood. Here, we utilized metabarcoding and metagenomics to investigate the responses of soil functional genes to N deposition along a natural soil pH gradient. Soil N content was uncorrelated with pH, enabling us to investigate their effects separately. Soil acidity strongly and negatively affected the relative abundances of most cluster of orthologous gene categories of the metabolism supercategory. Similarly, soil acidity negatively affected the diversity of functional genes related to carbon and N but not phosphorus cycling. Multivariate analyses showed that soil pH was the most important factor affecting microbial and functional gene composition, while the effects of N deposition were less important. Relative abundance of KEGG functional modules related to different parts of the studied cycles showed variable responses to soil acidity and N deposition. Furthermore, our results suggested that the diversity-function relationship reported for other organisms also applies to soil microbiomes. Since N deposition and soil pH affected microbial taxonomic and functional composition to a different extent, we conclude that N deposition effects might be primarily mediated through soil acidification in forest ecosystems.

Potential effect of key soil bacterial taxa on the increase of rice yield under milk vetch rotation

Legume crop rotation is often adopted in rice cultivation to improve soil productivity. However, little is known about the role of microbes under legume rotation in affecting soil productivity. To elucidate this, a long-term paddy cropping experiment was set up to study the relationship between crop yield, soil chemical properties, and key microbial taxa under a double-rice and milk vetch rotation. Milk vetch rotation significantly improved soil chemical properties compared to no fertilization treatment, and soil phosphorus was a major factor correlated with crop yield. Long-term legume rotation increased soil bacterial alpha diversity and changed soil bacterial community. After milk vetch rotation, the relative abundances of Bacteroidota, Desulfobacterota, Firmicutes, and Proteobacteria increased while those of Acidobacteriota, Chloroflexi, and Planctomycetota decreased. Moreover, milk vetch rotation increased the relative abundance of phosphorus-related gene K01083 (bpp), which was significantly correlated with soil phosphorus content and crop yield. Network analysis showed that taxa of Vicinamibacterales were positively correlated with total phosphorus and available phosphorus, which was a potential taxon contributing to the availability of soil phosphorus stock. Our results indicated that milk vetch rotation could enrich key taxa with latent phosphate-solubilizing ability, increase the content of soil available phosphorus, and finally enhance crop yield. This could provide scientific guidance for better crop production.

Phosphorus transformation behavior and phosphorus cycling genes expression in food waste composting with hydroxyapatite enhanced by phosphate-solubilizing bacteria

This study aimed to explore the effect of phosphate-solubilizing bacteria (PSB) Bacillus inoculation in the cooling stage on hydroxyapatite dissolution, phosphorus (P) forms transformation, and bacterial P cycling genes in food waste composting with hydroxyapatite. Results indicated that PSB inoculation promoted the dissolution of hydroxyapatite, increased P availability of compost by 8.1% and decreased the ratio of organic P to inorganic P by 10.2% based on sequential fractionation and ³¹P nuclear magnetic resonance spectroscopy. Illumina sequencing indicated Bacillus relative abundance after inoculation increased up to one time higher than control after the cooling stage. Network analysis and metabolic function of bacterial community analysis suggested inorganic P solubilizing genes of Bacillus and organic P mineralization genes of other genera were improved after inoculation in the core module. Therefore, bioaugmentation of PSB in the cooling stage may be a potential way to improve P bioavailability of bone and food waste in composting.

Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability

BACKGROUND

For achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability.

RESULTS

We found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass.

CONCLUSIONS

Our results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification. Video Abstract.

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion

Introduction

Plant invasion can profoundly alter ecosystem processes driven by microorganisms. The fundamental mechanisms linking microbial communities, functional genes, and edaphic characteristics in invaded ecosystems are, nevertheless, poorly understood.

Methods

Here, soil microbial communities and functions were determined across 22 Amaranthus palmeri (A. palmeri) invaded patches by pairwise 22 native patches located in the Jing-Jin-Ji region of China using high-throughput amplicon sequencing and quantitative microbial element cycling technologies.

Results

As a result, the composition and structure of rhizosphere soil bacterial communities differed significantly between invasive and native plants according to principal coordinate analysis. A. palmeri soils exhibited higher abundance of Bacteroidetes and Nitrospirae, and lower abundance of Actinobacteria than native soils. Additionally, compared to native rhizosphere soils, A. palmeri harbored a much more complex functional gene network with higher edge numbers, average degree, and average clustering coefficient, as well as lower network distance and diameter. Furthermore, the five keystone taxa identified in A. palmeri rhizosphere soils belonged to the orders of Longimicrobiales, Kineosporiales, Armatimonadales, Rhizobiales and Myxococcales, whereas Sphingomonadales and Gemmatimonadales predominated in the native rhizosphere soils. Moreover, random forest model revealed that keystone taxa were more important indicators of soil functional attributes than edaphic variables in both A. palmeri and native rhizosphere soils. For edaphic variables, only ammonium nitrogen was a significant predictor of soil functional potentials in A. palmeri invaded ecosystems. We also found keystone taxa in A. palmeri rhizosphere soils had strong and positive correlations with functional genes compared to native soils.

Discussion

Our study highlighted the importance of keystone taxa as a driver of soil functioning in invaded ecosystem.

Response of sediment microbial communities to different levels of PAC contamination and exposure time

Coagulants such as polyaluminium chloride (PAC) are widely used for removing phosphorus from eutrophic water, but its application for water treatment can potentially harm the environment. In this study, a four-timepoint exposure experiment was performed at week 1, 3, 7 and 10 to investigate how microbial communities in lake sediments respond to different concentrations of PAC (RS (raw lake water with nothing added), Low, Medium and High). The results showed that, while PAC can efficiently decrease the amount of C, N and P in lake water, the presence of residual aluminum and aluminum precipitates can greatly affect the microbial communities in lake sediments. In particular, different concentrations of PAC and exposure time affected the microbial diversity and structure of lake sediments, with changes being especially obvious at high concentration of PAC after 10 weeks of exposure. Moreover, the use of PAC significantly increased the relative abundances of Gammaproteobacteria and Competibacter, while reducing those of Thermodesulfovibrionia, Vicinamibacterales, and BSV26 in time- and concentration-dependent manners. Network analysis further showed strong correlations between differential bacterial species of PAC in high concentration at 10 weeks, which further suggested that PAC treatment changed the complex structure of microbiota in lake sediment. Finally, correlation analysis indicated a close connection between water parameters and differential species induced by PAC treatment. Overall, PAC contamination changed the microbial communities at different taxonomy levels and influenced the functional pathways to potentiate the P removal, and the results offered interesting insights into the use of PAC in water treatment and its impact on biogeochemical cycling. These results indicated that more attention need to be paid to the potential impact of chemical phosphorus removing reagents on the environment, including eutrophic water.

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.

Structure and Function Analysis of Cultivated Meconopsis integrifolia Soil Microbial Community Based on High-Throughput Sequencing and Culturability

(1) Background: The structure, function, and community interactions of soil microbial communities of cultivated Meconopsis integrifolia were characterized by studying this alpine flower and traditional endangered Tibetan medicine. (2) Methods: Soil bacteria and fungi were studied based on high-throughput sequencing technology. Bacteria were isolated using culturomics and functionally identified as IAA-producing, organic phosphorus-dissolving, inorganic phosphorus-dissolving, and iron-producing carriers. (3) Results: The dominant bacterial phyla were found to be Proteobacteria and Acidobacteria, and unclassified_Rhizobiales was the most abundant genus. Ascomycota and Mortierellomycota were the dominant fungal phyla. The bacteria were mainly carbon and nitrogen metabolizers, and the fungi were predominantly Saprotroph-Symbiotroph. The identified network was completely dominated by positive correlations, but the fungi were more complex than the bacteria, and the bacterial keystones were unclassified_Caulobacteraceae and Pedobacter. Most of the keystones of fungi belonged to the phyla Ascomycetes and Basidiomycota. The highest number of different species of culturable bacteria belonged to the genus Streptomyces, with three strains producing IAA, 12 strains solubilizing organic phosphorus, one strain solubilizing inorganic phosphorus, and nine strains producing iron carriers. (4) Conclusions: At the cost of reduced ecological stability, microbial communities increase cooperation toward promoting overall metabolic efficiency and enabling their survival in the extreme environment of the Tibetan Plateau. These pioneering results have value for the protection of endangered Meconopsis integrifolia under global warming and the sustainable utilization of its medicinal value.

In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling

BACKGROUND

Understanding the microbiome is crucial as it contributes to the metabolic health of the host and, upon dysbiosis, may influence disease development. With the recent surge in high-throughput sequencing technology, the availability of microbial genomic data has increased dramatically. Amplicon sequence-based analyses majorly profile microbial abundance and determine taxonomic markers. Furthermore, the availability of genome sequences for various microbial organisms has prompted the integration of genome-scale metabolic modelling that provides insights into the metabolic interactions influencing host health. However, the analysis from a single study may not be consistent, necessitating a meta-analysis.

RESULTS

We conducted a meta-analysis and integrated with constraint-based metabolic modelling approach, focusing on the microbiome of pacific white shrimp Penaeus vannamei, an extensively cultured marine candidate species. Meta-analysis revealed that Acinetobacter and Alteromonas are significant indicators of "health" and "disease" specific taxonomic biomarkers, respectively. Further, we enumerated metabolic interactions among the taxonomic biomarkers by applying a constraint-based approach to the community metabolic models (4416 pairs). Under different nutrient environments, a constraint-based flux simulation identified five beneficial species: Acinetobacter spWCHA55, Acinetobacter tandoii SE63, Bifidobacterium pseudolongum 49 D6, Brevundimonas pondensis LVF1, and Lutibacter profundi LP1 mediating parasitic interactions majorly under sucrose environment in the pairwise community. The study also reports the healthy biomarkers that can co-exist and have functionally dependent relationships to maintain a healthy state in the host.

CONCLUSIONS

Toward this, we collected and re-analysed the amplicon sequence data of P. vannamei (encompassing 117 healthy and 142 disease datasets). By capturing the taxonomic biomarkers and modelling the metabolic interaction between them, our study provides a valuable resource, a first-of-its-kind analysis in aquaculture scenario toward a sustainable shrimp farming.

Microbiome analysis revealed distinct microbial communities occupying different sized nodules in field-grown peanut

Legume nodulation is the powerhouse of biological nitrogen fixation (BNF) where host-specific rhizobia dominate the nodule microbiome. However, other rhizobial or non-rhizobial inhabitants can also colonize legume nodules, and it is unclear how these bacteria interact, compete, or combinedly function in the nodule microbiome. Under such context, to test this hypothesis, we conducted 16S-rRNA based nodule microbiome sequencing to characterize microbial communities in two distinct sized nodules from field-grown peanuts inoculated with a commercial inoculum. We found that microbial communities diverged drastically in the two types of peanut nodules (big and small). Core microbial analysis revealed that the big nodules were inhabited by Bradyrhizobium, which dominated composition (>99%) throughout the plant life cycle. Surprisingly, we observed that in addition to Bradyrhizobium, the small nodules harbored a diverse set of bacteria (~31%) that were not present in big nodules. Notably, these initially less dominant bacteria gradually dominated in small nodules during the later plant growth phases, which suggested that native microbial communities competed with the commercial inoculum in the small nodules only. Conversely, negligible or no competition was observed in the big nodules. Based on the prediction of KEGG pathway analysis for N and P cycling genes and the presence of diverse genera in the small nodules, we foresee great potential of future studies of these microbial communities which may be crucial for peanut growth and development and/or protecting host plants from various biotic and abiotic stresses.

Genomic Analysis of Pseudomonas asiatica JP233: An Efficient Phosphate-Solubilizing Bacterium

The bacterium Pseudomonas sp. strain JP233 has been reported to efficiently solubilize sparingly soluble inorganic phosphate, promote plant growth and significantly reduce phosphorus (P) leaching loss from soil. The production of 2-keto gluconic acid (2KGA) by strain JP233 was identified as the main active metabolite responsible for phosphate solubilization. However, the genetic basis of phosphate solubilization and plant-growth promotion remained unclear. As a result, the genome of JP233 was sequenced and analyzed in this study. The JP233 genome consists of a circular chromosome with a size of 5,617,746 bp and a GC content of 62.86%. No plasmids were detected in the genome. There were 5097 protein-coding sequences (CDSs) predicted in the genome. Phylogenetic analyses based on genomes of related Pseudomonas spp. identified strain JP233 as Pseudomonas asiatica. Comparative pangenomic analysis among 9 P. asiatica strains identified 4080 core gene clusters and 111 singleton genes present only in JP233. Genes associated with 2KGA production detected in strain JP233, included those encoding glucose dehydrogenase, pyrroloquinoline quinone and gluoconate dehydrogenase. Genes associated with mechanisms of plant-growth promotion and nutrient acquisition detected in JP233 included those involved in IAA biosynthesis, ethylene catabolism and siderophore production. Numerous genes associated with other properties beneficial to plant growth were also detected in JP233, included those involved in production of acetoin, 2,3-butanediol, trehalose, and resistance to heavy metals. This study provides the genetic basis to elucidate the plant-growth promoting and bio-remediation properties of strain JP233 and its potential applications in agriculture and industry.