Diversity of Phosphate Chemical Forms in Soils and Their Contributions on Soil Microbial Community Structure Changes

Restoring soil quality in semi-arid mining-degraded soils: Effects of different combinations of organic amendments on microbial nutrient cycling after 40 months of application

Medium-term effects of different organic amendments on the recovery of mining-degraded soils in a semi-arid limestone quarry were evaluated. Five organic amendments, including composts (garden pruning and greenhouse residues) and stabilised sewage sludge (alone and in mixtures), were compared to untreated soils and natural reference soils. After 40 months, different soil physico-chemical properties, total nutrient (organic carbon -C-, nitrogen -N- and phosphorus -P-) and labile P and N fractions were analysed together with bacterial functional groups catalysing major steps in P (phoD, appA, phnX, pstS) and N turnover (chiA, archaeal amoA, bacterial amoA, nirS, nirK, nosZ, nifH), as well as total bacterial biomass. Restoration altered soil properties, including decreasing pH by up to 10% and increasing total organic C (up to 3.54%), total N (up to 0.33%) and total P (up to 0.18%). Labile P- and N-fractions increased significantly, with ammonium and nitrate doubling in some cases. Microbial activity also rose significantly, with bacterial biomass and functional genes involved in P (phoD, pstS) and N turnover (chiA, nirS, nosZ) increasing 2-3000 times compared to non-restored soils. Sewage sludge had the most pronounced effect on physico-chemical properties, nutrient content and functional groups abundance, while greenhouse compost produced conditions resembling natural reference soils. These results demonstrated that organic amendments can rehabilitate degraded soils by enhancing nutrient content and bacterial community potential for N and P turnover. Organic amendments are thus a viable strategy for medium-term restoration of degraded soils in semi-arid climates.

Functional and Genomic Potential of Burkholderia contaminans PB_AQ24 Isolate for Boosting the Growth of Bamboo Seedlings in Heavy Metal Contaminated Soils

The present study investigated the genomic and functional potential of Burkholderia contaminans PB_AQ24, a bacterial strain isolated from the municipal solid waste dumpsite, for boosting the growth of Dendrocalamus strictus (Male bamboo) seedlings. The isolated strain exhibited high potency for metal solubilization and ACC (1-Aminocyclopropane-1-carboxylate) deaminase activity. Its genome harbored diverse genes responsible for nitrogen and phosphorus utilization (trpABCDES, iaaH, acdS, pstABCS, phoAUD, pqqABCDE, kdpABC, gln, and nirBD) and also an abundance of heavy metal tolerant genes (ftsH, hptX, iscX-fdx-hscAB-iscAUR, mgtA, corA, and copC). Seeds priming experiments carried out in heavy metal contaminated soils (such as waste dumpsite soil (WDS), fly ash dumpsite soil (FAS) and natural garden soil (NGS control)) augmented with Burkholderia contaminans sp. PB_AQ24 showed 85% sustenance of seedlings in WDS and 80% in FAS. The study thus highlighted the potential features in isolated bacterial strain Burkholderia sp. PB_AQ24 (NCBI accession no. JAQOUG000000000), which could boost the growth of bamboo seedlings in heavy metal contaminated soils and may be applied for restoration and rejuvenation of contaminated sites.

Advancements in phosphorus species profiling and bioavailability assessment with implications for phosphorus sustainability

Phosphorus (P) is an essential nutrient that governs ecosystem productivity, drives global biogeochemical cycles, and plays a central role in water-energy-food nexus. The increasing scarcity of P reserves and their environmental losses necessitate precise detection to monitor P in all contexts for effective and sustainable resource management. This review highlights recent advances in analytical techniques for P speciation and bioavailability across environmental matrices, including both bulk and single-cell methods. Furthermore, recent emerging insights into microbial P cycling were discussed, particularly the role of polyphosphate and polyphosphate-accumulating organisms in dynamic P transformations. By emphasizing the sustainability implications of P, we stress the importance of precise and quantitative detection methods to inform sustainable P management and mitigate the global P crisis.

Microbes, macrophages, and melanin: a unifying theory of disease as exemplified by cancer

It is widely accepted that cancer mostly arises from random spontaneous mutations triggered by environmental factors. Our theory challenges the idea of the random somatic mutation theory (SMT). The SMT does not fit well with Charles Darwin's theory of evolution in that the same relatively few mutations would occur so frequently and that these mutations would lead to death rather than survival of the fittest. However, it would fit well under the theory of evolution, if we were to look at it from the vantage point of pathogens and their supporting microbial communities colonizing humans and mutating host cells for their own benefit, as it does give them an evolutionary advantage and they are capable of selecting genes to mutate and of inserting their own DNA or RNA into hosts. In this article, we provide evidence that tumors are actually complex microbial communities composed of various microorganisms living within biofilms encapsulated by a hard matrix; that these microorganisms are what cause the genetic mutations seen in cancer and control angiogenesis; that these pathogens spread by hiding in tumor cells and M2 or M2-like macrophages and other phagocytic immune cells and traveling inside them to distant sites camouflaged by platelets, which they also reprogram, and prepare the distant site for metastasis; that risk factors for cancer are sources of energy that pathogens are able to utilize; and that, in accordance with our previous unifying theory of disease, pathogens utilize melanin for energy for building and sustaining tumors and metastasis. We propose a paradigm shift in our understanding of what cancer is, and, thereby, a different trajectory for avenues of treatment and prevention.

Application of Biochar-Immobilized Bacillus megaterium for Enhancing Phosphorus Uptake and Growth in Rice

Phosphorus (P) is an essential nutrient for rice growth, and the presence of phosphate-solubilizing bacteria (PSB) is an effective means to increase soil P content. However, the direct application of PSB may have minimal significance due to their low survival in soil. Biochar serves as a carrier that enhances microbial survival, and its porous structure and surface characteristics ensure the adsorption of Bacillus megaterium. Inoculating rice husk biochar-immobilized with Bacillus megaterium (BMB) resulted in dissolved inorganic and organic P levels of 39.55 and 31.97 mL L-1, respectively. Subsequently, rice pot experiments were conducted to investigate the response of soil microbial P mobilization and P uptake in rice to fertilizer inputs. The organic fertilizer (OF) combined with BMB treatment (MOF) showed the highest soil available phosphorus (AP) at 38 days, with a value of 7.83 mg kg-1, as well as increased the pqqC abundance while decreasing the abundance of phoD bacterial communities compared with the control. Furthermore, the bioavailable P reservoir (H2O-Pi and NaHCO3-Pi) in soil was greatly increased through the fertilizer input and microbial turnover, with the highest H2O-Pi (3.66 mg kg-1) in OF treatment and the highest NaHCO3-Pi (52.65 mg kg-1) in MOF treatment. Additionally, carbon utilization analysis was applied using the commercial Biolog system, revealing that the MOF treatment significantly increased the utilization of carbohydrates, polymers, and amino acid carbon sources. Moreover, compared to the control, MOF treatment significantly increased the shoot (0.469%) and root P (0.516%) content while promoting root development and thereby supporting rice growth. Our study demonstrates that the MOF treatment displayed higher P levels in both soil and rice plants, providing a theoretical basis for further understanding the role of biochar-based bacterial agents in rice P management.

Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks

Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia's avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.

How do high phosphate concentrations affect soil microbial communities after a century of ecosystem self-reclamation?

The use of rock phosphate (RP) instead of soluble phosphate fertilizers is preferred for the development of more sustainable agriculture. However, the impact of high concentrations in RP on bacterial and fungal communities remains poorly documented. Thus, next-generation sequencing was used to characterize bacterial and fungal communities in the soils and roots of four plant species growing naturally in a self-restored ecosystem, on former open-pit phosphate mines where past exploitation generated locally a substantial phosphate enrichment of the soil. Our results show that bacterial communities are dominated by Actinobacteria and Proteobacteria phyla, while the Ascomycota and Basidiomycota phyla predominate in the fungal community. The alpha and beta diversities of both bacterial and fungal communities differ significantly between the root and soil compartments but are not significantly affected by RP inputs. However, Amplicon Sequence Variants (ASVs) indicative of RP-enriched soils have been identified; among them are bacteria representative of Streptomyces, Bacillus, Mycobacterium or Agromyces. Implications of these results open new ways of reflection to understand the microbial response following RP-inputs and long-term soil restoration, as well as to formulate microbial-based bioinoculants for sustainable agriculture applications based on microorganisms better adapted to high concentrations of RP.

Phosphorus dynamics in volcanic soils of Weizhou Island, China: implications for environmental and agricultural applications

The dynamics of phosphorus are intricately governed by geological and ecological processes. Examining phosphorus dynamics in volcanic islands can enhance our comprehension of its behavior within such unique geological systems. However, research on phosphorus dynamics in volcanic islands remains limited. We investigated the phosphorus content of volcaniclastic rocks and basalt soils from Weizhou Island, China, to understand the influencing factors on phosphorus dynamics. The results indicate that in the volcaniclastic profile, phosphorus concentrates at 20-40 cm (17 mg/kg), decreases at 40-60 cm (11.9 mg/kg), and increases at 80-200 cm up to 46.4 mg/kg proximate to the bedrock, for the basalt profile, phosphorus content increases from the surface (80.2 mg/kg) towards the bedrock (83.9 mg/kg). The differences in phosphorus distribution between volcaniclastic rocks and basalts reflect the influence of parent material, rock weathering degree, carbonate content, topographic elevation, sea level changes, and geological activities. A strong positive correlation (R = 0.96907) between total and available phosphorus has been observed, suggesting that total phosphorus content effectively predicts available phosphorus content. Volcaniclastic rocks in wharves and high-elevation areas show low total phosphorus, while forest land with dense vegetation and neutral to alkaline soil supports higher total phosphorus due to enhanced bioavailability for plant absorption and utilization. Overall, the basalt soil of the volcanic island Weizhou Island demonstrates superior long-term fertility compared to the volcaniclastic soil. Despite its low total phosphorus content, it mainly exists in a highly bioavailable form, facilitating plant absorption, which is crucial for enhancing agricultural yields and ecosystem restoration on volcanic islands.

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.

Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity

Phosphorus is essential in all cells' structural, metabolic and regulatory functions. For fungal cells that import inorganic phosphate (Pi) up a steep concentration gradient, surface Pi transporters are critical capacitators of growth. Fungi must deploy Pi transporters that enable optimal Pi uptake in pH and Pi concentration ranges prevalent in their environments. Single, triple and quadruple mutants were used to characterize the four Pi transporters we identified for the human fungal pathogen Candida albicans, which must adapt to alkaline conditions during invasion of the host bloodstream and deep organs. A high-affinity Pi transporter, Pho84, was most efficient across the widest pH range while another, Pho89, showed high-affinity characteristics only within one pH unit of neutral. Two low-affinity Pi transporters, Pho87 and Fgr2, were active only in acidic conditions. Only Pho84 among the Pi transporters was clearly required in previously identified Pi-related functions including Target of Rapamycin Complex 1 signaling, oxidative stress resistance and hyphal growth. We used in vitro evolution and whole genome sequencing as an unbiased forward genetic approach to probe adaptation to prolonged Pi scarcity of two quadruple mutant lineages lacking all 4 Pi transporters. Lineage-specific genomic changes corresponded to divergent success of the two lineages in fitness recovery during Pi limitation. Initial, large-scale genomic alterations like aneuploidies and loss of heterozygosity eventually resolved, as populations gained small-scale mutations. Severity of some phenotypes linked to Pi starvation, like cell wall stress hypersensitivity, decreased in parallel to evolving populations' fitness recovery in Pi scarcity, while severity of others like membrane stress responses diverged from Pi scarcity fitness. Among preliminary candidate genes for contributors to fitness recovery, those with links to TORC1 were overrepresented. Since Pi homeostasis differs substantially between fungi and humans, adaptive processes to Pi deprivation may harbor small-molecule targets that impact fungal growth, stress resistance and virulence.

Synergistic variation of rhizosphere soil phosphorus availability and microbial diversity with stand age in plantations of the endangered tree species Parashorea chinensis

Introduction

Soil physicochemical properties and nutrient composition play a significant role in shaping microbial communities, and facilitating soil phosphorus (P) transformation. However, studies on the mechanisms of interactions between P transformation characteristics and rhizosphere microbial diversity in P-deficient soils on longer time scales are still limited.

Methods

In this study, rhizosphere soils were collected from a pure plantation of Parashorea chinensis (P. chinensis) at six stand ages in the subtropical China, and the dynamic transformation characteristics of microbial diversity and P fractions were analyzed to reveal the variation of their interactions with age.

Results

Our findings revealed that the rhizosphere soils across stand ages were in a strongly acidic and P-deficient state, with pH values ranging from 3.4 to 4.6, and available P contents ranging from 2.6 to 7.9 mg·kg-1. The adsorption of P by Fe3+ and presence of high levels of steady-state organic P highly restricted the availability of P in soil. On long time scales, acid phosphatase activity and microbial biomass P were the main drivers of P activation. Moreover, pH, available P, and ammonium nitrogen were identified as key factors driving microbial community diversity. As stand age increased, most of the nutrient content indicators firstly increased and then decreased, the conversion of other forms of P to bio-available P became difficult, P availability and soil fertility began to decline. However, bacteria were still able to maintain stable species abundance and diversity. In contrast, stand age had a greater effect on the diversity of the fungal community than on the bacteria. The Shannon and Simpson indices varied by 4.81 and 0.70 for the fungi, respectively, compared to only 1.91 and 0.06 for the bacteria. Microorganisms play a dominant role in the development of their relationship with soil P.

Discussion

In conclusion, rhizosphere microorganisms in P. chinensis plantations gradually adapt to the acidic, low P environment over time. This adaptation is conducive to maintaining P bioeffectiveness and alleviating P limitation.

Isolation and Identification of Acer truncatum Endophytic Fungus Talaromyces verruculosus and Evaluation of Its Effects on Insoluble Phosphorus Absorption Capacity and Growth of Cucumber Seedlings

The symbiosis between endophytic fungi and plants can promote the absorption of potassium, nitrogen, phosphorus, and other nutrients by plants. Phosphorus is one of the indispensable nutrient elements for plant growth and development. However, the content of available phosphorus in soil is very low, which limits the growth of plants. Phosphorus-soluble microorganisms can improve the utilization rate of insoluble phosphorus. In this study, Talaromyces verruculosus (T. verruculosus), a potential phosphorus-soluble fungus, was isolated from Acer truncatum, a plant with strong stress resistance, and its phosphorus-soluble ability in relation to cucumber seedlings under different treatment conditions was determined. In addition, the morphological, physiological, and biochemical indexes of the cucumber seedlings were assessed. The results show that T. verruculosus could solubilize tricalcium phosphate (TCP) and lecithin, and the solubilization effect of lecithin was higher than that of TCP. After the application of T. verruclosus, the leaf photosynthetic index increased significantly. The photosynthetic system damage caused by low phosphorus stress was alleviated, and the root morphological indexes of cucumber seedlings were increased. The plant height, stem diameter, and leaf area of cucumber seedlings treated with T. verruculosus were also significantly higher than those without treatment. Therefore, it was shown that T. verruculosus is a beneficial endophytic fungus that can promote plant growth and improve plant stress resistance. This study will provide a useful reference for further research on endophytic fungi to promote growth and improve plant stress resistance.

Cultural techniques capture diverse phosphate-solubilizing bacteria in rock phosphate-enriched habitats

Phosphorus (P) deficiency is a common problem in croplands where phosphate-based fertilizers are regularly used to maintain bioavailable P for plants. However, due to their limited mobility in the soil, there has been an increased interest in microorganisms that can convert insoluble P into a bioavailable form, and their use to develop phosphate-solubilizing bioinoculants as an alternative to the conventional use of P fertilizers. In this study, we proposed two independent experiments and explored two entirely different habitats to trap phosphate-solubilizing bacteria (PSBs). In the first experiment, PSBs were isolated from the rhizoplane of native plant species grown in a rock-phosphate (RP) mining area. A subset of 24 bacterial isolates from 210 rhizoplane morphotypes was selected for the inorganic phosphate solubilizing activities using tricalcium phosphate (TCP) as the sole P source. In the second experiment, we proposed an innovative experimental setup to select mycohyphospheric bacteria associated to arbuscular mycorrhizal fungal hyphae, indigenous of soils where agronomic plant have been grown and trapped in membrane bag filled with RP. A subset of 25 bacterial isolates from 44 mycohyphospheric morphotypes was tested for P solubilizing activities. These two bacterial subsets were then screened for additional plant growth-promoting (PGP) traits, and 16S rDNA sequencing was performed for their identification. Overall, the two isolation experiments resulted in diverse phylogenetic affiliations of the PSB collection, showing only 4 genera (24%) and 5 species (17%) shared between the two communities, thus underlining the value of the two protocols, including the innovative mycohyphospheric isolate selection method, for selecting a greater biodiversity of cultivable PSB. All the rhizoplane and mycohyphospheric PSB were positive for ammonia production. Indol-3-acetic acid (IAA) production was observed for 13 and 20 isolates, respectively among rhizoplane and mycohyphospheric PSB, ranging, respectively, from 32.52 to 330.27 μg mL-1 and from 41.4 to 963.9 μg mL-1. Only five rhizoplane and 12 mycohyphospheric isolates were positively screened for N2 fixation. Four rhizoplane PSB were identified as siderophore producers, while none of the mycohyphospheric isolates were. The phenotype of one PSB rhizoplane isolate, assigned to Pseudomonas, showed four additive PGP activities. Some bacterial strains belonging to the dominant genera Bacillus and Pseudomonas could be considered potential candidates for further formulation of biofertilizer in order to develop bioinoculant consortia that promote plant P nutrition and growth in RP-enriched soils.

Candida albicans' inorganic phosphate transport and evolutionary adaptation to phosphate scarcity

Phosphorus is essential in all cells' structural, metabolic and regulatory functions. For fungal cells that import inorganic phosphate (Pi) up a steep concentration gradient, surface Pi transporters are critical capacitators of growth. Fungi must deploy Pi transporters that enable optimal Pi uptake in pH and Pi concentration ranges prevalent in their environments. Single, triple and quadruple mutants were used to characterize the four Pi transporters we identified for the human fungal pathogen Candida albicans, which must adapt to alkaline conditions during invasion of the host bloodstream and deep organs. A high-affinity Pi transporter, Pho84, was most efficient across the widest pH range while another, Pho89, showed high-affinity characteristics only within one pH unit of neutral. Two low-affinity Pi transporters, Pho87 and Fgr2, were active only in acidic conditions. Only Pho84 among the Pi transporters was clearly required in previously identified Pi-related functions including Target of Rapamycin Complex 1 signaling and hyphal growth. We used in vitro evolution and whole genome sequencing as an unbiased forward genetic approach to probe adaptation to prolonged Pi scarcity of two quadruple mutant lineages lacking all 4 Pi transporters. Lineage-specific genomic changes corresponded to divergent success of the two lineages in fitness recovery during Pi limitation. In this process, initial, large-scale genomic alterations like aneuploidies and loss of heterozygosity were eventually lost as populations presumably gained small-scale mutations. Severity of some phenotypes linked to Pi starvation, like cell wall stress hypersensitivity, decreased in parallel to evolving populations' fitness recovery in Pi scarcity, while that of others like membrane stress responses diverged from these fitness phenotypes. C. albicans therefore has diverse options to reconfigure Pi management during prolonged scarcity. Since Pi homeostasis differs substantially between fungi and humans, adaptive processes to Pi deprivation may harbor small-molecule targets that impact fungal growth and virulence.

Effects of temperature-related changes on charred bone in soil: From P release to microbial community

Phosphorus (P) is one of the most common limited nutrients in terrestrial ecosystems. Animal bones, with abundant bioapatite, are considerable P sources in terrestrial ecosystems. Heating significantly promotes P release from bone bioapatite, which may alleviate P limitation in soil. This study aimed to explore P release from charred bone (CB) under heating at various temperatures (based on common natural heating). It showed that heating at ∼300 °C significantly increased the P release (up to ∼30 mg/kg) from CB compared with other heating temperatures. Then, the subsequent changes of available P and pH induced evident alternation of soil microbial community composition. For instance, CB heated at ∼300 °C caused elevation of phosphate-solubilizing fungi (PSF) abundance. This further stimulated P mobility in the soil. Meanwhile, the fungal community assembly process was shifted from stochastic to deterministic, whereas the bacterial community was relatively stable. This indicated that the bacterial community showed fewer sensitive responses to the CB addition. This study hence elucidated the significant contribution of heated bone materials on P supply. Moreover, functional fungi might assist CB treated by natural heating (e.g., fire) to construct P "Hot Spots".

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.

Phosphate solubilizing bacteria from soils with varying environmental conditions: Occurrence and function

Phosphate solubilizing bacteria (PSB) is an advantageous way to supply phosphate (P) to plants. The Mediterranean climate of Morocco, especially the low-lying areas, is semi-arid with nutrient-depleted soils in which small-scale, low-income farmers dominate without access to expensive inorganic fertilizers. However, there is not a wide range of PSBs suitable for various agroecological situations. Furthermore, our understanding of the soil and climatic variables that influence their development is limited. This study aims to examine the impacts of specific environmental factors, such as climate and soil, on the abundance, potential, and diversity of PSBs in four agricultural regions of Morocco. To assess the possible impact of these factors on the P solubilization capacity of PSBs and plant growth-promoting (PGP) traits, we analyzed the soil and climate of each sample studied. Similarly, we tested the P solubilization efficiency of the isolates. The bacteria were isolated in a National Botanical Research Institute's phosphate (NBRIP) agar medium. A total of 51 PSBs were studied in this work. The P-solubilization average of Rock P (RP) and Tricalcium P (TCP) of all strains that were isolated from each of the four regions ranged from 18.69 mg.L-1 to 40.43 mg.L-1 and from 71.71 mg.L-1 to 94.54 mg.L-1, respectively. The PGP traits of the isolated strains are positively correlated with the PSBs abundance and the sample characteristics (soil and climate). The morphological and biochemical characteristics of the strain allowed us to identify around nine different bacterial genera, including Bacillus, Pseudomonas, and Rhizobium. The findings showed that bacterial communities, density, and potency are closely correlated to various edapho-climatic conditions such as temperature, precipitation, soil nutrient status, and soil texture. These findings could be used to improve an effective plant-PSBs system and increase agricultural output by taking into account their specific ecological traits and plant growth mechanisms.

Phosphate-Solubilizing Bacteria: Advances in Their Physiology, Molecular Mechanisms and Microbial Community Effects

Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42- and H2PO4-, which are known as usable phosphorus. At present, the total phosphorus content of soils worldwide is 400-1000 mg/kg, of which only 1.00-2.50% is plant-available, which seriously affects the growth of plants and the development of agriculture, resulting in a high level of total phosphorus in soils and a scarcity of available phosphorus. Traditional methods of applying phosphorus fertilizer cannot address phosphorus deficiency problems; they harm the environment and the ore material is a nonrenewable natural resource. Therefore, it is imperative to find alternative environmentally compatible and economically viable strategies to address phosphorus scarcity. Phosphorus-solubilizing bacteria (PSB) can convert insoluble phosphorus in the soil into usable phosphorus that can be directly absorbed by plants, thus improving the uptake and utilization of phosphorus by plants. However, there is no clear and systematic report on the mechanism of action of PSB. Therefore, this paper summarizes the discovery process, species, and distribution of PSB, focusing on the physiological mechanisms outlining the processes of acidolysis, enzymolysis, chelation and complexation reactions of PSB. The related genes regulating PSB acidolysis and enzymatic action as well as genes related to phosphate transport and the molecular direction mechanism of its pathway are examined. The effects of PSB on the structure and abundance of microbial communities in soil are also described, illustrating the mechanism of how PSB interact with microorganisms in soil and indirectly increase the amount of available phosphorus in soil. And three perspectives are considered in further exploring the PSB mechanism in utilizing a synergistic multi-omics approach, exploring PSB-related regulatory genes in different phosphorus levels and investigating the application of PSB as a microbial fungicide. This paper aims to provide theoretical support for improving the utilization of soil insoluble phosphorus and providing optimal management of elemental phosphorus in the future.

Chemical fertilizer reduction combined with organic fertilizer affects the soil microbial community and diversity and yield of cotton

Introduction

The soil microbial community plays an important role in modulating cotton soil fertility. However, the effects of chemical fertilizer combined with organic fertilizer on soil chemical properties, microbial community structure, and crop yield and quality in arid areas are still unclear. This study aimed to explore the effects of different organic fertilizers on soil microbial community structure and diversity and cotton growth and yield.

Methods

High-throughput sequencing was used to study the soil bacteria and fungi in different growth stages of cotton. The field fertilization experiment had five treatments.

Results

The results indicated that the treatments of chemical fertilizer reduction combined with organic fertilizer significantly increased soil available nitrogen and phosphorus in cotton field. There were significant differences in the abundance of the bacterial and fungal communities in the dominant phyla among the treatments. At the phyla level, there were not significantly different in the diversity of bacteria and fungi among treatments. There were significant differences in the composition and diversity of bacterial and fungal communities during the entire cotton growth period (p = 0.001). The rhizosphere bacterial and fungal community structure was significantly affected by soil TK, NH4+, AK, TP, AN, and NO3-. The different fertilization treatments strongly influenced the modular structure of the soil bacterial and fungal community co-occurrence network. A reduction in chemical fertilizer combined with organic fertilizer significantly improved cotton stem diameter and seed yield, and the effect of the biological organic fertilizer on plant growth and yield formation was greater than that of ordinary organic fertilizer.

Discussion

This study provide a scientific and technical basis for the establishment of environmentally friendly green fertilization technology for cotton in arid areas and the promotion of sustainable development of cotton industry.

Growth stimulation of two legumes (Vicia faba and Pisum sativum) using phosphate-solubilizing bacteria inoculation

The application of chemical fertilizers for plant growth and protection is one of the reasons for the environment and ecosystem destruction, thus, sustainable agriculture is gaining popularity in research and among farming communities. Although most soils are high in total phosphorus (P), a large portion is unavailable to plants and regarded as a growth-limiting factor. P-solubilizing bacteria (PSB) exploitation is a newly developed bio-solution for enhancing rhizosphere P availability; however, the effect of these bacteria on soil quality and the different phases of plant growth remains unknown. This study aims to evaluate the impact of five strains of PSB, isolated from legume rhizosphere, on the growth of two plants (Vicia faba and Pisum sativum) and certain soil properties. The efficient strains of PSB used are characterized by the P-solubilization, the ACC deaminase activity, the fixation of N, and the IAA, HCN, and siderophores production. The activity of these bacteria is tested in vitro and in vivo under controlled conditions on the growth of the two plants supplemented with the rock P (RP). According to our findings, all PSBs strains outperformed the control in terms of enhancing the growth of the tested legumes with a percentage ranging from 77.78 to 88.88%, respectively. The results showed that all treatments significantly improved plant parameters like nitrogen- (N) and P-content in the plants (67.50, 23.11%), respectively. Also, an increase in the fresh and dry weights of above- (41.17, 38.57%) and below-ground biomasses (56.6, 42.28%), respectively. Compared to the control, this leads to an increase of 72% in root length, 40.91% in plant dry weight, and 40.07% in fresh weight. Rhizospheric soil in PSBs treatments displayed high levels of N, P, and organic matter. All treatments were found to have significantly higher levels of alkaline phosphatase, basal soil respiration, and β-glucosidase activity than the control. It is concluded that multi-traits PSB can be an alternative for utilizing chemical fertilizers to enhance soil quality and plant growth. Despite the potency of PSBs, its use as a source for the development of sustainable agriculture implies focusing on crop species and adaptation, stress tolerance and climate resilience.

Effects of moderate drought extension on bacterial network structure in the rhizosphere soil of Leymus chinensis in semi-arid grasslands

Introduction

Grasslands are home to complex bacterial communities whose dynamic interactions play a crucial role in organic matter and nutrient cycling. However, there is limited understanding regarding the impact of changes in rainfall amount and the duration of dry intervals on bacterial interactions.

Methods

To assess the impact of changes in precipitation volume and dry intervals on bacterial co-occurrence networks, we carried out precipitation manipulation experiments in the Eastern Eurasian Steppe of China.

Results and Discussion

We found that alterations in precipitation and dry intervals did not significantly affect bacterial alpha and beta diversity. However, we observed significant changes in the co-occurrence network structure of bacteria in the rhizosphere ecosystem, with the 12-day dry interval showing the most notable reduction in the number of degrees, edges, and clustering coefficient. Additionally, the study identified putative keystone taxa and observed that the moderately prolonged dry intervals between precipitation events had a major effect on the robustness of bacterial networks. The complexity and stability of the network were found to be positively correlated, and were primarily influenced by soil water content, phosphorous, and aboveground biomass, followed by available phosphorus (AP) and total biomass. These findings have the potential to enhance our comprehension of how bacterial co-occurrence pattern react to variations in dry intervals, by regulating their interactions in water-limited ecosystems. This, in turn, could aid in predicting the impact of precipitation regime alterations on ecosystem nutrient cycling, as well as the feedback between ecosystem processes and global climate change.

Impact of Two Phosphorus Fertilizer Formulations on Wheat Physiology, Rhizosphere, and Rhizoplane Microbiota

Phosphorus (P) is the second most important macronutrient for crop growth and a limiting factor in food production. Choosing the right P fertilizer formulation is important for crop production systems because P is not mobile in soils, and placing phosphate fertilizers is a major management decision. In addition, root microorganisms play an important role in helping phosphorus fertilization management by regulating soil properties and fertility through different pathways. Our study evaluated the impact of two phosphorous formulations (polyphosphates and orthophosphates) on physiological traits of wheat related to yield (photosynthetic parameters, biomass, and root morphology) and its associated microbiota. A greenhouse experiment was conducted using agricultural soil deficient in P (1.49%). Phenotyping technologies were used at the tillering, stem elongation, heading, flowering, and grain-filling stages. The evaluation of wheat physiological traits revealed highly significant differences between treated and untreated plants but not between phosphorous fertilizers. High-throughput sequencing technologies were applied to analyse the wheat rhizosphere and rhizoplane microbiota at the tillering and the grain-filling growth stages. The alpha- and beta-diversity analyses of bacterial and fungal microbiota revealed differences between fertilized and non-fertilized wheat, rhizosphere, and rhizoplane, and the tillering and grain-filling growth stages. Our study provides new information on the composition of the wheat microbiota in the rhizosphere and rhizoplane during growth stages (Z39 and Z69) under polyphosphate and orthophosphate fertilization. Hence, a deeper understanding of this interaction could provide better insights into managing microbial communities to promote beneficial plant-microbiome interactions for P uptake.

First Report on Novel Psychrotrophic Phosphorus-Solubilizing Ochrobactrum thiophenivorans EU-KL94 from Keylong Region in Great Himalayas and Their Role in Plant Growth Promotion of Oats (Avena sativa L.)

Cold stress leads to the disruption of the cellular homeostasis in plants and generation of reactive oxygen species (ROS) and productivity losses. In the present study, 94 psychrotrophic phosphorus-solubilizing bacteria with multiple plant growth-promoting (PGP) capabilities were isolated from rhizosphere of wheat. The most efficient strain EU-KL94 showing highest amount of solubilized phosphorus and maximum number of PGP attributes was identified using 16S rRNA sequencing as Ochrobactrum thiophenivorans. Ochrobactrum thiophenivorans EU-KL94 along with recommended doses of the chemical fertilizers as controls were used for alleviation of cold stress in oats. The strain improved the root and shoot length, dry and fresh weight, proline, glycine betaine, chlorophyll content as well as the superoxide dismutase (SOD) and glutathione reductase (GR) activities of oats under cold stress conditions. Ochrobactrum thiophenivorans with all promising plant growth activities under cold stress could be used as an environmental friendly strategy for mitigation of low temperature stress. To the best of our knowledge, Ochrobactrum thiophenivorans has been reported for the first time as P-solubilizer and as bioinoculants in oats for cold stress mitigation.

Phosphate Solubilization and Plant Growth Promotion by Pantoea brenneri Soil Isolates

Phosphate solubilizing microorganisms (PSMs) in soil have been shown to reduce mineral phosphate fertilizer supplementation and promote plant growth. Nevertheless, only several P-solubilizing microorganisms capable of solubilizing both organic and mineral sources of soil phosphorus have been identified up to now. The aim of this study was to evaluate the inorganic soil phosphate solubilizing activity of phytate-hydrolyzing Pantoea brenneri soil isolates. We showed that the strains efficiently solubilize a variety of inorganic phosphates. We optimized the media composition and culturing conditions to improve the solubilization efficiency of the strains and investigated the mechanisms of their phosphate solubilization. Through HPLC analysis, it was determined that P. brenneri produce oxalic, malic, formic, malonic, lactic, maleic, acetic, and citric acids as well as acid and alkaline phosphatases while growing on insoluble phosphate sources. Finally, we analyzed the influence of P. brenneri strains with multiple PGP-treats on plant growth in greenhouse experiments and showed their ability to promote growth of potato.

Pseudomonas aeruginosa and Bacillus cereus Isolated from Brazilian Cerrado Soil Act as Phosphate-Solubilizing Bacteria

The phosphate-solubilizing microorganism is essential for soil quality and plant development and can serve as an alternative to reduce such Brazilian needs for importing phosphate overseas. Here, we isolated and selected bacteria from Brazilian Cerrado soils capable of solubilize phosphate. We obtained 53 bacteria isolates, of which 23 could solubilize phosphate at a pH of 7.0, 17 could solubilize phosphate at a pH of 6.0, and 8 could solubilize at a pH of 5.5. Using 16S rRNA gene sequences, we identified nine bacteria species clustered in four groups: Bacillus sp., Pseudomonas sp., Priestia sp., and Klebsiella sp. Our results revealed that the UFT01 (P. aeruginosa) and UFT42 (B. cereus) isolates exhibited the best phosphate solubilization performance at all tested pH values. We further recorded higher levels of solubilization and phosphate availability six days after the soil inoculation with P. aeruginosa, and enzymatic analysis of the soil samples revealed that the P. aeruginosa-inoculated samples resulted in four-fold higher enzymatic activities when compared to non-inoculated soils. The B. cereus soil inoculation increased β-glucosidase activities and resulted in reduced the activities of arylsulfatase. Altogether, our findings demonstrated that P. aeruginosa and B. cereus isolated from Cerrado soils showed high phosphate solubilization potential.

Long-term water quality monitoring in agricultural catchments in Sweden: Impact of climatic drivers on diffuse nutrient loads

Water quality related to non-point source pollution continues to pose challenges in agricultural landscapes, despite two completed cycles of Water Framework Directive actions by farmers and landowners. Future climate projections will cause new challenges in landscape hydrology and subsequently, the potential responses in water quality. Investigating the nutrient trends in surface waters and studying the efficiency of mitigation measures revealed that loads and measures are highly variable both spatially and temporally in catchments with different agro-climatic and environmental conditions. In Sweden, nitrogen and phosphorus loads in eight agricultural catchments (470-3300 ha) have been intensively monitored for >20 years. This study investigated the relationship between precipitation, air temperature, and discharge patterns in relation to nitrogen (N) and phosphorus (P) loads at catchment outlets. The time series data analysis was carried out by integrating Mann-Kendall test, Pettitt break-points, and Generalized Additive Model. The results showed that the nutrient loads highly depend on water discharge, which had large variation in annual average (158-441 mm yr^-1). The annual average loads were also considerably different among the catchments with total N (TN) loads ranging from 6.76 to 35.73 kg ha^-1, and total P (TP) loads ranging from 0.11 to 1.04 kg ha^-1. The climatic drivers were highly significant indicators of nutrient loads but with varying degree of significance. Precipitation (28-962 mm yr^-1) was a significant indicator of TN loads in five catchments (loamy sand/sandy loam) while annual average temperature (6.5-8.7 °C yr^-1) was a significant driver of TN loads in six out of eight catchments. TP loads were associated with precipitation in two catchments and significantly correlated to water discharge in six catchments. Considering the more frequent occurrence of extreme weather events, it is necessary to tailor N and P mitigation measures to future climate-change features of precipitation, temperature, and discharge.

Microbial-Based Plant Biostimulants

Beneficial microorganisms offer essential ecological services to both natural and agricultural ecosystems [...].

Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms

Amplicon sequencing of bacterial or fungal marker sequences is currently the main method for the study of endophytic microorganisms in plants. However, it cannot obtain all types of microorganisms, including bacteria, fungi, protozoa, etc., in samples, nor compare the relative content between endophytic microorganisms and plants and between different types of endophytes. Therefore, it is necessary to develop a better analysis strategy for endophytic microorganism investigation. In this study, a new analysis strategy was developed to obtain endophytic microbiome information from plant transcriptome data. Results showed that the new strategy can obtain the composition of microbial communities and the relative content between plants and endophytic microorganisms, and between different types of endophytic microorganisms from the plant transcriptome data. Compared with the amplicon sequencing method, more endophytic microorganisms and relative content information can be obtained with the new strategy, which can greatly broaden the research scope and save the experimental cost. Furthermore, the advantages and effectiveness of the new strategy were verified with different analysis of the microbial composition, correlation analysis, inoculant content test, and repeatability test.

The Potential Applications of Commercial Arbuscular Mycorrhizal Fungal Inoculants and Their Ecological Consequences

Arbuscular mycorrhizal fungal (AMF) inoculants are sustainable biological materials that can provide several benefits to plants, especially in disturbed agroecosystems and in the context of phytomanagement interventions. However, it is difficult to predict the effectiveness of AMF inoculants and their impacts on indigenous AMF communities under field conditions. In this review, we examined the literature on the possible outcomes following the introduction of AMF-based inoculants in the field, including their establishment in soil and plant roots, persistence, and effects on the indigenous AMF community. Most studies indicate that introduced AMF can persist in the target field from a few months to several years but with declining abundance (60%) or complete exclusion (30%). Further analysis shows that AMF inoculation exerts both positive and negative impacts on native AMF species, including suppression (33%), stimulation (38%), exclusion (19%), and neutral impacts (10% of examined cases). The factors influencing the ecological fates of AMF inoculants, such as the inherent properties of the inoculum, dosage and frequency of inoculation, and soil physical and biological factors, are further discussed. While it is important to monitor the success and downstream impacts of commercial inoculants in the field, the sampling method and the molecular tools employed to resolve and quantify AMF taxa need to be improved and standardized to eliminate bias towards certain AMF strains and reduce discrepancies among studies. Lastly, inoculant producers must focus on selecting strains with a higher chance of success in the field, and having little or negligible downstream impacts.

Application of Indigenous Rhizospheric Microorganisms and Local Compost as Enhancers of Lettuce Growth, Development, and Salt Stress Tolerance

This study aimed to mitigate salt stress effects on lettuce by using native biostimulants (arbuscular mycorrhizal fungi (M, consortium), plant growth-promoting rhizobacteria (R, Z2, and Z4 strains), and compost (C)) applied alone or in combination under salinity stress (0, 50, and 100 mM NaCl). Physiological, biochemical, nutritional, mycorrhizal, growth, and soil characteristics were evaluated. Results revealed that growth and physiological traits were negatively affected by salinity. However, mycorrhizal colonization was enhanced under 100 mM NaCl after compost application. The applied biostimulants, particularly M and/or R improved the salinity tolerance of lettuce by increasing the dry biomass by 119% and 113% under 100 mM NaCl, respectively, for M and MR treatments. Similarly, MR enhanced stomatal conductance (47%), water content (260%), total chlorophyll (130%), phosphorus content (363%), and reduced the malondialdehyde (54%) and hydrogen peroxide (78%) compared to the control. Moreover, peroxidase activity (76%) and sugar content (36%) were enhanced by CM treatment, while protein (111%) and proline (104%) contents were significantly boosted by R treatment under 100 mM NaCl. Furthermore, glomalin content was enhanced by MR treatment under severe salinity. In conclusion, the applied biostimulants alone or in combination might help lettuce to tolerate salt stress and enhance its production in degraded areas.

Assessing spatial variability of selected soil properties in Upper Kabete Campus coffee farm, University of Nairobi, Kenya

This study aimed to evaluate spatial variability of selected soil parameters as a smart agricultural technology guide to precise fertilizer application. A farm designated as Field 3 which is under Arabica coffee within a bigger Soil Mapping Unit (SMU) was selected for a more detailed soil observation at a scale of 1:5000. Soil samples were taken at depths of 0–15 and 15–30 cm across 20 sample locations in grids and selected properties analysed in the laboratory. Kriging interpolation method was used to estimate the accuracy of interpolation through cross-validation of the top soil parameters. In 0 to 15 and 15–30 cm depth, soil reaction, percentage organic carbon and percent nitrogen showed low variability of 5.1% and 5.8%, 10.4% and 12.7%, 14.5% and 17.6% respectively. Phosphorus was deficient in both depths and showed moderate variability of 36.2% and 42.3% in 0–15 and 15–30 cm respectively. Calcium and Magnesium ranged from sufficient to rich and showed moderate and low variability in top and bottom depths, respectively. All micronutrients were sufficient in the soil. The soils were classified as Mollic Nitisols. Results showed that soil parameters varied spatially within the field therefore, there is need for variable input application depending on the levels of these elements and purchasing of fertilizer blends that are suitable for nutrient deficiencies. Precision agriculture is highly recommended in the field to capitalize on soil heterogeneity.

•

There is need for variable agricultural input application in farms.

•

Field spatial variability is a panacea to economically sound soil management.

•

Precision agriculture is recommended for profits and environmental protection.

Extraction and Identification of Effective Compounds from Natural Plants

Most botanical species contain various types of bioactive compounds. This study focusses on the extraction and identification of bioactive compounds from Calicotome spinosa (Gorse), including flavones, α-linolenic acid and sugar. During the investigation of gorse flowers, leaves and bark, flavones were isolated from the bark and leaves. Calicotome spinosa showed a total isoflavonoid content of 1.5% from the bark of gorse and 1.3% from the leaves. To find the best conditions for flavone extraction, samples of Calicotome spinosa were extracted with different solvents (methanol, water and acetonitrile). Methanol was found to be a suitable solvent to selectively extract flavone. An unsaturated cis fatty acid (α-linolenic acid, C18:3 ∆9, 12, 15) was identified as the principal component of the triacylglycerol fraction from the flowers. Hydrolyses process conditions were used to study Gorse wood. The results indicated that the wood of gorse is not a suitable substance for making paper. The extracted bioactive compounds were analysed using NMR, GCMS, UV, TLC and Fibre Analyser techniques. The extracted compounds offered uses as antioxidants and agricultural chemicals in addition to other benefits.