phoD Gene Abundance Research Articles

Effect of P Reduction on phoD-Harboring Bacteria Community in Solar Greenhouse Soil

Phosphorus (P) enrichment frequently occurs in the soil used in greenhouse vegetable production (GVP). Minimizing the application of P fertilizer represents a crucial approach to mitigating the accumulation of P in the soil and enhancing its utilization efficiency. However, the changes in bacterial communities and the turnover mechanism of soil P fractions related to soil P cycling after P fertilizer reduction are still unclear. To unravel these complexities, we devised three experimental treatments: conventional nitrogen (N), P, and potassium (K) fertilizer (N1P1K1); conventional N and K fertilizer without P (N1P0K1); and no fertilizer (N0P0K0). These experiments were conducted to elucidate the effects of P reduction on cucumber plant growth, soil P fractions, and the phoD-harboring bacterial community in the P-rich greenhouse soil. The results showed that there were no significant differences between the N1P1K1 and N1P0K1 treatments in terms of plant growth, yield, and P uptake, and the values for the N0P0K0 treatment were significantly lower than those for the N1P1K1 treatment. In a state of P depletion (N0P0K0, N1P0K1), the main P sources were Resin-Pi, NaHCO3-Pi, NaHCO3-Po, and NaOH-Pi. The contents of NaOH-Po and CHCl-Po in the N1P0K1 treatment increased significantly. Without P fertilizer, alkaline phosphatase (ALP) activity, phoD gene abundance, and bacterial community diversity were significantly increased. The abundance of Ensifer in the N0P0K0 and N1P0K1 treatments was 8 and 10.58 times that in the N1P1K1 treatment, respectively. Additionally, total phosphorus (TP) and available nitrogen (AN) were key factors affecting changes in the phoD bacterial community, while Shinella, Ensifer and Bradyrhizobium were the main factors driving the change in soil P fractions, and NaHCO3-Pi and NaOH-Pi were key factors affecting crop yield. Therefore, reducing the application of P fertilizer will increases the diversity of phoD-gene-harboring bacterial communities and promote organic P mineralization, thus maintaining the optimal crop yield.

Biotic regulation of phoD-encoding gene bacteria on organic phosphorus mineralization in lacustrine sediments with distinct trophic levels

Organic phosphorus (Po) mineralization hydrolyzed by alkaline phosphatase (APase) can replenish bioavailable P load in the sediment water ecosystem of lakes. However, the understanding about the interaction between P load and bacteria community encoding APase generation in the sediment are still limited. Different P pools in the sediments from Taihu Lake, China were measured using sequential extraction procedure. The APAase activity (APA) were obtained accompanying with enzymatic dynamical parameters Vmax and Km. The abundances and diversity of gene phoD-harboring bacterial communities were assessed using high throughput sequencing. The analysis results showed the decrease of potentially bioavailable P fractions including MgCl2-P and Fe-P along sampling gradient southwards together with active P concentrations in the water. Conversely, increasing APA and absolute abundance of phoD gene were found with the decreasing of P loads southwards. Positive correlation (p < 0.05) between absolute abundance and APA indicated that phoD-encoding bacteria manipulated the APA and Po mineralization. Negative correlation (p < 0.01) suggested that the APA was restrained by high P load and was promoted under low P condition. However, higher Vmax and Km values suggested that high mineralization potential of Po maintained the high concentrations of potentially bioavailable P even the APA was restricted. The abundance increase of predominant genus Cobetia (from 15.51 to 24.34 %) mirrored by the reduced Calothrix abundance (from 24.65 to 1036 %) was speculated to be responsible for the APA promotion under low P condition. Higher diversity indices in the high P scenario suggested that high P load stimulated the ecological diversity of gene phoD-encoding bacteria community. Generally, rare taxa such as Burkholderia having high connected degrees in bacterial communities together with abundant genera synergistically manipulated the phoD gene abundance and APase generation. Interaction between P fractions and bacteria encoding phoD gene determined the eutrophication status in the lacustrine ecosystem.

Intensive Citrus Cultivation Suppresses Soil Phosphorus Cycling Microbial Activity

Soil microbes are key drivers in regulating the phosphorus cycle. Elucidating the microbial mineralization process of soil phosphorus-solubilizing bacteria is of great significance for improving nutrient uptake and yield of crops. This study investigated the mechanism by which citrus cultivation affects the soil microbial acquisition strategy for phosphorus by measuring the abundance of the phoD gene, microbial community diversity and structure, and soil phosphorus fractions in the soils of citrus orchards and adjacent natural forests. The results showed that citrus cultivation could lead to a decrease in soil pH and an accumulation of available phosphorus in the soil, with a content as high as 112 mg·kg-1, which was significantly higher than that of natural forests (3.7 mg·kg-1). Citrus cultivation also affected the soil phosphorus fractions, with citrus soil having higher levels of soluble phosphorus (CaCl2-P), citrate-extractable phosphorus (Citrate-P), and mineral-bound phosphorus (HCl-P). The phosphorus fractions of natural forest soils were significantly lower than those of citrus soils, whereas the phoD gene abundance and alkaline phosphatase activity were significantly higher in natural forest soils than in citrus soils. High-throughput sequencing results showed that the Shannon diversity index of phosphate-solubilizing bacteria in citrus soils was 4.61, which was significantly lower than that of natural forests (5.35). The microbial community structure in natural forests was also different from that of citrus soils. In addition, the microbial community composition of phosphate-solubilizing bacteria in citrus soils was also different from that of natural forests, with the relative abundance of Proteobacteria being lower in natural forest soils than in citrus soils. Therefore, citrus cultivation led to a shift of soil microbial acquisition strategy for phosphorus, with external phosphorus addition being the main strategy in citrus soils, whereas microbial mineralization of organic phosphorus was the main strategy in natural forest soils to meet their growth requirements.

Plant invasion alters soil phosphorus cycling on tropical coral islands: Insights from Wollastonia biflora and Chromolaena odorata invasions

Plants may modify soil biogeochemical properties that facilitate their invasion of new sites which may be mediated by soil microorganisms. We compared microbially-mediated soil phosphorus (P) cycling among sites with different degrees of invasion by Wollastonia biflora and Chromolaena odorata on two coral islands. Wollastonia biflora and C. odorata outcompeted all native species and invested more P in leaves (45–136% more than the native species). We found a decrease in the proportion of HCl–P and organic P, and a corresponding increase in the proportion of labile inorganic P (Pi) of the soil total P concentrations following plant invasion. Leaf P concentrations in invasive species were positively correlated with the proportion of labile Pi, suggesting that HCl–P and organic P were the major P sources for invasive plants, and that plant invasion increased soil P-cycling rates as a result of root carboxylate release (evidenced by greater leaf manganese concentrations) and enhanced soil alkaline phosphatase activity. The latter was confirmed by an increased soil phoD gene abundance after plant invasion. Soil P availability was elevated after plant invasion which was associated with increases in the release of root carboxylates and microbial activities that are involved in mobilization of HCl–P and mineralization of organic P, respectively, especially in the wet season. This, in turn, strongly increased leaf P concentrations of invasive species to sustain rapid plant growth, and presumably depriving competitors of P. These novel insights into soil P cycling through the enrichment of a specific soil microbial community and root carboxylate release in invaded ecosystems enhance our understanding of plant invasion mechanisms on coral islands.

Poultry litter biochar soil amendment affects microbial community structures, promotes phosphorus cycling and growth of barley (Hordeumvulgare)

Phosphorus (P) is a non-replaceable, finite component of fertilizers. The imbalanced resource distribution and possible depletion of P impose challenges on current crop production worldwide. The aim of this study was to assess the impact of poultry litter biochar on plant growth and P mobilizing capability of the microbiome in comparison to a mineral fertilizer application. Spring barley (Hordeum vulgare) was grown in microcosms using a P-limited soil, fertilized with 0 (control), 50 (fertilizer) kg P ha−1 or a poultry litter biochar amendment (biochar, 2% w/w). Biochar amended rhizospheres had significantly higher phosphonate-utilizing bacteria, phoC and phoD gene (acid and alkaline phosphatase) copy numbers and improved P availability. Spring barley dry matter yields were significantly higher for biochar and fertilizer over control; however, P uptake with biochar was higher than with fertilizer. Furthermore, biochar had higher arbuscular mycorrhizal colonization and significantly raised soil pH. Fingerprint-analysis showed significant differences between all treatments for bacterial and fungal communities. 16S rRNA gene-based sequencing analysis revealed increased relative abundance of the phyla Actinobacteriota and Chloroflexi in biochar compared to control, potentially contributing to the ameliorated plant growth conditions. Pearson correlations of both phyla was positive with a range of P cycling variables as well as Morgan's P but negative with acid phosphatase activity. FAPROTAX analysis revealed positive correlations of aromatic compound degradation with phoC and phoD gene abundance, highlighting a possible link between biodegradation and P release. In conclusion, poultry litter biochar could potentially replace mineral P fertilizer for sustainable plant growth in P depleted soil environments.

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.

Fertilization and cultivation management promotes soil phosphorus availability by enhancing soil P-cycling enzymes and the phosphatase encoding genes in bulk and rhizosphere soil of a maize crop in sloping cropland

Fertilization and cultivation managements exert significant effects on crop growth and soil-associated nutrients in croplands. However, there is a lack of knowledge regarding how these practices affect soil phosphorus-cycling enzymes and functional genes involved in regulating global P-cycling, especially under intense agricultural management practices in sloping croplands. A long-term field (15-year) trial was conducted in a 15° sloping field based on five treatments: no fertilizer amendments + downslope cultivation (CK); mixed treatment of mineral fertilizer and organic manure + downslope cultivation (T1); mineral fertilizer alone + downslope cultivation (T2); 1.5-fold mineral fertilizer + downslope cultivation (T3); and mineral fertilizer + contour cultivation (T4). Bulk and rhizosphere soil samples were collected after the maize crop was harvested to determine the P fraction, P-cycling enzymes, and phosphatase-encoding genes. Results indicated that fertilization management significantly increased the inorganic (Pi) and organic soil (Po) P fractions compared to CK, except for NaOH-extractable Po in T1 and T3 in bulk and rhizosphere soils, respectively. For the cultivation treatments, the content of Pi pools in the downslope cultivation of T1 and T3 was significantly larger than that in the contour cultivation of T4 in bulk and rhizosphere soils. However, the content of NaOH-extractable Po in T1 and T3 was lower compared to T4 in bulk soil and vice versa for the NaHCO3-P and HCl-Po fractions in the rhizosphere. We also found that fertilization and cultivation managements significantly increased the activity of acid phosphatase (ACP), alkaline phosphatase (ALP), phytase, phosphodiesterases (PDE), and phoC and phoD gene abundance in bulk and rhizosphere soils, with a larger effect on the activity of ALP and the phosphatase encoding phoD gene, especially in T1 and T3 in the rhizosphere. Soil organic carbon (SOC) and microbial biomass C and P (MBC and MBP) were the main predictors for regulating P-cycling enzymes and phoC- and phoD gene abundance. A strong association of P-cycling enzymes, especially ALP and phytase, and the abundance of phoD genes with the P fraction indicated that the soil P cycle was mainly mediated by microbial-related processes. Together, our results demonstrated that an adequate amount of mineral fertilizer alone or combined with organic fertilizer plus downslope cultivation is more effective in promoting soil P availability by enhancing the activity of ALP, phytase, and phoD genes. This provides valuable information for sustaining soil microbial-regulated P management practices in similar agricultural lands worldwide.

Land use change alters phosphatase enzyme activity and phosphatase-harboring microbial abundance in the subalpine ecosystem of southeastern Qinghai-Tibet Plateau, China

In the presence of limited phosphorus (P) in terrestrial ecosystems, exploring how land use change (LUC) affects phosphatase enzyme activity and microbial communities is important for managing soil P, because microorganisms carry out the majority of P cycling in the soil through producing phosphatase enzymes. In this study, we explored the impact of LUC on P availability, phosphatase enzyme, the abundance of phosphatase-encoding genes, and microorganisms. We collected 168 soil samples at soil depths of 0–20 cm and 20–40 cm from seven sampling sites, each of which represented by four different land uses: artificial forests (AF), farmlands (FL), natural forests (NF), and shrubland (SL). We analyzed phosphatase-encoding genes and microbes from metagenome datasets. Results indicated that P availability substantially increased following NF to FL conversion. In contrast, phosphatase enzyme activity significantly decreases when NF is converted to different land uses, due to the decline of soil organic carbon (SOC), moisture content (MC) and total nitrogen (TN). We have also detected 13 P solubilizing and mineralizing genes. The phoD and gcd were the dominant mineralizing and solubilizing genes, respectively. Farmland had higher gcd gene abundance, while NF had significantly higher phoD gene abundance. The gcd gene abundance were mainly governed by pH and total P, whereas pH and available P were the primary factors controlling phoD gene. MC, SOC and TN regulated other genes detected in this study. With regard to the dominant gcd-harboring phyla, Acidobacteria, Proteobacteria, Bacteroidetes and Gemmatimonadetes were the dominant, while Proteobacteria, Acidobacteria, Actinobacteria, and Candidatus_Rokubacteria were the dominant phoD-harboring phyla. The majority of gcd and phoD-harboring microorganisms were primarily controlled by pH, available P and total P. However, some phyla also regulated by MC, SOC, and TN. In general, our findings suggested that LUC significantly alters phosphatase enzymes and the abundance of phosphate-encoding genes and microbes. These changes have significant implications for soil P cycling.

Differences in available phosphorus in temperate and subtropical forest soils

Soil P availability is influenced by the acid phosphomonoesterase (ACP) activity, microbial biomass P (MBP), pH, and other soil properties. To date, there is no clear understanding about how the enzyme catalytic efficiency (Vmax/Km) and the abundance of the phoC and phoD genes that encode ACP and alkaline phosphomonoesterase (ALP) influence the available P contents at different depths in temperate and subtropical forest soils. We investigated how the soil enzyme kinetic parameters, phoC and phoD gene abundance, pH, total P contents, and other soil properties influenced the P availability in soils from a temperate forest (ChangBai Mountain) and a subtropical forest (QianYanZhou Plantation). The results showed that the DNA contents and the ACP and ALP activities were positively correlated with the available P contents in the temperate forest soil. The phoC and phoD gene abundance and the ALP activity were positively correlated with the available P contents in the subtropical forest soil. The ACP-Vmax/Km and DNA contents were positively correlated with the available P contents in topsoil (0–10 cm). The total P contents, pH, MBP, and ACP-Vmax/Km in subsoil (10–30 cm) were positively correlated with the available P contents. A structural equation model showed that DNA content had the greatest effect on the soil available P in temperate forest soil, and phoC and phoD gene abundance had the greatest effect on the soil available P in subtropical forest soil. The mechanism of H+ dissolution affected the P availability through low pH in the topsoil and weathering in the subsoil. Overall, these findings provided an improved understanding about how the catalytic efficiencies of ACP and ALP and the phoC and phoD gene abundance, influenced the P availability in temperate and subtropical forest soils at different depths. We also gained insights into how the P availability was affected by H+ dissolution and the parent material in topsoil and subsoil, respectively.

Organic Farming Favors phoD-Harboring Rhizospheric Bacterial Community and Alkaline Phosphatase Activity in Tropical Agroecosystem

The bacteria harboring phoD encodes alkaline phosphatase (ALP), a secretory enzyme that hydrolyzes organic phosphorous (P) to a usable form in the soil. The impact of farming practices and crop types on phoD bacterial abundance and diversity in tropical agroecosystems is largely unknown. In this research, the aim was to study the effect of farming practices (organic vs. conventional) and crop types on the phoD-harboring bacterial community. A high-throughput amplicon (phoD gene) sequencing method was employed for the assessment of bacterial diversity and qPCR for phoD gene abundance. Outcomes revealed that soils treated for organic farming have high observed OTUs, ALP activity, and phoD population than soils managed under conventional farming with the trend of maize > chickpea > mustard > soybean vegetated soils. The relative abundance of Rhizobiales exhibited dominance. Ensifer, Bradyrhizobium, Streptomyces, and Pseudomonas were observed as dominant genera in both farming practices. Overall, the study demonstrated that organic farming practice favors the ALP activity, phoD abundance, and OTU richness which varied across crop types with maize crops showing the highest OTUs followed by chickpea, mustard, and least in soybean cropping.

The spatio-temporal distribution of alkaline phosphatase activity and phoD gene abundance and diversity in sediment of Sancha Lake

The bacterial phoD gene encoding alkaline phosphatase (ALP) plays an important role in the release of soluble reactive phosphorus (SRP) from organic phosphorus in ecosystems. However, phoD gene diversity and abundance in ecosystems is poorly understood. In the present study, we sampled the surface sediments and the overlying water of Sancha Lake at 9 different sampling sites, a typical eutrophic sub-deep freshwater lake in China, in April 15 (spring) and November 3 (autumn), 2017. High-throughput sequencing and qPCR were performed to analyze the diversity and abundance of the bacterial phoD gene in the sediments. We further discussed the relationships between the diversity and abundance of the phoD gene and environmental factors and ALP activity. A total of 881,717 valid sequences were obtained from 18 samples and were classified into 41 genera, 31 families, 23 orders, 12 classes, and 9 phyla and grouped into 477 OTUs. The dominant phyla were Proteobacteria and Actinobacteria. The phylogenetic tree based on the sequences of the phoD gene was plotted and composed of three branches. The genetic sequences were aligned predominantly with genera Pseudomonas, Streptomyces, Cupriavidus, and Paludisphaer. The phoD-harboring bacterial community structure showed a significant difference in spring and autumn, but no apparent spatial heterogeneity. The phoD gene abundances at different sampling points were significantly higher in autumn than in spring. In autumn and spring, the phoD gene abundance was significantly higher in the tail of lake and where cage culture used to be intensive. pH value, dissolved oxygen (DO), total organic carbon (TOC), ALP, and phosphorus were important environmental factors affecting the diversity of the phoD gene and the phoD-harboring bacterial community structure. Changes in phoD-harboring bacterial community structure, phoD gene abundance, and ALP activity were negatively correlated with SRP in overlying water. Our study indicated phoD-harboring bacteria in the sediments of Sancha Lake with the characteristics of high diversity and significant spatial and temporal heterogeneity in abundance and community structure, which played a important role in the release of SRP.

Livestock grazing-exclusion under global warming scenario decreases phosphorus mineralization by changing soil food web structure in a Tibetan alpine meadow

The exclusion of grazing has been used extensively in alpine meadows on the Tibetan Plateau. Studies, however, have shown reported recent trends of decreasing concentrations of soil nutrients because of grazing exclusion and climate change. The effects of excluding grazing on the soil biogeochemical process of phosphorus cycling in alpine meadows are unclear, especially under climatic warming. We conducted a 5-year grazing-exclusion and warming-manipulation experiment to examine the effects of excluding grazing on fractions of soil phosphorus, microbial and nematode communities and enzymatic activities in treatments of low grazing intensity, grazing exclusion, and combined grazing exclusion and warming. Our results indicated that excluding grazing significantly decreased bacterivore and omnivore-predator densities, phoD gene abundance and alkaline phosphomonoesterase activity (in the 0–5 cm layer by −34, −41, −38 and −42 %) at altitudes of 3850 m, 4000 m, 4150 m and 4250 m, respectively. Structural equation modeling indicated that bacterivores positively affected phoD gene abundance, alkaline phosphomonoesterase activity and inorganic‑phosphorus fractions. Combined grazing exclusion and warming significantly decreased bacterivore and omnivore-predator densities but significantly increased fungivore density (in the 0–5 cm layer by 238, 172, 119 and 65 %) at altitudes of 3850, 4000, 4150 and 4250 m, respectively. Structural equation modeling also indicated that the combined grazing-exclusion and warming treatment increased the soil fungi and fungivores, but the higher abundances of fungi and fungivores did not significantly affect acid phosphomonoesterase activity or inorganic‑phosphorus fractions. Alternatively, the combined grazing-exclusion and warming treatment significantly increased the concentrations of amorphous and free aluminum, which were positively correlated with the maximum adsorption of phosphorus. The combined grazing-exclusion and warming treatment thus significantly decreased the availability of resin phosphorus (−63, −51, −81 and −67 %) in the 0–5 cm layer at altitudes of 3850, 4000, 4150 and 4250 m, respectively. Our results suggested that light grazing (0.5 yak ha−1 year−1) could increase phosphorus mineralization and the activity of soil enzymes in alpine meadows under global warming. An adequate load of livestock pressure at each altitude can be an effective management technique, mainly under warming, to maintain an adequate, sustainable and equilibrated phosphorus cycle in the plant-soil system.

Effects of Lake Sediment on Soil Properties, Crop Growth, and the phoD-Harboring Microbial Community

Removal of lake sediment has been shown to be an effective method for lake restoration. High phosphorus (P) content makes it possible for lake sediment to provide fertility for agricultural production. However, little research has focused on the responses of the soil-phosphorus-related microbial community to the sediment-derived fertilizer enriched in phosphorus content. The phoD-harboring gene, important to the global phosphorus cycle, encodes alkaline phosphatase hydrolyzing organic P in soil. Accordingly, a plot experiment was performed to compare the effects of four different fertilization treatments—no-fertilizer control (CK), 50% chemical fertilization with compressed sediment (CS), 50% chemical fertilization with original lake sediment (S), and conventional chemical fertilization treatment (CT)—on the phoD gene community using QPCR and high-throughput sequencing analysis. Relationships among soil physicochemical properties, phoD-harboring microbial community abundance and composition were also evaluated. Results showed that compared to CT, CS significantly increased soil organic matter (SOM) content by 20.29%, and S enhanced the humus content by 20.75% (p &lt; 0.05). There was no significant influence on phoD gene microbial community richness (Chao1 and Sobs indexes) and diversity (Shannon index) between all treatments. The CS treatment significantly altered the phoD community structure and enhanced the Chinese cabbage yield by 40.19% (p &lt; 0.05). Pearson analysis showed that phoD gene abundance (copy number) had significant and negative relationships with SOM, total nitrogen (TN), total phosphorus (TP), available nitrogen (AN), available phosphorus (AP), and the Chao1 index. Redundancy analysis showed that shifts in the phoD community structure were related to soil physicochemical properties (SOM, TN, TP, AN, AP, and humus) rather than soil pH. In conclusion, the compressed sediment can be used in farmland since it optimizes the phoD-harboring microbial community abundance, composition, and structure, and thus significantly increases the Chinese cabbage yield.

The relationships of bacterial-feeding nematodes, phoD-harboring bacteria and alkaline phosphomonoesterase activity under the combined application of organic and inorganic fertilizers in an alkaline soil

Bacterial-feeding nematodes have the potential to increase soil alkaline phosphomonoesterase (AlP) activity by affecting the composition of phoD-harboring bacterial community or the abundance of phoD gene. However, the relationships between bacterial-feeding nematodes, composition of phoD-harboring bacterial community, phoD gene abundance and AlP activity with inorganic plus organic fertilization in alkaline soil where AlP is dominant is yet to be properly understood. Four fertilization regimes: non-fertilized control (CK), chemical nitrogen (N), phosphorus (P) and potassium (K) fertilizers (NPK), crop straw plus chemical fertilizers (SNPK), as well as pig manure plus chemical fertilizers (MNPK), were used in determining the variation in soil bacterial-feeding nematodes, composition of phoD-harboring bacterial community, phoD gene abundance and AlP activity under different fertilization treatments as well as their relationships. Results showed that both inorganic and organic fertilizer application significantly enhanced the activity of soil AlP, which significantly decreased under NPK application compared with SNPK and MNPK treatments. Partial least squares path modeling showed that AlP activity was directly and positively affected by composition of phoD-harboring bacterial community and microbial biomass carbon (MBC), and the bacterial-feeding nematode dominant genus Eucephalobus, which was affected by MBC directly, could affect AlP activity in an indirect way by its significant direct positive effect on phoD-harboring bacterial community composition. Of those 12 top bacterial genera that harbored phoD, just the gram-positive bacteria Massilia and Saccharothrix showed significant positive correlation with AlP, while Saccharothrix showed obvious positive correlation with Eucephalobus. Overall, these results suggest that the dominant genus Eucephalobus may be the beneficial indigenous bacterial-feeding nematode that can increase the activity of soil AlP within the alkaline soil, which is affected by MBC directly and can be likely to positively affect the composition of phoD-harboring bacterial community through a passive food ingestion mechanism and then promote AlP activity indirectly, of which Saccharothrix is the intermediary bacteria for the increase in AlP activity caused by the bacterial-feeding nematode.

Stronger effects of maize rhizosphere than phosphorus fertilization on phosphatase activity and phosphorus-mineralizing-related bacteria in acidic soils

The bacterial phoC and phoD genes encode acid (ACP) and alkaline phosphatase (ALP), respectively, which mineralize organic phosphorus (P) to inorganic P. The relative importance of P fertilization and the plant rhizosphere on soil phosphatase activities and associated bacterial communities in acidic soils are poorly understood; additionally, the different responses of the phoC- and phoD-harboring bacterial communities remains undetermined. Here, we grow maize in an acidic soil (pH 4.40) supplemented with 0 (P0), 8.74 (Low phosphorus, LP) and 87.36 (High phosphorus, HP) mg P kg−1, and determined phosphatase activities and associated bacterial abundance and community composition in bulk and rhizosphere soils. The results showed that relative to bulk soils, rhizosphere showed higher ACP and ALP activities and phoC and phoD gene abundance, but this effect strength was reduced under HP treatment, except for phoC gene abundance. The rhizosphere effect increased α-diversity of phoC-harboring bacteria under P fertilization but reduced phoD-harboring bacterial α-diversity under P0 and LP treatments. The rhizosphere significantly influenced phoC- and phoD-harboring bacterial community compositions, with stronger effect on phoD-harboring bacteria; while P fertilization only affected phoD-harboring bacteria. Immigrated and extinct species play important roles in reshaping phoC- and phoD-harboring bacterial communities, respectively, in response to the rhizosphere effect. Overall, compared with P fertilization, the maize rhizosphere more strongly influenced soil phosphatase activities, phoC- and phoD-harboring bacterial communities in acidic soils, with phoD-harboring bacteria responding more strongly to the rhizosphere effect and P fertilization. Notably, the strength of the rhizosphere effect heavily relied on P fertilization level.

The characteristics of alkaline phosphatase activity and phoD gene community in heavy-metal contaminated soil remediated by biochar and compost

This research was carried out to determine the influence of biochar and compost addition on the characteristics of potential alkaline phosphatase (ALP) activity and phoD gene community in heavy metal polluted soils. The ALP activity, the abundance and structure of phoD gene were systematically determined. Results showed that biochar and compost significantly changed soil properties, and promoted the microbial transformation of phosphorus. Compost addition significantly increased the ALP activity. Biochar and compost addition markedly increased the phoD gene abundance. The addition of biochar increased the proportion of Actinobacteria, Euryarchaeota, and Proteobacteria. By contrast, Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria were the dominant taxa in soils with compost addition. Electrical conductivity critically controlled the expression of phoD and changed the structure of phoD-coding microbial communities in heavy-metal polluted soils that remediated by biochar and compost.

Long-term fertilization lowers the alkaline phosphatase activity by impacting the phoD-harboring bacterial community in rice-winter wheat rotation system

PhoD-harboring bacteria and the secreted alkaline phosphatases (ALP) are crucial in the regulation of soil phosphorus (P) cycling. However, the influential factors of these crucial indicators and their internal interactions remain controversial. Here, a long-term field experiment containing different fertilization regimes was conducted (chemical, organic, and no fertilizer applied). The results indicated that the richness and diversity of phoD-harboring bacterial community were significantly decreased after long-term fertilization. The applied fertilizer promoted the growth of competitive species, while phoD-harboring bacteria lost the advantage to outcompete other microorganisms after long-term fertilization. The decreased ALP activity was caused by the declined phoD gene abundance, which is attributed to the comprehensive effects of soil organic C (SOC), total nitrogen (TN), and various forms of P. The random forest models identified SOC, TN, and available P (AP) to be the dominant environmental factors in shaping the phoD-harboring bacterial community. In addition, some other forms of P such as organic P (Po), inorganic P (Pi) or total P (TP) also exerted significant effects. Different fertilization regimes changed the keystone genera that contributed significantly to soil ALP activities, while Pseudolabrys and Pseudomonas were predicted to be the most important genera regardless of different fertilization regimes. This study extends the understanding of the main process and mechanisms of P mobilization in response to different fertilization regimes.

Stoichiometric imbalances and the dynamics of phosphatase activity and the abundance of phoC and phoD genes with the development of Cunninghamia lanceolata (Lamb.) Hook plantations

Soil phosphatase and P-cycling functional genes, such as phoC and phoD, are crucial factors in regulating terrestrial P cycling, especially in highly weathered subtropical and tropical soils. Soil element stoichiometry (especially available C:N:P by measuring dissolved organic C (DOC):available N (AN):Olsen P plays an essential role in biogeochemical P cycling, but how it affects phosphatase activity and the abundance of phoC and phoD genes following afforestation is unclear. Here, we investigated how soil C:N:P stoichiometry affected the dynamics of soil phosphatase activity and the abundance of phoC and phoD genes in an age sequence of 6-, 12-, 18-, 25-, 32-, and 49-year-old Chinese fir plantations. The results showed that the phosphatase activity and the abundance of phoC gene were overall higher in 18- and 25-year-old plantations than in the other four plantations. The abundance of phoD gene gradually increased with stand age. Phosphatase activity significantly and positively correlated with DOC:Olsen P and AN:Olsen P ratios, but not with DOC:AN ratio. Soil phosphatase activity significantly positively correlated with phoC gene abundance, but not with phoD gene abundance, indicating that the phoC gene abundance is the dominant predictor of the microbial functional potential for secreting phosphatase. Further analysis suggested that the ratios of DOC:Olsen P and AN:Olsen P, total N, DOC, AN, Olsen P, and microbial biomass C were the main predictors of phoC gene abundance and that DOC:AN, total P, AN, Olsen P, and microbial biomass C were the main predictors of phoD gene abundance. These findings together highlight the importance of soil available element stoichiometry regulating microbial functional genes, with potential implications for subtropical and tropical biogeochemical processes and for understanding how soil available C:N:P stoichiometry regulates P biotransformation.

Soil Microbial Community Succession Based on PhoD and Gcd Genes along a Chronosequence of Sand-Fixation Forest

Revegetation by planting shrubs on moving sand dunes is widely used to control desertification in arid/semi-arid areas. The soil including microbial community can gradually be improved along with plantation development. The purposes of this study were (1) to investigate the responses of microbial communities involved in the mineralization of soil organic phosphorus (OP) and dissolution of inorganic P (IOP) in the development of sand-fixating plantation and (2) to discuss the interactions between P turnover microbial communities and soil properties. We assessed the compositions of soil phoD gene (one of the Pho regulons encoding alkaline phosphomonoesterases) and gcd gene (encoding glucose dehydrogenase) in microbial community by using high-throughput Illumina MiSeq sequencing in a chronosequence of Caragana microphylla plantations (0-, 10-, 20-, and 37-year plantations and a native C. microphylla shrub forest) in Horqin Sandy Land, Northeast China. Soil properties including soil nutrients, enzymatic activity, and P fractions were also determined. The abundance of phoD and gcd genes linearly increased with the plantation age. However, the diversity of soil phoD microbes was more abundant than that of gcd. The phoD gene abundance and the fractions of total OP and IOP were positively correlated with the activity of phosphomonoesterase. Actinobacteria and Streptomycetaceae were the dominant phoD taxa, while Proteobacteria and Rhizobiaceae were the dominant gcd taxa. Plantation development facilitated the progressive successions of soil phoD and gcd communities resulting from the increase in the abundance of dominant taxa. Total soil N, NH4-N, and available K were the main factors affecting the structures of phoD and gcd communities, while pH was not significantly influencing factor in such arid and nutrient-poor sandy soil. Many phoD or gcd OTUs were classified into Rhizobium and Bradyrhizobium, suggesting the coupling relationship between soil P turnover and N fixation.

Adaptation of phoD-harboring bacteria to broader environmental gradients at high elevations than at low elevations in the Shennongjia primeval forest

Disentangling responses of phoD-harboring bacteria to environmental factors in different habitats, crucial for understanding the ecosystem’s potential for organic phosphorus mineralization and plant productivity, is an important but poorly investigated subject. Using MiSeq sequencing and multiple statistical analyses, we investigated activity, abundance, taxonomic and phylogenetic diversity of phoD-harboring bacteria at low (<1500 m) and high (>1500 m) elevations in the Shennongjia primeval forest. We found significant difference in phoD gene abundance and no significant divergence in alkaline phosphomonoesterase activity between low elevations and high elevations. Soil phoD-harboring bacteria showed stronger phylogenetic signals and broader environmental thresholds at high elevations than at low elevations based on threshold indicator taxa analysis, Blomberg’s K statistic, and Fritz-Purvis D-test. In addition, phoD-harboring bacteria showed closer phylogenetic clustering at high elevations than at low elevations. Null model reflected that community assembly at low elevations was determined by both deterministic and stochastic processes, and community assembly at high elevations was mainly determined by stochastic processes. To our knowledge, this study first reports that phoD-harboring bacteria are less environmentally constrained and have stronger environmental adaptation at high elevations than at low elevations. Our findings expand knowledge of the diversity maintenance of phoD-harboring bacteria at low and high elevations, and might offer the prediction of potential changes in organic phosphorus mineralization in the Shennongjia primeval forest.