A widely distributed phosphate-insensitive phosphatase presents a route for rapid organophosphorus remineralization in the biosphere

Analysis of microbial dynamics in the soybean root-associated environments from community to single-cell levels

Plant root-associated environments such as the rhizosphere, rhizoplane, and endosphere, are notably different from non-root-associated soil environments. However, the microbial dynamics in these spatially divided compartments remain unexplored. In this study, we propose a combinational analysis of single-cell genomics with 16S rRNA gene sequencing. This method enabled us to understand the entire soil microbiome and individual root-associated microorganisms. We applied this method to soybean microbiomes and revealed that their composition was different between the rhizoplane and rhizosphere in the early growth stages, but became more similar as growth progressed. In addition, a total of 610 medium- to high-quality single-amplified genomes (SAGs) were acquired, including plant growth-promoting rhizobacteria (PGPR) candidates while genomes with high GC content tended to be missed by SAGs. The whole-genome analyses of the SAGs suggested that rhizoplane-enriched Flavobacterium solubilizes organophosphate actively and Bacillus colonizes roots more efficiently. Single-cell genomics, together with 16S rRNA gene sequencing, enabled us to connect microbial taxonomy and function, and assess microorganisms at a strain resolution even in the complex soil microbiome.

A distinct, high-affinity, alkaline phosphatase facilitates occupation of P-depleted environments by marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus, the two most abundant phototrophs on Earth, thrive in oligotrophic oceanic regions. While it is well known that specific lineages are exquisitely adapted to prevailing in situ light and temperature regimes, much less is known of the molecular machinery required to facilitate occupancy of these low-nutrient environments. Here, we describe a hitherto unknown alkaline phosphatase, Psip1, that has a substantially higher affinity for phosphomonoesters than other well-known phosphatases like PhoA, PhoX, or PhoD and is restricted to clade III Synechococcus and a subset of high light I-adapted Prochlorococcus strains, suggesting niche specificity. We demonstrate that Psip1 has undergone convergent evolution with PhoX, requiring both iron and calcium for activity and likely possessing identical key residues around the active site, despite generally very low sequence homology. Interrogation of metagenomes and transcriptomes from TARA oceans and an Atlantic Meridional transect shows that psip1 is abundant and highly expressed in picocyanobacterial populations from the Mediterranean Sea and north Atlantic gyre, regions well recognized to be phosphorus (P)-deplete. Together, this identifies psip1 as an important oligotrophy-specific gene for P recycling in these organisms. Furthermore, psip1 is not restricted to picocyanobacteria and is abundant and highly transcribed in some α-proteobacteria and eukaryotic algae, suggesting that such a high-affinity phosphatase is important across the microbial taxonomic world to occupy low-P environments.

Mechanism of organic phosphorus transformation and its impact on the primary production in a deep oligotrophic plateau lake during stratification

Global warming is leading to extended stratification in deep lakes, which may exacerbate phosphorus (P) limitation in the upper waters. Conversion of labile dissolved organic P (DOP) is a possible adaptive strategy to maintain primary production. To test this, the spatiotemporal distributions of various soluble P fractions and phosphomonesterase (PME)/phosphodiesterase (PDE) activities were investigated in Lake Fuxian during the stratification period and the transition capacity of organic P and its impact on primary productivity were evaluated. The results indicated that the DOP concentration (mean 0.20 ± 0.05 μmol L-1) was significantly higher than that of dissolved inorganic P (DIP) (mean 0.08 ± 0.03 μmol L-1) in the epilimnion and metalimnion, which were predominantly composed of orthophosphate monoester (monoester-P) and orthophosphate diesters (diester-P). The low ratio of diester-P / monoester-P and high activities of PME and PDE indicate DOP mineralization in the epilimnion and metalimnion. We detected a DIP threshold of approximately 0.19 μmol L-1, corresponding to the highest total PME activity in the lake. Meta-analysis further demonstrated that DIP thresholds of PME activities were prevalent in oligotrophic (0.19 μmol L-1) and mesotrophic (0.74 μmol L-1) inland waters. In contrast to the phosphate-sensitive phosphatase PME, dissolved PDE was expressed independent of phosphate availability and its activity invariably correlated with chlorophyll a, suggesting the involvement of phytoplankton in DOP utilization. This study provides important field evidence for the DOP transformation processes and the strategy for maintaining primary productivity in P-deficient scenarios, which contributes to the understanding of P cycles and the mechanisms of system adaptation to future long-term P limitations in stratified waters.

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

Characterization of an extremophile bacterial acid phosphatase derived from metagenomics analysis

Acid phosphatases are enzymes that play a crucial role in the hydrolysis of various organophosphorous molecules. A putative acid phosphatase called FS6 was identified using genetic profiles and sequences from different environments. FS6 showed high sequence similarity to type C acid phosphatases and retained more than 30% of consensus residues in its protein sequence. A histidine-tagged recombinant FS6 produced in Escherichia coli exhibited extremophile properties, functioning effectively in a broad pH range between 3.5 and 8.5. The enzyme demonstrated optimal activity at temperatures between 25 and 50°C, with a melting temperature of 51.6°C. Kinetic parameters were determined using various substrates, and the reaction catalysed by FS6 with physiological substrates was at least 100-fold more efficient than with p-nitrophenyl phosphate. Furthermore, FS6 was found to be a decamer in solution, unlike the dimeric forms of crystallized proteins in its family.

Harnessing Phosphorous (P) Fertilizer-Insensitive Bacteria to Enhance Rhizosphere P Bioavailability in Legumes

Phosphorous (P) is widely used in agriculture; yet, P fertilizers are a nonrenewable resource. Thus, mechanisms to improve soil P bioavailability need to be found. Legumes are efficient in P acquisition and, therefore, could be used to develop new technologies to improve soil P bioavailability. Here, we studied different species and varieties of legumes and their rhizosphere microbiome responses to low-P stress. Some varieties of common beans, cowpeas, and peas displayed a similar biomass with and without P fertilization. The rhizosphere microbiome of those varieties grown without P was composed of unique microbes displaying different levels of P solubilization and mineralization. When those varieties were amended with P, some of the microbes involved in P solubilization and mineralization decreased in abundance, but other microbes were insensitive to P fertilization. The microbes that decreased in abundance upon P fertilization belonged to groups that are commonly used as biofertilizers such as Pseudomonas and Azospirillum. The microbes that were not affected by P fertilization constitute unique species involved in P mineralization such as Arenimonas daejeonensis, Hyphomicrobium hollandicum, Paenibacillus oenotherae, and Microlunatus speluncae. These P-insensitive microbes could be used to optimize P utilization and drive future sustainable agricultural practices to reduce human dependency on a nonrenewable resource.

Root microbiota confers rice resistance to aluminium toxicity and phosphorus deficiency in acidic soils

Aluminium (Al) toxicity impedes crop growth in acidic soils and is considered the second largest abiotic stress after drought for crops worldwide. Despite remarkable progress in understanding Al resistance in plants, it is still unknown whether and how the soil microbiota confers Al resistance to crops. Here we found that a synthetic community composed of highly Al-resistant bacterial strains isolated from the rice rhizosphere increased rice yield by 26.36% in acidic fields. The synthetic community harvested rhizodeposited carbon for successful proliferation and mitigated soil acidification and Al toxicity through extracellular protonation. The functional coordination between plants and microbes offers a promising way to increase the usage of legacy phosphorus in topsoil. These findings highlight the potential of microbial tools for advancing sustainable agriculture in acidic soils.

Effects of Phosphorus Limitation on the Bioavailability of DOM Released by Marine Heterotrophic Prokaryotes

Heterotrophic prokaryotes (HP) contribute largely to dissolved organic matter (DOM) processing in the ocean, but they also release diverse organic substances. The bioavailability of DOM released by HP under varying environmental conditions has not been fully elucidated. In this study, we investigated the bioavailability of DOM released by a single bacterial strain (Sphingopyxis alaskensis) and 2 natural HP communities grown under P-replete and P-limited conditions. The released DOM (HP-DOM) was used as a substrate for natural HP communities at a coastal site in the Northwestern Mediterranean Sea. We followed changes in HP growth, enzymatic activity, diversity, and community composition together with the consumption of HP-DOM fluorescence (FDOM). HP-DOM produced under P-replete and P-limited conditions promoted significant growth in all incubations. No clear differences in HP-DOM lability released under P-repletion and P-limitation were evidenced based on the HP growth, and P-limitation was not demonstrated to decrease HP-DOM lability. However, HP-DOM supported the growth of diverse HP communities, and P-driven differences in HP-DOM quality were selected for different indicator taxa in the degrading communities. The humic-like fluorescence, commonly considered recalcitrant, was consumed during the incubations when this peak was initially dominating the FDOM pool, and this consumption coincided with higher alkaline phosphatase activity. Taken together, our findings emphasize that HP-DOM lability is dependent on both DOM quality, which is shaped by P availability, and the composition of the consumer community.

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.

Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning

Bacteroidetes are prevalent in soil ecosystems and are associated with various eukaryotic hosts, including plants, animals, and humans. The ubiquity and diversity of Bacteroidetes exemplify their impressive versatility in niche adaptation and genomic plasticity. Over the past decade, a wealth of knowledge has been obtained on the metabolic functions of clinically relevant Bacteroidetes, but much less attention has been given to Bacteroidetes living in close association with plants. To improve our understanding of the functional roles of Bacteroidetes for plants and other hosts, we review the current knowledge of their taxonomy and ecology, in particular their roles in nutrient cycling and host fitness. We highlight their environmental distribution, stress resilience, genomic diversity, and functional importance in diverse ecosystems, including, but not limited to, plant-associated microbiomes.

The facilitating role of phycospheric heterotrophic bacteria in cyanobacterial phosphonate availability and Microcystis bloom maintenance

BACKGROUND

Phosphonates are the main components in the global phosphorus redox cycle. Little is known about phosphonate metabolism in freshwater ecosystems, although rapid consumption of phosphonates has been observed frequently. Cyanobacteria are often the dominant primary producers in freshwaters; yet, only a few strains of cyanobacteria encode phosphonate-degrading (C-P lyase) gene clusters. The phycosphere is defined as the microenvironment in which extensive phytoplankton and heterotrophic bacteria interactions occur. It has been demonstrated that phytoplankton may recruit phycospheric bacteria based on their own needs. Therefore, the establishment of a phycospheric community rich in phosphonate-degrading-bacteria likely facilitates cyanobacterial proliferation, especially in waters with scarce phosphorus. We characterized the distribution of heterotrophic phosphonate-degrading bacteria in field Microcystis bloom samples and in laboratory cyanobacteria "phycospheres" by qPCR and metagenomic analyses. The role of phosphonate-degrading phycospheric bacteria in cyanobacterial proliferation was determined through coculturing of heterotrophic bacteria with an axenic Microcystis aeruginosa strain and by metatranscriptomic analysis using field Microcystis aggregate samples.

RESULTS

Abundant bacteria that carry C-P lyase clusters were identified in plankton samples from freshwater Lakes Dianchi and Taihu during Microcystis bloom periods. Metagenomic analysis of 162 non-axenic laboratory strains of cyanobacteria (consortia cultures containing heterotrophic bacteria) showed that 20% (128/647) of high-quality bins from eighty of these consortia encode intact C-P lyase clusters, with an abundance ranging up to nearly 13%. Phycospheric bacterial phosphonate catabolism genes were expressed continually across bloom seasons, as demonstrated through metatranscriptomic analysis using sixteen field Microcystis aggregate samples. Coculturing experiments revealed that although Microcystis cultures did not catabolize methylphosphonate when axenic, they demonstrated sustained growth when cocultured with phosphonate-utilizing phycospheric bacteria in medium containing methylphosphonate as the sole source of phosphorus.

CONCLUSIONS

The recruitment of heterotrophic phosphonate-degrading phycospheric bacteria by cyanobacteria is a hedge against phosphorus scarcity by facilitating phosphonate availability. Cyanobacterial consortia are likely primary contributors to aquatic phosphonate mineralization, thereby facilitating sustained cyanobacterial growth, and even bloom maintenance, in phosphate-deficient waters. Video Abstract.

Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System

Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.

Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils

Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.

Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles

In marine systems, the availability of inorganic phosphate can limit primary production leading to bacterial and phytoplankton utilization of the plethora of organic forms available. Among these are phospholipids that form the lipid bilayer of all cells as well as released extracellular vesicles. However, information on phospholipid degradation is almost nonexistent despite their relevance for biogeochemical cycling. Here, we identify complete catabolic pathways for the degradation of the common phospholipid headgroups phosphocholine (PC) and phosphorylethanolamine (PE) in marine bacteria. Using Phaeobacter sp. MED193 as a model, we provide genetic and biochemical evidence that extracellular hydrolysis of phospholipids liberates the nitrogen-containing substrates ethanolamine and choline. Transporters for ethanolamine (EtoX) and choline (BetT) are ubiquitous and highly expressed in the global ocean throughout the water column, highlighting the importance of phospholipid and especially PE catabolism in situ. Thus, catabolic activation of the ethanolamine and choline degradation pathways, subsequent to phospholipid metabolism, specifically links, and hence unites, the phosphorus, nitrogen, and carbon cycles.

Roles of phosphate-solubilizing bacteria in mediating soil legacy phosphorus availability

Phosphorus (P), an essential macronutrient for all life on Earth, has been shown to be a vital limiting nutrient element for plant growth and yield. P deficiency is a common phenomenon in terrestrial ecosystems across the world. Chemical phosphate fertilizer has traditionally been employed to solve the problem of P deficiency in agricultural production, but its application has been limited by the non-renewability of raw materials and the adverse influence on the ecological health of the environment. Therefore, it is imperative to develop efficient, economical, environmentally friendly and highly stable alternative strategies to meet the plant P demand. Phosphate-solubilizing bacteria (PSB) are able to improve plant productivity by increasing P nutrition. Pathways to fully and effectively use PSB to mobilize unavailable forms of soil P for plants has become a hot research topic in the fields of plant nutrition and ecology. Here, the biogeochemical P cycling in soil systems are summarized, how to make full use of soil legacy P via PSB to alleviate the global P resource shortage are reviewed. We highlight the advances in multi-omics technologies that are helpful for exploring the dynamics of nutrient turnover and the genetic potential of PSB-centered microbial communities. Furthermore, the multiple roles of PSB inoculants in sustainable agricultural practices are analyzed. Finally, we project that new ideas and techniques will be continuously infused into fundamental and applied research to achieve a more integrated understanding of the interactive mechanisms of PSB and rhizosphere microbiota/plant to maximize the efficacy of PSB as P activators.

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

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

Years of sand fixation with Caragana korshinskii drive the enrichment of its rhizosphere functional microbes by accumulating soil N

C. korshinskii is one of the most widely-planted sand-fixing legumes in northwest China and exploring its rhizosphere microbiome is of great ecological importance. However, the effect of long-term sand fixation on the composition, diversity, and underlying functions of microbes in the C. korshinskii rhizosphere in dryland ecosystems remain unclear. Here, we performed high-throughput sequencing using a 16S rRNA (absolute quantification) and bacterial functional annotation of prokaryotic taxa (FAPROTAX) analysis and an ITS (relative quantification) and fungal functional guild (FUNGuild) analysis to investigate the C. korshinskii rhizosphere microbiome and metabolic functional groups at different sand-fixing ages (six years, CK6; twelve years, CK12; and eighteen years, CK18) and determined the physicochemical properties of the rhizosphere soil. Results showed that the key bacterial taxa of the rhizosphere were significantly more abundant in CK18 than in CK12 and CK6 at the phylum-class-genus level, and that fungal Glomeromycota was also significantly more abundant in the CK18 rhizosphere compared to CK12 and CK6. Among these bacterial taxa, the enrichment effect of key, functional, genus-level species of bacteria was the most obvious, including Rhizobium, Ensifer, Neorhizobium, Mesorhizobium, Streptomyces, Sphingomonas, and Flavobacterium, which are N-fixing and/or phosphate-solubilizing groups. The significant improvement seen in the physicochemical properties of the CK18 rhizosphere soil, including the higher total nitrogen (TN), available nitrogen (AN), pH, electrical conductivity (EC), higher N:P ratio, and lower C:N ratio, all demonstrated the relationship between the rhizosphere microbes and soil carbon (C) and nitrogen (N) cycling. A redundancy analysis (RDA) of different taxonomic levels indicated a close positive relationship between rhizosphere microbes and AN. In addition, the functional groups of the C. korshinskii rhizosphere bacteria were closely related to soil AN and were mainly composed of chemoheterotrophy and aerobic chemoheterotrophy. A Spearman correlation analysis revealed that these functional groups were mainly identified from bacterial Actinobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, and fungal Glomeromycota. Our study provides evidence that the rhizosphere microbes of C. korshinskii are closely related to the accumulation of N in the restoration of desert ecosystems, and that the ecological functional processes they are involved in mainly involve C and N cycles, which play an important role in desertification reversal.

Rethinking the biotic and abiotic remineralization of complex phosphate molecules in soils and sediments

Phosphorus (P) is an essential macronutrient for all living organisms. Despite a diversity of P compounds in the environment, orthophosphate is the most bioavailable form of P. Remineralization of complex P molecules (e.g., organic P and phosphoanhydrides) into orthophosphate is traditionally considered to be carried out primarily by enzymes. Natural minerals are recently viewed to be abiotic catalysts (as compared to the organic phosphatases) to facilitate the cleavage of terminal P-O-C/P bonds and remineralization of complex P compounds. However, quantitative comparison between biotic and abiotic remineralization pathways of complex P molecules is still missing, impeding our capability to assess the importance and contribution of abiotic P remineralization in the environment. This study compares the hydrolysis rates of six organic phosphates and three inorganic phosphoanhydrides by representative enzymes (acid and alkaline phosphatases) and natural oxide minerals (hematite, birnessite, and boehmite). The results show that enzymes and minerals have different substrate preferences. Specifically, alkaline phosphatase hydrolyzes phosphate monoesters faster than phosphoanhydrides, whereas acid phosphatase and minerals show higher hydrolysis rates toward phosphoanhydrides than phosphate monoesters. Although the hydrolysis rates by enzymes (~μM hr^-1) are orders of magnitude higher than those by minerals (~μM d^-1), normalization of the rates by the natural abundance of enzymes and minerals leads to comparable contributions of both processes in soils and sediments. These results highlight the significance of natural minerals in the remineralization of complex P compounds, a process that was traditionally overlooked but with important implications for constraining P biogeochemical cycling in the environment.

Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions

Advances in DNA sequencing technologies have drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Important ecological interactions being performed by microbes can be investigated by analyzing the extracellular protein fraction. Here, we combined a unique protein extraction method and an iterative bioinformatics pipeline to capture and identify extracellular proteins (metaexoproteomics) synthesized in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analyzed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1,885 plant, insect, and microbial proteins were identified across bulk and rhizosphere samples. Metaexoproteomics identified a significant shift in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This included stimulation of rhizosphere-specialized bacteria, such as Gammaproteobacteria, Betaproteobacteria, and Flavobacteriia, and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralization. Our metaproteomic assessment of the “active” plant microbiome at the field-scale demonstrates the importance of moving beyond metagenomics to determine ecologically important plant-microbe interactions underpinning plant health.

IMPORTANCE Plant-microbe interactions are critical to ecosystem function and crop production. While significant advances have been made toward understanding the structure of the plant microbiome, learning about its full functional role is still in its infancy. This is primarily due to an incomplete ability to determine in situ plant-microbe interactions actively operating under field conditions. Proteins are the functional entities of the cell. Therefore, their identification and relative quantification within a microbial community provide the best proxy for which microbes are the most metabolically active and which are driving important plant-microbe interactions. Here, we provide the first metaexoproteomics assessment of the plant microbiome using field-grown oilseed rape as the model crop species, identifying key taxa responsible for specific ecological interactions. Gaining a mechanistic understanding of the plant microbiome is central to developing engineered plant microbiomes to improve sustainable agricultural approaches and reduce our reliance on nonrenewable resources.

PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes

BACKGROUND

Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database.

RESULTS

In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments.

CONCLUSIONS

We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.

The role of organic nutrients in structuring freshwater phytoplankton communities in a rapidly changing world

Carbon, nitrogen, and phosphorus are critical macroelements in freshwater systems. Historically, researchers and managers have focused on inorganic forms, based on the premise that the organic pool was not available for direct uptake by phytoplankton. We now know that phytoplankton can tap the organic nutrient pool through a number of mechanisms including direct uptake, enzymatic hydrolysis, mixotrophy, and through symbiotic relationships with microbial communities. In this review, we explore these mechanisms considering current and projected future anthropogenically-driven changes to freshwater systems. In particular, we focus on how naturally- and anthropogenically- derived organic nutrients can influence phytoplankton community structure. We also synthesize knowledge gaps regarding phytoplankton physiology and the potential challenges of nutrient management in an organically dynamic and anthropogenically modified world. Our review provides a basis for exploring these topics and suggests several avenues for future work on the relation between organic nutrients and eutrophication and their ecological implications in freshwater systems.

Integration of small RNA, degradome, and transcriptome sequencing data illustrates the mechanism of low phosphorus adaptation in Camellia oleifera

Phosphorus (P) is an indispensable macronutrient for plant growth and development, and it is involved in various cellular biological activities in plants. Camellia oleifera is a unique high-quality woody oil plant that grows in the hills and mountains of southern China. However, the available P content is deficient in southern woodland soil. Until now, few studies focused on the regulatory functions of microRNAs (miRNAs) and their target genes under low inorganic phosphate (Pi) stress. In this study, we integrated small RNA, degradome, and transcriptome sequencing data to investigate the mechanism of low Pi adaptation in C. oleifera. We identified 40,689 unigenes and 386 miRNAs by the deep sequencing technology and divided the miRNAs into four different groups. We found 32 miRNAs which were differentially expressed under low Pi treatment. A total of 414 target genes of 108 miRNAs were verified by degradome sequencing. Gene ontology (GO) functional analysis of target genes found that they were related to the signal response to the stimulus and transporter activity, indicating that they may respond to low Pi stress. The integrated analysis revealed that 31 miRNA-target pairs had negatively correlated expression patterns. A co-expression regulatory network was established based on the profiles of differentially expressed genes. In total, three hub genes (ARF22, WRKY53, and SCL6), which were the targets of differentially expressed miRNAs, were discovered. Our results showed that integrated analyses of the small RNA, degradome, and transcriptome sequencing data provided a valuable basis for investigating low Pi in C. oleifera and offer new perspectives on the mechanism of low Pi tolerance in woody oil plants.