Phosphorus forms affect the hyphosphere bacterial community involved in soil organic phosphorus turnover

Arbuscular mycorrhizal fungi and Streptomyces: brothers in arms to shape the structure and function of the hyphosphere microbiome in the early stage of interaction

BACKGROUND

Fungi and bacteria coexist in a wide variety of environments, and their interactions are now recognized as the norm in most agroecosystems. These microbial communities harbor keystone taxa, which facilitate connectivity between fungal and bacterial communities, influencing their composition and functions. The roots of most plants are associated with arbuscular mycorrhizal (AM) fungi, which develop dense networks of hyphae in the soil. The surface of these hyphae (called the hyphosphere) is the region where multiple interactions with microbial communities can occur, e.g., exchanging or responding to each other's metabolites. However, the presence and importance of keystone taxa in the AM fungal hyphosphere remain largely unknown.

RESULTS

Here, we used in vitro and pot cultivation systems of AM fungi to investigate whether certain keystone bacteria were able to shape the microbial communities growing in the hyphosphere and potentially improved the fitness of the AM fungal host. Based on various AM fungi, soil leachates, and synthetic microbial communities, we found that under organic phosphorus (P) conditions, AM fungi could selectively recruit bacteria that enhanced their P nutrition and competed with less P-mobilizing bacteria. Specifically, we observed a privileged interaction between the isolate Streptomyces sp. D1 and AM fungi of the genus Rhizophagus, where (1) the carbon compounds exuded by the fungus were acquired by the bacterium which could mineralize organic P and (2) the in vitro culturable bacterial community residing on the surface of hyphae was in part regulated by Streptomyces sp. D1, primarily by inhibiting the bacteria with weak P-mineralizing ability, thereby enhancing AM fungi to acquire P.

CONCLUSIONS

This work highlights the multi-functionality of the keystone bacteria Streptomyces sp. D1 in fungal-bacteria and bacterial-bacterial interactions at the hyphal surface of AM fungi. Video Abstract.

Organic phosphorus levels change the hyphosphere phoD-harboring bacterial community of Funneliformis mosseae

The phoD-harboring bacterial community is responsible for organic phosphorus (P) mineralization in soil and is important for understanding the interactions between arbuscular mycorrhizal (AM) fungi and phosphate-solubilizing bacteria (PSB) at the community level for organic P turnover. However, current understanding of the phoD-harboring bacterial community associated with AM fungal hyphae responses to organic P levels remains incomplete. Here, two-compartment microcosms were used to explore the response of the phoD-harboring bacterial community in the hyphosphere to organic P levels by high-throughput sequencing. Extraradical hyphae of Funneliformis mosseae enriched the phoD-harboring bacterial community and organic P levels significantly altered the composition of the phoD-harboring bacterial community in the Funneliformis mosseae hyphosphere. The relative abundance of dominant families Pseudomonadaceae and Burkholderiaceae was significantly different among organic P treatments and were positively correlated with alkaline phosphatase activity and available P concentration in the hyphosphere. Furthermore, phytin addition significantly decreased the abundance of the phoD gene, and the latter was significantly and negatively correlated with available P concentration. These findings not only improve the understanding of how organic P influences the phoD-harboring bacterial community but also provide a new insight into AM fungus-PSB interactions at the community level to drive organic P turnover in soil.

Nutrient-dependent cross-kingdom interactions in the hyphosphere of an arbuscular mycorrhizal fungus

Introduction

The hyphosphere of arbuscular mycorrhizal (AM) fungi is teeming with microbial life. Yet, the influence of nutrient availability or nutrient forms on the hyphosphere microbiomes is still poorly understood.

Methods

Here, we examined how the microbial community (prokaryotic, fungal, protistan) was affected by the presence of the AM fungus Rhizophagus irregularis in the rhizosphere and the root-free zone, and how different nitrogen (N) and phosphorus (P) supplements into the root-free compartment influenced the communities.

Results

The presence of AM fungus greatly affected microbial communities both in the rhizosphere and the root-free zone, with prokaryotic communities being affected the most. Protists were the only group of microbes whose richness and diversity were significantly reduced by the presence of the AM fungus. Our results showed that the type of nutrients AM fungi encounter in localized patches modulate the structure of hyphosphere microbial communities. In contrast we did not observe any effects of the AM fungus on (non-mycorrhizal) fungal community composition. Compared to the non-mycorrhizal control, the root-free zone with the AM fungus (i.e., the AM fungal hyphosphere) was enriched with Alphaproteobacteria, some micropredatory and copiotroph bacterial taxa (e.g., Xanthomonadaceae and Bacteroidota), and the poorly characterized and not yet cultured Acidobacteriota subgroup GP17, especially when phytate was added. Ammonia-oxidizing Nitrosomonas and nitrite-oxidizing Nitrospira were significantly suppressed in the presence of the AM fungus in the root-free compartment, especially upon addition of inorganic N. Co-occurrence network analyses revealed that microbial communities in the root-free compartment were complex and interconnected with more keystone species when AM fungus was present, especially when the root-free compartment was amended with phytate.

Conclusion

Our study showed that the form of nutrients is an important driver of prokaryotic and eukaryotic community assembly in the AM fungal hyphosphere, despite the assumed presence of a stable and specific AM fungal hyphoplane microbiome. Predictable responses of specific microbial taxa will open the possibility of using them as co-inoculants with AM fungi, e.g., to improve crop performance.

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.

Arbuscular mycorrhizal fungi enhance plant phosphorus uptake through stimulating hyphosphere soil microbiome functional profiles for phosphorus turnover

The extraradical hyphae of arbuscular mycorrhizal (AM) fungi are colonized by different bacteria in natural and agricultural systems, but the mechanisms by which AM fungi interact with the hyphosphere soil microbiome and influence soil organic phosphorus (P) mobilization remain unclear. We grew Medicago in two-compartment microcosms, inoculated with Rhizophagus irregularis, or not, in the root compartment and set up P treatments (without P, with P addition as KH₂ PO₄ or nonsoluble phytate) in the hyphal compartment. We studied the processes of soil P turnover and characterized the microbiome functional profiles for P turnover in the hyphosphere soil by metagenomic sequencing. Compared with the bulk soil, the hyphosphere soil of R. irregularis was inhabited by a specific bacterial community and their functional profiles for P turnover was stimulated. At the species level, the shift in hyphosphere soil microbiome was characterized by the recruitment of the genome bin2.39 harbouring both gcd and phoD genes and genome bin2.97 harbouring the phoD gene, which synergistically drove nonsoluble phytate mobilization in the hyphosphere soil. Our results suggest that AM fungi recruits a specific hyphosphere soil microbiome and stimulated their functional profiles for P turnover to enhance utilization of phytate.

Effects of different fertilization methods on Lolium multiflorum Lam. growth and bacterial community in waste slag

Waste slag has low nutrient content, so it has insufficient nutrient cycling and transformation in the soil ecosystem. There are few studies on the application of oligotrophic phosphate-solubilizing bacteria and phosphate (P) fertilizer to improve the properties of waste slags. In this study, three oligotrophic bacterial strains with P solubilizing activity, namely, Bacillus subtilis 2C (7.23 μg/mL), Bacillus subtilis 6C (4.07 μg/mL), and Bacillus safensis 2N (5.05 μg/mL), were isolated from waste slags. In the pot experiment, compared with no application of P fertilizer, inoculation of Bacillus subtilis 2C with a 50% recommended dose of P fertilizer significantly increased the available phosphorus (AP), total phosphorus (TP), and total nitrogen (TN) in slag by 33.16%, 76.70%, and 233.33%, respectively. The N, P uptake and fresh weight of Lolium multiflorum Lam. were significantly improved by 114.15%, 139.02%, and 100%, respectively. The analysis of the bacterial community showed that the application of P fertilizer decreased the diversity and richness of the bacterial community, and with the addition of phosphorus fertilizer and Bacillus subtilis 2C, the bacterial community in the slag developed towards eutrophication. Redundancy analysis (RDA) showed that the TP content in the slag was significantly correlated with the bacterial community (P = 0.001, < 0.01), followed by the TN content. This study on different P fertilizer application methods can provide some basic ideas for improving the performance of waste slag.

A core microbiome in the hyphosphere of arbuscular mycorrhizal fungi has functional significance in organic phosphorus mineralization

The mycorrhizal pathway is an important phosphorus (P) uptake pathway for more than two-thirds of land plants. The arbuscular mycorrhizal (AM) fungi-associated hyphosphere microbiome has been considered as the second genome of mycorrhizal P uptake pathway and functionality in mobilizing soil organic P (Po). However, whether there is a core microbiome in the hyphosphere and how this is implicated in mining soil Po are less understood. We established on-site field trials located in humid, semiarid, and arid zones and a microcosm experiment in a glasshouse with specific AM fungi and varying soil types to answer the above questions. The hyphosphere microbiome of AM fungi enhanced soil phosphatase activity and promoted Po mineralization in all sites. Although the assemblage of hyphosphere microbiomes identified in three climate zones was mediated by environmental factors, we detected a core set in three sites and the subsequent microcosm experiment. The core members were co-enriched in the hyphosphere and dominated by Alphaproteobacteria, Actinobacteria, and Gammaproteobacteria. Moreover, these core bacterial members aggregate into stable guilds that contributed to phosphatase activity. The core hyphosphere microbiome is taxonomically conserved and provides functions, with respect to the mineralization of Po, that AM fungi lack.

Responses of Bacterial Community Structure, Diversity, and Chemical Properties in the Rhizosphere Soil on Fruiting-Body Formation of Suillus luteus

Mycorrhiza helper bacteria (MHB) play an important role in driving mycorrhizal formation. There are few reports on the relationship between bacteria and fruiting growths. Taking mycorrhizal rhizosphere soil from sporocarps of the S. luteus and non-mycorrhizal rhizosphere soil of the host plant (Larix gmelinii), we measured the bacterial community structure and diversity and chemical properties to clarify the effect of bacteria on fruiting-body formation. The bacterial diversity was significantly higher in mycorrhizal rhizosphere soil (p < 0.05) than that in non-mycorrhizal rhizosphere soil. The relative abundance of Burkholderia, Bradyrhizobium, Pseudomonas, and Rhizobium was significantly higher (p < 0.05) in mycorrhizal rhizosphere soil than in non-mycorrhizal rhizosphere soil. The soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), total potassium (TK), ammonium nitrogen (AN), available phosphorus (AP), available potassium (AK), and the activity of catalase, urease, and phosphatase in mycorrhizal rhizosphere soil were significantly higher (p < 0.05) than those in non-mycorrhizal rhizosphere soil. A redundancy analysis (RDA) showed that dominant bacteria are closely related to soil enzyme activity and physicochemical properties (p < 0.05). The boletus recruits a large number of bacteria around the plant roots that speed up nutrient transformation and increase the soil nutrient content, providing an important guarantee for mycelium culture and fruiting-body formation. These findings provide ideas for the nutritional supply of boletus sporocarps and lay the theoretical foundation for the efficient artificial cultivation of boletus.

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.

Arbuscular mycorrhizal fungi conducting the hyphosphere bacterial orchestra

More than two-thirds of terrestrial plants acquire nutrients by forming a symbiosis with arbuscular mycorrhizal (AM) fungi. AM fungal hyphae recruit distinct microbes into their hyphosphere, the narrow region of soil influenced by hyphal exudates. They thereby shape this so-called second genome of AM fungi, which significantly contributes to nutrient mobilization and turnover. We summarize current insights into characteristics of the hyphosphere microbiome and the role of hyphal exudates on orchestrating its composition. The hyphal exudates not only contain carbon-rich compounds but also promote bacterial growth and activity and influence the microbial community structure. These effects lead to shifts in function and cause changes in organic nutrient cycling, making the hyphosphere a unique and largely overlooked functional zone in ecosystems.

Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization

Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.

Benefits of phosphate solubilizing bacteria on belowground crop performance for improved crop acquisition of phosphorus

Although research on plant growth promoting bacteria began in the 1950s, basic and applied research on bacteria improving use of phosphorus (P) continues to be a priority among many agricultural research institutions. Ultimately, identifying agriculturally beneficial microbes, notably P solubilizing bacteria (PSB), that enhance the efficient use of P supports more sustainable cropping systems and the judicious use of mineral nutrients. In parallel, there is more attention on improving crop root P acquisition of existing soil P pools as well as by increasing the proportion of fertilizer P that is taken up by crops. Today, new lines of research are emerging to investigate the co-optimization of PSB-fertilizer-crop root processes for improved P efficiency and agricultural performance. In this review, we compile and summarize available findings on the beneficial effects of PSB on crop production with a focus on crop P acquisition via root system responses at the structural, functional and transcriptional levels. We discuss the current state of knowledge on the mechanisms of PSB-mediated P availability, both soil- and root-associated, as well as crop uptake via P solubilization, mineralization and mobilization, mainly through the production of organic acids and P-hydrolyzing enzymes, and effects on phytohormone signaling for crop root developement. The systematic changes caused by PSB on crop roots are discussed and contextualized within promising functional trait-based frameworks. We also detail agronomic profitability of P (mineral and organic) and PSB co-application, in amended soils and inoculated crops, establishing the connection between the influence of PSB on agroecosystem production and the impact of P fertilization on microbial diversity and crop functional traits for P acquisition.

Different Arbuscular Mycorrhizal Fungi Cocolonizing on a Single Plant Root System Recruit Distinct Microbiomes

Plant roots are usually colonized by various arbuscular mycorrhizal (AM) fungal species, which vary in morphological, physiological, and genetic traits. This colonization constitutes the mycorrhizal nutrient uptake pathway (MP) and supplements the pathway through roots. Simultaneously, the extraradical hyphae of each AM fungus is associated with a community of bacteria. However, whether the community structure and function of the microbiome on the extraradical hyphae differ between AM fungal species remains unknown. In order to understand the community structure and the predicted functions of the microbiome associated with different AM fungal species, a split-root compartmented rhizobox cultivation system, which allowed us to inoculate two AM fungal species separately in two root compartments, was used. We inoculated two separate AM fungal species combinations, (i) Funneliformis mosseae and Gigaspora margarita and (ii) Rhizophagus intraradices and G. margarita, on a single root system of cotton. The hyphal exudate-fed, active microbiome was measured by combining 13C-DNA stable isotope probing with MiSeq sequencing. We found that different AM fungal species, which were simultaneously colonizing a single root system, hosted active microbiomes that were distinct from one another. Moreover, the predicted potential functions of the different microbiomes were distinct. We conclude that the arbuscular mycorrhizal fungal component of the system is responsible for the recruitment of distinct microbiomes in the hyphosphere. The potential significance of the predicted functions of the microbial ecosystem services is discussed.IMPORTANCE Arbuscular mycorrhizal (AM) fungi form tight symbiotic relationships with the majority of terrestrial plants and play critical roles in plant P acquisition, adding a further dimension of complexity. The plant-AM fungus-bacterium system is considered a continuum, with the bacteria colonizing not only the plant roots, but also the associated mycorrhizal hyphal network, known as the hyphosphere microbiome. Plant roots are usually colonized by different AM fungal species which form an independent phosphorus uptake pathway from the root pathway, i.e., the mycorrhizal pathway. The community structure and function of the hyphosphere microbiome of different AM species are completely unknown. In this novel study, we found that arbuscular mycorrhizal fungi cocolonizing on single plant roots recruit their own specific microbiomes, which should be considered in evaluating plant microbiome form and function. Our findings demonstrate the importance of understanding trophic interactions in order to gain insight into the plant-AM fungus-bacterium symbiosis.