Organic nitrogen utilisation by an arbuscular mycorrhizal fungus is mediated by specific soil bacteria and a protist

Unraveling the diversity of hyphal explorative traits among Rhizophagus irregularis genotypes

Differences in functioning among various genotypes of arbuscular mycorrhizal (AM) fungi can determine their fitness under specific environmental conditions, although knowledge of the underlying mechanisms still is very fragmented. Here we compared seven homokaryotic isolates (genotypes) of Rhizophagus irregularis, aiming to characterize the range of intraspecific variability with respect to hyphal exploration of organic nitrogen (N) resources, and N supply to plants. To this end we established two experiments (one in vitro and one in open pots) and used 15N-chitin as the isotopically labeled organic N source. In Experiment 1 (in vitro), mycelium of all AM fungal genotypes transferred a higher amount of 15N to the plants than the passive transfer of 15N measured in the non-mycorrhizal (NM) controls. Noticeably, certain genotypes (e.g., LPA9) showed higher extraradical mycelium biomass production but not necessarily greater 15N acquisition than the others. Experiment 2 (in pots) highlighted that some of the AM fungal genotypes (e.g., MA2, STSI) exhibited higher rates of targeted hyphal exploration of chitin-enriched zones, indicative of distinct N exploration patterns from the other genotypes. Importantly, there was a high congruence of hyphal exploration patterns between the two experiments (isolate STSI always showing highest efficiency of hyphal exploration and isolate L23/1 being consistently the lowest), despite very different (micro) environmental conditions in the two experiments. This study suggests possible strategies that AM fungal genotypes employ for efficient N acquisition, and how to measure them. Implications of such traits for local mycorrhizal community assembly still need to be understood.

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.

Soil organic matter dynamics mediated by arbuscular mycorrhizal fungi - an updated conceptual framework

Arbuscular mycorrhizal (AM) fungi play an important role in soil organic matter (SOM) formation and stabilization. Previous studies have emphasized organic compounds produced by AM fungi as persistent binding agents for aggregate formation and SOM storage. This concept overlooks the multiple biogeochemical processes mediated by AM fungal activities, which drive SOM generation, reprocessing, reorganization, and stabilization. Here, we propose an updated conceptual framework to facilitate a mechanistic understanding of the role of AM fungi in SOM dynamics. In this framework, four pathways for AM fungi-mediated SOM dynamics are included: 'Generating', AM fungal exudates and biomass serve as key sources of SOM chemodiversity; 'Reprocessing', hyphosphere microorganisms drive SOM decomposition and resynthesis; 'Reorganizing', AM fungi mediate soil physical changes and influence SOM transport, redistribution, transformation, and storage; and 'Stabilizing', AM fungi drive mineral weathering and organo-mineral interactions for SOM stabilization. Moreover, we discuss the AM fungal role in SOM dynamics at different scales, especially when translating results from small scales to complex larger scales. We believe that working with this conceptual framework can allow a better understanding of AM fungal role in SOM dynamics, therefore facilitating the development of mycorrhiza-based technologies toward soil health and global change mitigation.

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.

Concepts and consequences of the hyphosphere core microbiome for arbuscular mycorrhizal fungal fitness and function

Arbuscular mycorrhizal (AM) fungi-associated hyphosphere microbiomes can be considered as the second genome of the mycorrhizal phosphorus uptake pathway. Their composition can be thought of as a stably recurring component of a holobiont, defined by the hyphosphere core microbiome, which is thought to benefit AM fungal fitness. Here, we review evidence indicating the existence of the hyphosphere core microbiome, highlight its functions linked to those functions lacking in AM fungi, and further explore the mechanisms by which different core members ensure their stable coexistence. We conclude that deciphering and utilizing the hyphosphere core microbiome provides an entry point for understanding the complex interactions among plants, AM fungi, and bacteria.

The potential of arbuscular mycorrhizal fungi to enhance metallic micronutrient uptake and mitigate food contamination in agriculture: prospects and challenges

Optimizing agroecosystems and crops for micronutrient uptake while reducing issues with inorganic contaminants (metal(loid)s) is a challenging task. One promising approach is to use arbuscular mycorrhizal fungi (AMF) and investigate the physiological, molecular and epigenetic changes that occur in their presence and that lead to changes in plant metal(loid) concentration (biofortification of micronutrients or mitigation of contaminants). Moreover, it is important to understand these mechanisms in the context of the soil microbiome, particularly those interactions of AMF with other soil microbes that can further shape crop nutrition. To address these challenges, a two-pronged approach is recommended: exploring molecular mechanisms and investigating microbiome management and engineering. Combining both approaches can lead to benefits in human health by balancing nutrition and contamination caused by metal(loid)s in the agro-ecosystem.

Arbuscular Mycorrhizal Fungus Alleviates Charged Nanoplastic Stress in Host Plants via Enhanced Defense-Related Gene Expressions and Hyphal Capture

Contamination of small-sized plastics is recognized as a factor of global change. Nanoplastics (NPs) can readily enter organisms and pose significant ecological risks. Arbuscular mycorrhizal (AM) fungi are the most ubiquitous and impactful plant symbiotic fungi, regulating essential ecological functions. Here, we first found that an AM fungus, Rhizophagus irregularis, increased lettuce shoot biomass by 25-100% when exposed to positively and negatively charged NPs vs control, although it did not increase that grown without NPs. The stress alleviation was attributed to the upregulation of gene expressions involving phytohormone signaling, cell wall metabolism, and oxidant scavenging. Using a root organ-fungus axenic growth system treated with fluorescence-labeled NPs, we subsequently revealed that the hyphae captured NPs and further delivered them to roots. NPs were observed at the hyphal cell walls, membranes, and spore walls. NPs mediated by the hyphae were localized at the root epidermis, cortex, and stele. Hyphal exudates aggregated positively charged NPs, thereby reducing their uptake due to NP aggregate formation (up to 5000 nm). This work demonstrates the critical roles of AM fungus in regulating NP behaviors and provides a potential strategy for NP risk mitigation in terrestrial ecosystems. Consequent NP-induced ecological impacts due to the affected AM fungi require further attention.

Impacts of Arbuscular Mycorrhizal Fungi on Metabolites of an Invasive Weed Wedelia trilobata

The invasive plant Wedelia trilobata benefits in various aspects, such as nutrient absorption and environmental adaptability, by establishing a close symbiotic relationship with arbuscular mycorrhizal fungi (AMF). However, our understanding of whether AMF can benefit W. trilobata by influencing its metabolic profile remains limited. In this study, Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was conducted to analyze the metabolites of W. trilobata under AMF inoculation. Metabolomic analysis identified 119 differentially expressed metabolites (DEMs) between the groups inoculated with AMF and those not inoculated with AMF. Compared to plants with no AMF inoculation, plants inoculated with AMF showed upregulation in the relative expression of 69 metabolites and downregulation in the relative expression of 50 metabolites. AMF significantly increased levels of various primary and secondary metabolites in plants, including amino acids, organic acids, plant hormones, flavonoids, and others, with amino acids being the most abundant among the identified substances. The identified DEMs mapped 53 metabolic pathways, with 7 pathways strongly influenced by AMF, particularly the phenylalanine metabolism pathway. Moreover, we also observed a high colonization level of AMF in the roots of W. trilobata, significantly promoting the shoot growth of this plant. These changes in metabolites and metabolic pathways significantly affect multiple physiological and biochemical processes in plants, such as free radical scavenging, osmotic regulation, cell structure stability, and material synthesis. In summary, AMF reprogrammed the metabolic pathways of W. trilobata, leading to changes in both primary and secondary metabolomes, thereby benefiting the growth of W. trilobata and enhancing its ability to respond to various biotic and abiotic stressors. These findings elucidate the molecular regulatory role of AMF in the invasive plant W. trilobata and provide new insights into the study of its competitive and stress resistance mechanisms.

Microbial community interactions determine the mineralization of soil organic phosphorus in subtropical forest ecosystems

In subtropical forest ecosystems with few phosphorus (P) inputs, P availability and forest productivity depend on soil organic P (Po) mineralization. However, the mechanisms by which the microbial community determines the status and fate of soil Po mineralization remain unclear. In the present study, soils were collected from three typical forest types: secondary natural forest (SNF), mixed planting, and monoculture forest of Chinese fir. The P fractions, Po-mineralization ability, and microbial community in the soils of different forest types were characterized. In addition, we defined Po-mineralizing taxa with the potential to interact with the soil microbial community to regulate Po mineralization. We found that a higher labile P content persisted in SNF and was positively associated with the Po-mineralization capacity of the soil microbial community. In vitro cultures of soil suspensions revealed that soil Po mineralization of three forest types was distinguished by differences in the composition of fungal communities. We further identified broad phylogenetic lineages of Po-mineralizing fungi with a high intensity of positive interactions with the soil microbial community, implying that the facilitation of Po-mineralizing taxa is crucial for soil P availability. Our dilution experiments to weaken microbial interactions revealed that in SNF soil, which had the highest interaction intensity of Po-mineralizing taxa with the community, Po-mineralization capacity was irreversibly lost after dilution, highlighting the importance of microbial diversity protection in forest soils. In summary, this study demonstrates that the interactions of Po-mineralizing microorganisms with the soil microbial community are critical for P availability in subtropical forests.IMPORTANCEIn subtropical forest ecosystems with few phosphorus inputs, phosphorus availability and forest productivity depend on soil organic phosphorus mineralization. However, the mechanisms by which the microbial community interactions determine the mineralization of soil organic phosphorus remain unclear. In the present study, soils were collected from three typical forest types: secondary natural forest, mixed planting, and monoculture forest of Chinese fir. We found that a higher soil labile phosphorus content was positively associated with the organic phosphorus mineralization capacity of the soil microbial community. Soil organic phosphorus mineralization of three forest types was distinguished by the differences in the composition of fungal communities. The positive interactions between organic phosphorus-mineralizing fungi and the rest of the soil microbial community facilitated organic phosphorus mineralization. This study highlights the importance of microbial diversity protection in forest soils and reveals the microbial mechanism of phosphorus availability maintenance in subtropical forest ecosystems.

Tropical tree ectomycorrhiza are distributed independently of soil nutrients

Mycorrhizae, a form of plant-fungal symbioses, mediate vegetation impacts on ecosystem functioning. Climatic effects on decomposition and soil quality are suggested to drive mycorrhizal distributions, with arbuscular mycorrhizal plants prevailing in low-latitude/high-soil-quality areas and ectomycorrhizal (EcM) plants in high-latitude/low-soil-quality areas. However, these generalizations, based on coarse-resolution data, obscure finer-scale variations and result in high uncertainties in the predicted distributions of mycorrhizal types and their drivers. Using data from 31 lowland tropical forests, both at a coarse scale (mean-plot-level data) and fine scale (20 × 20 metres from a subset of 16 sites), we demonstrate that the distribution and abundance of EcM-associated trees are independent of soil quality. Resource exchange differences among mycorrhizal partners, stemming from diverse evolutionary origins of mycorrhizal fungi, may decouple soil fertility from the advantage provided by mycorrhizal associations. Additionally, distinct historical biogeographies and diversification patterns have led to differences in forest composition and nutrient-acquisition strategies across three major tropical regions. Notably, Africa and Asia's lowland tropical forests have abundant EcM trees, whereas they are relatively scarce in lowland neotropical forests. A greater understanding of the functional biology of mycorrhizal symbiosis is required, especially in the lowland tropics, to overcome biases from assuming similarity to temperate and boreal regions.

Arbuscular mycorrhizal fungi suppress ammonia-oxidizing bacteria but not archaea across agricultural soils

Arbuscular mycorrhizal (AM) fungi are supposedly competing with ammonia-oxidizing microorganisms (AO) for soil nitrogen in form of ammonium. Despite a few studies directly addressing AM fungal and AO interactions, mostly in artificial cultivation substrates, it is not yet clear whether AM fungi can effectively suppress AO in field soils containing complex indigenous microbiomes. To fill this knowledge gap, we conducted compartmentalized pot experiments using four pairs of cropland and grassland soils with varying physicochemical properties. To exclude the interference of roots, a fine nylon mesh was used to separate the rhizosphere and mesh bags, with the latter being filled with unsterile field soils. Inoculation of plants with AM fungus Rhizophagus irregularis LPA9 suppressed AO bacteria (AOB) but not archaea (AOA) in the soils, indicating how soil nitrification could be suppressed by AM fungal presence/activity. In addition, in rhizosphere filled with artificial substrate, AM inoculation did suppress both AOB and AOA, implying more complex interactions between roots, AO, and AM fungi. Besides, we also observed that indigenous AM fungi contained in the field soils eventually did colonize the roots of plants behind the root barrier, and that the extent of such colonization was higher if the soil has previously been taken from cropland than from grassland. Despite this, the effect of experimental AM fungal inoculation on suppression of indigenous AOB in the unsterile field soils did not vanish. It seems that studying processes at a finer temporal scale, using larger buffer zones between rhizosphere and mesh bags, and/or detailed characterization of indigenous AM fungal and AO communities would be needed to uncover further details of the biotic interactions between the AM fungi and indigenous soil AO.

Unveiling the crucial role of soil microorganisms in carbon cycling: A review

Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.

The addition of discrimination inhibitors stimulations discrimination potential and N2O emissions were linked to predation among microorganisms in long term nitrogen application and straw returning systems

Introduction

Ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) have been proven to be key microorganisms driving the ammonia oxidation process. However, under different fertilization practices, there is a lack of research on the impact of interaction between predators and AOA or AOB on nitrogen cycling at the multi-trophic level.

Methods

In this study, a network-oriented microscopic culture experiment was established based on four different long-term fertilization practices soils. We used the nitrification inhibitors 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxide-3-oxyl (PTIO) and 3, 4-Dimethylpyrazole phosphate (DMPP) inhibited AOA and AOB, respectively, to explore the impact of interaction between protists and AOA or AOB on nitrogen transformation.

Results

The results showed that long-term nitrogen application promoted the potential nitrification rate (PNR) and nitrous oxide (N2O) emission, and significantly increased the gene abundance of AOB, but had no obvious effect on AOA gene abundance. DMPP significantly reduced N2O emission and PNR, while PTIO had no obvious effect on them. Accordingly, in the multi-trophic microbial network, Cercozoa and Proteobacteria were identified as keystone taxa of protists and AOB, respectively, and were significantly positively correlated with N2O, PNR and nitrate nitrogen. However, Nitrososphaerota archaeon as the keystone species of AOA, had an obvious negative linkage to these indicators. The structural equation model (SEM) showed that AOA and AOB may be competitors to each other. Protists may promote AOB diversity through direct trophic interaction with AOA.

Conclusion

The interaction pattern between protists and ammonia-oxidizing microorganisms significantly affects potential nitrification rate and N2O emission, which has important implications for soil nitrogen cycle.

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.

Soil organic carbon loss decreases biodiversity but stimulates multitrophic interactions that promote belowground metabolism

Soil organic carbon (SOC) plays an essential role in mediating community structure and metabolic activities of belowground biota. Unraveling the evolution of belowground communities and their feedback mechanisms on SOC dynamics helps embed the ecology of soil microbiome into carbon cycling, which serves to improve biodiversity conservation and carbon management strategy under global change. Here, croplands with a SOC gradient were used to understand how belowground metabolisms and SOC decomposition were linked to the diversity, composition, and co-occurrence networks of belowground communities encompassing archaea, bacteria, fungi, protists, and invertebrates. As SOC decreased, the diversity of prokaryotes and eukaryotes also decreased, but their network complexity showed contrasting patterns: prokaryotes increased due to intensified niche overlap, while that of eukaryotes decreased possibly because of greater dispersal limitation owing to the breakdown of macroaggregates. Despite the decrease in biodiversity and SOC stocks, the belowground metabolic capacity was enhanced as indicated by increased enzyme activity and decreased enzymatic stoichiometric imbalance. This could, in turn, expedite carbon loss through respiration, particularly in the slow-cycling pool. The enhanced belowground metabolic capacity was dominantly driven by greater multitrophic network complexity and particularly negative (competitive and predator-prey) associations, which fostered the stability of the belowground metacommunity. Interestingly, soil abiotic conditions including pH, aeration, and nutrient stocks, exhibited a less significant role. Overall, this study reveals a greater need for soil C resources across multitrophic levels to maintain metabolic functionality as declining SOC results in biodiversity loss. Our researchers highlight the importance of integrating belowground biological processes into models of SOC turnover, to improve agroecosystem functioning and carbon management in face of intensifying anthropogenic land-use and climate change.

An improved method for extraction of soil fungal mycelium

Fungal mycelium is a major component of the soil microbiome. The soil hyphosphere represents a complex and dynamic niche for specific microorganisms, where multitrophic interactions occur, affecting ecosystem processes. However, extracting fungal mycelium from the soil to enable its taxonomical, chemical, and structural characterisation is challenging in the absence of a fast, efficient, and low-cost procedure. In this study, an old method (Bingle and Paul 1985), based on successive soil wet filtrations and density gradient centrifugation, was improved and tested in three different soil types (silty clay, silty clay loam, and loamy sand). The improved method reduced the number of filtrations by about five times and the centrifugation time from 40 min to 1 min. It avoided using any chemical substance which may impair further chemical analyses or DNA isolation and amplification. The method efficiency was about 50 % in the clay and 23 % in the sandy soils. However, a pre-step consisting of removing the fine-root fragments and other debris under the stereomicroscope may increase the method efficiency to more than 65 %, independent of the soil type.•A simple, efficient, and low-cost method suitable for extracting soil mycelium from a large number of samples.•The protocol includes successive soil wet filtrations and sucrose gradient centrifugation.•The method efficiency increases if the fine-root fragments and other debris are previously removed from the soil.

Unrevealing the potential of microbes in decomposition of organic matter and release of carbon in the ecosystem

Organic matter decomposition is a biochemical process with consequences affecting climate change and ecosystem productivity. Once decomposition begins, C is lost as CO2 or sequestered into more recalcitrant carbon difficult to further degradation. As microbial respiration releases carbon dioxide into the atmosphere, microbes act as gatekeepers in the whole process. Microbial activities were found to be the second largest CO2 emission source in the environment after human activities (industrialization), and research investigations suggest that this may have affected climate change over the past few decades. It is crucial to note that microbes are major contributors in the whole C cycle (decomposition, transformation, and stabilization). Therefore, imbalances in the C cycle might be causing changes in the entire carbon content of the ecosystem. The significance of microbes, especially soil bacteria in the terrestrial carbon cycle requires more attention. This review focuses on the factors that affect microorganism behavior during the breakdown of organic materials. The key factors affecting the microbial degradation processes are the quality of the input material, nitrogen, temperature, and moisture content. In this review, we suggest that to address global climate change and its effects on agricultural systems and vice versa, there is a need to double-up on efforts and conduct new research studies to further evaluate the potential of microbial communities to reduce their contribution to terrestrial carbon emission.

Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil

Anthropogenic nitrogen inputs lead to a high ammonium (NH4+)/nitrate (NO3-) ratio in the soil, which restricts hyphal spreading of soil fungi. Access of symbiotic fungi to roots is a prerequisite for plant-fungal interactions. Hyphosphere bacteria protect fungi from environmental stress, yet the impact of hyphosphere bacteria on adaptation of host fungi to NH4+-enriched conditions remains unclear. By developing soil microcosm assays, we report that a plant-symbiotic fungus, Phomopsis liquidambaris, harbors specific hyphosphere bacteria that facilitate hyphal spreading and assist in the root colonization in NH4+-enriched soil. Genetic manipulation, 16S rRNA gene analysis and coinoculation assays revealed that the genus Enterobacter was enriched in the hyphosphere of NH4+-sensitive wild-type compared to NH4+-preferring nitrite reductase-deficient strain. The representative Enterobacter sp. SZ2-promoted hyphal spreading is only evident in nonsterilized soil. We further identified an increased abundance and diversity of ammonia-oxidizing archaea (AOA) and a synchronously decreased NH4+:NO3- ratio following SZ2 inoculation. Microbial supplementation and inhibitor assays showed that AOA-mediated reduction in NH4+:NO3- ratio is responsible for SZ2-enhanced fungal adaptation to NH4+-enriched conditions. The Ph. liquidambaris-Enterobacter-AOA triple interaction promoted rice growth in NH4+-enriched soil. Our study reveals the essential role of hyphosphere microorganism-based hyphal spreading in plant-fungal symbiosis establishment within nitrogen-affected agroecosystems.

Old-growth Acer macrophyllum trees host a unique suite of arbuscular mycorrhizal fungi and other root-associated fungal taxa in their canopy soil environment

Canopy soils occur on tree branches throughout the temperate rainforests of the Pacific Northwest Coast and are recognized as a defining characteristic of these ecosystems. Certain tree species extend adventitious roots into these canopy soil environments. Yet, research on adventitious root-associated fungi remains limited. Our study used microscopy to compare fungal colonization intensity between canopy and forest floor roots of old-growth bigleaf maple (Acer macrophyllum) trees. Subsequently, two high-throughput sequencing platforms were used to explore the spatial and seasonal variation of root-associated fungi between the two soil environments over one year. We found that canopy and forest floor roots had similar colonization intensity and were associating with a diversity of arbuscular mycorrhizal fungi and other potential symbionts, many of which were resolved to species level. Soil environment and seasonality affected root-associated fungal community composition, and several fungal species were indicative of the canopy soil environment. In Washington State's (USA) temperate old-growth rainforests, these canopy soil environments host a unique suite of root-associated fungi. The presence of arbuscular mycorrhizae provides further evidence that adventitious roots form fungal associations to exploit canopy soils for resources, and there may be novel relationships forming with other fungi. These soils may be providing a redundancy compartment (i.e., "nutrient reserve"), imparting a resiliency to disturbances for certain old-growth trees.

Straw amendment and nitrification inhibitor controlling N losses and immobilization in a soil cooling-warming experiment

It is common practice in agriculture to apply high‑carbon amendments, e.g. straw, or nitrification inhibitors (NI) to reduce soil nitrogen (N) losses. However, little is known on the combined effects of straw and NI and how seasonal soil temperature variations further affect N immobilization. We conducted a 113-day mesocosm experiment with different levels of ¹⁵N-fertilizer application (N0: control; N1: 125 kg N ha^-1; N2: 250 kg N ha^-1) in an agricultural soil, amended with either wheat straw, NI or a combination of both in order to investigate N retention and loss from soil after a cooling-warming phase simulating a seasonal temperature shift, i.e., 30 days cooling phase at 7 °C and 10 days warming phase at 21 °C. Subsequently, soils were planted with barley as phytometers to study ¹⁵N-transfer to a following crop. Straw addition significantly reduced soil N-losses due to microbial N immobilization. Although carbon added as straw led to increased N₂O emissions at high N fertilization, this was partly counterbalanced by NI. Soil cooling-warming strongly increased ammonification (+77 %), while nitrification was suppressed, and straw-induced microbial N immobilization dominated. N immobilized after straw addition was mineralized at the end of the experiment as indicated by structural equation models. Re-mineralization in N2 was sufficient, but still suboptimal in N0 and N1 at critical times of early barley growth. N-use efficiency of the ¹⁵N tracer decreased with fertilization intensity from 50 % in N1 to 35 % in N2, and straw amendment reduced NUE to 25 % at both fertilization rates. Straw amendment was most powerful in reducing N-losses (-41 %), in particular under variable soil temperature conditions, but NI enforced its effects by reducing N₂O emission (-40 %) in N2 treatment. Sufficient N-fertilization coupled with straw application is required to adjust the timely re-mineralization of N for subsequent crops.

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.

Direct nitrogen, phosphorus and carbon exchanges between Mucoromycotina 'fine root endophyte' fungi and a flowering plant in novel monoxenic cultures

Most plants form mycorrhizal associations with mutualistic soil fungi. Through these partnerships, resources are exchanged including photosynthetically fixed carbon for fungal-acquired nutrients. Recently, it was shown that the diversity of associated fungi is greater than previously assumed, extending to Mucoromycotina fungi. These Mucoromycotina 'fine root endophytes' (MFRE) are widespread and generally co-colonise plant roots together with Glomeromycotina 'coarse' arbuscular mycorrhizal fungi (AMF). Until now, this co-occurrence has hindered the determination of the direct function of MFRE symbiosis. To overcome this major barrier, we developed new techniques for fungal isolation and culture and established the first monoxenic in vitro cultures of MFRE colonising a flowering plant, clover. Using radio- and stable-isotope tracers in these in vitro systems, we measured the transfer of 33 P, 15 N and 14 C between MFRE hyphae and the host plant. Our results provide the first unequivocal evidence that MFRE fungi are nutritional mutualists with a flowering plant by showing that clover gained both 15 N and 33 P tracers directly from fungus in exchange for plant-fixed C in the absence of other micro-organisms. Our findings and methods pave the way for a new era in mycorrhizal research, firmly establishing MFRE as both mycorrhizal and functionally important in terrestrial ecosystems.

Knowns and unknowns of the soil fungal necrobiome

Dead microbial cells, commonly referred to as necromass, are increasingly recognized as an important source of both persistent carbon as well as nutrient availability in soils. Studies of the microbial communities associated with decomposing fungal necromass have accumulated rapidly in recent years across a range of different terrestrial ecosystems. Here we identify the primary ecological patterns regarding the structure and dynamics of the fungal necrobiome as well as highlight new research frontiers that will likely be key to gaining a full understanding of fungal necrobiome composition and its associated role in soil biogeochemical cycling. Because many members of the fungal necrobiome are culturable, combining laboratory functional assays with field-based surveys and experiments will allow ongoing studies of the fungal necrobiome to move from largely descriptive to increasingly predictive.

Hyphosphere interactions between Rhizophagus irregularis and Rahnella aquatilis promote carbon-phosphorus exchange at the peri-arbuscular space in Medicago truncatula

Arbuscular mycorrhizal (AM) fungi form a continuum between roots and soil. One end of this continuum is comprised of the highly intimate plant-fungus interface with intracellular organelles for nutrient exchange, while on the other end the fungus interacts with bacteria to compensate for the AM fungus' inability to take up organic nutrients from soil. How both interfaces communicate in this highly complex tripartite mutualism is widely unknown. Here, the effects of phosphate-solubilizing bacteria (PSB) Rahnella aquatilis dwelling at the surface of the extraradical hyphae of Rhizophagus irregularis was analysed based on the expression of genes involved in C-P exchange at the peri-arbuscular space (PAS) in Medicago truncatula. The interaction between AM fungus and PSB resulted in an increase in uptake and transport of Pi along the extraradical hyphae and its transfer from AM fungus to plant. In return, this was remunerated by a transfer of C from plant to AM fungus, improving the C-P exchange at the PAS. These results demonstrated that a microorganism (i.e., a PSB) developing at the hyphosphere interface can affect the C-P exchange at the PAS between plant and AM fungus, suggesting a fine-tuned communication operated between three organisms via two distantly connected interfaces.

A shift from inorganic to organic nitrogen-dominance shapes soil microbiome composition and co-occurrence networks

Soil microbiomes are characterized by their composition and networks, which are linked to soil nitrogen (N) availability. In nature, inorganic N dominates at one end and organic N dominates at the other end along soil N gradients; however, little is known about how this shift influences soil microbiome composition and co-occurrence networks, as well as their controls. To this end, we conducted an experiment with the host plant Solidago canadensis, which was subject to three N regimes: inorganic N-dominated, co-dominated by inorganic and organic N (CIO), and organic N-dominated. Organic N dominance exhibited stronger effects on the composition and co-occurrence networks of soil microbiomes than inorganic N dominance. The predominant control was plant traits for bacterial and fungal richness, and soil pH for keystone species. Relative to the CIO regime, inorganic N dominance did not affect fungal richness and increased keystone species; organic N dominance decreased fungal richness and keystone species. Pathogenic fungi and arbuscular mycorrhizal fungi were suppressed by organic N dominance but not by inorganic N dominance. These findings suggest that the shift from soil inorganic N-dominance to soil organic N-dominance could strongly shape soil microbiome composition and co-occurrence networks by altering species diversity and topological properties.

Arbuscular Mycorrhiza and Nitrification: Disentangling Processes and Players by Using Synthetic Nitrification Inhibitors

Both plants and their associated arbuscular mycorrhizal (AM) fungi require nitrogen (N) for their metabolism and growth. This can result in both positive and negative effects of AM symbiosis on plant N nutrition. Either way, the demand for and efficiency of uptake of mineral N from the soil by mycorrhizal plants are often higher than those of nonmycorrhizal plants. In consequence, the symbiosis of plants with AM fungi exerts important feedbacks on soil processes in general and N cycling in particular. Here, we investigated the role of the AM symbiosis in N uptake by Andropogon gerardii from an organic source (¹⁵N-labeled plant litter) that was provided beyond the direct reach of roots. In addition, we tested if pathways of ¹⁵N uptake from litter by mycorrhizal hyphae were affected by amendment with different synthetic nitrification inhibitors (dicyandiamide [DCD], nitrapyrin, or 3,4-dimethylpyrazole phosphate [DMPP]). We observed efficient acquisition of ¹⁵N by mycorrhizal plants through the mycorrhizal pathway, independent of nitrification inhibitors. These results were in stark contrast to ¹⁵N uptake by nonmycorrhizal plants, which generally took up much less ¹⁵N, and the uptake was further suppressed by nitrapyrin or DMPP amendments. Quantitative real-time PCR analyses showed that bacteria involved in the rate-limiting step of nitrification, ammonia oxidation, were suppressed similarly by the presence of AM fungi and by nitrapyrin or DMPP (but not DCD) amendments. On the other hand, abundances of ammonia-oxidizing archaea were not strongly affected by either the AM fungi or the nitrification inhibitors. IMPORTANCE Nitrogen is one of the most important elements for all life on Earth. In soil, N is present in various chemical forms and is fiercely competed for by various microorganisms as well as plants. Here, we address competition for reduced N (ammonia) between ammonia-oxidizing prokaryotes and arbuscular mycorrhizal fungi. These two functionally important groups of soil microorganisms, participating in nitrification and plant mineral nutrient acquisition, respectively, have often been studied in separation in the past. Here, we showed, using various biochemical and molecular approaches, that the fungi systematically suppress ammonia-oxidizing bacteria to an extent similar to that of some widely used synthetic nitrification inhibitors, whereas they have only a limited impact on abundance of ammonia-oxidizing archaea. Competition for free ammonium is a plausible explanation here, but it is also possible that the fungi produce some compounds acting as so-called biological nitrification inhibitors.

Separation of triacylglycerols containing positional isomers of hexadecenoic acids by enantiomeric liquid chromatography-mass spectrometry

Triacylglycerols (TAGs) containing positional isomers of hypogeic (Hy), palmitoleic (Po), and palmitvaccenic (Pv) acids from three microorganisms (top-fermenting brewer's yeast Saccharomyces cerevisiae, green alga Coccomyxa elongata, and arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis) were analyzed. Dozens of regioisomers and enantiomers of TAGs containing one, two or three hexadecenoic acids have been identified by means of reversed phase chromatography/mass spectrometry (RP-HPLC/MS). The regioisomers of TAGs containing two palmitic acids and any hexadecenoic acid were separated. Analysis of regioisomers of TAGs having one Pv residue showed that asymmetric molecular species such as PvPP or PPPv were dominant in Rhizophagus. TAGs were also analyzed on a chiral phase column and nine molecular species of TAGs containing two palmitic and any of three hexadecenoic acids were separated and identified. In the case of TAGs containing one palmitic and two hexadecenoic acids, the separation was successful only if the hexadecenoic acids were identical. Separation of TAGs containing three hexadecenoic acids was successful only if all three hexadecenoic acids were identical. Regardless of the type of TAG, it was found that TAGs in the AM fungus and containing palmitvaccenic acid bound at the sn-1 position of the glycerol backbone were dominant, suggesting similarity in the biosynthesis of the different TAGs. The covalent adduct chemical ionization method was used for identification of TAGs as adduct with (1-methyleneimino)-1-ethenyl ion, which reacted with double bond of the unsaturated fatty acid. Tandem MS thus makes it possible to identify TAGs containing various hexadecenoic acids.

Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field

Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species-level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genus-level clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere) we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere-associated clade. We extended our approach to show that closely related Cercozoa encounter divergent AM fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field-scale is driven by niche-based processes shaped by evolutionary legacy of adaptation to conditions primarily related to soil compartment, followed by soil layer, giving a deeper understanding on the selection pressures that shaped their evolution.

Track and trace: how soil labelling techniques have revealed the secrets of resource transport in the arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) fungi colonise plant roots, and by doing so forge the 'mycorrhizal uptake pathway(s)' (MUP) that provide passageways for the trade of resources across a specialised membrane at the plant-fungus interface. The transport of nutrients such as phosphorus (P), nitrogen and zinc from the fungus, and carbon from the plant, via the MUP have mostly been quantified using stable or radioactive isotope labelling of soil in a specialised hyphae-only compartment. Recent advances in the study of AM fungi have used tracing studies to better understand how the AM association will function in a changing climate, the extent to which the MUP can contribute to P uptake by important crops, and how AM fungi trade resources in interaction with plants, other AM fungi, and friend and foe in the soil microbiome. The existing work together with well-designed future experiments will provide a valuable assessment of the potential for AM fungi to play a role in the sustainability of managed and natural systems in a changing climate.

Ensuring future food security and resource sustainability: insights into the rhizosphere

Feeding the world’s growing population requires continuously increasing crop yields with less fertilizers and agrochemicals on limited land. Focusing on plant belowground traits, especially root-soil-microbe interactions, holds a great promise for overcoming this challenge. The belowground root-soil-microbe interactions are complex and involve a range of physical, chemical, and biological processes that influence nutrient-use efficiency, plant growth and health. Understanding, predicting, and manipulating these rhizosphere processes will enable us to harness the relevant interactions to improve plant productivity and nutrient-use efficiency. Here, we review the recent progress and challenges in root-soil-microbe interactions. We also highlight how root-soil-microbe interactions could be manipulated to ensure food security and resource sustainability in a changing global climate, with an emphasis on reducing our dependence on fertilizers and agrochemicals.

Multimodal correlative imaging and modelling of phosphorus uptake from soil by hyphae of mycorrhizal fungi

Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore-space, and models of AMF-enhanced P-uptake are poorly validated. We used synchrotron X-ray computed tomography to visualize mycorrhizas in soil and synchrotron X-ray fluorescence/X-ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling. We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co-locate with areas of high P and low Al, and preferentially associate with organic-type P species over Al-rich inorganic P. We discovered that AMF avoid Al-rich areas as a source of P. Sulphur-rich regions were found to be correlated with higher hyphal density and an increased organic-associated P-pool, whilst oxidized S-species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome-related. Our experimentally-validated model led to an estimate of P-uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated - a result with significant implications for the modelling of plant-soil-AMF interactions.

Microgranular fertilizer and biostimulants as alternatives to diammonium phosphate fertilizer in maize production on marshland soils in northwest Germany

The eutrophication of groundwater through widespread diammonium phosphate (DAP) fertilization and excessive farm fertilizer is one of the major problems in European agriculture. Organomineral microgranular fertilizers that have a reduced phosphorus (P) content, alone or in combination with biostimulants, offer promising alternatives to DAP fertilization. We conducted a field experiment with maize (Zea mays) on a marshland soil site in order to compare the yield increase and the phosphorus balance of DAP and microgranular fertilizer variants. P content of the soil on the study site is 3.9 g P per 100 g soil. Treatments involved a combination of two fertilizers, namely DAP or a P-reduced microgranular slow-release organomineral fertilizer (Startec) and the biostimulants mycorrhiza, humic substances and soil bacteria, applied individually or along with two of the above biostimulants. Fertilizer variants were also tested individually without additional biostimulants. One in four plots was used as a control, treated only with biogas slurry, to identify site-specific spatial variability and to implement correction factors to process raw data using standardized methods. Startec performed as well as DAP in terms of both the yield and corn cob ratio, while the P excess was lower in plots treated with Startec (av. = 4.5 kg P2O5 ha-1 ) compared to DAP (av. = 43.7 kg P2O5 ha-1 ). The latter differences are of statistical significance. Individual biostimulants and a combination of multiple biostimulants rarely resulted in significantly higher yields, with the exception of some combinations with humic substances and mycorrhiza in individual years. The influence of the climatic conditions in each of the years was higher than the influence of the biostimulants. However, average increases in yield over three years would be economically beneficial for farmers in the case of the applied humic substances product and mycorrhiza. An adequate alternative to DAP was found in the form of a P-reduced microgranular fertilizer from Startec.