Fungal Community Responses to Past and Future Atmospheric CO2 Differ by Soil Type

Rare taxa mediate microbial carbon and nutrient limitation in the rhizosphere and bulk soil under sugarcane-peanut intercropping systems

Introduction

Microbial carbon (C) and nutrient limitation exert key influences on soil organic carbon (SOC) and nutrient cycling through enzyme production for C and nutrient acquisition. However, the intercropping effects on microbial C and nutrient limitation and its driving factors between rhizosphere and bulk soil are unclear.

Methods

Therefore, we conducted a field experiment that covered sugarcane-peanut intercropping with sole sugarcane and peanut as controls and to explore microbial C and nutrient limitation based on the vector analysis of enzyme stoichiometry; in addition, microbial diversity was investigated in the rhizosphere and bulk soil. High throughput sequencing was used to analyze soil bacterial and fungal diversity through the 16S rRNA gene and internal transcribed spacer (ITS) gene at a phylum level.

Results

Our results showed that sugarcane-peanut intercropping alleviated microbial C limitation in all soils, whereas enhanced microbial phosphorus (P) limitation solely in bulk soil. Microbial P limitation was also stronger in the rhizosphere than in bulk soil. These results revealed that sugarcane-peanut intercropping and rhizosphere promoted soil P decomposition and facilitated soil nutrient cycles. The Pearson correlation results showed that microbial C limitation was primarily correlated with fungal diversity and fungal rare taxa (Rozellomycota, Chyltridiomycota, and Calcarisporiellomycota) in rhizosphere soil and was correlated with bacterial diversity and most rare taxa in bulk soil. Microbial P limitation was solely related to rare taxa (Patescibacteria and Glomeromycota) in rhizosphere soil and related to microbial diversity and most rare taxa in bulk soil. The variation partitioning analysis further indicated that microbial C and P limitation was explained by rare taxa (7%-35%) and the interactions of rare and abundant taxa (65%-93%).

Conclusion

This study indicated the different intercropping effects on microbial C and nutrient limitation in the rhizosphere and bulk soil and emphasized the importance of microbial diversity, particularly rare taxa.

Degradation of agricultural waste is dependent on chemical fertilizers in long-term paddy-dry rotation field

The practice of returning straw to agricultural fields is a globally employed technique. Such agricultural fields also receive a significant amount of nitrogen (N) and phosphorus (P) fertilizers, because these two macronutrients are essential for plant growth and development. However, the consequences of such macronutrients input on straw decomposition, soil dissolved organic matter (DOM), key microbes, and lignocellulolytic enzymes are still unclear. In a similar aim, we designed a long-term straw returning study without and with different N and P nutrient supplementation: CK (N0P0), T1 (N120P0), T2 (N120P60), T3 (N120P90), T4 (N120P120), T5 (N0P90), T6 (N60P90), and T7 (N180P90), and evaluated their impact on rice and oilseed rape yield, soil DOM, enzymes, lignocellulose content, microbial diversity, and composition. We found straw returning improved overall yield in all treatments and T7 showed the highest yield for oilseed rape (30.31-38.87 g/plant) and rice (9.14-9.91 t/ha) during five-years of study. The fertilizer application showed a significant impact on soil physicochemical properties, such as water holding capacity and soil porosity decreased, and bulk density increased in fertilized treatments, as compared to CK. Similarly, significantly low OM, cellulose, hemicellulose, and lignin content were found in T7, T4, T3, and T2, while high values were found in CK and T5, respectively. The fluorescence excitation-emission matrix spectra of DOM of different treatments revealed that T3, T7, T4, and T6 showed high peak M (microbial by-products), peak A and peak C (humic acid-like) as compared to others. The microbial composition was also distinctive in each treatment and a high relative abundance of Chloroflexi, Actinobacteriota, Ascomycota, and Basidiomycota were found in T2 and T3 treatments, respectively. These findings indicate that the decomposition of straw in the agricultural field was dependent on nutrients input, which facilitated key microbial growth and impacted positively on lignocellulolytic enzymes, which further aided the breakdown of all components of straw in the field efficiently. On the other hand, high input of chemical based fertilizers to soil can lead to several environmental issues, such as nutrient imbalance, nutrient runoff, soil pH change and changes in microbial activities. Keeping that in consideration, we recommend moderate fertilizer dosage (N120P90) in such fields to achieve higher decomposition of crop straw with a small yield compromise.

Characterization of the arbuscular mycorrhizal fungal community associated with rosewood in threatened Miombo forests

Understanding the dynamics of arbuscular mycorrhizal fungi (AMF) in response to land use change is important for the restoration of degraded forests. Here, we investigated the AMF community composition in the roots of Pterocarpus tinctorius sampled from agricultural and forest fallow soils rich in aluminum and iron. By sequencing the large subunit region of the rRNA gene, we identified a total of 30 operational taxonomic units (OTUs) in 33 root samples. These OTUs belonged to the genera Rhizophagus, Dominikia, Glomus, Sclerocystis, and Scutellospora. The majority of these OTUs did not closely match any known AMF species. We found that AMF species richness was significantly influenced by soil properties and overall tree density. Acidic soils with high levels of aluminum and iron had a low mean AMF species richness of 3.2. Indicator species analyses revealed several AMF OTUs associated with base saturation (4 OTUs), high aluminum (3 OTUs), and iron (2 OTUs). OTUs positively correlated with acidity (1 OTU), iron, and available phosphorus (2 OTUs) were assigned to the genus Rhizophagus, suggesting their tolerance to aluminum and iron. The results highlight the potential of leguminous trees in tropical dry forests as a reservoir of unknown AMF species. The baseline data obtained in this study opens new avenues for future studies, including the use of indigenous AMF-based biofertilizers to implement ecological revegetation strategies and improve land use.

Fungal communities in soils under global change

Soil fungi play indispensable roles in all ecosystems including the recycling of organic matter and interactions with plants, both as symbionts and pathogens. Past observations and experimental manipulations indicate that projected global change effects, including the increase of CO₂ concentration, temperature, change of precipitation and nitrogen (N) deposition, affect fungal species and communities in soils. Although the observed effects depend on the size and duration of change and reflect local conditions, increased N deposition seems to have the most profound effect on fungal communities. The plant-mutualistic fungal guilds - ectomycorrhizal fungi and arbuscular mycorrhizal fungi - appear to be especially responsive to global change factors with N deposition and warming seemingly having the strongest adverse effects. While global change effects on fungal biodiversity seem to be limited, multiple studies demonstrate increases in abundance and dispersal of plant pathogenic fungi. Additionally, ecosystems weakened by global change-induced phenomena, such as drought, are more vulnerable to pathogen outbreaks. The shift from mutualistic fungi to plant pathogens is likely the largest potential threat for the future functioning of natural and managed ecosystems. However, our ability to predict global change effects on fungi is still insufficient and requires further experimental work and long-term observations. Citation: Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P (2022). Fungal communities in soils under global change. Studies in Mycology 103: 1-24. doi: 10.3114/sim.2022.103.01.

Soil Ventilation Benefited Strawberry Growth via Microbial Communities and Nutrient Cycling Under High-Density Planting

In order to increase O₂ concentration in the rhizosphere and reduce the continuous cropping obstacles under high-density cultivation, ventilation is often used to increase soil aeration. Yet, the effect of ventilation on soil microbial communities and nutrient cycling and, further, the extent to which they influence strawberry growth under greenhouse conditions are still poorly understood. Thus, four treatments—no ventilation + low planting density (LD), ventilation + LD, no ventilation + high planting density (HD), and ventilation + HD—of strawberry “Red cheeks” (Fragaria × ananassa Duch. cv. “Benihopp”) were studied in a greenhouse for 3 years. The ventilation pipe (diameter = 10 cm) was buried in the soil at a depth of 15 cm from the surface and fresh air was sent to the root zone through the pipe by a blower. Ten pipes (one pipeline in a row) were attached to a blower. Soil samples were collected using a stainless-steel corer (five-point intra-row sampling) for the nutrient and microbial analyses. The composition and structure of the soil bacterial and fungal communities were analyzed by high-throughput sequencing of the 16S and 18S rRNA genes, and functional profiles were predicted using PICRUSt and FUNGuild, respectively. The results showed that soil ventilation increased the net photosynthetic rate (Pn), transpiration rate (Tr), and water use efficiency (WUE) of strawberry plants across two growth stages [vegetative growth stage (VGS) and fruit development stage (FDS)]. Soil ventilation increased its available nutrient contents, but the available nutrient contents were reduced under the high planting density compared with low planting density. Both the O₂ concentration and O₂:CO₂ ratio were increased by ventilation; these were positively correlated with the relative abundance of Bacilli, Gamma-proteobacteria, Blastocatella, as well as Chytridiomycota and Pezizomycetes. Conversely, ventilation decreased soil CO₂ concentration and the abundance of Beta-proteobacteria and Gemmatimonadetes. The greater planting density increased the relative abundance of Acidobacteria (oligotrophic group). Ventilation altered soil temperature and pH along with carbon and nitrogen functional profiles in the VGS (more nitrogen components) and FDS (more carbon components), which benefited strawberry plant growth under high planting density. The practice of soil ventilation provides a strategy to alleviate hypoxia stress and continuous cropping obstacles for improving crop production in greenhouse settings.

Multiple constraints cause positive and negative feedbacks limiting grassland soil CO2 efflux under CO2 enrichment

Terrestrial ecosystems are increasingly enriched with resources such as atmospheric CO₂ that limit ecosystem processes. The consequences for ecosystem carbon cycling depend on the feedbacks from other limiting resources and plant community change, which remain poorly understood for soil CO₂ efflux, J_CO2, a primary carbon flux from the biosphere to the atmosphere. We applied a unique CO₂ enrichment gradient (250 to 500 µL L^-1) for eight years to grassland plant communities on soils from different landscape positions. We identified the trajectory of J_CO2 responses and feedbacks from other resources, plant diversity [effective species richness, exp(H)], and community change (plant species turnover). We found linear increases in J_CO2 on an alluvial sandy loam and a lowland clay soil, and an asymptotic increase on an upland silty clay soil. Structural equation modeling identified CO₂ as the dominant limitation on J_CO2 on the clay soil. In contrast with theory predicting limitation from a single limiting factor, the linear J_CO2 response on the sandy loam was reinforced by positive feedbacks from aboveground net primary productivity and exp(H), while the asymptotic J_CO2 response on the silty clay arose from a net negative feedback among exp(H), species turnover, and soil water potential. These findings support a multiple resource limitation view of the effects of global change drivers on grassland ecosystem carbon cycling and highlight a crucial role for positive or negative feedbacks between limiting resources and plant community structure. Incorporating these feedbacks will improve models of terrestrial carbon sequestration and ecosystem services.

Investigating the mycobiome of the Holcomb Creosote Superfund Site

Even though many fungi are known to degrade a range of organic chemicals and may be advantageous for targeting hydrophobic chemicals with low bioavailability due to their ability to secrete extracellular enzymes, fungi are not commonly leveraged in the context of bioremediation. Here we sought to examine the fungal microbiome (mycobiome) at a model creosote polluted site to determine if fungi were prevalent under high PAH contamination conditions as well as to identify potential mycostimulation targets. Several significant positive associations were detected between OTUs and mid-to high-molecular weight PAHs. Several OTUs were closely related to taxa that have previously been identified in culture-based studies as PAH degraders. In particular, members belonging to the Ascomycota phylum were the most diverse at higher PAH concentrations suggesting this phylum may be promising biostimulation targets. There were nearly three times more positive correlations as compared to negative correlations, suggesting that creosote-tolerance is more common than creosote-sensitivity in the fungal community. Future work including shotgun metagenomic analysis would help confirm the presence of specific degradation genes. Overall this study suggests that mycobiome and bacterial microbiome analyses should be performed in parallel to devise the most optimal in situ biostimulation treatment strategies.

Tree growth rate regulate the influence of elevated CO2 on soil biochemical responses under tropical condition

Tree growth rate can complicate our understandings of plant belowground responses to elevated CO₂ (eCO₂) in tropical ecosystems. We studied the effects of eCO₂ on plant growth parameters, and rhizospheric soil properties including soil organic carbon (SOC), glomalin related soil protein (GRSP), microbial biomass C (C_mic), CO₂ efflux (C_efflux), and microbial extracellular enzyme activities under two tropical tree saplings of fast-growing Tectona grandis (Teak) and slow-growing Butea monosperma (Butea). We exposed these saplings to eCO₂ (∼550 ppm) and ambient CO₂ (aCO₂; ∼395 ppm) in the Indo-Gangetic plain region, and further (after 10 and 46 months) measured the changes in their rhizospheric soil properties. With respect to aCO₂ treatment, eCO₂ significantly increased plant height, stem and shoot weight, and total plant biomass of Teak. However, these plant traits did not considerably differed between eCO₂ and aCO₂ treatments of Butea. The eCO₂ induced greater extent of increase in rhizospheric soil properties including SOC fractions (particulate OC, non-particulate OC and total OC), GRSP fractions (easily extractable- GRSP, difficulty extractable- GRSP and total- GRSP), C_mic, C_efflux and extracellular enzyme activities (phosphatase, dehydrogenase, β-glucosidase and fluorescein diacetate) were observed under Teak compared with Butea. Compared with aCO₂ treatment, eCO₂ slightly reduced soil available N and P under the Teak, but no changes were apparent between eCO₂ and aCO₂ treatments of the Butea. The greater extent of responses from soil variables observed after longer period (46 months) of CO₂ exposure. The multivariate analysis confirmed that eCO₂ treatment with Teak is more responsive compared with other treatments of Teak and Butea. This contrasting rhizospheric soil feedback to eCO₂ between two tropical trees, suggesting fast-growing species will be more responsive to future climate. Such species will have a competitive advantage over coexisting less responsive species (e.g. Butea) under future eCO₂ climate.

Bacterial community response to a preindustrial-to-future CO2 gradient is limited and soil specific in Texas Prairie grassland

Rising atmospheric CO₂ concentration directly stimulates plant productivity and affects nutrient dynamics in the soil. However, the influence of CO₂ enrichment on soil bacterial communities remains elusive, likely due to their complex interactions with a wide range of plant and soil properties. Here, we investigated the bacterial community response to a decade long preindustrial-to-future CO₂ gradient (250-500 ppm) among three contrasting soil types using 16S rRNA gene amplicon sequencing. In addition, we examined the effect of seasonal variation and plant species composition on bacterial communities. We found that Shannon index (H') and Faith's phylogenetic diversity (PD) did not change in response to the CO₂ gradient (R²  = 0.01, p > 0.05). CO₂ gradient and season also had a negligible effect on overall community structure, although silty clay soil communities were better structured on a CO₂ gradient (p < 0.001) among three soils. Similarly, CO₂ gradient had no significant effect on the relative abundance of different phyla. However, we observed soil-specific variation of CO₂ effects in a few individual families. For example, the abundance of Pirellulaceae family decreased linearly with CO₂ gradient, but only in sandy loam soils. Conversely, the abundance of Micromonosporaceae and Gaillaceae families increased with CO₂ gradient in clay soils. Soil water content (SWC) and nutrient properties were the key environmental constraints shaping bacterial community structure, one manifestation of which was a decline in bacterial diversity with increasing SWC. Furthermore, the impact of plant species composition on community structure was secondary to the strong influence of soil properties. Taken together, our findings indicate that bacterial communities may be largely unresponsive to indirect effects of CO₂ enrichment through plants. Instead, bacterial communities are strongly regulated by edaphic conditions, presumably because soil differences create distinct environmental niches for bacteria.

Impacts of Atmospheric CO2 and Soil Nutritional Value on Plant Responses to Rhizosphere Colonization by Soil Bacteria

Concerns over rising atmospheric CO₂ concentrations have led to growing interest in the effects of global change on plant-microbe interactions. As a primary substrate of plant metabolism, atmospheric CO₂ influences below-ground carbon allocation and root exudation chemistry, potentially affecting rhizosphere interactions with beneficial soil microbes. In this study, we have examined the effects of different atmospheric CO₂ concentrations on Arabidopsis rhizosphere colonization by the rhizobacterial strain Pseudomonas simiae WCS417 and the saprophytic strain Pseudomonas putida KT2440. Rhizosphere colonization by saprophytic KT2440 was not influenced by sub-ambient (200 ppm) and elevated (1,200 ppm) concentrations of CO₂, irrespective of the carbon (C) and nitrogen (N) content of the soil. Conversely, rhizosphere colonization by WCS417 in soil with relatively low C and N content increased from sub-ambient to elevated CO₂. Examination of plant responses to WCS417 revealed that plant growth and systemic resistance varied according to atmospheric CO₂ concentration and soil-type, ranging from growth promotion with induced susceptibility at sub-ambient CO₂, to growth repression with induced resistance at elevated CO₂. Collectively, our results demonstrate that the interaction between atmospheric CO₂ and soil nutritional status has a profound impact on plant responses to rhizobacteria. We conclude that predictions about plant performance under past and future climate scenarios depend on interactive plant responses to soil nutritional status and rhizobacteria.

Relationships between soil fungal and woody plant assemblages differ between ridge and valley habitats in a subtropical mountain forest

Elucidating interactions of above-ground and below-ground communities in different habitat types is essential for understanding biodiversity maintenance and ecosystem functioning. Using 454 pyrosequencing of ITS2 sequences we examined the relationship between subtropical mountain forest soil fungal communities, abiotic conditions, and plant communities using correlation and partial models. Ridge and valley habitats with differing fungal communities were delineated. Total, saprotrophic and pathogenic fungal richness were significantly correlated with plant species richness and/or soil nutrients and moisture in the ridge habitat, but with habitat convexity or basal area of Castanopsis eyrei in the valley habitat. Ectomycorrhizal (EM) fungal richness was significantly correlated with basal area of C. eyrei and total EM plants in the ridge and valley habitats, respectively. Total, saprotrophic, pathogenic and EM fungal compositions were significantly correlated with plant species composition and geographic distance in the ridge habitat, but with various combinations of plant species composition, plant species richness, soil C : N ratio and pH or no variables in the valley habitat. Our findings suggest that mechanisms influencing soil fungal diversity and community composition differ between ridge and valley habitats, and relationships between fungal and woody plant assemblages depend on habitat types in the subtropical forest ecosystem.

Host Plant Physiology and Mycorrhizal Functioning Shift across a Glacial through Future [CO2] Gradient

Rising atmospheric carbon dioxide concentration ([CO2]) may modulate the functioning of mycorrhizal associations by altering the relative degree of nutrient and carbohydrate limitations in plants. To test this, we grew Taraxacum ceratophorum and Taraxacum officinale (native and exotic dandelions) with and without mycorrhizal fungi across a broad [CO2] gradient (180-1,000 µL L-1). Differential plant growth rates and vegetative plasticity were hypothesized to drive species-specific responses to [CO2] and arbuscular mycorrhizal fungi. To evaluate [CO2] effects on mycorrhizal functioning, we calculated response ratios based on the relative biomass of mycorrhizal (MBio) and nonmycorrhizal (NMBio) plants (RBio = [MBio - NMBio]/NMBio). We then assessed linkages between RBio and host physiology, fungal growth, and biomass allocation using structural equation modeling. For T. officinale, RBio increased with rising [CO2], shifting from negative to positive values at 700 µL L-1 [CO2] and mycorrhizal effects on photosynthesis and leaf growth rates drove shifts in RBio in this species. For T. ceratophorum, RBio increased from 180 to 390 µL L-1 and further increases in [CO2] caused RBio to shift from positive to negative values. [CO2] and fungal effects on plant growth and carbon sink strength were correlated with shifts in RBio in this species. Overall, we show that rising [CO2] significantly altered the functioning of mycorrhizal associations. These symbioses became more beneficial with rising [CO2], but nonlinear effects may limit plant responses to mycorrhizal fungi under future [CO2]. The magnitude and mechanisms driving mycorrhizal-CO2 responses reflected species-specific differences in growth rate and vegetative plasticity, indicating that these traits may provide a framework for predicting mycorrhizal responses to global change.

Resilience of Fungal Communities to Elevated CO2

Soil filamentous fungi play a prominent role in regulating ecosystem functioning in terrestrial ecosystems. This necessitates understanding their responses to climate change drivers in order to predict how nutrient cycling and ecosystem services will be influenced in the future. Here, we provide a quantitative synthesis of ten studies on soil fungal community responses to elevated CO2. Many of these studies reported contradictory diversity responses. We identify the duration of the study as an influential parameter that determines the outcome of experimentation. Our analysis reconciles the existing globally distributed experiments on fungal community responses to elevated CO2 and provides a framework for comparing results of future CO2 enrichment studies.

Plant community change mediates the response of foliar δ(15)N to CO 2 enrichment in mesic grasslands

Rising atmospheric CO2 concentration may change the isotopic signature of plant N by altering plant and microbial processes involved in the N cycle. CO2 may increase leaf δ(15)N by increasing plant community productivity, C input to soil, and, ultimately, microbial mineralization of old, (15)N-enriched organic matter. We predicted that CO2 would increase aboveground productivity (ANPP; g biomass m(-2)) and foliar δ(15)N values of two grassland communities in Texas, USA: (1) a pasture dominated by a C4 exotic grass, and (2) assemblages of tallgrass prairie species, the latter grown on clay, sandy loam, and silty clay soils. Grasslands were exposed in separate experiments to a pre-industrial to elevated CO2 gradient for 4 years. CO2 stimulated ANPP of pasture and of prairie assemblages on each of the three soils, but increased leaf δ(15)N only for prairie plants on a silty clay. δ(15)N increased linearly as mineral-associated soil C declined on the silty clay. Mineral-associated C declined as ANPP increased. Structural equation modeling indicted that CO2 increased ANPP partly by favoring a tallgrass (Sorghastrum nutans) over a mid-grass species (Bouteloua curtipendula). CO2 may have increased foliar δ(15)N on the silty clay by reducing fractionation during N uptake and assimilation. However, we interpret the soil-specific, δ(15)N-CO2 response as resulting from increased ANPP that stimulated mineralization from recalcitrant organic matter. By contrast, CO2 favored a forb species (Solanum dimidiatum) with higher δ(15)N than the dominant grass (Bothriochloa ischaemum) in pasture. CO2 enrichment changed grassland δ(15)N by shifting species relative abundances.