Fungal community response to long‐term soil warming with potential implications for soil carbon dynamics

Responses of vascular plant fine roots and associated microbial communities to whole-ecosystem warming and elevated CO2 in northern peatlands

Warming and elevated CO2 (eCO2) are expected to facilitate vascular plant encroachment in peatlands. The rhizosphere, where microbial activity is fueled by root turnover and exudates, plays a crucial role in biogeochemical cycling, and will likely at least partially dictate the response of the belowground carbon cycle to climate changes. We leveraged the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment, to explore the effects of a whole-ecosystem warming gradient (+0°C to 9°C) and eCO2 on vascular plant fine roots and their associated microbes. We combined trait-based approaches with the profiling of fungal and prokaryote communities in plant roots and rhizospheres, through amplicon sequencing. Warming promoted self-reliance for resource uptake in trees and shrubs, while saprophytic fungi and putative chemoorganoheterotrophic bacteria utilizing plant-derived carbon substrates were favored in the root zone. Conversely, eCO2 promoted associations between trees and ectomycorrhizal fungi. Trees mostly associated with short-distance exploration-type fungi that preferentially use labile soil N. Additionally, eCO2 decreased the relative abundance of saprotrophs in tree roots. Our results indicate that plant fine-root trait variation is a crucial mechanism through which vascular plants in peatlands respond to climate change via their influence on microbial communities that regulate biogeochemical cycles.

Enhancing soil health and nutrient cycling through soil amendments: Improving the synergy of bacteria and fungi

The synergy between bacteria and fungi is a key determinant of soil health and have a positive effect on plant development under drought conditions, with the potentially enhancing the sustainability of amending soil with natural materials. However, identifying how soil amendments influence plant growth is often difficult due to the complexity of microorganisms and their links with different soil amendment types and environmental factors. To address this, we conducted a field experiment to examine the impact of soil amendments (biochar, Bacillus mucilaginosus, Bacillus subtilis and super absorbent polymer) on plant growth. We also assessed variations in microbial community, links between fungi and bacteria, and soil available nutrients, while exploring how the synergistic effects between fungus and bacteria influenced the response of soil amendments to plant growth. This study revealed that soil amendments reduced soil bacterial diversity but increased the proportion of the family Enterobacteriaceae, Nitrosomonadaceae, and also increased soil fungal diversity and the proportion of the sum of the family Lasiosphaeriaceae, Chaetomiaceae, Pleosporaceae. Changes in soil microbial communities lead to increase the complexity of microbial co-occurrence networks. Furthermore, this heightened network complexity enhanced the synergy of soil bacteria and fungi, supporting bacterial functions related to soil nutrient cycling, such as metabolic functions and genetic, environmental, and cellular processes. Hence, the BC and BS had 3.0-fold and 0.5-fold greater root length densities than CK and apple tree shoot growth were increased by 62.14 %,50.53 % relative to CK, respectively. In sum, our results suggest that the synergistic effect of bacteria and fungi impacted apple tree growth indirectly by modulating soil nutrient cycling. These findings offer a new strategy for enhancing the quality of arable land in arid and semi-arid regions.

Nitrogen availability mediates soil carbon cycling response to climate warming: A meta-analysis

Global climate warming may induce a positive feedback through increasing soil carbon (C) release to the atmosphere. Although warming can affect both C input to and output from soil, direct and convincing evidence illustrating that warming induces a net change in soil C is still lacking. We synthesized the results from field warming experiments at 165 sites across the globe and found that climate warming had no significant effect on soil C stock. On average, warming significantly increased root biomass and soil respiration, but warming effects on root biomass and soil respiration strongly depended on soil nitrogen (N) availability. Under high N availability (soil C:N ratio < 15), warming had no significant effect on root biomass, but promoted the coupling between effect sizes of root biomass and soil C stock. Under relative N limitation (soil C:N ratio > 15), warming significantly enhanced root biomass. However, the enhancement of root biomass did not induce a corresponding C accumulation in soil, possibly because warming promoted microbial CO₂ release that offset the increased root C input. Also, reactive N input alleviated warming-induced C loss from soil, but elevated atmospheric CO₂ or precipitation increase/reduction did not. Together, our findings indicate that the relative availability of soil C to N (i.e., soil C:N ratio) critically mediates warming effects on soil C dynamics, suggesting that its incorporation into C-climate models may improve the prediction of soil C cycling under future global warming scenarios.

Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long-term warming

Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mechanisms have been suggested to explain the long-term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year-old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationships between temperature sensitivity of physiology (growth, respiration, carbon use efficiency, and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation of microbial respiration, but only in summer, when warming had exacerbated the seasonally-induced, already small dissolved organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon increased the extracellular enzymatic pool and its temperature sensitivity. We propose that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes to decadal warming. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming effects on these soils.

Distinct patterns of soil bacterial and fungal community assemblages in subtropical forest ecosystems under warming

Climate change globally affects soil microbial community assembly across ecosystems. However, little is known about the impact of warming on the structure of soil microbial communities or underlying mechanisms that shape microbial community composition in subtropical forest ecosystems. To address this gap, we utilized natural variation in temperature via an altitudinal gradient to simulate ecosystem warming. After 6 years, microbial co-occurrence network complexity increased with warming, and changes in their taxonomic composition were asynchronous, likely due to contrasting community assembly processes. We found that while stochastic processes were drivers of bacterial community composition, warming led to a shift from stochastic to deterministic drivers in dry season. Structural equation modelling highlighted that soil temperature and water content positively influenced soil microbial communities during dry season and negatively during wet season. These results facilitate our understanding of the response of soil microbial communities to climate warming and may improve predictions of ecosystem function of soil microbes in subtropical forests.

Experimental warming increases fungal alpha diversity in an oligotrophic maritime Antarctic soil

The climate of maritime Antarctica has altered since the 1950s. However, the effects of increased temperature, precipitation and organic carbon and nitrogen availability on the fungal communities inhabiting the barren and oligotrophic fellfield soils that are widespread across the region are poorly understood. Here, we test how warming with open top chambers (OTCs), irrigation and the organic substrates glucose, glycine and tryptone soy broth (TSB) influence a fungal community inhabiting an oligotrophic maritime Antarctic fellfield soil. In contrast with studies in vegetated soils at lower latitudes, OTCs increased fungal community alpha diversity (Simpson's index and evenness) by 102-142% in unamended soil after 5 years. Conversely, OTCs had few effects on diversity in substrate-amended soils, with their only main effects, in glycine-amended soils, being attributable to an abundance of Pseudogymnoascus. The substrates reduced alpha and beta diversity metrics by 18-63%, altered community composition and elevated soil fungal DNA concentrations by 1-2 orders of magnitude after 5 years. In glycine-amended soil, OTCs decreased DNA concentrations by 57% and increased the relative abundance of the yeast Vishniacozyma by 45-fold. The relative abundance of the yeast Gelidatrema declined by 78% in chambered soil and increased by 1.9-fold in irrigated soil. Fungal DNA concentrations were also halved by irrigation in TSB-amended soils. In support of regional- and continental-scale studies across climatic gradients, the observations indicate that soil fungal alpha diversity in maritime Antarctica will increase as the region warms, but suggest that the accumulation of organic carbon and nitrogen compounds in fellfield soils arising from expanding plant populations are likely, in time, to attenuate the positive effects of warming on diversity.

Organic amendments enhance soil microbial diversity, microbial functionality and crop yields: A meta-analysis

Fertilization plays an important role in changing soil microbial diversity, which is essential for determining crop yields. Yet, the influence of organic amendments on microbial diversity remains uncertain, and few studies have addressed the relative importance of microbial diversity versus other drivers of crop yields. Here, we synthesize 219 studies worldwide and found that organic amendments significantly increased microbial diversity components (i.e., Shannon, richness, and phylogenetic diversity) and shifted microbial community structure compared to mineral-only fertilization. The performance of microbial alpha diversity varied substantially with organic amendment types, microbial groups and changes in soil pH. Both microbial diversity and community structure exhibited significantly positive relationships with microbial functionality and crop yields. In addition, soil abiotic properties and microbial functionality had a much stronger impact on crop yields than microbial diversity and climate factors. Partial least squares path modeling showed that soil microbial diversity was an important underlying factor driving crop yields via boosting soil microbial functionality. Overall, our findings provide robust evidence for the positive diversity-functions relationships, emphasizing that substituting mineral fertilizers with organic amendments is a promising way to conserve microbial diversity and promote soil microbial functions and crop yields.

Coupling of plant and mycorrhizal fungal diversity: its occurrence, relevance, and possible implications under global change

First principles predict that diversity at one trophic level often begets diversity at other levels, suggesting plant and mycorrhizal fungal diversity should be coupled. Local-scale studies have shown positive coupling between the two, but the association is less consistent when extended to larger spatial and temporal scales. These inconsistencies are likely due to divergent relationships of different mycorrhizal fungal guilds to plant diversity, scale dependency, and a lack of coordinated sampling efforts. Given that mycorrhizal fungi play a central role in plant productivity and nutrient cycling, as well as ecosystem responses to global change, an improved understanding of the coupling between plant and mycorrhizal fungal diversity across scales will reduce uncertainties in predicting the ecosystem consequences of species gains and losses.

Warming has a minor effect on surface soil organic carbon in alpine meadow ecosystems on the Qinghai-Tibetan Plateau

The alpine meadow ecosystem on the Qinghai-Tibetan Plateau (QTP) is very sensitive to warming and plays a key role in regulating global carbon (C) cycling. However, how warming affects the soil organic carbon (SOC) pool and related C inputs and outputs in alpine meadow ecosystems on the QTP remains unclear. Here, we combined two field experiments and a meta-analysis on field experiments to synthesize the responses of the SOC pool and related C cycling processes to warming in alpine meadow ecosystems on the QTP. We found that the SOC content of surface soil (0-10 cm) showed a minor response to warming, but plant respiration was accelerated by warming. In addition, the warming effect on SOC was not correlated with experimental and environmental variables, such as the method, magnitude and duration of warming, initial SOC content, mean annual temperature, and mean annual precipitation. We conclude that the surface SOC content is resistant to climate warming in alpine meadow ecosystems on the QTP.