Short-term precipitation exclusion alters microbial responses to soil moisture in a wet tropical forest

Impact of aridity rise and arid lands expansion on carbon-storing capacity, biodiversity loss, and ecosystem services

Drylands, comprising semi-arid, arid, and hyperarid regions, cover approximately 41% of the Earth's land surface and have expanded considerably in recent decades. Even under more optimistic scenarios, such as limiting global temperature rise to 1.5°C by 2100, semi-arid lands may increase by up to 38%. This study provides an overview of the state-of-the-art regarding changing aridity in arid regions, with a specific focus on its effects on the accumulation and availability of carbon (C), nitrogen (N), and phosphorus (P) in plant-soil systems. Additionally, we summarized the impacts of rising aridity on biodiversity, service provisioning, and feedback effects on climate change across scales. The expansion of arid ecosystems is linked to a decline in C and nutrient stocks, plant community biomass and diversity, thereby diminishing the capacity for recovery and maintaining adequate water-use efficiency by plants and microbes. Prolonged drought led to a -3.3% reduction in soil organic carbon (SOC) content (based on 148 drought-manipulation studies), a -8.7% decrease in plant litter input, a -13.0% decline in absolute litter decomposition, and a -5.7% decrease in litter decomposition rate. Moreover, a substantial positive feedback loop with global warming exists, primarily due to increased albedo. The loss of critical ecosystem services, including food production capacity and water resources, poses a severe challenge to the inhabitants of these regions. Increased aridity reduces SOC, nutrient, and water content. Aridity expansion and intensification exacerbate socio-economic disparities between economically rich and least developed countries, with significant opportunities for improvement through substantial investments in infrastructure and technology. By 2100, half the world's landmass may become dryland, characterized by severe conditions marked by limited C, N, and P resources, water scarcity, and substantial loss of native species biodiversity. These conditions pose formidable challenges for maintaining essential services, impacting human well-being and raising complex global and regional socio-political challenges.

A Gulf Stream frontal eddy harbors a distinct microbiome compared to adjacent waters

Mesoscale oceanographic features, including eddies, have the potential to alter productivity and other biogeochemical rates in the ocean. Here, we examine the microbiome of a cyclonic, Gulf Stream frontal eddy, with a distinct origin and environmental parameters compared to surrounding waters, in order to better understand the processes dominating microbial community assembly in the dynamic coastal ocean. Our microbiome-based approach identified the eddy as distinct from the surround Gulf Stream waters. The eddy-associated microbial community occupied a larger area than identified by temperature and salinity alone, increasing the predicted extent of eddy-associated biogeochemical processes. While the eddy formed on the continental shelf, after two weeks both environmental parameters and microbiome composition of the eddy were most similar to the Gulf Stream, suggesting the effect of environmental filtering on community assembly or physical mixing with adjacent Gulf Stream waters. In spite of the potential for eddy-driven upwelling to introduce nutrients and stimulate primary production, eddy surface waters exhibit lower chlorophyll a along with a distinct and less even microbial community, compared to the Gulf Stream. At the population level, the eddy microbiome exhibited differences among the cyanobacteria (e.g. lower Trichodesmium and higher Prochlorococcus) and in the heterotrophic alpha Proteobacteria (e.g. lower relative abundances of specific SAR11 phylotypes) versus the Gulf Stream. However, better delineation of the relative roles of processes driving eddy community assembly will likely require following the eddy and surrounding waters since inception. Additionally, sampling throughout the water column could better clarify the contribution of these mesoscale features to primary production and carbon export in the oceans.

Is allelochemical synthesis in Casuarina equisetifolia plantation related to litter microorganisms?

Productivity decline of Casuarina equisetifolia plantation and difficulty in natural regeneration remains a serious problem because of allelopathy. Previous studies have confirmed that 2,4-di-tert-butylphenol (2,4-DTBP) are the major allelochemicals of the C. equisetifolia litter exudates. The production of these allelochemicals may derive from decomposition of litter or from the litter endophyte and microorganisms adhering to litter surfaces. In the present study, we aimed to evaluate the correlation between allelochemicals in litter and endophytic and epiphytic fungi and bacteria from litter. A total of 100 fungi and 116 bacteria were isolated from the interior and surface of litter of different forest ages (young, half-mature, and mature plantation). Results showed that the fermentation broth of fungal genera Mycosphaerella sp. and Pestalotiopsis sp., and bacterial genera Bacillus amyloliquefaciens, Burkholderia-Paraburkholderia, and Pantoea ananatis had the strongest allelopathic effect on C. equisetifolia seeds. Allelochemicals, such as 2,4-DTBP and its analogs were identified in the fermentation broths of these microorganisms using GC/MS analysis. These results indicate that endophytic and epiphytic fungi and bacteria in litters are involved in the synthesis of allelochemicals of C. equisetifolia. To further determine the abundance of the allelopathic fungi and bacteria, Illumina MiSeq high-throughput sequencing was performed. The results showed that bacterial genera with strong allelopathic potential were mainly distributed in the young and half-mature plantation with low abundance, while the abundance of fungal genera Mycosphaerella sp. and Pestalotiopsis sp. were higher in the young and mature plantations. In particular, the abundance of Mycosphaerella sp. in the young and mature plantations were 501.20% and 192.63% higher than in the half-mature plantation, respectively. Overall, our study demonstrates that the litter fungi with higher abundance in the young and mature plantation were involved in the synthesis of the allelochemical 2,4-DTBP of C. equisetifolia. This finding may be important for understanding the relationship between autotoxicity and microorganism and clarifying the natural regeneration problem of C. equisetifolia.

Feedback in tropical forests of the Anthropocene

Tropical forests are complex systems containing myriad interactions and feedbacks with their biotic and abiotic environments, but as the world changes fast, the future of these ecosystems becomes increasingly uncertain. In particular, global stressors may unbalance the feedbacks that stabilize tropical forests, allowing other feedbacks to propel undesired changes in the whole ecosystem. Here, we review the scientific literature across various fields, compiling known interactions of tropical forests with their environment, including the global climate, rainfall, aerosols, fire, soils, fauna, and human activities. We identify 170 individual interactions among 32 elements that we present as a global tropical forest network, including countless feedback loops that may emerge from different combinations of interactions. We illustrate our findings with three cases involving urgent sustainability issues: (1) wildfires in wetlands of South America; (2) forest encroachment in African savanna landscapes; and (3) synergistic threats to the peatland forests of Borneo. Our findings reveal an unexplored world of feedbacks that shape the dynamics of tropical forests. The interactions and feedbacks identified here can guide future qualitative and quantitative research on the complexities of tropical forests, allowing societies to manage the nonlinear responses of these ecosystems in the Anthropocene.

Responses of Fungal Community Structure and Functional Composition to Short-Term Fertilization and Dry Season Irrigation in Eucalyptus urophylla × Eucalyptus grandis Plantation Soils

Plantation forests productivity is severely limited by the seasonal drought and fertilization practices in South China. Soil nutrient and water availability influence soil fungal community, functional group diversity and the variation of plant productivity; however, the effects of irrigation and fertilization on fungal responses have rarely been studied. Here, we investigate the responses of fungal community structure and functional groups in Eucalyptus plantation soils to short-term fertilization (F), dry-season irrigation (W), short-term fertilization combined with dry-season irrigation (FW), and control (CK) treatments for ten months. A higher proportion of Basidiomycota was observed in the irrigation and/or fertilization treatments; conversely, lower proportions of Ascomycota and Mucoromycotina were observed in the only irrigation and fertilization treatments. Higher soil carbon contents and symbiotroph fungi (mainly Ectomycorrhizas) proportion were detected in the FW treatment, while low proportions of saprophytic and pathogenic fungi were observed in the FW treatment when compared with those in other treatments. These results may indicate that Eucalyptus tree growth under irrigation and fertilization condition was better than under fertilization only, irrigation only, or neither management. The results highlight that short-term fertilization and dry-season irrigation can shift fungal community structure and functional groups by regulating available soil moisture and nutrients. They also provide a theoretical basis for the development of more appropriate management approaches in the early stages of forest plantation.

Resistance and resilience of soil prokaryotic communities in response to prolonged drought in a tropical forest

Global climate changes such as prolonged duration and intensity of drought can lead to adverse ecological consequences in forests. Currently little is known about soil microbial community responses to such drought regimes in tropical forests. In this study, we examined the resistance and resilience of topsoil prokaryotic communities to a prolongation of the dry season in terms of diversity, community structure and co-occurrence patterns in a French Guianan tropical forest. Through excluding rainfall during and after the dry season, a simulated prolongation of the dry season by five months was compared to controls. Our results show that prokaryotic communities increasingly diverged from controls with the progression of rain exclusion. Furthermore, prolonged drought significantly affected microbial co-occurrence networks. However, both the composition and co-occurrence networks of soil prokaryotic communities immediately ceased to differ from controls when precipitation throughfall returned. This study thus suggests modest resistance but high resilience of microbial communities to a prolonged drought in tropical rainforest soils.

Changes in microbial communities at different soil depths through the first rainy season following severe wildfire in North China artificial Pinus tabulaeformis forest

Wildfire could result in dramatic changes to soil temperatures and environments, with immediate, short- or long-lasting impacts on soil microbes. However, relatively little research has documented how fire disturbance, soil depth, time variation and their interactions affect soil microbial communities in wet conditions. This study investigated a severe wildfire influenced on bacterial and fungal communities at four soil depths (0-5, 5-10, 10-15 and 15-20 cm) after two quarters (with similar precipitation and exactly during the rainy season). Soil sampling was conducted in a burned site relative to an undisturbed contiguous site in the North China artificial Pinus tabulaeformis forest. Results indicated that fire had significant effects on bacterial and fungal richness, diversity, composition and structure, including most impacts on the surface mineral soil (0-5 cm) within the first period post-fire and minor impacts on the subsoils (5-20 cm) up to the second period. The microbial richness and some dominant taxa in the undisturbed soils changed with time and depth, suggesting spatiotemporal variation in soil microbial communities although the effects of rainfall were weakened. These differences in microbes between burned and undisturbed soils were mainly driven by soil pH, whereas organic matter and available potassium mediated the distribution of microbial communities along depth and time, respectively. In addition, fungal community was more sensitive to fire and time than bacterial community but an opposite result was found in depth. Nevertheless, soil microbes showed some signs of adaptation to fire. This work advocate that non-intervention should be considered in the short term after a fire or low-intensity water replenishment in the case of aridity.

Home-field advantage in soil respiration and its resilience to drying and rewetting cycles

Climate change is expected to increase extreme weather events, such as more extreme drought and rainfall incidences, with consequences for ecosystem carbon (C) cycling. An understanding of how drying and rewetting (DRW) events affect microbe-mediated soil processes is therefore critical to the predictions of future climate. Here, a reciprocal-transplant experiment was conducted using two soils originated from distinct climate and agricultural managements to evaluate how soil biotic and abiotic properties regulate soil respiration and its resilience to simulated DRW cycles. We found that regardless of the DRW intensity, the effects of microbial community on soil respiration and its resilience to DRW cycles were dependent on soil type. Soil microbial communities yielded higher respiration rates and resilience in native than foreign soils under both one and four DRW cycles, supporting the "home-field advantage" hypothesis. Structural equation modeling demonstrated that soil pH and total C directly influenced soil respiration, but effects of soil abiotic properties on respiration resilience were mediated by microbial communities. Among microbial drivers, the microbial C utilization capacity (as characterized by community-level physiological profile, C-acquisition enzyme activities and microbial metabolic quotients) was the best predictor of respiration resilience to DRW cycles, followed by microbial biomass carbon/nitrogen ratio and microbial community composition. Our study suggests that soil microbial communities may have adapted to their historical conditions, which facilitates the resilience of soil respiration to changing environments, but this adaptation may accelerate C loss from soils facing increasingly variable climate.

Soil Microbes Trade-Off Biogeochemical Cycling for Stress Tolerance Traits in Response to Year-Round Climate Change

Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.

Effects of seasonal precipitation change on soil respiration processes in a seasonally dry tropical forest

Precipitation is projected to change intensity and seasonal regime under current global projections. However, little is known about how seasonal precipitation changes will affect soil respiration, especially in seasonally dry tropical forests. In a seasonally dry tropical forest in South China, we conducted a precipitation manipulation experiment to simulate a delayed wet season (DW) and a wetter wet season (WW) over a three-year period. In DW, we reduced 60% throughfall in April and May to delay the onset of the wet season and irrigated the same amount water into the plots in October and November to extend the end of the wet season. In WW, we irrigated 25% annual precipitation into plots in July and August. A control treatment (CT) receiving ambient precipitation was also established. Compared with CT, DW significantly increased soil moisture by 54% during October to November, and by 30% during December to April. The treatment of WW did not significantly affect monthly measured soil moisture. In 2015, DW significantly increased leaf area index and soil microbial biomass but decreased fine root biomass. In contrast, WW significantly decreased fine root biomass and forest floor litter stocks. Soil respiration was not affected by DW, which could be attributed to the increased microbial biomass offsetting the decrease in fine root biomass. In contrast, WW significantly increased soil respiration from 3.40 to 3.90 μmol m-2 s-1 in the third year, mainly due to the increased litter decomposition and soil pH (from 4.48 to 4.68). The present study suggests that both a delayed wet season and a wetter wet season will have significant impacts on soil respiration-associated ecosystem components. However, the ecosystem components can respond in different directions to the same change in precipitation, which ultimately affected soil respiration.

Soil bacterial community responses to altered precipitation and temperature regimes in an old field grassland are mediated by plants

The structure and function of soil microbiomes often change in response to experimental climate manipulations, suggesting an important role in ecosystem feedbacks. However, it is difficult to know if microbes are responding directly to environmental changes or are more strongly impacted by plant responses. We investigated soil microbial responses to precipitation and temperature manipulations at the Boston-Area Climate Experiment in Massachusetts, USA, in both vegetated and bare plots to parse direct vs. plant-mediated responses to multi-factor climate change. We assessed the bacterial community in vegetated soils in 2009, two years after the experiment was initiated, and bacterial and fungal community in vegetated and bare soils in 2011. The bacterial community structure was significantly changed by the treatments in vegetated soils. However, such changes in the bacterial community across the treatments were absent in the 2011 bare soils. These results suggest that the bacterial communities in vegetated soils were structured via plant community shifts in response to the abiotic manipulations. Co-variation between bacterial community structure and temperature sensitivities and stoichiometry of potential enzyme activities in the 2011 vegetated soils suggested a link between bacterial community structure and ecosystem function. This study emphasizes the importance of plant-soil-microbial interactions in mediating responses to future climate change.

A unified conceptual framework for prediction and control of microbiomes

Microbiomes impact nearly all systems on Earth, and despite vast differences among systems, we contend that it is possible and highly beneficial to develop a unified conceptual framework for understanding microbiome dynamics that is applicable across systems. The ability to robustly predict and control environmental and human microbiomes would provide impactful opportunities to sustain and improve the health of ecosystems and humans alike. Doing so requires understanding the processes governing microbiome temporal dynamics, which currently presents an enormous challenge. We contend, however, that new opportunities can emerge by placing studies of both environmental and human microbiome temporal dynamics in the context of a unified conceptual framework. Our conceptual framework poses that factors influencing the temporal dynamics of microbiomes can be grouped into three broad categories: biotic and abiotic history, internal dynamics, and external forcing factors. Both environmental and human microbiome science study these factors, but not in a coordinated or consistent way. Here we discuss opportunities for greater crosstalk across these domains, such as leveraging specific ecological concepts from environmental microbiome science to guide optimization of strategies to manipulate human microbiomes towards improved health. To achieve unified understanding, it is necessary to have a common body of theory developed from explicit iteration between models and molecular-based characterization of microbiome dynamics across systems. Only through such model-experiment iteration will we eventually achieve prediction and control across microbiomes that impact ecosystem sustainability and human health.

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest

The high diversity of tree species has traditionally been considered an important controller of belowground processes in tropical rainforests. However, soil water availability and resources are also primary regulators of soil bacteria in many ecosystems. Separating the effects of these biotic and abiotic factors in the tropics is challenging because of their high spatial and temporal heterogeneity. To determine the drivers of tropical soil bacteria, we examined tree species effects using experimental tree monocultures and secondary forests at La Selva Biological Station in Costa Rica. A randomized block design captured spatial variation and we sampled at four dates across two years to assess temporal variation. We measured bacteria richness, phylogenetic diversity, community composition, biomass, and functional potential. All bacteria parameters varied significantly across dates. In addition, bacteria richness and phylogenetic diversity were affected by the interaction of vegetation type and date, whereas bacteria community composition was affected by the interaction of vegetation type and block. Shifts in bacteria community richness and composition were unrelated to shifts in enzyme function, suggesting physiological overlap among taxa. Based on the observed temporal and spatial heterogeneity, our understanding of tropical soil bacteria will benefit from additional work to determine the optimal temporal and spatial scales for sampling. Understanding spatial and temporal variation will facilitate prediction of how tropical soil microbes will respond to future environmental change.

Ectomycorrhizal fungi slow soil carbon cycling

Respiration of soil organic carbon is one of the largest fluxes of CO2 on earth. Understanding the processes that regulate soil respiration is critical for predicting future climate. Recent work has suggested that soil carbon respiration may be reduced by competition for nitrogen between symbiotic ectomycorrhizal fungi that associate with plant roots and free-living microbial decomposers, which is consistent with increased soil carbon storage in ectomycorrhizal ecosystems globally. However, experimental tests of the mycorrhizal competition hypothesis are lacking. Here we show that ectomycorrhizal roots and hyphae decrease soil carbon respiration rates by up to 67% under field conditions in two separate field exclusion experiments, and this likely occurs via competition for soil nitrogen, an effect larger than 2 °C soil warming. These findings support mycorrhizal competition for nitrogen as an independent driver of soil carbon balance and demonstrate the need to understand microbial community interactions to predict ecosystem feedbacks to global climate.

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests

Tropical ecosystems remain poorly understood and this is particularly true for belowground soil fungi. Soil fungi may respond to plant identity when, for example, plants differentially allocate resources belowground. However, spatial and temporal heterogeneity in factors such as plant inputs, moisture, or nutrients can also affect fungal communities and obscure our ability to detect plant effects in single time point studies or within diverse forests. To address this, we sampled replicated monocultures of four tree species and secondary forest controls sampled in the drier and wetter seasons over 2 years. Fungal community composition was primarily related to vegetation type and spatial heterogeneity in the effects of vegetation type, with increasing divergence partly reflecting greater differences in soil pH and soil moisture. Across wetter versus drier dates, fungi were 7% less diverse, but up to four-fold more abundant. The combined effects of tree species and seasonality suggest that predicted losses of tropical tree diversity and intensification of drought have the potential to cascade belowground to affect both diversity and abundance of tropical soil fungi.

Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism

Global climate models predict a future of increased severity of drought in many tropical forests. Soil microbes are central to the balance of these systems as sources or sinks of atmospheric carbon (C), yet how they respond metabolically to drought is not well-understood. We simulated drought in the typically aseasonal Luquillo Experimental Forest, Puerto Rico, by intercepting precipitation falling through the forest canopy. This approach reduced soil moisture by 13% and water potential by 0.14 MPa (from -0.2 to -0.34). Previous results from this experiment have demonstrated that the diversity and composition of these soil microbial communities are sensitive to even small changes in soil water. Here, we show prolonged drought significantly alters the functional potential of the community and provokes a clear osmotic stress response, including the production of compatible solutes that increase intracellular C demand. Subsequently, a microbial population emerges with a greater capacity for extracellular enzyme production targeting macromolecular carbon. Significantly, some of these drought-induced functional shifts in the soil microbiota are attenuated by prior exposure to a short-term drought suggesting that acclimation may occur despite a lack of longer-term drought history.