Microbes, memory, and moisture: predicting microbial moisture responses and their impact on carbon cycling

Protists and fungi: Reinforcing urban soil ecological functions against flash droughts

Rising instances of flash droughts are contributing to notable variability in soil moisture across terrestrial ecosystems. These phenomena challenge urban ecosystem services, yet the reaction of soil ecological functions (SEFs) to such events is poorly understood. This study investigates the responses of SEFs (about nutrient metabolism capacity and potential) and the microbiome under two specific scenarios: a flooding-drought sequence and a direct drought condition. Using quantitative microbial element cycling analysis, high-throughput sequencing, and enzyme activity measurements, we found that unlike in forests, the microbial composition in urban soils remained unchanged during flash drought conditions. However, SEFs were affected in both settings. Correlation analysis and Mantel test showed that forest soils exhibited more complex interactions among soil moisture, properties, and microbial communities. Positive linear correlation revealed that bacteria were the sole drivers of SEFs. Interestingly, while multi-threshold results suggested bacterial α diversity impeded the maximization of SEFs in urban soils, fungi and protists had a beneficial impact. Cross-domain network of urban soils had higher number of nodes and edges, but lower average degree and robustness than forest soils. Mantel test revealed that fungi and protist had significant correlations with bacterial composition in forest soils, but not in urban soils. In the urban network, the degree and eigenvector centrality of bacterial, fungal and protistan ASVs were significantly lower compared to those in the forest. These results suggest that the lower robustness of the microbial network in urban soils is attributed to limited interactions among fungi, consumer protists, and bacteria, contributing to the failure of microbial-driven ecological functions. Overall, our findings emphasize the critical role of fungi and protists in shielding urban soils from drought-induced disturbances and in enhancing the resistance of urban ecological functions amidst environmental changes.

Persistent legacy effects on soil metagenomes facilitate plant adaptive responses to drought

Both chronic and acute drought alter the composition and physiology of soil microbiomes, with implications for globally important processes including carbon cycling and plant productivity. When water is scarce, selection favors microbes with thicker peptidoglycan cell walls, sporulation ability, and constitutive osmolyte production (Schimel, Balser, and Wallenstein 2007)-but also the ability to degrade complex plant-derived polysaccharides, suggesting that the success of plants and microbes during drought are inextricably linked. However, communities vary enormously in their drought responses and subsequent interactions with plants. Hypothesized causes of this variation in drought resilience include soil texture, soil chemistry, and historical precipitation patterns that shaped the starting communities and their constituent species (Evans, Allison, and Hawkes 2022). Currently, the physiological and molecular mechanisms of microbial drought responses and microbe-dependent plant drought responses in diverse natural soils are largely unknown (de Vries et al. 2023). Here, we identify numerous microbial taxa, genes, and functions that characterize soil microbiomes with legacies of chronic water limitation. Soil microbiota from historically dry climates buffered plants from the negative effects of subsequent acute drought, but only for a wild grass species native to the same region, and not for domesticated maize. In particular, microbiota with a legacy of chronic water limitation altered the expression of a small subset of host genes in crown roots, which mediated the effect of acute drought on transpiration and intrinsic water use efficiency. Our results reveal how long-term exposure to water stress alters soil microbial communities at the metagenomic level, and demonstrate the resulting "legacy effects" on neighboring plants in unprecedented molecular and physiological detail.

Microbial communities mediate the effect of cover cropping on soil ecosystem functions under precipitation reduction in an agroecosystem

Cover cropping is a sustainable agricultural practice that profoundly influences soil microbial communities and ecosystem functions. However, the responses of soil ecosystem functions and microbial communities to cover cropping under the projected changes in precipitation, remain largely unexplored. To address this gap, a field experiment with cover cropping (control, hairy vetch, ryegrass, and hairy vetch plus ryegrass) and precipitation reduction (ambient precipitation and 50 % reduction in ambient precipitation) treatments was conducted from 2018 to 2020 in an agroecosystem located in the Guanzhong Plain of China. Soil ecosystem functions related to nutrient storage, nutrient cycling, and organic matter decomposition were measured to assess the soil multifunctionality index and bacterial and fungal communities were determined by Illumina NovaSeq sequencing. The results indicated that cover cropping enhanced soil multifunctionality index, and reduced precipitation strengthened this effect. Microbial community composition, rather than microbial diversity, was significantly altered by cover cropping regardless of precipitation reduction. Cover cropping increased the microbial network complexity and stability, but this effect was dampened by reduced precipitation. The microbial community composition and network complexity significantly and positively correlated with soil multifunctionality index under ambient and reduced precipitation conditions. Linear regression analyses and structural equation models collectively demonstrated that the increase in soil multifunctionality index was attributed to cover cropping-induced changes in microbial community composition and network complexity, irrespective of precipitation reduction. This study highlights the crucial role of microbial communities in driving the response of soil multifunctionality to cover cropping in the context of reduced precipitation, which has important implications for agricultural management and sustainability under future climate change scenarios.

Rainfall effect on soil respiration depends on antecedent soil moisture

Climate change has a discernible influence on rainfall patterns, thus potentially affecting the intricate dynamics of soil respiration (Rs) and soil carbon storage. However, we still lack a profound understanding of the determinants of Rs response to rainfall events. Here, utilizing a comprehensive 10-year dataset (2004-2013), we explored the direction and magnitude of Rs response to rainfall events and the underlying determinants in a temperate forest. Based on the identified 368 rainfall events over the study period, we demonstrate that rainfall suppresses Rs when the soil moisture is optimal and moist in the growing season, whereas its effect on Rs during the non-growing season is minimal. Notably, antecedent soil moisture, rather than rainfall amount, shows a substantial impact on Rs during the growing season (coefficient of determination (R2) = 0.37 for antecedent soil moisture, and R2 < 0.01 for rainfall amount). Incorporating antecedent soil moisture significantly enhances the explanatory power (R2) from 0.09 to 0.45 regarding the relative changes in Rs following rainfall events. Our results highlight the environmental dependency of Rs response to rainfall events and suggest that incorporating the role of antecedent soil moisture could enhance predictability and reduce uncertainty in ecosystem modeling.

Decreased snow depth inhibits litter decomposition via changes in litter microbial biomass and enzyme activity

Decreased snow depth resulting from global warming has the potential to significantly impact biogeochemical cycles in cold forests. However, the specific mechanisms of how snow reduction affects litter decomposition and the underlying microbial processes remain unclear, this knowledge gap limits our ability to precisely predict ecological processes within cold forest ecosystems under climate change. Hence, a field experiment was conducted in a subalpine forest in southwestern China, involving a gradient of snow reduction levels (control, 50 %, 100 %) to investigate the effects of decreased snow on litter decomposition, as well as microbial biomass and activity, specifically focused on two common species: red birch (Betula albosinensis) and masters larch (Larix mastersiana). After one year of incubation, the decomposition rate (k-value) of the two types of litter ranged from 0.12 to 0.24 across three snow treatments. A significant lower litter mass loss, microbial biomass and enzyme activity were observed under decreased snow depth in winter. Furthermore, a hysteresis inhibitory effect of snow reduction on hydrolase activity was observed in the following growing season. Additionally, the high initial quality (lower C/N ratio) of red birch litter facilitated the colonization by a greater quantity of microorganisms, making it more susceptible to snow reduction compared to the low-quality masters larch litter. Structural equation models indicated that decreased snow depth hindered litter decomposition by altering the biological characterization of litter (e.g., microbial biomass and enzyme activity) and environmental variables (e.g., mean temperature and moisture content). The findings suggest that the potential decline in snow depth could inhibit litter decomposition by reducing microbial biomass and activity, implying that the future climate change may alter the material cycling processes in subalpine forest ecosystems.

Exploring the biotic and abiotic drivers influencing nata de coco production by Komagataeibacter nataicola in pre-fermented coconut water

In China and Southeast Asia, pre-fermented coconut water is commonly used for the production of nata de coco, a jelly-like fermented food that consists of bacterial cellulose (BC). The inherent natural fermentation process of coconut water introduces uncontrollable variables, which can lead to unstable yields during BC production. This study involved the collection of spontaneously pre-fermented coconut water over a five-month production cycle. The aim was to evaluate the microbiota and metabolite profile, as well as determine its impact on BC synthesis by Komagataeibacter nataicola. Significant variations in the microbial community structure and metabolite profile of pre-fermented coconut water were observed across different production months, these variations had significant effects on BC synthesis by K. nataicola. A total of 52 different bacterial genera and 32 different fungal genera were identified as potential biotic factors that can influence BC production. Additionally, several abiotic factors, including lactate (VIP = 4.92), mannitol (VIP = 4.22), ethanol (VIP = 2.67), and ascorbate (VIP = 1.61), were found to be potential driving forces affecting BC synthesis by K. nataicola. Upon further analysis, the correlation network indicated that 14 biotic factors had a significant contribution to BC production in three strains of K. nataicola. These factors included 8 bacterial genera, such as Limosilactobacillus and Lactiplantibacillus, and 6 fungal genera, such as Meyerozyma and Ogataea. The abiotic factors lactate, mannitol, and ethanol showed a positive correlation with the BC yield. This study provides significant insights into controlling the fermentation processes of pre-fermented coconut water in industrial settings.

Long-term plastic mulching decreases rhizoplane soil carbon sequestration by decreasing microbial anabolism

Ridge-furrow with plastic mulching (RFPM) is a widely used agricultural practice in rain-fed farmlands. However, the impact of microbial related metabolism on soil organic carbon (SOC) is not fully understood. Amino sugar analysis, high-throughput sequencing, and high-throughput qPCR approaches are combined to investigate this topic, based on a long-term experiment. Treatments include flat planting without mulching (FP), ridge-furrow without mulching (RF), and RFPM. RFPM significantly decreases rhizoplane SOC contents, while bulk SOC contents change insignificantly across treatments. In terms of microbial metabolic pathways, RFPM decreases indicators of the in vivo metabolic pathway, whereas those of the ex vivo pathway are increased. In terms of microbial community features, core taxa module #1 is dominated by Sphingomonadaceae. These are putative high yield (Y) strategists, according to the microbial life-history strategy framework. They are closely related to the in vivo pathway and are most predictive for SOC; their abundance is highest under FP and lowest under RFPM. Core taxa module #2 is dominated by Chitinophagaceae, putative resource acquisition (A) strategists, that are closely related to the ex vivo pathway. Their abundance in the rhizoplane is highest under RFPM and lowest under FP. The RFPM-induced decline in SOC occurs simultaneously with the abundance of A-strategists with in vivo pathway but not the Y-strategists with ex vivo pathway. Overall, the result of this study shows a trade-off. In RFPM practice, the ex vivo microbial pathway is enhanced along with the abundance of A-strategists. This is not the case for the in vivo pathway and associated abundance of Y-strategists, which are closely associated with SOC. Our findings underlined the impact of rhizoplane microbial metabolic pathways on SOC status is key to agricultural practices in drylands such as RFPM, and advanced our understanding of how microbes affect the carbon cycling in dryland farming.

Microbial drought resistance may destabilize soil carbon

Droughts are becoming more frequent and intense with climate change. As plants and microbes respond to drought, there may be consequences for the vast stocks of organic carbon stored in soils. If microbes sustain their activity under drought, soils could lose carbon, especially if inputs from plants decline. Empirical and theoretical studies reveal multiple mechanisms of microbial drought resistance, including tolerance and avoidance. Physiological responses allow microbes to acclimate to drought within minutes to days. Along with dispersal, shifts in community composition could allow microbiomes to maintain functioning despite drought. Microbes might also adapt to drier conditions through evolutionary processes. Together, these mechanisms could result in soil carbon losses larger than currently anticipated under climate change.

Resilience of ecosystem service delivery in grasslands in response to single and compound extreme weather events

Extreme weather events are increasing in frequency and magnitude with profound effects on ecosystem functioning. Further, there is now a greater likelihood that multiple extreme events are occurring within a single year. Here we investigated the effect of a single drought, flood or compound (flood + drought) extreme event on temperate grassland ecosystem processes in a field experiment. To assess system resistance and resilience, we studied changes in a wide range of above- and below-ground indicators (plant diversity and productivity, greenhouse gas emissions, soil chemical, physical and biological metrics) during the 8 week stress events and then for 2 years post-stress. We hypothesized that agricultural grasslands would have different degrees of resistance and resilience to flood and drought stress. We also investigated two alternative hypotheses that the combined flood + drought treatment would either, (A) promote ecosystem resilience through more rapid recovery of soil moisture conditions or (B) exacerbate the impact of the single flood or drought event. Our results showed that flooding had a much greater effect than drought on ecosystem processes and that the grassland was more resistant and resilient to drought than to flood. The immediate impact of flooding on all indicators was negative, especially for those related to production, and climate and water regulation. Flooding stress caused pronounced and persistent shifts in soil microbial and plant communities with large implications for nutrient cycling and long-term ecosystem function. The compound flood + drought treatment failed to show a more severe impact than the single extreme events. Rather, there was an indication of quicker recovery of soil and microbial parameters suggesting greater resilience in line with hypothesis (A). This study clearly reveals that contrasting extreme weather events differentially affect grassland ecosystem function but that concurrent events of a contrasting nature may promote ecosystem resilience to future stress.

Drought legacies and ecosystem responses to subsequent drought

Climate change is expected to increase the frequency and severity of droughts. These events, which can cause significant perturbations of terrestrial ecosystems and potentially long-term impacts on ecosystem structure and functioning after the drought has subsided are often called 'drought legacies'. While the immediate effects of drought on ecosystems have been comparatively well characterized, our broader understanding of drought legacies is just emerging. Drought legacies can relate to all aspects of ecosystem structure and functioning, involving changes at the species and the community scale as well as alterations of soil properties. This has consequences for ecosystem responses to subsequent drought. Here, we synthesize current knowledge on drought legacies and the underlying mechanisms. We highlight the relevance of legacy duration to different ecosystem processes using examples of carbon cycling and community composition. We present hypotheses characterizing how intrinsic (i.e. biotic and abiotic properties and processes) and extrinsic (i.e. drought timing, severity, and frequency) factors could alter resilience trajectories under scenarios of recurrent drought events. We propose ways for improving our understanding of drought legacies and their implications for subsequent drought events, needed to assess the longer-term consequences of droughts on ecosystem structure and functioning.