Challenges in upscaling laboratory studies to ecosystems in soil microbiology research

Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale

Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.

Effects of freeze-thaw cycles on soil greenhouse gas emissions: A systematic review

In the context of global warming, increasingly widespread and frequent freezing and thawing cycles (FTCs) will have profound effects on the biogeochemical cycling of soil carbon and nitrogen. FTCs can increase soil greenhouse gas (GHG) emissions by reducing the stability of soil aggregates, promoting the release of dissolved organic carbon, decreasing the number of microorganisms, inducing cell rupture, and releasing carbon and nitrogen nutrients for use by surviving microorganisms. However, the similarity and disparity of the mechanisms potentially contributing to changes in GHGs have not been systematically evaluated. The present study consolidates the most recent findings on the dynamics of soil carbon and nitrogen, as well as GHGs, in relation to FTCs. Additionally, it analyzes the impact of FTCs on soil GHGs in a systematic manner. In this study, particular emphasis is given to the following: (i) the reaction mechanism involved; (ii) variations in soil composition in different types of land (e.g., forest, peatland, farmland, and grassland); (iii) changes in soil structure in response to cycles of freezing temperatures; (iv) alterations in microbial biomass and community structure that may provide further insight into the fluctuations in GHGs after FTCs. The challenges identified included the extension of laboratory-scale research to ecosystem scales, the performance of in-depth investigation of the coupled effects of carbon, nitrogen, and water in the freeze-thaw process, and analysis of the effects of FTCs through the use of integrated research tools. The results of this study can provide a valuable point of reference for future experimental designs and scientific investigations and can also assist in the analysis of the attributes of GHG emissions from soil and the ecological consequences of the factors that influence these emissions in the context of global permafrost warming.

The proliferation of beneficial bacteria influences the soil C, N, and P cycling in the soybean-maize intercropping system

Soybean-maize intercropping system can improve the utilization rate of farmland and the sustainability of crop production systems. However, there is a significant gap in understanding the interaction mechanisms between soil carbon (C), nitrogen (N), and phosphorus (P) cycling functional genes, rhizosphere microorganisms, and nutrient availability. To reveal the key microorganisms associated with soil nutrient utilization and C, N, and P cycling function in the soybean-maize intercropping system, we investigated the changes in soil properties, microbial community structure, and abundance of functional genes for C, N, and P cycling under soybean-maize intercropping and monocropping at different fertility stages in a pot experiment. We found that there was no significant difference in the rhizosphere microbial community between soybean-maize intercropping and monocropping at the seeding stage. As the reproductive period progressed, differences in microbial community structure between intercropping and monocropping gradually became significant, manifesting the advantages of intercropping. During the intercropping process of soybean and maize, the relative abundance of beneficial bacteria in soil rhizosphere significantly increased, particularly Streptomycetaceae and Pseudomonadaceae. Moreover, the abundances of C, N, and P cycling functional genes, such as abfA, mnp, rbcL, pmoA (C cycling), nifH, nirS-3, nosZ-2, amoB (N cycling), phoD, and ppx (P cycling), also increased significantly. Redundancy analysis and correlation analysis showed that Streptomycetaceae and Pseudomonadaceae were significantly correlated with soil properties and C, N, and P cycling functional genes. In brief, soybean and maize intercropping can change the structure of microbial community and promote the proliferation of beneficial bacteria in the soil rhizosphere. The accumulation of these beneficial bacteria increased the abundance of C, N, and P cycling functional genes in soil and enhanced the ability of plants to fully utilize environmental nutrients and promoted growth.

Microbial evolution-An under-appreciated driver of soil carbon cycling

Although substantial advances in predicting the ecological impacts of global change have been made, predictions of the evolutionary impacts have lagged behind. In soil ecosystems, microbes act as the primary energetic drivers of carbon cycling; however, microbes are also capable of evolving on timescales comparable to rates of global change. Given the importance of soil ecosystems in global carbon cycling, we assess the potential impact of microbial evolution on carbon-climate feedbacks in this system. We begin by reviewing the current state of knowledge concerning microbial evolution in response to global change and its specific effect on soil carbon dynamics. Through this integration, we synthesize a roadmap detailing how to integrate microbial evolution into ecosystem biogeochemical models. Specifically, we highlight the importance of microscale mechanistic soil carbon models, including choosing an appropriate evolutionary model (e.g., adaptive dynamics, quantitative genetics), validating model predictions with 'omics' and experimental data, scaling microbial adaptations to ecosystem level processes, and validating with ecosystem-scale measurements. The proposed steps will require significant investment of scientific resources and might require 10-20 years to be fully implemented. However, through the application of multi-scale integrated approaches, we will advance the integration of microbial evolution into predictive understanding of ecosystems, providing clarity on its role and impact within the broader context of environmental change.

Soil respiration and controls in warmer winter: A snow manipulation study in postfire and undisturbed black pine forests

Climate change impacts drive warmer winters, reduced snowfall, and forest fires. In 2020, a wildfire scorched about 1508 hectares of black pine (Pinus nigra Arnold) forests in Türkiye. Whether the combined effects of lack of snow and forest fires significantly alter winter soil respiration (Rs) and soil temperature remains poorly understood. A field experiment was conducted in the postfire and undisturbed black pine forests during the winter to quantify Rs rates as affected by lack of snow and forest fire. We applied four treatments: snow-exclusion postfire (SEPF), snow postfire (SPF), snow-exclusion-undisturbed forest (SEUF), and snow undisturbed forest (SUF). The SEPF exhibited the significantly lowest mean Rs rates (0.71 μmol m-2 s-1) compared to the SPF (1.02 μmol m-2 s-1), SEUF (1.44 μmol m-2 s-1), and SUF (1.48 μmol m-2 s-1). The Rs also showed significant variations with time (p < .0001). However, treatments and time revealed no statistically significant interaction effects (p = .6801). Total winter Rs (January-March) ranged from 4.47 to 4.59 Mt CO2 ha-1 in the undisturbed forest and 2.20 to 3.16 Mt CO2 ha-2 in the postfire site. The Rs showed a significantly positive relationship (p < .0001) with the soil (0.59) and air (0.46) temperatures and a significantly negative relationship (p = .0017) with the soil moisture (-0.20) at the 5 cm depth. In contrast, the Rs indicated a negative but not statistically significant relationship (p = .0932) with the soil moisture (-0.16) at the 10 cm soil depth. The combined effects of lack of snow and forest fire significantly decreased Rs, thus conserving the soil's organic carbon stocks and reducing the CO2 contribution to the atmosphere. In contrast, a warmer winter significantly increased Rs rates in the undisturbed forest, suggesting an acceleration of soil organic carbon losses and providing positive feedback to climate change.

Changing soil available substrate primarily caused by fertilization management contributed more to soil respiration temperature sensitivity than microbial community thermal adaptation

Substrate depletion and microbial community thermal adaptation are major mechanisms that regulate the temperature sensitivity (Q10) of soil microbial respiration. Traditionally, the Q10 of soil microbial respiration is measured using laboratory incubation, which has limits in the continuous input of available substrates and the time scale for microbial community thermal adaptation. How the available substrate and the soil microbial community regulate the Q10 of soil microbial respiration under natural warming conditions remains unclear. To fill this gap in knowledge, a long-term field experiment was conducted consisting of two years of soil respiration observations combined with a soil available substrate and microbial community thermal adaptation analysis under seasonal warming conditions. The Q10 of soil respiration was calculated using the square root method, and it was more affected by the available substrate than by microbial community thermal adaptation. Fertilization management has a stronger effect on soil available substrate than temperature. As the temperature increased, NH4-N proved itself to be important for the bacterial community in the process of Q10 regulation, while dissolved organic carbon and nitrogen were key factors for the fungal community. Based on the niche breadth of microbial community composition, the changing Q10 of the soil respiration was not only closely associated with the specialist community, but also the generalist and neutralist communities. Furthermore, bacterial community thermal adaptation primarily occurred through shifts in the abundances of specialists and neutralists, while changes in species richness and species replacement occurred for the fungal generalists and neutralists. This work indicates that changing available nitrogen and DOC primarily caused by fertilization management contributed more in regulating the Q10 of soil microbial respiration than microbial community thermal adaptation, and there are different mechanisms for bacterial and fungal community thermal adaptation under warming.

The mixed blessings of rare earth element supplements for tomatoes and ferns

Rare earth elements (REEs) constitute a key group of critical minerals that are strategic for the global low-carbon economy and several United Nations Sustainable Development Goals. Their expected escalating emissions into the environment from emerging anthropogenic sources can negatively affect natural ecosystems. However, their hormetic effects make these elements effective fertilizers to promote crop production. Here, we investigate the response of tomatoes and ferns to REE exposure (La, Gd, Yb). While ferns were unresponsive to REEs, these elements promote evident benefits in tomatoes, e.g., elevating nutrient uptake, higher photosynthetic capacity and phytohormone enhancement to allocate energy to green tissue and root development. Nevertheless, the non-selective cation uptake incurs risks of accumulating non-essential elements in edible tissues. These evident benefits of REEs on crops support applications in agricultural production systems, create added value to the global distribution and promote better material flow management of REEs as strategic and critical resources.

Shifts in soil ammonia-oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions

Anthropogenic nitrogen (N) loading alters soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize 68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N-stimulation of nitrification, but does so via climate-related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N-availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate-related shifts in soil ammonia-oxidizing community maintain the N-stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.

Revisiting the relationships between soil nitrous oxide emissions and microbial functional gene abundances

A conceptual framework proposes that soil N2 O emissions are more likely related to microbial functional gene abundances based on laboratory experiments than in-situ observations. This framework has largely contributed to reconciling the disputation on linking soil N2 O emissions with functional gene abundances, but the direct evidence is lacking. Wei et al. (2023) provided new evidence to support this framework, showing that O2 dynamics were a better predictor of in-situ soil N2 O emissions than were functional gene abundances. Before the observations can inform N2 O modeling and support sustainable nitrogen management, however, some additional efforts are needed to revisit the relationships between in-situ soil N2 O emissions and functional gene abundances.

Shift from flooding to drying enhances the respiration of soil aggregates by changing microbial community composition and keystone taxa

Changes in the water regime are among the crucial factors controlling soil carbon dynamics. However, at the aggregate scale, the microbial mechanisms that regulate soil respiration under flooding and drying conditions are obscure. In this research, we investigated how the shift from flooding to drying changes the microbial respiration of soil aggregates by affecting microbial community composition and their co-occurrence patterns. Soils collected from a riparian zone of the Three Gorges Reservoir, China, were subjected to a wet-and-dry incubation experiment. Our data illustrated that the shift from flooding to drying substantially enhanced soil respiration for all sizes of aggregate fractions. Moreover, soil respiration declined with aggregate size in both flooding and drying treatments. The keystone taxa in bacterial networks were found to be Acidobacteriales, Gemmatimonadales, Anaerolineales, and Cytophagales during the flooding treatment, and Rhizobiales, Gemmatimonadales, Sphingomonadales, and Solirubrobacterales during the drying treatment. For fungal networks, Hypocreales and Agaricalesin were the keystone taxa in the flooding and drying treatments, respectively. Furthermore, the shift from flooding to drying enhanced the microbial respiration of soil aggregates by changing keystone taxa. Notably, fungal community composition and network properties dominated the changes in the microbial respiration of soil aggregates during the shift from flooding to drying. Thus, our study highlighted that the shift from flooding to drying changes keystone taxa, hence increasing aggregate-scale soil respiration.

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.

Linking between soil properties, bacterial communities, enzyme activities, and soil organic carbon mineralization under ecological restoration in an alpine degraded grassland

Soil organic carbon (SOC) mineralization is affected by ecological restoration and plays an important role in the soil C cycle. However, the mechanism of ecological restoration on SOC mineralization remains unclear. Here, we collected soils from the degraded grassland that have undergone 14 years of ecological restoration by planting shrubs with Salix cupularis alone (SA) and, planting shrubs with Salix cupularis plus planting mixed grasses (SG), with the extremely degraded grassland underwent natural restoration as control (CK). We aimed to investigate the effect of ecological restoration on SOC mineralization at different soil depths, and to address the relative importance of biotic and abiotic drivers of SOC mineralization. Our results documented the statistically significant impacts of restoration mode and its interaction with soil depth on SOC mineralization. Compared with CK, the SA and SG increased the cumulative SOC mineralization but decreased C mineralization efficiency at the 0-20 and 20-40 cm soil depths. Random Forest analyses showed that soil depth, microbial biomass C (MBC), hot-water extractable organic C (HWEOC), and bacterial community composition were important indicators that predicted SOC mineralization. Structural equal modeling indicated that MBC, SOC, and C-cycling enzymes had positive effects on SOC mineralization. Bacterial community composition regulated SOC mineralization via controlling microbial biomass production and C-cycling enzyme activities. Overall, our study provides insights into soil biotic and abiotic factors in association with SOC mineralization, and contributes to understanding the effect and mechanism of ecological restoration on SOC mineralization in a degraded grassland in an alpine region.