Decomposition responses to climate depend on microbial community composition

Effects of canopy gaps on microclimate, soil biological activity and their relationship in a European mixed floodplain forest

Forest canopy gaps can influence understorey microclimate and ecosystem functions such as decomposition. Gaps can arise from silviculture or tree mortality, increasingly influenced by climate change. However, to what degree canopy gaps affect the buffered microclimate in the understorey under macroclimatic changes is unclear. We, therefore, investigated the effect of forest gaps differing in structure and size (25 gaps: single tree gaps up to 0.67 ha cuttings) on microclimate and soil biological activity compared to closed forest in a European mixed floodplain forest. During the investigation period in the drought year 2022 between May and October, mean soil moisture and temperature as well as soil and air temperature fluctuations increased with increasing openness. In summer, the highest difference of monthly means between cuttings and closed forest in the topsoil was 3.98 ± 9.43 % volumetric moisture and 2.05 ± 0.89 °C temperature, and in the air at 30 cm height 0.61 ± 0.35 °C temperature. For buffering, both the over- and understorey tree layers appeared as relevant with a particularly strong influence of understorey density on soil temperature. Three experiments, investigating soil biological activity by quantifying decomposition rates of tea and wooden spatulas as well as mesofauna feeding activity with bait-lamina stripes, revealed no significant differences between gaps and closed forest. However, we found a positive significant effect of mean soil temperature on feeding activity throughout the season. Although soil moisture decreased during this period, it showed no counteracting effect on feeding activity. Generally, very few significant relationships were observed between microclimate and soil biological activity in single experiments. Despite the dry growing season, decomposition rates remained high, suggesting temperature had a stronger influence than soil moisture. We conclude that the microclimatic differences within the gap gradient of our experiment were not strong enough to affect soil biological activity considerably.

Soil microbial identity explains home-field advantage for litter decomposition

Unraveling the mechanisms of home-field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking. To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool-temperate forests. Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome-wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss. The results indicated that the unique relationships between plant litter and soil microbes through plant-soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land-use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land-use change on decomposition processes in forest ecosystems.

Putting soil microbes on first: identifying the engines of home-field advantage in litter decomposition

This article is a Commentary on Shigyo et al. (2024); 243: 2146–2156.

Warming alters cascading effects of a dominant arthropod predator on fungal community composition in the Arctic

Rapid climate change in the Arctic is altering microbial structure and function, with important consequences for the global ecosystem. Emerging evidence suggests organisms in higher trophic levels may also influence microbial communities, but whether warming alters these effects is unclear. Wolf spiders are dominant Arctic predators whose densities are expected to increase with warming. These predators have temperature-dependent effects on decomposition via their consumption of fungal-feeding detritivores, suggesting they may indirectly affect the microbial structure as well. To address this, we used a fully factorial mesocosm experiment to test the effects of wolf spider density and warming on litter microbial structure in Arctic tundra. We deployed replicate litter bags at the surface and belowground in the organic soil profile and analyzed the litter for bacterial and fungal community structure, mass loss, and nutrient characteristics after 2 and 14 months. We found there were significant interactive effects of wolf spider density and warming on fungal but not bacterial communities. Specifically, higher wolf spider densities caused greater fungal diversity under ambient temperature but lower fungal diversity under warming at the soil surface. We also observed interactive treatment effects on fungal composition belowground. Wolf spider density influenced surface bacterial composition, but the effects did not change with warming. These findings suggest a widespread predator can have indirect, cascading effects on litter microbes and that effects on fungi specifically shift under future expected levels of warming. Overall, our study highlights that trophic interactions may play important, albeit overlooked, roles in driving microbial responses to warming in Arctic terrestrial ecosystems.

IMPORTANCE

The Arctic contains nearly half of the global pool of soil organic carbon and is one of the fastest warming regions on the planet. Accelerated decomposition of soil organic carbon due to warming could cause positive feedbacks to climate change through increased greenhouse gas emissions; thus, changes in ecological dynamics in this region are of global relevance. Microbial structure is an important driver of decomposition and is affected by both abiotic and biotic conditions. Yet how activities of soil-dwelling organisms in higher trophic levels influence microbial structure and function is unclear. In this study, we demonstrate that predicted changes in abundances of a dominant predator and warming interactively affect the structure of litter-dwelling fungal communities in the Arctic. These findings suggest predators may have widespread, indirect cascading effects on microbial communities, which could influence ecosystem responses to future climate change.

Substrate complexity buffers negative interactions in a synthetic community of leaf litter degraders

Leaf litter microbes collectively degrade plant polysaccharides, influencing land-atmosphere carbon exchange. An open question is how substrate complexity-defined as the structure of the saccharide and the amount of external processing by extracellular enzymes-influences species interactions. We tested the hypothesis that monosaccharides (i.e. xylose) promote negative interactions through resource competition, and polysaccharides (i.e. xylan) promote neutral or positive interactions through resource partitioning or synergism among extracellular enzymes. We assembled a three-species community of leaf litter-degrading bacteria isolated from a grassland site in Southern California. In the polysaccharide xylan, pairs of species stably coexisted and grew equally in coculture and in monoculture. Conversely, in the monosaccharide xylose, competitive exclusion and negative interactions prevailed. These pairwise dynamics remained consistent in a three-species community: all three species coexisted in xylan, while only two species coexisted in xylose, with one species capable of using peptone. A mathematical model showed that in xylose these dynamics could be explained by resource competition. Instead, the model could not predict the coexistence patterns in xylan, suggesting other interactions exist during biopolymer degradation. Overall, our study shows that substrate complexity influences species interactions and patterns of coexistence in a synthetic microbial community of leaf litter degraders.

Nanomaterials in the environment and their pragmatic voyage at various trophic levels in an ecosystem

In the development of nanotechnology, nanomaterials (NMs) have a huge credential in advancing the existing follow-ups of analytical and diagnosis techniques, drug designing, agricultural science, electronics, cosmetics, sports, textiles and water purification. However, NMs have also grasped attention of researchers onto their toxicity. In the present review, initially the development of notable NMs such as metal and metal-oxide nanoparticles (NPs), magnetic NPs, carbon-based NMs and quantum dots intended to be commercialized along with their applications are discussed. This is followed by the current scenario of NMs in the environment to widen the outlook on the concentration of NPs in the environmental compartments and the frequency of organism exposed to NPs at varied trophic levels. In order to understand the physiochemical and morphological significance of NPs in exhibiting toxicity, fate of NPs in the environment is briefly deliberated. This is further geared-up to glance in-sightedly on the organisms starting from primary producer to primary consumer, secondary consumer, tertiary consumer and decomposers encountering NPs in their habitual niche. The state of NPs to which organisms are exposed, mechanism of NP uptake and toxicity, anomalies faced at each trophic level, concentration of NPs that is liable to cause toxicity and, biotransfer of NPs to the next generation and trophic level are detailed. Finally, the future prospects on bioaccumulation and biomagnification of NP-based products are conversed. Thus, the review would be noteworthy in unveiling the significance of NPs in forthcoming years combined with threat towards each organism in an ecosystem.

Sheep dung deposition disrupted the soil microbiome in degraded grassland but not in non-degraded grassland

Grazing is the most extensive land use in grassland worldwide, wherein the soil microbiome is known to support multiple ecosystem functions. Yet, the experimental impact of livestock grazing and dung deposits on the soil microbiome in degraded grassland remains poorly understood. We examined the effects of sheep dung depositions on the bacterial and fungal microbiome of two grasslands: non-degraded and degraded (long-term overgrazing) in northern China. Specifically, sheep dung was experimentally added to the soil and its effects on the soil microbial community were determined 3 months later (corresponding to livestock excreta deposited throughout the entire growing season of grassland, June to September). Our results showed that sheep dung additions showed negative effects on the soil microbiome of already degraded grassland, while with a diminished impact on the non-degraded grassland. In particular, dung deposition decreased soil microbial Shannon index, notably significantly reducing fungal diversity in degraded grassland. Moreover, sheep dung deposition modifies soil bacterial community structure and diminishes bacterial community network complexity. The alteration of soil pH caused by sheep dung deposition partially explains the decline in microbial diversity in degraded grassland. However, sheep dung did not alter the relative abundance and community composition of bacterial and fungal dominant phyla either in the non-degraded or in the degraded grassland. In conclusion, the short-term deposition of sheep dung exerted a detrimental influence on the microbial community in degraded grassland soil. It contributes new experimental evidence regarding the adverse effects of livestock grazing, particularly through dung deposition, on the soil microbiome in degraded grassland. This knowledge is crucial for guiding managers in conserving the soil microbiome in grazed grasslands.

Mycorrhizal fungi modify decomposition: a meta-analysis

It has been proposed that ectomycorrhizal fungi can reduce decomposition while arbuscular mycorrhizal fungi may enhance it. These phenomena are known as the 'Gadgil effect' and 'priming effect', respectively. However, it is unclear which one predominates globally. We evaluated whether mycorrhizal fungi decrease or increase decomposition, and identified conditions that mediate this effect. We obtained decomposition data from 43 studies (97 trials) conducted in field or laboratory settings that controlled the access of mycorrhizal fungi to substrates colonized by saprotrophs. Across studies, mycorrhizal fungi promoted decomposition of different substrates by 6.7% overall by favoring the priming effect over the Gadgil effect. However, we observed significant variation among studies. The substrate C : N ratio and absolute latitude influenced the effect of mycorrhizal fungi on decomposition and contributed to the variation. Specifically, mycorrhizal fungi increased decomposition at low substrate C : N and absolute latitude, but there was no discernable effect at high values. Unexpectedly, the effect of mycorrhizal fungi was not influenced by the mycorrhizal type. Our findings challenge previous assumptions about the universality of the Gadgil effect but highlight the potential of mycorrhizal fungi to negatively influence soil carbon storage by promoting the priming effect.

Diversity and biogeography of bacterial community in the Ili River network varies locally and regionally

Microorganisms in rivers indeed play a crucial role in nutrient cycling within aquatic ecosystems. Understanding the assembly mechanisms of bacterial communities in river networks is essential for predicting their special composition and functional characteristics in natural rivers. This study employed 16S rRNA gene amplicon sequence variation (ASVs) to scrutinize the bacterial community within the uniquely topographical Ili River network. The bacterial community composition varied across the three tributaries with distinct sources and the mainstream. The confluence of various sources diminished the diversity of the bacterial community and altered the functionality of within mainstream. We suggest that strong dispersal limitation predominantly shaped the community at the regional scale (46.6 %), underscoring the significant contribution of headwater sites to bacterial community composition. Contrary to expectation, the bacterial resources in the mainstream were not enriched by the higher diversity in three tributaries. Instead, confluence disturbance potentially increased the undominated processes (36.7 %) and alter the bacterial community composition at the local scale of the mainstream. The intricate coalescence at the confluence could potentially be an intriguing causative factor. Our research indicates that the composition of bacterial communities within intricate river networks exhibits biogeographic patterns, simultaneously influenced by river confluence and geographical features, necessitating multi-scale analysis.

Thinning enhances forest soil C storage by shifting the soil toward an oligotrophic condition

Forests are significant carbon reservoirs, with approximately one-third of this carbon stored in the soil. Forest thinning, a prevalent management technique, is designed to enhance timber production, preserve biodiversity, and maintain ecosystem functions. Through its influence on biotic and abiotic factors, thinning can profoundly alter soil carbon storage. Yet, the full implications of thinning on forest soil carbon reservoirs and the mechanisms underpinning these changes remain elusive. In this study, we undertook a two-year monitoring initiative, tracking changes in soil extracellular enzyme activities (EEAs), microbial communities, and other abiotic parameters across four thinning intensities within a temperate pine forest. Our results show a marked increase in soil carbon stock following thinning. However, thinning also led to decreased dissolved organic carbon (DOC) content and a reduced DOC to soil organic carbon (SOC) ratio, pointing toward a decline in soil carbon lability. Additionally, fourier transform infrared spectroscopy (FTIR) analysis revealed an augmented relative abundance of aromatic compounds after thinning. There was also a pronounced increase in absolute EEAs (per gram of dry soil) post-thinning, implying nutrient limitations for soil microbes. Concurrently, the composition of bacterial and fungal communities shifted toward oligotrophic dominance post thinning. Specific EEAs (per gram of soil organic matter) exhibit a significant reduction following thinning, indicating a deceleration in organic matter decomposition rates. In essence, our findings reveal that thinning transitions soil toward an oligotrophic state, dampening organic matter decomposition, and thus bolstering the soil carbon storage potential of forest. This study provides enhanced insights into the nuanced relationship between thinning practices and forest soil carbon dynamics, serving as a robust foundation for enlightened forest management strategies.

Changes in nutrient availability substantially alter bacteria and extracellular enzymatic activities in Antarctic soils

In polar regions, global warming has accelerated the melting of glacial and buried ice, resulting in meltwater run-off and the mobilization of surface nutrients. Yet, the short-term effects of altered nutrient regimes on the diversity and function of soil microbiota in polyextreme environments such as Antarctica, remains poorly understood. We studied these effects by constructing soil microcosms simulating augmented carbon, nitrogen, and moisture. Addition of nitrogen significantly decreased the diversity of Antarctic soil microbial assemblages, compared with other treatments. Other treatments led to a shift in the relative abundances of these microbial assemblages although the distributional patterns were random. Only nitrogen treatment appeared to lead to distinct community structural patterns, with increases in abundance of Proteobacteria (Gammaproteobateria) and a decrease in Verrucomicrobiota (Chlamydiae and Verrucomicrobiae).The effects of extracellular enzyme activities and soil parameters on changes in microbial taxa were also significant following nitrogen addition. Structural equation modeling revealed that nutrient source and extracellular enzyme activities were positive predictors of microbial diversity. Our study highlights the effect of nitrogen addition on Antarctic soil microorganisms, supporting evidence of microbial resilience to nutrient increases. In contrast with studies suggesting that these communities may be resistant to change, Antarctic soil microbiota responded rapidly to augmented nutrient regimes.

Sphingomonas clade and functional distribution with simulated climate change

Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R2 = 0.465) and clade composition (R2 = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.

Impacts of litter microbial community on litter decomposition in the absence of soil microorganisms

What is the effect of phyllosphere microorganisms on litter decomposition in the absence of colonization by soil microorganisms? Here, we simulated the litter standing decomposition stage in the field to study the differences in the composition and structure of the phyllosphere microbial community after the mixed decomposition of Populus × canadensis and Pinus sylvestris var. mongolica litter. After 15 months of mixed decomposition, we discovered that litters that were not in contact with soil had an antagonistic effect (the actual decomposition rate was 18.18%, which is lower than the expected decomposition rate) and the difference between the litters themselves resulted in a negative response to litter decomposition. In addition, there was no significant difference in bacterial and fungal community diversity after litter decomposition. The litter bacterial community was negatively responsive to litter properties and positively responsive to the fungal community. Importantly, we found that bacterial communities had a greater impact on litter decomposition than fungi. This study has enriched our understanding of the decomposition of litter itself and provided a theoretical basis for further exploring the "additive and non-additive effects" of litter decomposition and the mechanism of microbial drive.

IMPORTANCE

The study of litter decomposition mechanism plays an important role in the material circulation of the global ecosystem. However, previous studies have often looked at contact with soil as the starting point for decomposition. But actually, standing litter is very common in forest ecosystems. Therefore, we used field simulation experiments to simulate the decomposition of litters without contact with soil for 15 months, to explore the combined and non-added benefits of the decomposition of mixed litters, and to study the influence of microbial community composition on the decomposition rate while comparing the differences of microbial communities.

Warming Leads to Changes in Soil Organic Carbon Molecules Due to Decreased Mineral Protection

Climate change affects the content and composition of soil organic carbon (SOC). However, warming-induced changes in the SOC compounds remain unknown. Using nuclear magnetic resonance spectroscopy, molecular mixing models, and Fourier transform ion cyclotron resonance mass spectrometry, we analyzed the variations and relationships in molecular compounds in Mollisol with 10-56 g C kg-1 soil-1 by translocating soils under six climate regimes. We found that increased temperature and precipitation were negatively correlated with carbohydrate versus lipid and lignin versus protein. The former was consistent across soils with varying SOC contents, but the latter decreased as the SOC content increased. The carbohydrate-lipid correlations were related to dithionite-citrate-extractable Fe, while the lignin-protein correlations were linked to changes in moisture and pyrophosphate-extractable Fe/Al. Our findings indicate that the reduction in the mineral protection of SOC is associated with molecular alterations in SOC under warming conditions.

Biological Interactions Mediate Soil Functions by Altering Rare Microbial Communities

Soil microbes, the main driving force of terrestrial biogeochemical cycles, facilitate soil organic matter turnover. However, the influence of the soil fauna on microbial communities remains poorly understood. We investigated soil microbiota dynamics by introducing competition and predation among fauna into two soil ecosystems with different fertilization histories. The interactions significantly affected rare microbial communities including bacteria and fungi. Predation enhanced the abundance of C/N cycle-related genes. Rare microbial communities are important drivers of soil functional gene enrichment. Key rare microbial taxa, including SM1A02, Gammaproteobacteria, and HSB_OF53-F07, were identified. Metabolomics analysis suggested that increased functional gene abundance may be due to specific microbial metabolic activity mediated by soil fauna interactions. Predation had a stronger effect on rare microbes, functional genes, and microbial metabolism compared to competition. Long-term organic fertilizer application increased the soil resistance to animal interactions. These findings provide a comprehensive understanding of microbial community dynamics under soil biological interactions, emphasizing the roles of competition and predation among soil fauna in terrestrial ecosystems.

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.

Fungal community composition predicts forest carbon storage at a continental scale

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

Depth effects on bacterial community altitudinal patterns and assembly processes in the warm-temperate montane forests of China

Soil bacterial communities are essential for ecosystem function, yet their response along altitudinal gradients in different soil strata remains unclear. Understanding bacterial community co-occurrence networks and assembly patterns in mountain ecosystems is crucial for comprehending microbial ecosystem functions. We utilized Illumina MiSeq sequencing to study bacterial diversity and assembly patterns of surface and subsurface soils across a range of elevations (700 to 2100 m) on Dongling Mountain. Our results showed significant altitudinal distribution patterns concerning bacterial diversity and structure in the surface soil. The bacterial diversity exhibited a consistent decrease, while specific taxa demonstrated unique patterns along the altitudinal gradient. However, no altitudinal dependence was observed for bacterial diversity and community structure in the subsurface soil. Additionally, a shift in bacterial ecological groups is evident with changing soil depth. Copiotrophic taxa thrive in surface soils characterized by higher carbon and nutrient content, while oligotrophic taxa dominate in subsurface soils with more limited resources. Bacterial community characteristics exhibited strong correlations with soil organic carbon in both soil layers, followed by pH in the surface soil and soil moisture in the subsurface soil. With increasing depth, there is an observable increase in taxa-taxa interaction complexity and network structure within bacterial communities. The surface soil exhibits greater sensitivity to environmental perturbations, leading to increased modularity and an abundance of positive relationships in its community networks compared to the subsurface soil. Furthermore, the bacterial community at different depths was influenced by combining deterministic and stochastic processes, with stochasticity (homogenizing dispersal and undominated) decreasing and determinism (heterogeneous selection) increasing with soil depth.

Composition of DOM along the depth gradients in the paddy field treated with crop straw for 10 years

Crop straw return is a widely used agricultural management practice. The addition of crop straw significantly alters the pool of dissolved organic matter (DOM) in agricultural soils and plays a pivotal role in the global carbon (C) cycle, which is sensitive to climate change. The DOM concentration and composition at different soil depths could regulate the turnover and further storage of organic C in terrestrial systems. However, it is still unclear how crop straw return influences the change in DOM composition in rice paddy soils. Therefore, a field experiment was conducted in which paddy soil was amended with crop straw for 10 years. Two crop straw-addition treatments [NPK with 50% crop straw (NPK+1/2S) and NPK with 100% crop straw (NPK + S)], a conventional mineral fertilization control (NPK) and a non-fertilized control were included. Topsoil (0-20 cm) and subsoil (20-40 cm) samples were collected to investigate the soil DOM concentration and compositional structure of the profile. Soil nutrients, iron (Fe) fraction, microbial biomass carbon (MBC), and concentration and optical properties (UV-Vis and fluorescence spectra) of soil DOM were determined. Here, we found that the DOM in the topsoil was more humified than that in the subsoil. The addition of crop straw further decreased the humidification degree of DOM in the subsoil. In crop straw-amended topsoil, microbial decomposition controlled the composition of DOM and induced the formation of aromatic DOM. In the straw-treated subsoil, selective adsorption by poorly crystalline Fe(oxyhydr)oxides and microbial decomposition controlled the composition of DOM. In particular, the formation of protein-like compounds could have played a significant role in the microbial degradation of DOM in the subsoil. Overall, this work conducted a case study within long-term agricultural management to understand the changes in DOM composition along the soil profile, which would be further helpful for evaluating C cycling in agricultural ecosystems.

Male, female, and mixed-sex poplar plantations support divergent soil microbial communities

Males and females of dioecious plants have sex-specific adaptations to diverse habitats. The effects of inter- and intrasexual interactions in poplar plantations on composition, structure, and function of soil microbiota have not been explored in degraded areas. We conducted a series of greenhouse and field experiments to investigate how belowground competition, soil microbial communities, and seasonal variation nitrogen content differ among female, male, and mixed-sex Populus cathayana plantations. In the greenhouse experiment, female neighbors suppressed the growth of males under optimal nitrogen conditions. However, male neighbors enhanced stable isotope ratio of nitrogen (δ15 N) of females under intersexual competition. In the field, the root length density, root area density, and biomass of fine roots were lower in female plantations than in male or mixed-sex plantations. Bacterial networks of female, male, and mixed-sex plantations were characterized by different composition of hub nodes, including connectors, modules, and network hubs. The sex composition of plantations altered bacterial and fungal community structures according to Bray-Curtis distances, with 44% and 65% of variance explained by the root biomass, respectively. The total soil nitrogen content of mixed-sex plantation was higher than that in female plantation in spring and summer. The mixed-sex plantation also had a higher β-1,4-N-acetyl-glucosaminidase activity in summer and a higher nitrification rate in autumn than the other two plantations. The seasonal soil N content, nitrification rate, and root distribution traits demonstrated spatiotemporal niche separation in the mixed-sex plantation. We argue that a strong female-female competition and limited nitrogen content could strongly impede plant growth and reduce the resistance of monosex plantations to climate change and the mixed-sex plantations constitutes a promising way to restore degraded land.

Multiple spatial scales of bacterial and fungal structural and functional traits affect carbon mineralization

Studying the functional heterogeneity of soil microorganisms at different spatial scales and linking it to soil carbon mineralization is crucial for predicting the response of soil carbon stability to environmental changes and human disturbance. Here, a total of 429 soil samples were collected from typical paddy fields in China, and the bacterial and fungal communities as well as functional genes related to carbon mineralization in the soil were analysed using MiSeq sequencing and GeoChip gene microarray technology. We postulate that CO2 emissions resulting from bacterial and fungal carbon mineralization are contingent upon their respective carbon consumption strategies, which rely on the regulation of interactions between biodiversity and functional genes. Our results showed that the spatial turnover of the fungal community was 2-4 times that of the bacterial community from hundreds of meters to thousands of kilometres. The effect of spatial scale exerted a greater impact on the composition rather than the functional characteristics of the microbial community. Furthermore, based on the establishment of functional networks at different spatial scales, we observed that both bacteria and fungi within the top 10 taxa associated with carbon mineralization exhibited a prevalence of generalist species at the regional scale. This study emphasizes the significance of spatial scaling patterns in soil bacterial and fungal carbon degradation functions, deepening our understanding of how the relationship between microbial decomposers and soil heterogeneity impacts carbon mineralization and subsequent greenhouse gas emissions.

Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system

Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.

Shifts in bacterial traits under chronic nitrogen deposition align with soil processes in arbuscular, but not ectomycorrhizal-associated trees

Nitrogen (N) deposition increases soil carbon (C) storage by reducing microbial activity. These effects vary in soil beneath trees that associate with arbuscular (AM) and ectomycorrhizal (ECM) fungi. Variation in carbon C and N uptake traits among microbes may explain differences in soil nutrient cycling between mycorrhizal associations in response to high N loads, a mechanism not previously examined due to methodological limitations. Here, we used quantitative Stable Isotope Probing (qSIP) to measure bacterial C and N assimilation rates from an added organic compound, which we conceptualize as functional traits. As such, we applied a trait-based approach to explore whether variation in assimilation rates of bacterial taxa can inform shifts in soil function under chronic N deposition. We show taxon-specific and community-wide declines of bacterial C and N uptake under chronic N deposition in both AM and ECM soils. N deposition-induced reductions in microbial activity were mirrored by declines in soil organic matter mineralization rates in AM but not ECM soils. Our findings suggest C and N uptake traits of bacterial communities can predict C cycling feedbacks to N deposition in AM soils, but additional data, for instance on the traits of fungi, may be needed to connect microbial traits with soil C and N cycling in ECM systems. Our study also highlights the potential of employing qSIP in conjunction with trait-based analytical approaches to inform how ecological processes of microbial communities influence soil functioning.

Desiccation induces varied responses within a soil bacterial genus

Desiccation impacts a suite of physiological processes in microbes by elevating levels of damaging reactive oxygen species and inducing DNA strand breaks. In response to desiccation-induced stress, microbes have evolved specialized mechanisms to help them survive. Here, we performed a 128-day lab desiccation experiment on nine strains from three clades of an abundant soil bacterium, Curtobacterium. We sequenced RNA from each strain at three time points to investigate their response. Curtobacterium was highly resistant to desiccation, outlasting both Escherichia coli and a famously DNA damage-resistant bacterium, Deinococcus radiodurans. However, within the genus, there were also 10-fold differences in survival rates among strains. Transcriptomic profiling revealed responses shared within the genus including up-regulation of genes involved in DNA damage repair, osmolyte production, and efflux pumps, but also up-regulation of pathways and genes unique to the three clades. For example, trehalose synthesis gene otsB, the chaperone groEL, and the oxygen scavenger katA were all found in either one or two clades but not the third. Here, we provide evidence of considerable variation in closely related strains, and further elucidation of the phylogenetic conservation of desiccation tolerance remains an important goal for microbial ecologists.

Microbial ecological clusters structured by environments drive maize residue decomposition at the continental scale

Environmental factors (e.g., climate and edaphic factors) indirectly regulate residue decomposition via microbial communities. Microbial ecological clusters (eco-clusters) structured by specific environmental factors have consequences for ecosystem functions. However, less is known about how microbial eco-clusters affect residue decomposition, especially over broad geographic scales. We collected agricultural soils from adjacent pairs of upland and paddy fields along a latitudinal gradient from the cold-temperature zone to the tropical zone, and conducted a microcosm experiment with 13C-labelled maize residue to explore the continental pattern of maize residue-derived 13CO2 (RDC), and whether and how microbial eco-clusters drive and predict RDC. Results showed that RDC decreased with latitude in both upland and paddy fields. Further, we identified 21 well-defined eco-clusters according to microbial environmental preferences, which explained 51.15 % of the spatial variations in RDC. The eco-clusters of high-total annual precipitation (TAP), high-mean annual temperature (MAT), low-pH, and some low-nutrient-associated exerted a positive effect on RDC. These eco-clusters contained many taxa belonging to the Actinobacteriota, Firmicutes, and Sordariomycetes, and their relative abundance decreased with latitude. Upland soils displayed 2.40-fold of RDC over paddy soils. Low-pH and high-organic matter (OM) eco-clusters were found to be the most prominent predictors of RDC in upland and paddy fields, respectively. Finally, we constructed a continental atlas of RDC in both upland and paddy fields based on eco-clusters and high-resolution climate and soil data. Overall, our study provides important evidence that historical environment-shaped microbial eco-clusters can drive and predict residue decomposition, providing new insights into how environmental factors indirectly regulate residue decomposition.

Testing the contribution of dispersal to microbial succession following a wildfire

IMPORTANCE

Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.

Bacterial community structure and assembly dynamics hinge on plant litter quality

Litter decomposition is a fundamental ecosystem process controlling the biogeochemical cycling of energy and nutrients. Using a 360-day lab incubation experiment to control for environmental factors, we tested how litter quality (low C/N deciduous vs. high C/N coniferous litter) governed the assembly and taxonomic composition of bacterial communities and rates of litter decomposition. Overall, litter mass loss was significantly faster in soils amended with deciduous (DL) rather than coniferous (CL) litter. Communities degrading DL were also more taxonomically diverse and exhibited stochastic assembly throughout the experiment. By contrast, alpha-diversity rapidly declined in communities exposed to CL. Strong environmental selection and competitive biological interactions induced by molecularly complex, nutrient poor CL were reflected in a transition from stochastic to deterministic assembly after 180 days. Constraining how the diversity and assembly of microbial populations modulates core ecosystem processes, such as litter decomposition, will become increasingly important under novel climate conditions, and as policymakers and land managers emphasize soil carbon sequestration as a key natural climate solution.

Role of microplastics in microbial community structure and functions in urban soils

Evidence from the laboratory suggests that microplastics (MPs) can harm soil microorganisms, affecting the structures and functions of microbial communities. The impact of soil MPs on microbes in actual urban environments with high human activity levels, however, has not been well reported. To investigate the MP effect on urban soil microorganisms under complex scenarios, we analyzed 42 soil samples from standardized plots of 7 urban functional zones. We report that urban green spaces are important for studying microbial diversity in the study area, and they also contribute to the global homogenization of soil microbes and genes. Bacterial communities in soils enriched with various MPs showed greater differences in OTUs than fungi. Compared to low-MP soils, most ARGs and nutrient cycling genes had similar or slightly lower abundances in soils with high levels of MPs. The coupling of pollutant factors with MPs as independent variables had significant explanatory power for both positive and negative correlations in PLS-PM analysis. Specifically, PET and PP MPs explained 3.54% and 6.03%, respectively, of the microbial community and functional genes. This study fills knowledge gaps on the effects of MPs on urban soil microbial communities in real environments, facilitating better management of urban green spaces.

Investigating the eco-evolutionary response of microbiomes to environmental change

Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.

Climate warming has direct and indirect effects on microbes associated with carbon cycling in northern lakes

Northern lakes disproportionately influence the global carbon cycle, and may do so more in the future depending on how their microbial communities respond to climate warming. Microbial communities can change because of the direct effects of climate warming on their metabolism and the indirect effects of climate warming on groundwater connectivity from thawing of surrounding permafrost, especially at lower landscape positions. Here we used shotgun metagenomics to compare the taxonomic and functional gene composition of sediment microbes in 19 peatland lakes across a 1600-km permafrost transect in boreal western Canada. We found microbes responded differently to the loss of regional permafrost cover than to increases in local groundwater connectivity. These results suggest that both the direct and indirect effects of climate warming, which were respectively associated with loss of permafrost and subsequent changes in groundwater connectivity interact to change microbial composition and function. Archaeal methanogens and genes involved in all major methanogenesis pathways were more abundant in warmer regions with less permafrost, but higher groundwater connectivity partly offset these effects. Bacterial community composition and methanotrophy genes did not vary with regional permafrost cover, and the latter changed similarly to methanogenesis with groundwater connectivity. Finally, we found an increase in sugar utilization genes in regions with less permafrost, which may further fuel methanogenesis. These results provide the microbial mechanism for observed increases in methane emissions associated with loss of permafrost cover in this region and suggest that future emissions will primarily be controlled by archaeal methanogens over methanotrophic bacteria as northern lakes warm. Our study more generally suggests that future predictions of aquatic carbon cycling will be improved by considering how climate warming exerts both direct effects associated with regional-scale permafrost thaw and indirect effects associated with local hydrology.

Dispersal changes soil bacterial interactions with fungal wood decomposition

Although microbes are the major agent of wood decomposition - a key component of the carbon cycle - the degree to which microbial community dynamics affect this process is unclear. One key knowledge gap is the extent to which stochastic variation in community assembly, e.g. due to historical contingency, can substantively affect decomposition rates. To close this knowledge gap, we manipulated the pool of microbes dispersing into laboratory microcosms using rainwater sampled across a transition zone between two vegetation types with distinct microbial communities. Because the laboratory microcosms were initially identical this allowed us to isolate the effect of changing microbial dispersal directly on community structure, biogeochemical cycles and wood decomposition. Dispersal significantly affected soil fungal and bacterial community composition and diversity, resulting in distinct patterns of soil nitrogen reduction and wood mass loss. Correlation analysis showed that the relationship among soil fungal and bacterial community, soil nitrogen reduction and wood mass loss were tightly connected. These results give empirical support to the notion that dispersal can structure the soil microbial community and through it ecosystem functions. Future biogeochemical models including the links between soil microbial community and wood decomposition may improve their precision in predicting wood decomposition.

Contrasting geochemical and fungal controls on decomposition of lignin and soil carbon at continental scale

Lignin is an abundant and complex plant polymer that may limit litter decomposition, yet lignin is sometimes a minor constituent of soil organic carbon (SOC). Accounting for diversity in soil characteristics might reconcile this apparent contradiction. Tracking decomposition of a lignin/litter mixture and SOC across different North American mineral soils using lab and field incubations, here we show that cumulative lignin decomposition varies 18-fold among soils and is strongly correlated with bulk litter decomposition, but not SOC decomposition. Climate legacy predicts decomposition in the lab, and impacts of nitrogen availability are minor compared with geochemical and microbial properties. Lignin decomposition increases with some metals and fungal taxa, whereas SOC decomposition decreases with metals and is weakly related with fungi. Decoupling of lignin and SOC decomposition and their contrasting biogeochemical drivers indicate that lignin is not necessarily a bottleneck for SOC decomposition and can explain variable contributions of lignin to SOC among ecosystems.

Global patterns and edaphic-climatic controls of soil carbon decomposition kinetics predicted from incubation experiments

Knowledge about global patterns of the decomposition kinetics of distinct soil organic matter (SOM) pools is crucial to robust estimates of land-atmosphere carbon fluxes under climate change. However, the current Earth system models often adopt globally-consistent reference SOM decomposition rates (k_ref), ignoring effects from edaphic-climate heterogeneity. Here, we compile a comprehensive set of edaphic-climatic and SOM decomposition data from published incubation experiments and employ machine-learning techniques to develop models capable of predicting the expected sizes and k_ref of multiple SOM pools (fast, slow, and passive). We show that soil texture dominates the turnover of the fast pools, whereas pH predominantly regulates passive SOM decomposition. This suggests that pH-sensitive bacterial decomposers might have larger effects on stable SOM decomposition than previously believed. Using these predictive models, we provide a 1-km resolution global-scale dataset of the sizes and k_ref of these SOM pools, which may improve global biogeochemical model parameterization and predictions.

Litter accumulation and fire risks show direct and indirect climate-dependence at continental scale

Litter decomposition / accumulation are rate limiting steps in soil formation, carbon sequestration, nutrient cycling and fire risk in temperate forests, highlighting the importance of robust predictive models at all geographic scales. Using a data set for the Australian continent, we show that among a range of models, >60% of the variance in litter mass over a 40-year time span can be accounted for by a parsimonious model with elapsed time, and indices of aridity and litter quality, as independent drivers. Aridity is an important driver of variation across large geographic and climatic ranges while litter quality shows emergent properties of climate-dependence. Up to 90% of variance in litter mass for individual forest types can be explained using models of identical structure. Results provide guidance for future decomposition studies. Algorithms reported here can significantly improve accuracy and reliability of predictions of carbon and nutrient dynamics and fire risk.

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.

Future climate conditions accelerate wheat straw decomposition alongside altered microbial community composition, assembly patterns, and interaction networks

Although microbial decomposition of plant litter plays a crucial role in nutrient cycling and soil fertility, we know less about likely links of specific microbial traits and decomposition, especially in relation to climate change. We study here wheat straw decomposition under ambient and manipulated conditions simulating a future climate scenario (next 80 years) in agroecosystems, including decay rates, macronutrient dynamics, enzyme activity, and microbial communities. We show that future climate will accelerate straw decay rates only during the early phase of the decomposition process. Additionally, the projected climate change will increase the relative abundance of saprotrophic fungi in decomposing wheat straw. Moreover, the impact of future climate on microbial community assembly and molecular ecological networks of both bacteria and fungi will strongly depend on the decomposition phase. During the early phase of straw decomposition, stochastic processes dominated microbial assembly under ambient climate conditions, whereas deterministic processes highly dominated bacterial and fungal communities under simulated future climate conditions. In the later decomposition phase, similar assembly processes shaped the microbial communities under both climate scenarios. Furthermore, over the early phases of decomposition, simulated future climate enhanced the complexity of microbial interaction networks. We concluded that the impact of future climate on straw decay rate and associated microbial traits like assembly processes and inter-community interactions is restricted to the early phase of decomposition.

Functional significance of microbial diversity in arid soils: biological soil crusts and nitrogen fixation as a model system

Microbial communities respond to changes in environmental conditions; however, how compositional shifts affect ecosystem processes is still not well-understood and it is often assumed that different microbial communities will function equally under similar environmental conditions. We evaluated this assumption of functional redundancy using biological soil crusts (BSCs) from two arid ecosystems in Mexico with contrasting climate conditions (hot and cold deserts) following an experimental approach both in the field (reciprocal transplants) and in laboratory conditions (common garden), focusing on the community's composition and potential for nitrogen fixation. Potential of nitrogen fixation was assessed through the acetylene reduction assay. Community composition and diversity was determined with T-RFLPs of nifH gene, high throughput sequencing of 16S rRNA gene amplicons and metagenomic libraries. BSCs tended to show higher potential nitrogen fixation rates when experiencing temperatures more similar to their native environment. Moreover, changes in potential nitrogen fixation, taxonomic and functional community composition, and diversity often depended on an interactive effect of origin of the communities and the environment they experienced. We interpret our results as legacy effects that result from ecological specialization of the BSC communities to their native environment. Overall, we present evidence of nonfunctional redundancy of BSCs in terms of nitrogen fixation.

Effects of vegetation shift from needleleaf to broadleaf species on forest soil CO2 emission

Forest soil harbors diverse microbial communities with decisive roles in ecosystem processes. Vegetation shift from needleleaf to broadleaf species is occurring across the globe due to climate change and anthropogenic activities, potentially change forest soil microbial communities and C cycle. However, our knowledge on the impact of such vegetation shift on soil microbial community and activities, and its consequences on forest soil C dynamics are still not well established. Here, we examined the seasonal variation of soil CO₂ emission, soil extracellular enzyme activities (EEAs), and soil bacterial, fungal communities in subtropical forest from broadleaf, needleleaf, and mixed stands. In addition, soil CO₂ emission and soil EEAs were measured in temperate forest during the growing season. Soil organic matter (SOM) content significantly differs between broadleaf and needleleaf forests and primarily distinguish various soil chemical and microbial characteristics. Significantly higher EEAs and soil CO₂ emission in broadleaf forest compared to needleleaf forest were observed both in subtropical and temperate forests. The relative abundance of Basidiomycota positively correlated with SOM and EEAs and indirectly increase soil CO₂ emission whereas the relative abundance of Ascomycota exhibits opposite trend, suggesting that soil fungal communities play a key role in determining the different microbial activities between broadleaf and needleleaf stands. The temperature sensitivity of soil CO₂ emission was significantly higher in broadleaf forest compared to needleleaf forest, further suggesting that the soil organic carbon in broadleaf forests is more vulnerable to warming.

Linkages between the molecular composition of dissolved organic matter and soil microbial community in a boreal forest during freeze-thaw cycles

Soil dissolved organic matter (DOM) plays a vital role in biogeochemical processes. Global warming leads to increased freeze-thaw cycles (FTCs) in boreal forest soils, which can change DOM production and consumption. However, the interactions between the chemical composition of DOM molecules and the microbial communities that drive C decomposition in the context of freeze-thaw are poorly understood. Here, a FTCs incubation experiment was conducted. Combined with pyrolysis gas chromatography-mass spectrometry and high-throughput sequencing techniques, the relationships between DOM chemodiversity and microbial community structure were assessed. Results indicated that both low-frequency (2FTCs) and high-frequency freeze-thaw cycles (6FTCs) significantly increased soil dissolved organic carbon (DOC) contents in the surface (0-10 cm) and subsurface (50-60 cm) soil layers. In the topsoil, FTCs significantly reduced the relative abundance of aromatic compounds, but increased the relative proportions of alkanes, phenols, fatty acid methyl esters (Me) and polysaccharides in the DOM. In the subsuface soil layer, only the relative abundance of Me in the 6FTCs treatment increased significantly. The response of bacterial communities to FTCs was more sensitive than that of fungi, among which only the relative abundance of Gammaproteobacteria increased by FTCs. Moreover, the relative abundance of these taxa was positively correlated with the increment of DOC. Co-occurrence networks confirmed DOM-bacterial interactions, implying that specific microorganisms degrade specific substrates. At class level, Gammaproteobacteria were significantly positively correlated with labile C (polysaccharides and alkanes), whereas other bacterial classes such as Actinobacteria, Alphaproteobacteria, and Thermoleophilia were significantly positively correlated with aromatic compounds in the topsoil. Collectively, FTCs tended to activate DOM and enhance its biodegradability of DOM, potentially hampering DOC accumulation and C sequestration. These findings highlight the potential of DOM molecular mechanisms to regulate the functional states of soil bacterial communities under increased FTCs.

Rapid bacterial and fungal successional dynamics in first year after chaparral wildfire

The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition with Illumina MiSeq sequencing of 16S and ITS2 amplicons. Fire severely reduced bacterial biomass by 47%, bacterial richness by 46%, fungal biomass by 86%, and fungal richness by 68%. The burned bacterial and fungal communities experienced rapid succession, with 5-6 compositional turnover periods. Analogous to plants, turnover was driven by "fire-loving" pyrophilous microbes, many of which have been previously found in forests worldwide and changed markedly in abundance over time. Fungal secondary succession was initiated by the Basidiomycete yeast Geminibasidium, which traded off against the filamentous Ascomycetes Pyronema, Aspergillus, and Penicillium. For bacteria, the Proteobacteria Massilia dominated all year, but the Firmicute Bacillus and Proteobacteria Noviherbaspirillum increased in abundance over time. Our high-resolution temporal sampling allowed us to capture post-fire microbial secondary successional dynamics and suggest that putative tradeoffs in thermotolerance, colonization, and competition among dominant pyrophilous microbes control microbial succession with possible implications for ecosystem function.

Assessment of selenium and zinc enriched sludge and duckweed as slow-release micronutrient biofertilizers for Phaseolus vulgaris growth

Selenium (Se) and zinc (Zn) are essential micronutrients that are often lacking in the diet of humans and animals. Application of mineral Se and Zn fertilizers into soils may lead to a waste of Se and Zn due to the fast leaching and low utilization by plants. Slow-release Se and Zn biofertilizer may therefore be beneficial. This study aims to assess the potential of SeZn-enriched duckweed and sludge produced from wastewater as slow-release Se and Zn biofertilizers. Pot experiments with green beans (Phaseolus vulgaris) and sampling of Rhizon soil pore water were conducted to evaluate the bioavailability of Se and Zn in sandy and loamy soils mixed with SeZn-enriched duckweed and sludge. Both the Se and Zn concentrations in the soil pore water increased upon amending the two biomaterials. The concentration of Se released from SeZn-enriched duckweed rapidly decreased in the first 21 days and slowly declined afterwards, while it remained stable during the entire experiment upon application of SeZn-enriched sludge. The Zn content in the soil pore water gradually increased over time. The application of SeZn-enriched duckweed and sludge significantly increased the Se concentrations in plant tissues, in particular in the form of organic Se-methionine in seeds, without a negative impact on plant growth when an appropriate dose was applied (1 mg Se/kg soil). While, it did not increase Zn concentrations in plant seeds. The results indicate that the SeZn-enriched duckweed and sludge could be only used as organic Se biofertilizers for Se-deficient soils. Particularly, the SeZn-enriched sludge dominated with elemental nano-Se was an effective Se source and slow-release Se biofertilizer. These results could offer a theoretical reference to choose an alternative to chemical Se fertilizers for biofortification, avoiding the problem of Se losses by leaching from mineral Se fertilizers while recovering resources from wastewater. This could contribute to the driver for a future circular economy.

Photovoltaic panels have altered grassland plant biodiversity and soil microbial diversity

Introduction

Human concerns about fossil fuel depletion, energy security and environmental degradation have driven the rapid development of solar photovoltaic (PV) power generation. Most of the photovoltaic power generation plants are concentrated in desert, grassland and arable land, which means the change of land use type. However, there is still a gap in the research of the PV panel layout on grassland plant species diversity and ecological function.

Methods

In this study, Illumina high-throughput sequencing technology was used to investigate the effects of PV panel arrangement on grassland plant species diversity and soil microbial diversity. In view of the differences in the microclimate at different sites of the PV panels, quadrates were arranged in front edge (FE), beneath the center of each panel (BP), back edge (BE), the uncovered interspace adjacent to each panel (IS) and the undisturbed grassland around the PV panels (Control), respectively.

Results

PV panels (especially FE) significantly increased the total aboveground productivity (total AGB) and plant species diversity in grasslands. FE increased precipitation accumulation and plant species diversity directly and indirectly changed the diversity of soil bacterial and fungal communities. PV panels decreased the relative abundance of Actinobacteriota, while increased the relative abundance of Proteobacteria, Acidobacteriota, and Methylomirabilota. EC, Margalef' s richness and total AGB were the main factors affecting the composition of bacterial communities, while alkaline hydrolysis nitrogen (AN) and available phosphorus (AP) were the main factors affecting the composition of fungal communities.

Discussion

In conclusion, the arrangement of PV panels increased the plant species diversity and soil microorganisms in grassland. This study provides important information for further understanding the impact of PV panels on grassland ecosystem function and is of great significance for maintaining grassland ecosystem function.

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning

Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly; however, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. Here, we characterized the rate and composition of bacteria dispersing into surface soil via three dispersal routes (from the air above the vegetation, from nearby vegetation and leaf litter near the soil surface, and from the bulk soil and litter below the top layer). We then quantified the impact of those routes on microbial community composition and functioning in the topmost litter layer. The bacterial dispersal rate onto the surface layer was low (7900 cells/cm2/day) relative to the abundance of the resident community. While bacteria dispersed through all three routes at the same rate, only dispersal from above and near the soil surface impacted microbiome composition, suggesting that the composition, not rate, of dispersal influenced community assembly. Dispersal also impacted microbiome functioning. When exposed to dispersal, leaf litter decomposed faster than when dispersal was excluded, although neither decomposition rate nor litter chemistry differed by route. Overall, we conclude that the dispersal routes transport distinct bacterial communities that differentially influence the composition of the surface soil microbiome.

A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome

MOTIVATION

PERMANOVA is currently the most commonly used method for testing community-level hypotheses about microbiome associations with covariates of interest. PERMANOVA can test for associations that result from changes in which taxa are present or absent by using the Jaccard or unweighted UniFrac distance. However, such presence-absence analyses face a unique challenge: confounding by library size (total sample read count), which occurs when library size is associated with covariates in the analysis. It is known that rarefaction (subsampling to a common library size) controls this bias but at the potential costs of information loss and the introduction of a stochastic component into the analysis.

RESULTS

Here, we develop a non-stochastic approach to PERMANOVA presence-absence analyses that aggregates information over all potential rarefaction replicates without actual resampling, when the Jaccard or unweighted UniFrac distance is used. We compare this new approach to three possible ways of aggregating PERMANOVA over multiple rarefactions obtained from resampling: averaging the distance matrix, averaging the (element-wise) squared distance matrix and averaging the F-statistic. Our simulations indicate that our non-stochastic approach is robust to confounding by library size and outperforms each of the stochastic resampling approaches. We also show that, when overdispersion is low, averaging the (element-wise) squared distance outperforms averaging the unsquared distance, currently implemented in the R package vegan. We illustrate our methods using an analysis of data on inflammatory bowel disease in which samples from case participants have systematically smaller library sizes than samples from control participants.

AVAILABILITY AND IMPLEMENTATION

We have implemented all the approaches described above, including the function for calculating the analytical average of the squared or unsquared distance matrix, in our R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A quantitative analysis of microbial community structure-function relationships in plant litter decay

Soil microbes play a central role in ecosystem element cycling. Yet a central question in microbial ecology remains unanswered: to what extent does the taxonomic composition of soil microbial communities mediate biogeochemical process rates? In this quantitative review, we explore the mechanisms that lead to variation in the strength of microbial community structure-function relationships over space and time. To evaluate these mechanisms, we conduct a meta-analysis of studies that have monitored the decomposition of sterilized plant litter inoculated with different microbial assemblages. We find that the influence of microbial community composition on litter decay is pervasive and strong, rivalling in magnitude the influence of litter chemistry on decomposition. However, no single environmental or experimental attribute was correlated with variation in the inoculum effect. These results emphasize the need to better understand ecological dynamics within microbial communities, particularly emergent features such as cross-feeding networks, to improve predictions of soil biogeochemical function.

Plant biodiversity promotes sustainable agriculture directly and via belowground effects

While the positive relationship between plant biodiversity and ecosystem functioning (BEF) is well established, the extent to which this is mediated via belowground microbial processes is poorly understood. Growing evidence suggests that plant community structure influences soil microbial diversity, which in turn promotes functions desired for sustainable agriculture. Here, we outline the 'plant-directed' and soil microbe-mediated mechanisms expected to promote positive BEF. We identify how this knowledge can be utilized in plant diversification schemes to maximize ecosystem functioning in agroecosystems, which are typically species poor and sensitive to biotic and abiotic stressors. In the face of resource overexploitation and global change, bridging the gaps between biodiversity science and agricultural practices is crucial to meet food security in the Anthropocene.

Life in the Wheat Litter: Effects of Future Climate on Microbiome and Function During the Early Phase of Decomposition

Even though it is widely acknowledged that litter decomposition can be impacted by climate change, the functional roles of microbes involved in the decomposition and their answer to climate change are less understood. This study used a field experimental facility settled in Central Germany to analyze the effects of ambient vs. future climate that is expected in 50-80 years on mass loss and physicochemical parameters of wheat litter in agricultural cropland at the early phase of litter decomposition process. Additionally, the effects of climate change were assessed on microbial richness, community compositions, interactions, and their functions (production of extracellular enzymes), as well as litter physicochemical factors shaping their colonization. The initial physicochemical properties of wheat litter did not change between both climate conditions; however, future climate significantly accelerated litter mass loss as compared with ambient one. Using MiSeq Illumina sequencing, we found that future climate significantly increased fungal richness and altered fungal communities over time, while bacterial communities were more resistant in wheat residues. Changes on fungal richness and/or community composition corresponded to different physicochemical factors of litter under ambient (Ca²⁺, and pH) and future (C/N, N, P, K⁺, Ca²⁺, pH, and moisture) climate conditions. Moreover, highly correlative interactions between richness of bacteria and fungi were detected under future climate. Furthermore, the co-occurrence networks patterns among dominant microorganisms inhabiting wheat residues were strongly distinct between future and ambient climates. Activities of microbial β-glucosidase and N-acetylglucosaminidase in wheat litter were increased over time. Such increased enzymatic activities were coupled with a significant positive correlation between microbial (both bacteria and fungi) richness and community compositions with these two enzymatic activities only under future climate. Overall, we provide evidence that future climate significantly impacted the early phase of wheat litter decomposition through direct effects on fungal communities and through indirect effects on microbial interactions as well as corresponding enzyme production.