● Under warming soil respiration was higher, but soil microbial biomass was lower.

Global warming is expected to increase the rate of soil carbon (C) efflux through enhanced soil microbial processes, mainly in systems, such as high elevation wetlands, storing large quantities of soil organic C. Here, we assessed the impact of experimental warming on respiration and microbial communities of high Andean wetland soils of the Puna region located at three different elevations (3793, 3862, 4206 m a.s.l.). We incubated soils at 10°C and 25°C for 68 days and measured the soil respiration rate and its temperature sensitivity (Q₁₀). Furthermore, we measured biomass and composition and enzymatic activity of soil microbial communities, and initial and final soil C content. Although warming increased soil respiration rates, with more pronounced effect in soils sampled from 4206 m a.s.l., Q₁₀ did not differ between elevations. Soil C content was higher at the highest elevation. Soil microbial biomass, but not enzymatic activity, was lower for warmed soil samples. However, the biomass-specific respiration and biomass-specific enzymatic activity were higher under warming, and in soil from the highest elevation wetland. These results suggest that, in the short-term, warming could stimulate resource allocation to respiration rather than microbial growth, probably related to a reduction in the microbial carbon use efficiency. Simultaneously, soils with higher soil C concentrations could release more CO₂, despite the similar Q₁₀ in the different wetlands. Overall, the soil of these high Andean wetlands could become C sources instead of C sinks, in view of forecasted increasing temperatures, with C-losses at regional scale.

● Core taxa play an important role in regulating soil carbon metabolism.

Characterizing the ecological roles of core soil microbial species in soil carbon metabolism is critically important for enhancing carbon sequestration in agricultural systems; however, no studies to date have determined the effects of core soil microbial taxa on carbon metabolism under various long-term fertilization practices. Here, we collected soil samples from field plots that had been subjected to different fertilization practices for nearly 30 years and examined the long-term effects of fertilization on the preferences of core soil bacterial taxa for different carbon sources. We also examined the relative contribution of core soil bacterial taxa in utilization of different carbon source types in Biolog Eco microplates. Long-term fertilization treatment had a significant effect on soil properties and bacterial community structure. The core taxa were closely related to soil carbon source utilization. The co-occurrence network showed that the major ecological clusters containing core taxa made key contributions to soil carbon source utilization. The organic fertilization increased the abundance of a core cluster with a low weighted average rrn copy number. This ecological cluster was the most important factor affecting soil carbon source utilization even among soil physicochemical factors considered. Our findings indicate that core taxa characterized by oligotrophic bacteria have a major effect on carbon source utilization in Ultisols.

● P. frumentum biomass could be improved by appropriating returning measures.

The use of green manure returning to field is a common practice in conservation tillage. However, there is limited research on how different amounts of alfalfa can affect saline-alkali soil properties, bacterial community characteristics, and subsequent productivity. In this study, five different amounts of alfalfa return were investigated to understand the biological relationships between rhizospheres soil properties, bacterial communities, potential functions, and the Purus frumentum biomass. The results showed that the biomass was highest when 75% of the alfalfa was returned to the field. This particular amount was associated with relatively low soil pH and electrical conductivity. Additionally, it increased the relative abundance of beneficial bacterial taxa in both core and non-core bacteria. Statistical analysis revealed significant differences in both core (RANOSIM = 0.871, P = 0.001) and non-core (RANOSIM = 0.947, P = 0.001) bacterial communities among the different amounts of alfalfa return based on non-metric multidimensional scaling analysis. Core bacterial taxa and their potential ecological functions were more closely related to plant biomass compared to non-core bacteria based on correlation analysis and multiple regression analysis. Therefore, our results indicate that optimizing the amount of alfalfa return can improve subsequent plant biomass. Regulating soil physicochemical properties and influencing core microbial community structure are of great significance for soil functional stability and crop productivity sustainability.

● EDU reduces O₃ sensitivity of alfalfa by mediating antioxidant enzyme activities.

Ozone (O₃) is a phytotoxic air pollutant, both ethylenediurea (EDU) and arbuscular mycorrhizal (AM) fungi can affect plant O₃ sensitivity. However, the underlying mechanisms of EDU and AM fungi on plant O₃ sensitivity are unclear, and whether the combined application of the two can alleviate O₃ damage has not been verified. In this study, an open-top chamber experiment was conducted to examine the effects of EDU and AM inoculation on growth and physiological parameters of alfalfa (Medicago sativa L.) plants under O₃ enrichment. The results showed that EDU significantly decreased O₃ visible injury (28.67%−68.47%), while AM inoculation significantly increased O₃ visible injury. Mechanistically, the reduction of plant O₃ sensitivity by EDU was mediated by antioxidant enzyme activities rather than stomatal conductance. Although AM inoculation increased antioxidant enzyme activities (4.99%−211.23%), it significantly increased stomatal conductance (42.69%) and decreased specific leaf weight (12.98%), the negative impact was overwhelming. Therefore, AM inoculation increased alfalfa’s O₃ sensitivity. Furthermore, we found AM inoculation increased stomatal conductance by increasing stomatal density. The research indicated EDU was sufficient to counteract the negative effects of AM inoculation on O₃ sensitivity. The combined application of EDU and AM fungi could largely alleviate the adverse effects of O₃ on plant performance.

● Fungi are more sensitive to precipitation than bacteria.

Precipitation scenario alteration leads to grievous ecological consequences in ecosystems, especially on the Qinghai-Tibet Plateau. Bacterial and fungal community and their abundant and rare taxa in soil ecosystems may respond differently to the changed precipitation. Therefore, more attention needs to be paid to the sensitivity of bacteria and fungi and their abundant and rare taxa to precipitation shifts. The responses of bacterial and fungal populations and their abundant and rare taxa concerning diversity, assembly, and interactions to manipulative changes of precipitation were explored via imitating no precipitation, little precipitation, and medium precipitation using 16S rRNA gene and ITS amplicon sequencing. The results indicated that the change rate of fungal Simpson diversity with precipitation was higher than that of bacteria. The slope of the modified stochasticity ratio (MST) value of fungi to precipitation was steeper than that of bacteria. The Simpson diversity and the MST value of abundant and rare taxa within bacteria had no difference with precipitation. In contrast, those of abundant taxa within fungi varied more than rare ones with precipitation. By unveiling the differential responses of microbial populations with discrepant characteristics, this study allowed us to understand the different microbial communities responding to rainfall on the Qinghai-Tibet Plateau.

● A new fairy ring fungus was reported in this study.

Fairy rings are common in diverse global biomes and often appear as lush vegetation in one to three concentric zones caused by the spread of mycelia in grassland ecosystems. However, the underlying mechanisms and environmental adaptation of fairy rings remain largely unclear. In this study, two fairy rings (A and B) caused by Agaricus xanthodermus were sampled on the Qinghai-Tibet Plateau during a time when fairy rings are most obvious. By conducting a vegetation survey and high-throughput sequencing, the changes of plants and soil microorganisms to fairy ring fungi were examined. Plant above-ground biomass at both fairy rings was greatly increased by fairy ring fungi, but the response of dominant plant species is different at two fairy ring sites. In addition, bacterial and fungal communities significantly varied within distinct sampling zones across the fairy rings, and showed variable genus-specific responses at two fairy ring sites. At fairy ring A, soil available N:P ratio was essential in shaping the structure of plant and microbial community, while soil available N concentration was the most important predictor at fairy ring B. Taken together, our results indicated Agaricus xanthodermus fairy rings have variable effects on alpine meadow plants and soil microbes at different habitats. We propose that the impacts of fairy ring fungi on plants and microbes are determined by the level of soil available N concentration and available N:P ratio. These results contribute to a better understanding of the mechanisms through which fairy rings affect the vegetation of alpine meadows.

● Dicyandiamide decreased N₂O emissions even under 40°C.

Heat waves associated with global warming and extreme climates would arouse serious consequences on nitrogen (N) cycle. However, the responses of the functional guilds to different temperatures, especially high temperature and the cascading effect on N₂O emissions remain unclear. An incubation study was conducted to examine the effect of different temperatures (20°C, 30°C, and 40°C) and fertilizer types (urea and manure) on N₂O-producers and N₂O-reducers, as well as the efficacy of dicyandiamide (DCD) on N₂O emissions in a vegetable soil. Results showed that ammonia oxidizers and nirS-type denitrifiers were well adapted to high temperature (40°C) with manure application, while the fungal nirK-denitrifiers had better tolerance with urea application. The nosZ clade I microbes had a strong adaptability to various temperatures regardless of fertilization type, while the growth of nosZ clade II group microbes in non-fertilized soil (control) were significantly inhibited at higher temperature. The N₂O emissions were significantly decreased with increasing temperature and DCD application (up to 60%, even at 40°C). Under high temperature conditions, fungal denitrifiers play a significant role in N-limited soils (non-fertilized) while nirS-type denitrifiers was more important in fertilized soils in N₂O emissions, which should be specially targeted when mitigating N₂O emissions under global warming climate.

● Fungi are more sensitive to long-term nitrogen addition than bacteria.

Nitrogen (N) addition can significantly affect the amount of soil carbon (C) pools through biological routes, and microbial residues are important components of soil carbon pools. However, it remains unclear how N addition affects the accumulation of soil microbial residues in meadow grasslands. This study analyzed the effects of N addition on microbial residues in a meadow grassland soil, and the key factors affecting the accumulation of microbial residues under N addition were analyzed in combination with soil physicochemical properties and microbial community structure. The results showed that N addition significantly changed the structure of the microbial communities and the accumulation of microbial residues, mainly manifested by a significant decrease in fungal biomass and the fungal/bacterial ratio (F/B), but had no significant effect on bacterial or total microbial biomass (PLFAs). N addition significantly increased the accumulation of fungal residues (7.45%), but had no significant effect on the accumulation of bacterial residues or total amino sugar (TAS). We found that fungal residues were more affected by soil environmental factors than bacterial residues. The results of the random forest analysis showed that bacterial biomass under N addition was the most important predictor of soil bacterial residues, whereas total N (TN), pH and F/B were the most important predictors of soil fungal residue. In summary, our results indicate that fungal communities and residues accumulation play important roles in regulating the response of grassland soil C to N addition, further enhancing our understanding of the mechanisms of soil carbon pool to N addition.

● Metatranscriptomics uncovers the dynamic expression of functional genes in soil environments, providing insights into the intricate metabolic activities within microbial communities.

Metatranscriptomics is a cutting-edge technology for exploring the gene expression by, and functional activities of, the microbial community across diverse ecosystems at a given time, thereby shedding light on their metabolic responses to the prevailing environmental conditions. The double-RNA approach involves the simultaneous analysis of rRNA and mRNA, also termed structural and functional metatranscriptomics. By contrast, mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles, but requires either deep sequencing or effective rRNA depletion. In this review, we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional metatranscriptomics. In particular, we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields, such as rhizobiomes, antibiotic resistomes, methanomes, and viromes. Our review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.

● Responses of soil DIRB to lignocellulosic fractions during a 6-week microcosm incubation were investigated.

Dissimilatory iron reducing bacteria (DIRB) are phylogenetically and physiologically diverse in paddy soils, where iron reduction closely couples with the oxidation of rice straw-derived carbon in the straw returning scenarios. However, few studies have addressed the niche differentiation within DIRB groups during the degradation of lignocellulosic fractions of rice straw. This study conducted a 6-week microcosm incubation experiment to reveal the distinct responses of DIRB groups under specific lignocellulosic fraction amendments with and without ferrihydrite (Fh) addition in a flooded paddy Ultisol. Results showed that the total absolute abundance of the 19 detected DIRB groups did not vary significantly during the incubation. Anaeromyxobacter, Bacillus, and Clostridium were the dominant DIRB groups for all lignocellulosic treatments whereas Thermincola was dominant but only under xylan amendment with Fh addition. DIRB-nodes in the co-occurrence networks of bacterial community mainly belonged to Anaeromyxobacter and Bacillus. Clostridium and Thermincola, Alkaliphilus and Anaeromyxobacter, and Alicyclobacillus, Desulfobulbus, and Desulfosporosinus were specifically proliferated under xylan, cellulose, and lignin amendments, respectively. Whether the proliferation was limited by insufficient ferric iron varied by bacterial group. These findings suggested the lignocellulosic fraction-induced niche differentiation within DIRB groups, which advanced our understanding of the ecology of DIRB in paddy soils under straw returning.

● Flue gas desulfurization gypsum and clover planting alleviated the soil salinization stress.

The coastal area of Shandong Province, characterized by coastal saline tidal soil, is one of the main production areas of winter jujube in China. However, the low soil fertility and poor soil structure in jujube orchard restricted the development of the jujube industry. The objectives of this study were to 1) evaluate the effect of application of flue gas desulfurization (FGD) gypsum and clover planting on soil quality improvement and soil microbial community structure of jujube orchard; 2) investigate the effects of two measures on the nutrition and quality of winter jujube. The results showed that FGD gypsum reduced the soil total salt content by 65.6%, and clover planting increased the soil organic matter content by 30.7%, which effectively alleviated the soil salinization stress and improved the soil structure. Soil pH and total phosphorus (TP) were the main determinants influencing bacterial community composition, and TP was the dominant factor of the fungal community composition in the saline-alkali soils. Meanwhile, FGD gypsum addition and clover planting significantly increased the sugar degree and Vc content of winter jujube, thus improved jujube quality, and further contributed to the ecological sustainable development of winter jujube industry.

● Integrated grain cropping systems promote soil health (SH) and sustainability.

Tropical soils are prone to degradation. Adoption of conservation agricultural practices is essential to improve soil health, which is influenced by soil microbes. In this study we analyzed shifts in microbial biomass and activity (MBA) and microbial community structure (MCS) based on fatty acid methyl esthers (FAMEs) between five no-till agricultural practices: maize monoculture (MM); maize annualy intercropped with Urochloa decumbens (M/Ud); M/Ud with soybean rotation every other year (M/Ud–S); M/Ud keeping the pasture for the next two years (M/Ud–Ud–Ud); and maize intercropped with U. ruziziensis keeping the pasture for the next two years (M/Ur–Ur–Ur). Results indicated that MBA was affected by the inclusion of Urochloa intercropping and by rotation with soybean. Systems under a longer residence time with Urochloa in the field had higher β-glucosidase activity and soil basal respiration, indicating a greater microbial activity. MCS was less affected than MBA by the investigated cropping systems. MCS changed only in the continuous pasture systems, which were enriched in arbuscular mycorrhyzal fungi (AMF). Additionally, the continuous pasture systems had lower microbial stress ratios than the other agricultural practices. In sum, our study showed that utilization of Urochloa spp. under longer periods in no-till agricultural practices contributes to increase microbial activity, AMF abundance and decrease microbial stress ratio. These changes are primarily beneficial for soil health.

● Soil erosion resulted in homogenization of bacterial communities in the watershed.

Sediment source tracing can accurately provide a theoretical basis for controlling soil erosion effectively, by identifying the most serious types of land use. Traditional sediment tracing methods are based on physical, chemical, biological, and composite fingerprinting, which have not included microbes. As high-throughput sequencing becomes more prevalent, microorganisms can provide more information than what we think. Thus, whether the microorganism can also be used as a special fingerprint factor for sediment source identification during soil erosion, we have tested it by using microbial source tracking tool FEAST to quantify the microbe contribution from five types of eroded land (including dryland, urban, paddy field, forest and grassland) to the depositional areas (Niubitan) in the Yuanjiang basin. The source microbial community in the erosive area was heterogeneous, and assembly process analysis further demonstrated that the source tracking results could reach higher accuracy. The results of FEAST showed that dryland (35.50%), urban (17.21%), paddy field (8.14%), and forest (1.07%) were the major contributors to Niubitan. Our results follow the general soil erosion rules and prove its validity. Taken together, a new perspective is provided by these results for tracing sediment sources in erosion-sedimentary systems.

● We assess the recovery of microbial networks underneath crust to repeated rainfall.

Biological soil crusts (BSCs) are an important multi-trophic component of arid ecosystems in the Mediterranean region. In a mesocosm experiment, the authors investigated how the network of interactions among the members of the soil microbial communities in four types of soil sample responded when soils were exposed to two simulated extreme rain events. The four types of soil samples were: covered by Cladonia rangiformis and previously hydrated (+BSC+H), covered by C. rangiformis and dried (+BSC-H), uncovered and hydrated (-BSC+H), uncovered and dried (-BSC-H). Network analysis was based on the co-occurrence patterns of microbes; microbes were assessed by the phospholipid fatty acids analysis. The authors further explored the relations between networks’ metrics and soil functions denoted by enzymatic activity and soil chemical variables. All networks exhibited Small world properties, moderate values of clustering coefficient and eigen centrality, indicating the lack of hub nodes. The networks in -BSC-H soils appeared coherent during the pre-rain phases and they became modular after rains, while those in +BSC-H soils kept their connectivity till the second rain but this then collapsed. The network metrics that were indicative of cohesive networks tended to be related to enzyme activity while those that characterized the loose networks were related to Ca, K, Mg, NH₄⁺ and organic N. In all mesocosms except for +BSC-H, networks’ fragmentation after the second heavy rain was milder than after the first one, supporting the idea of community acclimatization. The response of microbial networks to heavy rains was characterized by the tendency to exhibit degradation-reconstruction phases. The network collapse in the crusted only mesocosms showed that the communities beneath crusts in arid areas were extremely vulnerable to recurring heavy rain events.

• Sugar addition caused vigorous proliferation of wilt pathogen.

Sugars are frequently and abundantly found in root exudates, but influence of specific sugars on the fate of soil-borne pathogens, microbiome structure, and particularly microbial interactions are not well understood. A 42-day of microcosm incubation was conducted with two soils: a natural watermelon Fusarium wilt pathogen (i.e., Fusarium oxysporum f. sp. niveum (FON))-infested soil (Low-FON soil) and the soil further receiving the wilt pathogen inocula (High-FON soil). Both soils were supplemented with four simple sugars before incubation. The results show that, in both soils, FON was enriched by all sugars although co-living with tremendously diverse microbes; and bacterial richness, evenness, and diversity were decreased and bacterial community structure was changed by all sugars. Bacterial richness and evenness were negatively correlated with FON quantity in both Low-FON and High-FON soils, indicating that FON may tend to live in soil with low alpha-diversity. In both Low-FON and High-FON soils, the sugar-spiked networks had more links, higher density, larger modules, and shorter harmonic geodesic distance, suggesting greater potentials for microbial interaction and niche-sharing. The positive links between some of the keystone taxa and FON indicates that these keystone taxa may have promoted FON. This may be one of reasons why FON could proliferate vigorously after sugar supplementation.

• Fungal communities were more sensitive to N fertilizers than P, K fertilizers.

Nitrogen (N), phosphate (P), and potassium (K) are the three most important nutrients applied into agricultural soils, but the impacts of their single or combined application on soil fungal community structure and stability are still open questions. Using qPCR and Illumina Miseq sequencing, the variation of soil fungal communities in response to long-term addition of N, P, or K fertilization alone and their combinations in a Mollisol field was investigated in this study. In addition, the fungal community resistance indices and network structure were studied. Results showed that N fertilizations (N, NK, NP and NPK treatments) rather than P, K fertilizations (P, K and PK treatments) significantly increased fungal abundance, but decreased fungal diversity and shifted fungal community structures when compared to non-fertilization (NoF). Additionally, N fertilization treatments presented lower resistance of fungal communities to environment disturbances than those of P, K fertilization treatments. More numbers and higher abundances of changed fungal taxa at the genus and OTU levels were induced by N fertilizations rather than by addition of P, K fertilizers. In addition, N fertilizations induced a more changeable fungal network and complex pathogenic subnetwork with many positive interactions among responding plant pathogens (RP, the changeable plant pathogens induced by fertilizers addition compared to NoF) when compared to P, K fertilizations. These RP directly and negatively influenced fungal community resistance examined by structural equation modeling (SEM), which were indirectly detrimental to soybean yields. Our findings revealed that addition of N fertilizers significantly disturbed fungal communities and promoted pathogenic interactions, and provided insights into the optimization of fertilization strategies toward agricultural sustainability.

• Both organic and inorganic fertilizations stimulate soil aggregation.

Differently sized soil aggregates, with non-uniform distribution of space and nutrients, provide spatially heterogeneous microenvironments for microorganisms and are important for controlling microbial community ecology and biogeochemistry in soils. Here, we investigated the prokaryotic communities within different aggregate-size fractions: macroaggregate (>0.25 mm), microaggregate (0.053–0.25 mm) and silt+ clay (<0.053 mm). These were isolated from fluvo-aquic soils under 39-year fertilization strategies: no fertilizer (CK), chemical fertilizer (NPK), manure fertilizer (M), and combination of manure and chemical fertilizers (MNPK). The results showed that the proportion of macroaggregate, soil aggregate-associated organic carbon (SOC) content and aggregate stability were all significantly increased by both manure and chemical fertilizations. Organic fertilizations (M and MNPK) more effectively boosted formation and stability of macroaggregates and enhanced SOC concentration than NPK. The distribution patterns of microorganisms in aggregates were primarily shaped by fertilization and aggregate size. They explained 76.9% of the variance in bacterial community compositions. Fertilizations, especially with organic fertilizers primarily transitioned bacterial communities from slow-growing oligotrophic groups (e.g., Chloroflexi) dominance to fast-growing copiotrophic groups (e.g., Proteobacteria and Bacteroidetes) dominance across all aggregate sizes. Macroaggregates possessed a more stable bacterial community and efficiency of resource transfer, while smaller aggregates increased antagonism and weakened mutualism among bacterial communities. Overall, combination of manure and chemical fertilizers was crucial for increasing SOC content and aggregation, leading to a clear shift in bacterial community structures at aggregate scale.

• Continuous chlorine treatment have no obvious effect on soil microbial community structure and composition.

Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic. However, at present, little is known about the impact of residual chlorine on the soil micro-ecological environment. Herein, we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water, and then analyzed the influence on the soil microbial community using metagenomics. After 14-d continuous chlorine treatment, there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil. Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment, it recovered to the original status. The abundance of several resistance genes changed by 7 d and recovered by 14 d. According to our results, the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth (shoot length and fresh weight) and soil micro-ecology. In general, our study assisted with environmental risk assessments relating to the application of chlorine-containing disinfectants and minimization of risks to the environment during disease control, such as COVID-19.

• 10-year of CC was a cut-off point in separating soil bacterial community structures.

Soil-borne plant diseases cause major economic losses globally. This is partly because their epidemiology is difficult to predict in agricultural fields, where multiple environmental factors could determine disease outcomes. Here we used a combination of field sampling and direct experimentation to identify key abiotic and biotic soil properties that can predict the occurrence of bacterial wilt caused by pathogenic Ralstonia solanacearum. By analyzing 139 tomato rhizosphere soils samples isolated from six provinces in China, we first show a clear link between soil properties, pathogen density and plant health. Specifically, disease outcomes were positively associated with soil moisture, bacterial abundance and bacterial community composition. Based on soil properties alone, random forest machine learning algorithm could predict disease outcomes correctly in 75% of cases with soil moisture being the most significant predictor. The importance of soil moisture was validated causally in a controlled greenhouse experiment, where the highest disease incidence was observed at 60% of maximum water holding capacity. Together, our results show that local soil properties can predict disease occurrence across a wider agricultural landscape, and that management of soil moisture could potentially offer a straightforward method for reducing crop losses to R. solanacearum

• Biocrust succession alters diazotrophic diversity and community compositions.

The diazotrophic community in biological soil crusts (biocrusts) is the key supplier of nitrogen in dryland. To date, there is still limited information on how biocrust development influences the succession of diazotrophic community, and what are the most important factors mediating diazotrophic communities during biocrust succession. Using the high throughput nifH amplicon sequencing, the diazotrophs in soils at different developmental stages of biocrust were comparatively studied. The results evidenced the decrease of TOC/TN ratio and pH value with biocrust development. Nostoc and Scytonema were the most dominant diazotrophic genera at all biocrust stages, while Azospirillum and Bradyrhizobium were abundant only in bare soil. Diazotrophic co-occurrence networks tended to be less complex and less connected with biocrust succession. The soil TOC/TN ratio was the most dominant factor mediating diazotrophic diversity, community composition and assembly processes, while diazotrophic-diversity and NO3⁻-N/NH4⁺-N ratio were positively correlated with the nitrogenase activity during biocrust succession. This study provided novel understandings of nitrogen fixation and succession patterns of diazotrophic community, by showing the effects of biocrust succession on diazotrophic diversity, community composition, community assembly and co-occurrence networks, and recognizing TOC/TN ratio as the most dominant factor mediating diazotrophs during biocrust succession.

• Soil phosphorus shaped both abundant and rare bacterial communities.

Uncovering the mechanisms underlying the diversity patterns of abundant and rare species is crucial for terrestrial biodiversity maintenance. However, the response of abundant and rare community assembly to ecological succession has not been explored, particularly considering soil profiles. Here 300 soil samples were collected from reforestation ecosystems from depths of up to 300 cm and horizontal distances of 30-90 cm from a tree. We revealed that soil phosphorus not only affected alpha diversity and community structure, but also mediated the balance of stochastic and deterministic processes for abundant and rare sub-communities, which exhibited contrasting assembly strategies. The abundant sub-community changed from variable selection to stochasticity with the increase of phosphorus, while the rare sub-community shifted from homogeneous selection to stochasticity. Dispersal limitation was the main assembly process in the abundant sub-community, while the rare sub-community was governed primarily by homogeneous selection. Moreover, the relative influence of deterministic processes increased with succession for both sub-communities. At the scale of a single tree, stochastic processes increased with soil depth in rare sub-community, while deterministic processes increased with the radius from a single tree in the abundant sub-community. Overall, our results highlight the importance of the soil phosphorus-driven assembly process in understanding the re-assembly and maintenance of soil bacterial diversity.

• The riverbed-oxbow lake bed-floodplain-terrace continuum.

Continuous landscape components along the lateral riverside are affected by both hydrologic connectivity and disconnectivity. In recent years, anthropogenic activities and climate changes have caused wetland shrinkage and land degradation along the lateral riverside of many arid and semiarid regions. Since microorganisms are major drivers of soil biochemical cycling, it is essential to examine soil microbial communities along the lateral landscape continuum to understand their ecosystem functioning and predict future land changes. Here, we collected samples along a lateral riverbed center-riverbed edge-oxbow lake-floodplain-terrace continuum in the Xilin River Basin, Inner Mongolia, China. The floodplain had the highest microbial diversity and heterogeneity, with Bacteroidetes, β- and ©-Proteobacteria being the most abundant taxa. In contrast, the terrace had the lowest microbial diversity and heterogeneity, with Acidobacteria, Actinobacteria, Verrucomicrobia, Gemmatimonadetes, and α-Proteobacteria as the most abundant taxa. Silt particle, salinity, and moisture were the most influential factors for bacterial communities along the riverside continuum. Altogether, we demonstrate that dominant bacterial lineages, soil particles, and moisture-related factors are valuable indicators of this continuum, which can be leveraged for early prediction of drought-induced wetland shrinkage and grassland desertification.

• Topsoil diversity was greater in phenosoils than genosoils, but the trend was reversed in subsoils.

Human disturbances to soils can lead to dramatic changes in soil physical, chemical, and biological properties. The influence of agricultural activities on the bacterial community over different orders of soil and at depth is still not well understood. We used the concept of genoform and phenoform to investigate the vertical (down to 1 m depth) soil bacterial community structure in paired genosoils (undisturbed forests) and phenosoils (cultivated vineyards) in different soil orders. The study was conducted in the Hunter Valley area, New South Wales, Australia, where samples were collected from 3 different soil orders (Calcarosol, Chromosol, and Kurosol), and each soil order consists of a pair of genosoil and phenosoil. The bacterial community structure was analyzed using high-throughput sequencing of 16S rRNA. Results showed that bacterial-diversity decreased with depth in phenosoils, however, the trend is less obvious in genoform profiles. Topsoil diversity was greater in phenosoils than genosoils, but the trend was reversed in subsoils. Thus, cropping not only affected topsoil bacteria community but also decreased its diversity in the subsoil. Bacterial community in topsoils was influenced by both soil orders and soil forms, however, in subsoils it was more impacted by soil orders. Constrained Analysis of Principal Coordinates revealed that cropping increased the similarity of bacterial structures of different soil orders. This study highlighted the strong influence of agricultural activities on soil microbial distribution with depth, which is controlled by soil orde

• Straw returning significantly affects silicon fraction transformation;

Returning crop straw into the soil is an important practice to balance biogenic and bioavailable silicon (Si) pool in paddy, which is crucial for the healthy growth of rice. However, owing to little knowledge about soil microbial communities responsible for straw degradation, how straw return affects Si bioavailability, its uptake, and rice yield remains elusive. Herein, we investigate the change of soil Si fractions and microbial community in a 39-year-old paddy field amended by a long-term straw return. Results show that rice straw return significantly increased soil bioavailable Si and rice yield from 29.9% to 61.6% and from 14.5% to 23.6%, respectively, when compared to NPK fertilization alone. Straw return significantly altered soil microbial community abundance. Acidobacteria was positively and significantly related to amorphous Si, while Rokubacteria at phylum level, Deltaproteobacteria, and Holophagae at class level was negatively and significantly related to organic matter adsorbed and Fe/Mn-oxide-combined Si in soils. Redundancy analysis of their correlations further demonstrated that Si status significantly explained 12% of soil bacterial community variation. These findings suggest that soil bacteria community and diversity interact with Si mobility by altering its transformation, thus resulting in the balance of various nutrient sources to drive biological Si cycle in agroecosystem.

• We measured soil variables along the profile in two alpine ecosystems.

Microbial biomass and extracellular enzyme activities control the rate of soil organic carbon decomposition, thereby affecting soil carbon pool. However, seasonal dynamics of soil microbial properties at different depths of the soil profile remain unclear. In this study, we sampled soils in the early, middle and late growing season at different soil depths (0–100 cm) in two alpine ecosystems (meadow and shrubland) on the Tibetan Plateau. We measured plant belowground biomass, soil properties, microbial biomass and extracellular enzyme activities. We found that soil properties changed significantly with sampling time and soil depth. Specifically, most of soil properties consistently decreased with increasing soil depth, but inconsistently varied with sampling time. Moreover, root biomass and microbial biomass decreased with increasing soil depth and increased with sampling time during the growing season. However, microbial extracellular enzyme activities and their vector properties all changed with depth, but did not vary significantly with time. Taken together, these results show that soil properties, microbial biomass and extracellular enzyme activities mostly decline with increasing depth of the soil profile, and soil properties and microbial biomass are generally more variable during the growing season than extracellular enzyme activities across the soil profile in these alpine ecosystems. Further studies are needed to investigate the changes in soil microbial community composition and function at different soil depths over the growing season, which can enhance our mechanistic understanding of whole-profile soil carbon dynamics of alpine ecosystems under climate change.

•Intercropping effects on yield advantages are crop species specific.

Less attention has been given to soil enzymes that contribute to beneficial rhizosphere interactions in intercropping systems. Therefore, we performed a field experiment by growing faba bean, lupine, and maize in mono and mixed cultures in a moderately fertile soil. We measured shoot biomass and the kinetic parameters (maximal velocity (V_max) and Michaelis-constant (K_m)) of three key enzymes in the rhizosphere: Leucine-aminopeptidase (LAP), β-1,4-N-acetylglucosaminidase (NAG), and phosphomonoesterase (PHO). Faba bean benefitted in mixed cultures by greater shoot biomass production with both maize and lupine compared to its expected biomass in monoculture. Next, LAP and NAG kinetic parameters were less responsive to mono and mixed cultures across the crop species. In contrast, both the V_max and K_m values of PHO increased in the faba bean rhizosphere when grown in mixed cultures with maize and lupine. A positive relative interaction index for shoot P and N uptake for faba bean showed its net facilitative interactions in the mixed cultures. Overall, these results suggest that over-productivity in intercropping is crop-specific and the positive intercropping effects could be modulated by P availability. We argue that the enzyme activities involved in nutrient cycling should be incorporated in further research.

• Soil fungal community composition varied significantly between study sites.

Soil fungi and aboveground plant play vital functions in terrestrial ecosystems, while the relationship between aboveground plant diversity and the unseen soil fungal diversity remains unclear. We established 6 sites from the west to the east of the temperate steppe that vary in plant diversity (plant species richness: 7-32) to explore the relationship between soil fungal diversity and aboveground plant diversity. Soil fungal community was characterized by applying 18S rRNA gene sequencing using MiSeq PE300 and aligned with Silva 132 database. As a result, soil fungal community was predominately composed of species within the Ascomycota (84.36%), Basidiomycota (7.22%) and Mucoromycota (6.44%). Plant species richness occupied the largest explanatory power in structuring soil fungal community (19.05%–19.78%). The alpha (α) diversity of the whole soil fungi and Ascomycota showed a hump-backed pattern with increasing plant species richness, and the beta (β) diversity of the whole soil fungi and Ascomycota increased with increasing plant β diversity. Those results indicated that soil fungi and external resources were well balanced at the 20-species level of plant and the sites were more distinct in the composition of their plant communities also harbored more distinct soil fungal communities. Thus, plant diversity could predict both soil fungal α and β diversity in the temperate steppe of northeastern China.

• Infestations of Lespedeza cuneata alter soil microbial communities and their actions.

Invasive plant species may alter soil characteristics or interact with the soil microbial community resulting in a competitive advantage. Our objectives were to determine: i) if invasive plant species alter soil properties; and ii) the long-term effects of invasive plant species on soil properties and subsequent implications on ecological restoration efforts. We focused on Lespedeza cuneata, a plant that may be allelopathic. Soil samples were collected from four locations in Central Missouri, USA: an old-field with abundant L. cuneata, two reconstructed sites, and a remnant prairie that has never been plowed. Soil health indictors were used to characterize soil properties at these sites. Nearly every soil property differed significantly between the unplowed prairie reference site and the other three sites. The reconstructed sites, however, generally did not differ from the invaded old-field. These results indicate that the reconstructed prairies are not fully recovered. Although above-ground traits, such as the plant community structure, appear similar to the prairie, the soil microbial community structure still resembles that of an invaded old-field site. These results indicate that more time may be needed before soil microbial populations fully recover after invasive plant removal.

• We evaluated effects of fungi on N₂O emission in Chinese milk vetch-containing soils.

Fungi play an important role in soil nitrous oxide (N₂O) emission in many agricultural soil systems. However, the effect of fungi on N₂O emission in Chinese milk vetch (CMV)-containing soils has not been examined sufficiently. This study investigated the contribution of bacteria and fungi to soil N₂O emission in CMV-amended soils. We compared soils from an experimental field in the Fujian Academy of Agricultural Sciences that had been treated with 30 000 kg of CMV per 667 m² per year with one that was not treated with CMV. We incubated soil using cycloheximide and streptomycin to differentiate fungal and bacterial N₂O emissions, respectively. Quantitative PCR (qPCR) was performed to investigate bacterial and fungal abundances in the two agricultural soil ecosystems. The contribution of fungi to soil N₂O emission in CMV-amended soils was greater than that in non-CMV-amended paddy soils, with fungi accounting for more than 56% of the emissions in CMV-amended soils. Quantitative PCR showed that the ratio of the internal transcribed spacer to 16S rDNA was significantly higher in CMV-amended soils than in non-CMV-amended paddy soils. Furthermore, soil properties, such as pH (P<0.05) and NH₄⁺ concentration (P<0.05), significantly and negatively affected N₂O emission by fungi in soil, whereas the total organic carbon (P<0.05) and NO₃^- concentration (P<0.05) showed significant positive effects. Fungi may be important contributors to N₂O production in CMV-amended soils, which may create challenges for mitigating N₂O production.