● Salt spray is a natural disturbance in coastal area of Southern China. ● Arbuscular mycorrhizal fungi can mediate the detrimental effects of salt spray. ● Leaf thickness and photosynthetic ability are key parameters. ● Combined fungi may be beneficial for trees grown in coastal areas.
Salt spray is a natural disturbance in coastal region. Arbuscular mycorrhizal fungi (AMF) are recognized as bio-ameliorators of soil salinity in plants. However, the mechanism through which AMF protects Cinnamomum camphora against aerial salinity remains unclear. To address this knowledge gap, plants were subjected to four fungal regimes, namely sterilized fungal inoculum, Glomus tortuosum, Funneliformis mosseae, or a combination of these two fungi, and exposed to three sprayed-salt regimes (0, 7, or 14 mg NaCl cm−2 d−1) in a greenhouse. Salt spray significantly decreased photosynthetic capabilities, total dry weight, and salinity tolerance of non-mycorrhizal plants. Mycorrhizal inoculation, particularly a combination of G. tortuosum and F. mosseae, evidently mitigated the detrimental effects induced by salt spray. Meanwhile, mycorrhiza-mediated protection depended on the intensity of sprayed salt and the identity of fungal taxa. Furthermore, the enhanced resistance of mycorrhizal C. camphora seedlings to aerial salinity was mainly owing to increased leaf thickness and photosynthetic capabilities. These findings imply that inoculation with combined fungi could be an optimal strategy for cultivating C. camphora plants in coastal regions. The results gained hold the potential to offer both theoretical and practical guidance for the managers of coastal ecosystems in soil restoration and conservation.
● Biocrusts are one of the most important components of the land cover in frozen ground regions on the Qinghai–Tibet Plateau, which increased the silt particle content, enhanced field moisture capacity, and reduced soil bulk density. ● Biocrusts significantly increased levels of SOC (22.6−30.8 g kg−1) and TN (2.1−2.8 g kg−1) within the 0–40 cm soil layer, while they had no significant influence on the TP contents. ● Biocrusts also had influence on the stoichiometry characteristics, and the C/N, C/P and N/P ratios of the biocrusts were all higher than that of the bare land, which revealed that biocrusts enhanced the contents of SOC and TN in presuccessional period of biocrusts and reduced the availability of P in their postsuccessional period.
Biocrusts (BSCs) are widely distributed in frozen ground regions on the Qinghai-Tibet Plateau, and they are considered an important component of cold ecosystems. However, the specific impacts of BSCs on frozen soil remains relatively unclear. The aim of our study was to clarify the influence of BSCs (light BSCs and dark BSCs in two different succession stages) on the physical properties and ecological stoichiometry characteristics of frozen soil. Our results showed that BSCs increased the silt particle content in 20–40 cm soil layer, leading to a decrease in soil bulk density. And the field water capacity increased about 10%–40% compared to bare land. Additionally, BSCs significantly increased the contents of soil organic carbon (SOC, 22.6–30.8 g kg−1) and total nitrogen (TN, 2.1–2.8 g kg−1) in the upper 40 cm soil layer, both of them were approximately 1.3–2.0 and 1.3–4.0 times higher than those observed in bare land. However, BSCs did not have significant influence on soil total phosphorus (TP). BSCs had a significant impact on the stoichiometric ratios within 40 cm. The C/N ratios of the two types of BSCs ranged from 8.8 to 13.5, the C/P ratios ranged from 6.6 to 13.8, and the N/P ratios ranged from 0.6 to 1.2, which were all higher than those of the bare land. There were no significant differences among the C/N, C/P, and N/P ratios between two types of BSCs. However, the increment of C/P and N/P ratios of dark BSCs were significantly higher than those of light BSCs within 0–30 cm, which indicated that a reduction in the availability of phosphorus during the later stages of BSCs succession. These findings provided a theoretical basis for further research on the ecological functions of BSCs in frozen ground regions.
● Dicyandiamide decreased N2O emissions even under 40°C. ● Ammonia oxidizers and nirS were well adapted to 40°C in manured soils. ● Fungal nirK tolerated high temperature better in urea than manure treatment. ● Compared to nosZ II, nosZ I adapted to all temperature regardless of fertilization. ● nirS -denitrifier dominated N2O emissions at high temperature in fertilized soil.
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.
● A new fairy ring fungus was reported in this study. ● Fairy ring fungi influence plants and soil microbes by promoting soil nutrients. ● The effect of fairy ring fungi on plants and soil microbes depends on the habitat type.
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.
● Soil resistomes of conventional and organic systems were similar in terms of ARG biodiversity. ● Soil resistomes of conventional and organic systems were different regarding individual ARGs. ● Uncultivated bacteria and archaea can contribute significantly to soil resistome.
Metagenomic studies of various soil environments have previously revealed the widespread distribution of antibiotic resistance genes (ARGs) around the globe. In this study, we applied shotgun metagenomics to investigate differences in microbial communities and resistomes in Chernozem soils that have been under long-term organic and conventional cropping practices. The organic cropping system was seeded with Triticum spelta without any fertilizer. The conventional cropping system was seeded with Tríticum durum Desf and used mineral fertilizer (NPK), that resulted in an increased amount of total and available carbon and nitrogen in soils. Across all samples, we identified a total of 21 ARG classes, among which the dominant were vancomycin, tetracycline and multidrug. Profiling of soil microbial communities revealed differences between the studied fields in the relative abundances of 14 and 53 genera in topsoil and subsoil, respectively. Correlation analysis showed significant correlations (positive and negative) among 18 genera and 6 ARGs, as well as between these ARGs and some chemical properties of soils. The analysis of metagenome-assembled genomes revealed that Nitrospirota, Thermoproteota, Actinobacteriota and Binatota phyla of archaea and bacteria serve as hosts for glycopeptide and fluoroquinolone/tetracycline ARGs. Collectively, the data obtained enrich knowledge about the consequences of human agricultural activities in terms of soil microbiome modification and highlight the role of nitrogen cycling taxa, including uncultivated genera, in the formation of soil resistome.
● Fungi are more sensitive to long-term nitrogen addition than bacteria. ● Long-term nitrogen addition significantly reduces fungal biomass, but promotes the accumulation of fungal residues in soil. ● Long-term nitrogen addition has no significant impact on bacterial biomass and residues.
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. ● mRNA enrichment from soil samples remains a formidable challenge due to the presence of inhibitory compounds, low RNA yields, and sample heterogeneity. ● Soil metatranscriptomics unravels the expression levels of genes involved in the real-time molecular dialogues between plants and rhizobionts, uncovering the dynamics of nutrient exchange, symbiotic interactions, and plant-microbe communication. ● Metatranscriptomics unlocks the active expression of the soil resistome, elucidating the mechanisms of resistance dissemination under anthropogenic activities. ● Metatranscriptomics provides comprehensive data regarding the identification, quantification, and evolutionary history of RNA viruses.
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.
● Bacterial networks became less connected with soil development along primary succession. ● Community composition was initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with decreasing pH. ● Most natural microorganisms in extreme habitats exist as consortia that provide robustness and extensive metabolic capabilities in structuring bacterial communities.
In microbial ecology, there is limited understanding of the mechanisms governing patterns in community structure across space and time. Here, we studied the changes of bacterial co-occurrence network structure over four primary successional soils after glacier retreat, including a sand dune system and three glacier foreland series, varying in timescale from centuries to millennia. We found that in all series, network structure was most complex in the earliest stages of succession, and became simpler over time. Richness and abundance of keystone species and network stability also declined over time. It appears that with less productive, nutrient poor and physiologically extreme conditions of early succession, closer interactions among bacterial species are ecologically selected for. These may take the form of consortia (with positive interactions) or stronger niche exclusion (with negative interactions). Additionally, we quantified the relative roles of different structuring processes on bacterial community using a bin-based null model analysis (iCAMP). With each successional series, community composition was initially governed by stochasticity, but as succession proceeded there was a progressive increase in deterministic selection over time, correlated with decreasing pH. Overall, our results show a consistency among the four series in long-term processes of community succession, with more integrated networks and greater stochasticity in early stages.
● Phyla Proteobacteria and Bacteroidetes dominated in the rhizosphere of tomatoes under RSD amendment. ● Stochastic processes dominated in bacterial community assembly for biochar and CF amendments. ● It is important to monitor and manage soil conditions before planting after RSD amendment.
Reductive soil disinfestation (RSD) is an important tool for sustainable agricultural productivity. However, the differences in soil bacterial communities and their community assembly processes among RSD and other treatment strategies (e.g., biochar and chemical fumigation) are still subject to open questions. In this study, soils subjected to various treatments–un-treated control (CK), chemical soil fumigation with CaCN2 (CF), 1% biochar (1%B), 3% biochar (3%B), and reductive soil disinfestation (RSD) are investigated. Soil samples were collected, incubated, and then used for growth of tomato plants. The Sloan neutral community model indicates that stochastic processes dominate in bacterial community assembly for both biochar and CF amendments. In contrast, this work shows that RSD treatment can have a strong impact on soil bacterial community composition. The relative abundance of Firmicutes increased during unplanted soil incubation, whereas Proteobacteria and Bacteroidetes dominated in the rhizosphere after planting of tomatoes. Normalized stochasticity ratio reveals that deterministic selection played an important role in the bacterial assembly under RSD amendment. We found that RSD amendment yielded lower biomass than that for other treatments after 28 days of tomato growth. Our results suggest that although RSD treatment has great potential to rebuild soil bacterial ecology by shaping bacterial communities and their assembly processes, it is important to monitor and manage soil conditions (e.g., soil nutrients or physical properties) before planting to ensure plant productivity.
● Soil aggregates affect soil respiration and its temperature sensitivity. ● Organic matter input boosts soil respiration, affected by temperature and aggregate size. ● Q 10 declines with increasing aggregate size, influenced by soil quality index. ● Microbial CUE drops with organic matter input, temperature and aggregate size increase.
Understanding the dynamics of soil respiration, microbial carbon use efficiency (CUE), and temperature sensitivity (Q10) in response to exogenous organic matter (EOM) input, soil aggregate size, and incubation temperature is crucial for predicting soil carbon cycling responses to environmental changes. In this study, these interactions were investigated by 180-day incubation of soil aggregates supplemented with EOM at various temperatures (5°C, 15°C and 25°C). The results reveal an ‘L-shaped’ trend in soil respiration on the time scale across all treatments, characterized by initial rapid declines followed by stability. EOM input and higher temperatures significantly enhance respiration rates. Notably, the respiratory rates of soil aggregates of different sizes exhibit distinct patterns based on the presence or absence of EOM. Under conditions without the addition of EOM, larger aggregates show relatively lower respiration rates. Conversely, in the presence of EOM, larger aggregates exhibit higher respiratory rates. Furthermore, Q10 decreases with increasing aggregate size. The relationship between Q10 and the substrate quality index (SQI) supports the carbon quality temperature (CQT) hypothesis, highlighting SQI’s influence on Q10 values, particularly during later incubation stages. Microbial CUE decreases with EOM input and rising temperatures. Meanwhile, aggregate size plays a role in microbial CUE, with smaller aggregates exhibiting higher CUE due to enhanced nutrient availability. In conclusion, the intricate interplay of EOM input, aggregate size, and temperature significantly shapes soil respiration, microbial CUE, and Q10. These findings underscore the complexity of these interactions and their importance in modeling soil carbon dynamics under changing environmental conditions.
● Nitrogen fertilizers’ effects on protists in three paddy field soils were analyzed. ● Different nitrogen fertilizers had distinctive effects on the protist communities. ● The effect of nitrogen fertilizers on protist communities slightly depended on the soil types. ● Predatory protists were the main groups that were affected by nitrogen fertilizers.
Protists are one of the most diverse and dominant microbial groups and they play critical roles in the soil ecosystem. Although nitrogen fertilizers have a profound impact on protist communities, still less is known about how different nitrogen fertilizer types affect protist community composition in different soil types. Here we investigated the effects of six inorganic nitrogen fertilizers (urea, ammonium nitrate, ammonium sulfate, potassium nitrate, ammonium chloride, and diammonium hydrogen phosphate) and an organic fertilizer (a mixture of rice husk and cow manure) on protist community composition in three paddy field soils using a high-throughput sequencing method. The effect of the fertilizers on the functional groups of protists, namely consumers (predators and decomposers), photoautotrophs, and parasites (plant pathogens and animal parasites) was also analyzed. The results showed that nitrogen fertilizers had distinctive effects on the beta diversity of the protists, while we also observed that the same fertilizer had slightly different effects depending on the soil type. Amoebozoa and Rhizaria were the most affected protist taxonomical groups, while predatory protists were the main functional groups that were affected by nitrogen fertilizers. Random forest analysis showed that most of the fertilizer-affected protists were predators, among which Cercozoa was the most affected taxa. In conclusion, our results provide important insights into the impact of nitrogen fertilizers on soil protist communities.
● ARGs and ARB in typical environments which exposed to antibiotics are prevalent. ● Nanoparticle- and photosensitizer-related technology can clear specific ARGs or ARB. ● CRISPR-Cas- and phage-related technology can eliminate particular ARGs or ARB. ● Antibiotic combination can be used to eliminate microbial resistance. ● Microbiome-specific technology can eradicate most types of ARGs or ARB in one shot.
Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment pose serious threats to environmental security and public health. There is an urgent need for methods to specifically and effectively control environmental pollution or pathogen infection associated with ARGs and ARB. This review aims to provide an overview of methods abating the prevalence and spread of ARGs and ARB from species to community level. At the species level, species-specific technologies, such as nanoparticle-, photosensitizer-, CRISPR-Cas-, and phage-related technology can be utilized to clear a particular class of ARGs or ARB, and in combination with low-dose antibiotics, a higher removal efficiency can be achieved. Moreover, the combination of antibiotics can be used to reverse microbial resistance and treat recurrent antibiotic resistant pathogen infections. At the community level, community-specific strategies, such as biochar, hyperthermophilic compost, and fecal microbiota transplantation can eradicate most types of ARGs or ARB in one shot, reducing the probability of resistance development. Though some progress has been made to eliminate ARGs and ARB in disease treatment or decontamination scenarios, further research is still needed to elucidate their mechanisms of action and scopes of application, and efforts should be made to explore novel strategies to counter the prevalence of antibiotic resistance.
● Organic fertilization increased the richness and abundance of beneficial communities. ● The increase in the beneficial communities resulted from soil property optimization. ● Organic fertilization enhanced the functionality of bacterial communities. ● Plants exhibited a preference for internalizing beneficial bacteria.
Soil microbiomes play a crucial role in maintaining ecological functions and are of great importance for soil health. Some of them could bring benefits to plants for growth promotion. Despite numerous studies have focused on specific beneficial bacteria and their interactions with soils and plants, we still lack a comprehensive understanding of beneficial communities in plant–soil continuums and their responses to agricultural activities. To address this gap, we carried out a microcosm experiment using 16S rRNA amplicon sequencing to explore the effects of organic fertilization on beneficial communities in plant–soil continuums and assess their potential multifunctionality. Our findings reveal that organic fertilization had a positive impact on the beneficial functionality of bacterial communities in plant–soil continuums. This improvement was primarily attributed to the optimized soil physicochemical conditions resulting from organic fertilization. Additionally, organic fertilization increased the complexity of bacterial co-occurrence networks in both soils and the endosphere. Keystone taxa in the endosphere undergone a shift of functions toward pathogen suppression as the result of organic fertilization. Furthermore, this study revealed that plants exhibited a preference for internalizing beneficial bacteria over other type of bacteria. We also provided new insights for evaluating the multifunctionality of microbiomes, and found that the functionality of beneficial communities in plant–soil continuums is enhanced by organic fertilization. All these findings suggested that organic fertilization can be an effective strategy for maintaining plant and soil health.
● Rubber-based agroforestry systems increased the complexity of fungal networks. ● Fungal community structure was strongly correlated with soil pH and SOC. ● Rubber-based agroforestry systems reduced the presence of certain pathogens.
Rubber-based agroforestry systems have been recognized as a practical and sustainable solution to promote the development of agriculture and the environment. However, interactions between fungal communities and these systems are still not sufficiently investigated. In this study, we compared the abundance, diversity, and community composition of soil fungi in four treatments, including rubber monoculture and three rubber-based agroforestry treatments involving intercropping with Camellia sinensis, Coffea liberica, and Theobroma cacao. The results revealed that the community composition exhibited significant variation between the four different treatments, while the overall soil α-diversity was relatively stable across all treatments. Soil pH and soil organic carbon were significantly related to the structure of the fungal community. In particular, the complexity of the functional fungal network increased in response to agroforestry treatments, promoting beneficial fungi and suppressing certain plant pathogens. These results suggest that rubber-based agroforestry systems can promote the health of soil microbial community composition, and therefore provide an effective approach to enhancing soil quality.
● Fungi are more sensitive to precipitation than bacteria. ● The susceptibility of abundant and rare bacteria to precipitation has no difference. ● Abundant taxa of fungi are more vulnerable to precipitation than rare ones.
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.
