● Microbial attributes were compared between soil fauna gut and plant rhizosphere. ● Manure applications decreased or increased gut or rhizosphere bacterial diversity. ● Stochastic or deterministic processes drove gut or rhizosphere bacterial assembly. ● Manure applications increased bacterial network complexity of gut and rhizosphere.
Diverse microbes inhabit animals and plants, helping their hosts perform multiple functions in agricultural ecosystems. However, the responses of soil fauna gut and plant rhizosphere microbiomes to livestock manure applications are still not well understood. Here we fed Protaetia brevitarsis larvae (PBL) with chicken manure and collected their frass. The frass and manure were applied as fertilizers to lettuce pots. We then compared the changes of microbial diversity, community assembly, and potential functions between the gut group (i.e., all PBL gut and frass samples) and the rhizosphere group (i.e., all rhizosphere soil samples). We revealed that manure applications (i.e., feeding or fertilization) decreased bacterial diversity in the gut group but increased that in the rhizosphere group. Particularly, the proportions of Bacilli in the gut group and Gammaproteobacteria in the rhizosphere group were increased (up to a maximum of 33.8% and 20.4%, respectively) after manure applications. Stochastic and deterministic processes dominated community assembly in the gut and rhizosphere microbiomes, respectively. Manure applications increased the microbial co-occurrence network complexity of both the gut and rhizosphere groups. Moreover, the proportions of functional taxa associated with human/animal pathogens in the gut group and carbon/nitrogen cycling in the rhizosphere group were enhanced (up to 2.6-fold and 24.6-fold, respectively). Our findings illustrate the different responses of microbial diversity, community assembly, and potential functions in soil fauna gut and plant rhizosphere to manure applications. The results could enhance our knowledge on the reasonable utilization of animal and plant microbiomes in agricultural management.
● Soil abundant taxa diversity positively related to multifunctionality under Hg stress. ● Microbial network complexity of soil abundant taxa supported the strength of SBF. ● Stochastic assembly of soil abundant subcommunity supported the strength of SBF. ● Stochastic ratio was the most important predictor for the strength of SBF.
It is known that soil microbial communities are intricately linked to multiple ecosystem functions and can maintain the relationship between soil biodiversity and multifunctionality (SBF) under environmental stresses. However, the relative contributions and driving forces of abundant and rare taxa within the communities in maintaining soil biodiversity-multifunctionality relationship under pollution stresses are still unclear. Here, we conducted microcosm experiments to estimate the importance of soil abundant and rare taxa in predicting these relationships under heavy metal mercury (Hg) stress in paired paddy and upland fields. The results revealed that the diversity of abundant taxa, rather than rare taxa, was positively related to multifunctionality, with the abundant subcommunity tending to maintain a larger proportion of soil functions including chitin degradation, protein degradation, and phosphorus mineralization. Soil multitrophic network complexity consisting of abundant species showed positive correlations with biodiversity and multifunctionality, and supported the strength of SBF within a network complexity range. Stochastic assembly processes of the abundant subcommunity were positively correlated with the strength of SBF, although stochastic processes decreased the biodiversity and the multifunctionality, respectively. After simultaneously accounting for multiple factors on the strength of SBF, we found that the stochastic community assembly ratio of abundant taxa was the most important predictor for SBF strength under Hg stress. Our results highlight the importance of abundant taxa in supporting soil multifunctionality, and elucidate the linkages between community assembly, network complexity and SBF relationship under environmental stresses.
● Rice planting decreased total iron but increased active iron. ● Iron activation varied greatly among different paddy soils but not in woodland soils. ● Paddy soil iron was mainly affected by pH, SOC and particle composition. ● The decrease of soil Fe was mainly in the form of Fec and was closely related to SOC.
Human activities have intensified the activity and morphological transformation of iron in soils, but there is a lack of quantitative assessment of the loss or of the transformation pattern. By studying Fe-rich rice soils in southern China and comparing them with corresponding woodland soils, it was found that rice planting reduced the total iron (Fet) content, mainly of crystalline iron (Fec), along soil profiles (0−100 cm) while increasing the content of active iron (Feo). The activation degree of Feo (Feo%) varied significantly among different parent materials in paddy soils but showed less variation in woodland soils. Regression analysis revealed significant correlations between both the content of Fec and the content of Feo in paddy soils with soil organic carbon (SOC) and particle composition (p < 0.05). The Feo% was primarily influenced by pH, SOC, and particle composition. The iron loss in paddy soil was mainly Fec and was closely related to SOC, whereas the transformation of active iron (Feo) was influenced by a combination of soil factors and environmental conditions. The results demonstrate that human activities accelerate the loss and activation of active iron in the soil, thereby altering the iron cycling process in rice paddy ecosystems.
● Comammox Nitrospira clade A and B showed contrasting responses to citrus planting. ● 54d9-like AOA and Nitrobacter -NOB dominated in the 5Y and 10Y soils. ● Nitrososphaera -like AOA and Nitrospira -like NOB dominated in the 20Y and 30Y soils. ● Soil pH and P content were the major factors shaping nitrifying communities.
Ammonia oxidizing bacteria (AOB), archaea (AOA), nitrite oxidizing bacteria (NOB) and complete ammonia oxidizers (comammox Nitrospira) are major players in nitrification. However, the distribution and community composition of these nitrifiers in intensively managed orchard soils are still unclear. Here, we chose soil samples from citrus orchards that had been planted for 5 years (5Y), 10 years (10Y), 20 years (20Y) and 30 years (30Y), and adjacent woodland (NF), to study the response of nitrifiers to long-term citrus plantation using quantitative PCR and MiSeq sequencing. Our results revealed that the ammonia and nitrite oxidation potentials in the 5Y soil were the highest, and decreased with increasing plantation age. The AOB abundance was higher in 5Y and 10Y soils than that in 20Y and 30Y soils. The abundance of comammox Nitrospira clade A increased with increasing plantation age, but comammox Nitrospira clade B showed the opposite tendency. MiSeq sequencing results indicated 54d9-like AOA and Nitrobacter-NOB were the dominant populations in 5Y and 10Y soils whereas Nitrososphaera-like AOA and Nitrospira-like NOB dominated in 20Y and 30Y soils. The conversion of woodland to orchard resulted in a significant shift of AOB population from Nitrosospira cluster 3a.1 to cluster 3a.2. In addition, soil pH and phosphorus (P) content were the major factors shaping nitrifying communities. This work suggested citrus plantation altered the distribution of community composition of nitrifiers by affecting soil chemical and physical conditions, and comammox Nitrospira could potentially play an important role in nitrification in intensive managed orchard soils.
● The nitrogen (N) and phosphorus (P) addition promotes the abundance of soybean soil nematodes. ● The addition of nitrogen can alleviate the suppression of phosphorus on nematodes. ● Phosphorus addition affects nematode abundance by ammonium nitrogen.
With global warming, the increasing of industrial and agricultural activities and demand for fossil fuels, large amounts of nitrogen and phosphorus compounds are released into the atmosphere, resulting in an annual increase in nitrogen and phosphorus deposition. The nematodes, as one of the main functional groups of soil organisms, occupy multiple trophic levels in soil detritus food networks. However, few studies on the effects of nitrogen and phosphorus on soil nematodes, and the results are uncertain. This experiment was conducted in soybean farmland and four treatments included control, nitrogen addition, phosphorus addition, and N + P addition. The results showed that both phosphorus and N + P addition significantly increased the abundance of soil nematodes, but that had no effects on soil nematodes richness. Redundancy analysis showed that nitrate nitrogen, soil moisture content, and pH were environmental factors driving different dietary changes in soil nematode communities. The effect of phosphorus addition on the abundance of nematode communities mainly affects ammonium nitrogen. Our findings revealed that nitrogen addition when phosphate fertilizer is added to soybean farmland will have a certain positive effect on the soil underground food web, which provides a basis for better explaining the effect of nitrogen and phosphorus addition on soybean farmland.
● CH4 emission rates followed an increased pattern during the growing season at Tibetan Plateau. ● Unique genes carried by abundant species were positively correlated with CH4 emission rates. ● Climate factors influenced CH4 emission rates by regulating microbial community and their genes.
Microorganisms play pivotal roles in soil methane (CH4) emissions and their functional genes are origins of a key mechanism for soil CH4-cycling. However, understanding of the roles of specific genes (e.g., unique or shared genes carried by species) underlying CH4-cycling remains elusive. Here, we measured CH4 emission rates and investigated variations in microbial community and the abundance of genes carried by species during the growing season in alpine meadow on the Tibetan Plateau. We discovered that CH4 emission rates increased from 394.4, 745.9, and 1092.7 µg CH4 m−2 h−1, in April, June, and August, respectively, and had a positive correlation with unique genes carried by abundant species during the growing season. Moreover, we found that unique genes carried by abundant species involved in methanogenesis processes have a higher abundance than methanotrophic processes. Further analysis indicated that climate factors (i.e., mean monthly temperature (MMT) and mean monthly precipitation (MMP)) influenced microbial community and their functional genes, and therefore affected the CH4 emission rates. Overall, the present study provides a novel insight into the variation of soil CH4 emissions from a functional gene perspective, highlighting the important roles of unique genes carried by abundant species in CH4 emissions in the Tibetan Plateau under seasonal variation.
● Changes in soil properties and microbial communities regulated rhizosphere protistan assemblages. ● Bacterial community was more sensitive to soil amendments than protists and fungi. ● Soil amendments trigger the role of specific protistan taxa Cercozoa on microbial interactions.
Understanding the responses of different rhizosphere microbial lineages to soil amendments during in situ remediation of Cd-contaminated soil is of great importance in the assessment of the restoration and crop health. Here, we evaluated the effects of lime (LM), biochar (BC), pig manure (PM), and a commercial Mg-Ca-Si conditioner (CMC) on the rice rhizosphere soil physicochemical properties and community assembly of bacteria, fungi, and protists in a six-year consecutive application of soil amendments field trial. Our results indicated that among the four amendments, the BC and CMC had the best efficiency in increasing soil pH, which were 5.2% and 16.2%, respectively. Despite the differences in soil Cd concentrations is not noticeable, all the soil amendment treatments significantly decreased the proportion of available Cd in total Cd compared to the control. Soil amendments significantly altered the diversity of bacterial community, while they had no effect on fungal and protistan communities. Linear discriminant analysis effect size (LEfSe) showed that the bacteria was more sensitive to soil amendment-induced changes. For protists, treatments with LM and BC changed the groups of protistan consumers, while treatments with PM and CMC significantly increased the relative abundances of protistan phototrophs. Co-occurrence network analysis revealed that soil amendments increased microbial network complexity and triggered the role of protists, especially for the predatory protists Cercozoa, on microbial trophic interactions. Further variation partitioning analysis revealed that edaphic properties, bacterial and fungal communities compositions together explained the 77% of the total variation in protistan community, and the stronger correlations between diversity of bacterial and protistan communities suggested that the bacteria community was a more important biotic driver of the protistan community. Overall, our findings demonstrate the distinct responses of rice rhizosphere microbial communities to soil amendment applications, highlighting the interactive associations between microbiomes, which is vital for enhancing our ability to develop effective strategies for sustainable soil management. This study enhances our understanding of the ecological roles of protists under soil amendment applications and highlights their potential contributions in bioremediation and environmental applications for Cd-contaminated soil.
● A new COX1 primer for soil nematode metabarcoding was designed, and this primer outperforms other commonly used COX1 primer pairs in species recovery and quantity of PCR products. ● The lack of reference database is the main reason that led to the low species recovery in COX1 metabarcoding. ● We expanded current NCBI database by adding 51 newly generated COX1 reference sequences.
Microscopic nematodes play important roles in soil ecosystems and often serve as bioindicators of soil health. The identification of soil nematodes is often difficult due to their limited diagnostic characters and high phenotypic plasticity. DNA barcoding and metabarcoding techniques are promising but lack universal primers, especially for mitochondrial COX1 gene. In this study a degenerated COX1 forward primer COIFGED was developed. The primer pair (COIFGED/JB5GED) outperforms other four commonly used COX1 primer pairs in species recovery and quantity of polymerase chain reaction (PCR) products. In metabarcoding analysis, the reads obtained from the new primer pair had the highest sequencing saturation threshold and amplicon sequence variant (ASV) diversity in comparison to other COX1 as well as 18S rRNA primers. The annotation of ASVs suggested the new primer pair initially recovered 9 and 6 out of 25 genera from mock communities, respectively, outperformed other COX1 primers, but underperformed the widely used 18S NF1/18Sr2b primers (16 out of 25 genera). By supplementing the COX1 database with our reference sequences, we recovered an additional 6 mock community species bringing the tally closer to that obtained with 18S primers. In summary, our newly designed COX1 primers significantly improved species recovery and thus can be supplementary or alternative to the conventional 18S metabarcoding.
● N fertilizer altered bacterial community compositions by changing soil nutrients. ● Bacterial ammonia oxidation became predominated with the increasing N rate. ● Excessive N input caused the information of a more complex microbial network. ● Intensified microbial competition by excessive N was due to negative link increase.
Nitrogen (N) fertilization drives the structure and function of soil microbial communities, which are crucial for regulating soil biogeochemical cycling and maintaining ecosystem stability. Despite the N fertilizer effects on soil microbial composition and diversity have been widely investigated, it is generally overlooked that ecosystem processes are carried out via complex associations among microbiome members. Here, we examined the effects of five N fertilization levels (0, 135, 180, 225, and 360 kg N ha−1) on microbial co-occurrence networks and key functional taxa such as ammonia-oxidizers in paddy soils. The results showed that N addition altered microbial community composition, which were positively related to soil total N and available phosphorus (P) contents. The abundance of ammonia-oxidizing archaea (AOA) significantly decreased after N addition, whereas ammonia-oxidizing bacteria (AOB) increased in N360 treatment. Compared with low-N group (N0 and N135), the high-N group (N225 and N360) shaped more complex microbial webs and thus improved the stability of the microbial community. Partial least squares path modeling further revealed that N fertilizer had a higher effect on microbial network complexity in the high-N group (0.83) than the low-N group (0.49). Although there were more positive links across all microbial networks, the proportion of negative links significantly increased in the high-N network, suggesting that excess N addition aggravated the competition among microbial species. Disentangling these interactions between microbial communities and N fertilization advances our understanding of biogeochemical processes in paddy soils and their effects on nutrient supply to rice production. Our findings highlighted that highly N-enriched paddy soils have more stable microbial networks and can better sustain soil ecological functions to cope with the ongoing environmental changes.
● Pattern and mitigation potential of crop-specific fertilizer-N losses were assessed. ● China showed high fertilizer-N losses due to high N application rates and low SOC. ● MAP, SOC, and soil pH are key parameters affecting fertilizer-N losses. ● At a given application rate, soils with higher SOC have lower fertilizer-N losses. ● Optimal N rate combined with SOC improvement could cut 34.8%−59.6% of N losses.
Understanding crop-specific fertilizer-nitrogen (N) loss patterns, driving factors, and mitigation potentials is vital for developing efficient mitigation strategies. However, analyses based on the gross magnitude of fertilizer-N losses within a growing season remain fragmented and inconclusive at a global scale. To address this gap, we conducted a global meta-analysis using 940 observations from 79 published 15N-tracing studies to assess the effects of natural factors, soil parameters, and N application rates on gross fertilizer-N losses in cereal-cropped soils. We found that China had the highest conventional fertilizer-N application and loss rates (230−255 and 75.9−114 kg N ha−1 season−1, respectively) and the lowest soil organic carbon (SOC) contents (10.6 g kg−1) among the countries examined. Mean annual precipitation, SOC content, and soil pH were key parameters affecting fertilizer-N losses in wheat-, maize-, and rice-cropped soils, respectively. Fertilizer-N application rates were positively correlated with N loss amounts, while higher SOC levels led to lower losses. Adopting optimized N application rates combined with improving SOC levels could potentially mitigate 34.8%−59.6% of N losses without compromising crop yields compared with conventional practices. This study underscores the critical role of SOC in reducing N losses and suggests that future research should focus on innovative strategies and efficient organic amendments for enhanced SOC sequestration.
● Herbicide-based weeds control impacts wheat crops as well. ● SynComs of Pseudomonas strains reduce the need for high-dose herbicides. ● 100% Axial provides less weed control compared to 75% Axial with C4 SynCom. ● Axial 75% with C4 SynCom promotes wheat growth than the 75% Axial alone.
To address environmental concerns and manage resistant weeds, there is a growing demand for eco-friendly alternatives. In this study, we propose the integration of synthetic communities (SynComs) to reduce herbicide consumption. Four SynComs, consisting of bacteria isolated from weed or wheat rhizospheres, were first evaluated under greenhouse conditions. All SynComs enhanced wheat growth, which was manifested by increased Soil Plant Analysis Development (SPAD) values and fresh biomass. At the same time, SynCom C4 effectively reduced SPAD values and fresh biomass of the infesting weed, Phalaris minor, when combined with low-dose Axial herbicide. A field trial was then conducted using the C4 SynCom and various doses of Axial (100%, 75%, 50%, and 25%). Remarkably, the combination of C4 with 50% and 75% Axial significantly improved wheat growth by mitigating the side effects of herbicide on wheat. Weed infestation reduced grain yield by 16% and 25% at the dose of 50% and 75% Axial, respectively. The combination of Axial with C4 rescued up to 22% of grain yield loss under infested weed compared with Axial alone. Our findings suggested that the combination of herbicides with SynComs exhibited synergistic effects for controlling Phalaris minor and promoting wheat growth, so that such combination provides a sustainable and eco-friendly weed control strategy.
● Conservation tillage increases soil microarthropod abundance at the global scale. ● The effect of conservative tillage on microarthropods is soil texture-dependent. ● This positive effect of conservation tillage is particularly evident in nutrient-poor soil areas. ● In temperate humid regions, however, this positive effect of conservation tillage is limited. ● The effect of conservative tillage on microarthropods varies with fauna group and climate regions.
Conservation tillage is crucial for preserving soil structure and fertility. However, the effects of no tillage on the abundance of soil microarthropods (Acari and Collembola) remain unclear, with contrasting results reported. To assess the global impact of no tillage, we compiled a data set consisting of 59 publications, from which we extracted 167 observations for microarthropod abundance, 193 observations for Acari abundance, and 176 observations for Collembola abundance. Our findings revealed significant increases in soil microarthropods (27.1%), Acari (22.1%), and Collembola (32.3%) compared to conventional tillage under no tillage. The impact varied with soil texture, precipitation, and soil nutrient availability. Furthermore, to assess the impact of reduced tillage, we extracted 46 observations for microarthropod abundance, 64 observations for Acari abundance, and 27 observations for Collembola abundance. Reduced tillage also showed positive effects, with a 28.4% increase in soil microarthropods and a 53.7% increase in Acari compared to conventional tillage. Our research demonstrates the beneficial effects of no tillage and reduced tillage on soil microarthropod abundance. However, the positive effect of conservation tillage on soil microarthropods differed in magnitude Collembola and Acari. Conservation tillage should be encouraged, particularly in regions with poor soil nutrients and high precipitation, to prevent further decline in soil microarthropod abundance.
Plastic pollution is a growing concern in soil ecosystems worldwide. The accumulation of (micro)plastic debris leads to a unique microenvironment, termed the “plastisphere.” Notably, the dynamics and behaviors of the soil plastisphere diverge from its marine counterpart, where it is initially defined, thereby likely exhibiting an uncharacterized feature in ecological effects and biogeochemistry. The understanding of the soil plastisphere holds significant implications for environmental science and practical applications in pollution management and agricultural practices. Compared with the oceanic plastisphere, research on the soil plastisphere is still in its infancy with limited but significant studies contributing to current knowledge. A recent seminal work by Rillig et al. (Rillig et al., 2023. Nature Reviews Microbiology. doi:10.1038/s41579-023-00967-2) has inspired us and provided comprehensive insights into the characteristics and function of the soil plastisphere. In this commentary, we present core aspects of the soil plastisphere, encompassing its microbial communities, biogeochemical processes, and ecological implications, as well as highlight current methodologies probing this domain.
● ARB was investigated in different soil types following manure application. ● CTC-manure induced more resistance of soil indigenous microbes in fluvo-aquic soil. ● Lactobacillus , Dyella , Ralstonia , and Bacillus were the key different genera. ● Manure control is an effective way to reduce the risk of soil ARB.
Swine manure, commonly applied as organic compost in agricultural fields, is an important reservoir of antibiotic-resistant bacteria (ARB). Previous work indicated that manure application led to more antibiotic resistance genes in red soil compared with black soil and fluvo-aquic soil. Accordingly, the influencing mechanisms of soil types on the distribution of ARB was worthy of further exploration by a soil column experiment. The results showed that a higher shift in the operational taxonomic units and the community composition of chlortetracycline (CTC)-resistant bacteria (CRB) were observed in fluvo-aquic soil than in black and red soils. CTC induced antibiotic resistance development in soil indigenous microorganisms (Streptomyces, Pseudomonas, Bacillus, Rhodococcus, and Paenibacillus), and the induction was most obvious in fluvo-aquic soil. Streptomyces was significantly positively correlated with pH and organic matter. Additionally, LEfSe analysis indicated that the key different genera were Microbacteriaceae (black soil), Lactobacillus, unclassified_c__Bacilli and Paenibacillus (fluvo-aquic soil), and Dyella, Ralstonia and Bacillus (red soil). It was concluded that manure application led to higher CRB risk in fluvo-aquic soil compared with black and red soils. Overall, appropriate methods according to soil types are important ways to reduce the risk of soil resistant bacteria during manure return.
