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Despite the importance of soil bacterial and fungal communities for ecosystem services and human welfare, how their ecological networks respond to climatic aridity have yet been evaluated. Here, we collected soil samples from 47 sites across 2500 km in coastal and inland areas of eastern Australia with contrasting status of aridity. We found that the diversity of both bacteria and fungi significantly differed between inland and coastal soils. Despite the significant differences in soil nutrient availability and stoichiometry between the inland and coastal regions, aridity was the most important predictor of bacterial and fungal community compositions. Aridity has altered the potential microbial migration rates and further impacted the microbial assembly processes by increasing the importance of stochasticity in bacterial and fungal communities. More importantly, ecological network analysis indicated that aridity enhanced the complexity and stability of the bacterial network but reduced that of the fungal network, possibly due to the contrasting impacts of aridity on the community-level habitat niche breadth and overlaps. Our work paves the way towards a more comprehensive understanding of how climate changes will alter soil microbial communities, which is integral to predicting their long-term consequences for ecosystem sustainability and resilience to future disturbances.

Arbuscular mycorrhizal (AM) fungi and soil invertebrates represent a large proportion of total soil biomass and biodiversity and are vital for plant performance, soil structure, and biogeochemical cycling. However, the role of soil invertebrates in AM fungi development remains elusive. In this opinion article, we summarize the ecological importance of AM fungi and soil invertebrates in the plant-soil continuum and highlight the effects of soil invertebrates on AM fungal hyphae development and functioning. In a context of global change, we envision that better mechanistic understanding of the complex feedback via chemical signaling pathways across the interactions between soil invertebrates and AM fungi is critical to predict their ecological consequences and will open new avenues for promoting ecosystem resilience and sustainability.

In this paper, a millimeter-wave (mmW) wideband high-isolation wide-angle scanning antenna is presented. The end-fire magnetoelectric (ME) dipole with wideband impedance characteristic and wide beamwidth is selected. Based on the ME dipole, a 1×4 subarray with a stripline feed network is constructed to get higher antenna efficiency. Then, four 1×4 subarrays are adopted to form a 4×4 array to realize the wide-angle scanning performance. Furthermore, to get better isolation between the subarrays, the beam is tilted on the non-scanning plane; in addition, the resonant split rings are added on the background of the subarrays. With these two measures, the isolation between the subarrays can be effectively reduced, with more than 20 dB over the entire bandwidth. Owing to the wide beamwidth of ME dipole and high isolation between the subarrays, the 4×4 array can obtain the wide-angle scanning characteristic. The final antenna covers an operating bandwidth of 19.5% (24.25-29.5 GHz) with return loss more than 10 dB, which can meet the band in the 5G standard. The beam can scan approximately ±55∘ with a realized gain reduction under 3 dB within the wide operating bandwidth. Also, the simulated radiation efficiency of the array is more than 77% over almost the entire band. The antenna will be a potential candidate to be applied in 5G applications.

It is a grand challenge to ensure the food security for a predicted world population of exceeding 9.7 billion by 2050, especially in an era of global climate change, land degradation and biodiversity loss. Current agricultural productions are mainly relying on synthetic chemical fertilisers to boost plant productivity but have undesirable effects on the environment and soil biodiversity. A promising direction in sustainable agriculture is to harness naturally occurring processes of beneficial plant-associated microbiomes to ensure sustained crop production and global food security. Despite the significant progress made in the development of beneficial microbes as inoculants to enhance plant performance, challenges remain with the translation of knowledge of plant and soil microbiomes to successful microbial products in the agricultural sector. Here, we highlight how fertilizer technology should be renovated by harnessing microbiome-based innovations to promote plant productivity and contribute to the end of hunger.

Soil bacteria are diverse and form complicated ecological networks through various microbial interactions, which play important roles in soil multi-functionality. However, the seasonal effects on the bacterial network, especially the relationship between bacterial network topological features and soil resistomes remains underexplored, which impedes our ability to unveil the mechanisms of the temporal-dynamics of antibiotic resistance genes (ARGs). Here, a field investigation was conducted across four seasons at the watershed scale. We observed significant seasonal variation in bacterial networks, with lower complexity and stability in autumn, and a wider bacterial community niche in summer. Similar to bacterial communities, the co-occurrence networks among ARGs also shift with seasonal change, particularly with respect to the topological features of the node degree, which on average was higher in summer than in the other seasons. Furthermore, the nodes with higher betweenness, stress, degree, and closeness centrality in the bacterial network showed strong relationships with the 10 major classes of ARGs. These findings highlighted the changes in the topological properties of bacterial networks that could further alter antibiotic resistance in soil. Together, our results reveal the temporal dynamics of bacterial ecological networks at the watershed scale, and provide new insights into antibiotic resistance management under environmental changes.

The intimate interactions of indigenous crops with their associated microbiomes during long-term co-evolution strengthen the capacity and flexibility of crops to cope with biotic and abiotic stresses. This represents a promising untapped field for searching novel tools to sustainably increase crop productivity. However, the current capability of harnessing the power of indigenous crop microbiomes for sustainable crop production is limited due to low efficiency of separating the targeted functional microbes. Here, we highlight the potential benefits and existing challenges of utilizing indigenous crop microbiomes to reduce agrochemical inputs and increase crop resistance to biotic and abiotic stresses. We propose a framework using Raman-spectroscopy-based single-cell-sorting technology combined with a synthetic community approach to design and optimize a functionally reliable ‘beneficial biome’ under controlled conditions. This framework will offer opportunities for sustainable agriculture and provide a new direction for future studies. Crop microbiomes provide plants with beneficial functions including increased nutrient acquisition and stress tolerance, but the current capability of utilizing indigenous crop microbiomes is limited due to low efficiency of separating the targeted functional microbes. A newly proposed framework using single-cell-sorting Raman spectroscopy combined with a synthetic community approach has the potential to design and optimize a ‘beneficial biome’.

The information on the effects of ZnONPs on soil biological processes and the resulting changes of ecosystem function is limited in wheat straw return agricultural soil. This study investigated the effects of ZnONPs on soil heterotrophic respiration and biochemical properties in wheat straw return farmland soil. An 84-day microcosm incubation experiment was implemented after the exposure of different doses of ZnONPs (0, 100, and 500 mg kg−1 dry soil) in a greenhouse under the temperature of 25 ± 3 °C. Soil heterotrophic respiration and soil enzyme activities were detected. Microbial community composition and diversity were analyzed by Illumina MiSeq platform. Heterotrophic respiration was significantly inhibited by ZnONPs at 500 mg kg−1. The activities of β-glucosidase, cellulose, and cellobiohydrolase decreased under high-level exposure of ZnONPs. The labile Zn2+ assimilated by soil microorganism was increased by 331% and 707%, respectively. Bacterial communities in the soil are more sensitive to ZnONPs than fungal ones. The changes of heterotrophic respiration were closely correlated with soil pH values and microbial compositions, especially fungal communities. Although ascomycetes were inhibited by ZnONPs, their abundance was the highest within soil fungal community. The inhibition of heterotrophic respiration was associated with the variation of soil fungal communities, although the bacterial communities are sensitive to ZnONPs. The microbiome modulation is necessary for the management of the decomposition of returned wheat straw in the field contaminated by ZnONPs. The effects of ZnONPs on soil ecological process should be considered when the application of fertilizers and pesticides which contain ZnONPs.

Applying organic fertilizers has been well documented to facilitate the dissemination of antibiotic resistance genes (ARGs) in soil ecosystems. However, the role of soil fauna in this process has been seldom addressed, which hampers our ability to predict the fate of and to manage the spread of ARGs. Here, using high-throughput quantitative polymerase chain reaction (HT-qPCR), we examined the effect of long-term (5-, 8-, and 10-year) fertilization treatments (control, inorganic fertilizers, and mixed fertilizers) on the transfer of ARGs between soil, nematodes, and earthworms. We found distinct fates for ARGs in the nematodes and earthworms, with the former having higher enriched levels of ARGs than the latter. Fertilization impacted the number and abundance of ARGs in soil, and fertilization duration altered the composition of ARGs. Shared ARGs among soil, nematodes, and earthworm guts supported by a fast expectation-maximization microbial source tracking analysis demonstrated the trophic transfer potential of ARGs through this short soil food chain. The transfer of ARGs was reduced by fertilization duration, which was mainly ascribed to the reduction of ARGs in the earthworm gut microbiota. This study identified the transfer of ARGs in the soil-nematode-earthworm food chain as a potential mechanism for a wider dissemination of ARGs in the soil ecosystem.

4 páginas.- 2 figuras.- 19 referencias.- Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41396-022-01225-8, Soils harbor the most diverse naturally evolved antibiotic resistance genes (ARGs) on Earth, with implications for human health and ecosystem functioning. How ARGs evolve as soils develop over centuries, to millennia (i.e., pedogenesis), remains poorly understood, which introduces uncertainty in predictions of the dynamics of ARGs under changing environmental conditions. Here we investigated changes in the soil resistome by analyzing 16 globally distributed soil chronosequences, from centuries to millennia, spanning a wide range of ecosystem types and substrate age ranges. We show that ARG abundance and diversity decline only after millions of years of soil development as observed in very old chronosequences. Moreover, our data show increases in soil organic carbon content and microbial biomass as soil develops that were negatively correlated with the abundance and diversity of soil ARGs. This work reveals natural dynamics of soil ARGs during pedogenesis and suggests that such ecological patterns are predictable, which together advances our understanding of the environmental drivers of ARGs in terrestrial environments., This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 702057. MD-B is supported by a project from the Spanish Ministry of Science and Innovation (PID2020-115813RA-I00), and a project PAIDI 2020 from the Junta de Andalucía (P20_00879).

The use of antibiotics in human medicine and animal husbandry has resulted in the continuous release of antibiotics into the environment, which imposes high selection pressure on bacteria to develop antibiotic resistance. The spread and aggregation of antibiotic resistance genes (ARGs) in multidrug-resistant pathogens is one of the most intractable clinical challenges. Numerous studies have been conducted to profile the patterns of ARGs in agricultural ecosystems, as this is closely related to human health and wellbeing. This paper provides an overview of the transmission of ARGs in agricultural ecosystems resulting from the application of animal manures and other organic amendments. The future need to control and mitigate the spread of antibiotic resistance in agricultural ecosystems is also discussed, particularly from a holistic perspective, and requires multiple sector efforts to translate fundamental knowledge into effective strategies.

The increasing and simultaneous pollution of plastic debris and antibiotic resistance in aquatic environments makes plastisphere a great health concern. However, the development process of antibiotic resistome in the plastisphere is largely unknown, impeding risk assessment associated with plastics. Here, we profiled the temporal dynamics of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial composition in the plastisphere from initial microbial colonization to biofilm formation in urban water. A total of 82 ARGs, 12 MGEs, and 63 bacterial pathogens were detected in the plastisphere and categorized as the pioneering, intermediate, and persistent ones. The high number of five MGEs and six ARGs persistently detected in the whole microbial colonization process was regarded as a major concern because of their potential role in disseminating antibiotic resistance. In addition to genomic analysis, D2O-labeled single-cell Raman spectroscopy was employed to interrogate the ecophysiology of plastisphere in a culture-independent way and demonstrated that the plastisphere was inherently more tolerant to antibiotics than bacterioplankton. Finally, by combining persistent MGEs, intensified colonization of pathogenic bacteria, increased tolerance to antibiotic, and potential trophic transfer into a holistic risk analysis, the plastisphere was indicated to constitute a hot spot to acquire and spread antibiotic resistance and impose a long-term risk to ecosystems and human health. These findings provide important insights into the antibiotic resistome and ecological risk of the plastisphere and highlight the necessity for comprehensive surveillance of plastisphere.

Protists, an integral component of soil microbiome, are one of the main predators of bacteria. Bacteria can produce toxic secondary metabolites, e.g., antibiotics to fight stress under the predation pressure of protists; however, impacts of antibiotics on the profile of protists in soils remain unclear. Here, we constructed a microcosm incubation to investigate the effects of two common antibiotics, oxytetracycline and ciprofloxacin, on the protistan and bacterial communities in an arable soil. Rhizaria were the most abundant protist supergroup, followed by Amoebozoa, Stramenopiles, and Aveolata. Among trophic functional groups, consumers were predominant within the protistan community. The protistan alpha-diversity was not significantly changed, while the bacterial alpha-diversity was decreased under the pressure of antibiotics. Nevertheless, the antibiotic exposure considerably reduced the relative abundance of protistan lineages in Rhizaria and Amoebozoa, which were the dominant supergroups of protistan consumers, while increased the relative abundance of other consumer and phototrophic protists. Altogether, we provide novel experimental evidence that the bacterivorous consumers, an important functional group of protists, were more sensitive to antibiotics than other functional groups. Our findings have potential implications for the induced alterations of protistan community and their ecological functions under the scenarios of projected increasing global antibiotic usage.

Tread particles (TPs) from vehicle tires are widely distributed in soil ecosystems; therefore, there is an urgent need to evaluate their effects on soil biota. In the present study, the soil worm Enchytraeus crypticus was incubated for 21 days in soil microcosms containing increasing concentrations of TPs (0, 0.0048%, 0.024%, 0.12%, 0.6%, and 3% of dry soil weight). High concentrations of zinc (Zn, 9407.4 mg kg-1) and polycyclic aromatic hydrocarbons (PAHs, 46.8 mg kg-1) were detected in the TPs, which resulted in their increased concentrations in soils amended with TPs. We demonstrated that TPs had an adverse effect on the survival (decreased by more than 25%) and reproduction (decreased by more than 50%) of the soil worms. Moreover, TP exposure disturbed the microbiota of the worm guts and surrounding soil. In addition, a covariation between bacterial and fungal communities was observed in the worm guts after exposure to TPs. Further analysis showed that TP exposure caused an enrichment of microbial genera associated with opportunistic pathogenesis in the worm guts. The combined results from this study indicate that TPs might threaten the terrestrial ecosystem by affecting soil fauna and their gut microbiota.

The soil-plant system is an important route for antibiotic resistance genes (ARGs) to spread from the environment to human beings. Through the study of ARGs in the soil-plant system, their distribution and transmission in soil organisms can be clarified, and the risk and rule of the transmission of ARGs in the food chain can be revealed, which provide a theoretical basis for controlling the pollution of resistance genes and guarantee human health. Therefore, it is also of great value in maintaining planetary health. This paper firstly summarize the important research progress of resistome in the soil (including soil fauna gut) and plant microbiomes, then highlight the flow of resistance genes in the soil-plant system, and finally propose that planetary health can be ensured by managing the flow of resistance genes in the soil-plant system and discuss future research directions.

Understanding the future distribution of antibiotic resistance in natural soil ecosystems is important to forecast their impacts on ecosystem and human health under projected climate change scenarios. Therefore, it is critical and timely to decipher the links between climate warming and antibiotic resistance, two of Earth's most imminent problems. Here, we explored the role of five-year simulated climate warming (+ 4 °C) on the diversity and proportions of soil antibiotic resistance genes (ARGs) across three seasons in both plantation and natural forest ecosystems. We found that the positive effects of warming on the number and proportions of ARGs were dependent on the sampling seasons (summer, autumn and winter), and seasonality was a key factor driving the patterns of ARG compositions in forest soils. Fifteen ARGs, conferring resistance to common antibiotics including aminoglycoside, beta-lactam, macrolide-lincosamide-streptogramin B, multidrug, sulfonamide, and tetracycline, were significantly enriched in the warming treatment. We showed that changes in soil properties and community compositions of bacteria, fungi and protists can explain the changes in soil ARGs under climate warming. Taken together, these findings advance our understanding of environmental ARGs under the context of future climate change and suggest that elevated temperature may promote the abundance of specific soil ARGs, with important implications for ecosystem and human health.

With the increasing global antibiotic uses in livestock husbandry, animal manures upon land application pose potential threats to the environments and soil microbiome. Nevertheless, effects of manures and antibiotic-administered manures on soil protists, an integral component of soil food web and primary regulators of bacteria, remain unknown. Here, we assessed impacts of cattle and poultry manures with or without an antibiotic tylosin on soil protists and their functional groups in a 130-day microcosm incubation. Protists were highly responsive to manure application, with a significant decline in their alpha diversity in all manure treatments. There were also significant temporal changes in the alpha diversity and composition of soil protists and their functional groups. Poultry manures had stronger negative influences on the community structure of protists compared to cattle manures, and more pronounced effects on protists were observed in tylosin-spiked manure treatments. Furthermore, many consumer, phototrophic and parasitic taxa were highly susceptible to all manure treatments at Day 50 and 130. Altogether, our findings demonstrate negative effects of animal manures and tylosin on soil protists. This study suggests that the applications of livestock manures and antibiotics may subsequently alter ecological functions of protists and their interactions with other soil microorganisms in agricultural systems.

Understanding the current and future distributions of plant pathogens is critical to predict the plant performance and related economic benefits in the changing environment. Yet, little is known about the roles of environmental drivers in shaping the profiles of fungal plant pathogens in phyllosphere, an important habitat of microbiomes on Earth. Here, using a large-scale investigation of Eucalyptus phyllospheric microbiomes in Australia and the multiple linear regression model, we show that precipitation is the most important predictor of fungal taxonomic diversity and abundance. The abundance of fungal plant pathogens in phyllosphere exhibited a positive linear relationship with precipitation. With this empirical dataset, we constructed current and future atlases of phyllosphere plant pathogens to estimate their spatial distributions under different climate change scenarios. Our atlases indicate that the abundance of fungal plant pathogens would increase especially in the coastal regions with up to 100-fold increase compared with the current abundance. These findings advance our understanding of the distributions of fungal plant pathogens in phyllospheric microbiomes under the climate change, which can improve our ability to predict and mitigate their impacts on plant productivity and economic losses. This article is protected by copyright. All rights reserved.

Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.

The discovery of comammox Nitrospira being capable of complete oxidising ammonia to nitrate radically challenged the conventional concept of two-step nitrification. However, the response of comammox Nitrospira to nitrification inhibitors (NIs) and their role in soil nitrification remain largely unknown, which has hindered our ability to predict the efficiency of NIs in agroecosystems. We evaluated the effect of four NIs, 2-chloro-6-(trichloromethyl) pyridine (nitrapyrin), 3,4-dimethylpyrazole phosphate (DMPP), allylthiourea (ATU) and dicyandiamide (DCD) on the growth of comammox Nitrospira, ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in two pasture and arable soils. The amendment of nitrogen fertiliser significantly increased soil nitrate concentrations over time, indicating a sustaining nitrification activity in both soils. The addition of all the four NIs effectively reduced the production of nitrate in both soils, but to varying degrees during incubation. The abundances of comammox Nitrospira clade A were significantly increased by addition of nitrogen fertilisers and significantly impeded by the four NIs in the pasture soil, but their abundances were only remarkably hindered by nitrapyrin in the arable soil. All the four NIs obviously inhibited the AOB abundances in both soils. Except for DMPP, the other three NIs effectively suppressed the AOA abundances in both soils. We provided new evidence that growth of comammox Nitrospira clade A can be stimulated by nitrogen fertilisers and inhibited by various nitrification inhibitors, suggesting their potential role in nitrification of agricultural soils.

The importance of diet in regulating the gut microbiome of globally distributed and functionally important soil generalist invertebrates such as collembolans remain poorly understood. Here, we studied a model collembolan (Folsomia candida) and found that diet (bacteria, plant litters, yeast, mixed food) is a critical factor in regulating the microbial diversity and community composition of this important soil organism. Collembolans fed with litter exhibited the lowest bacterial diversity and were dominated by Ochrobactrum. Conversely, collembolans fed with mixed diets resulted in the highest bacterial diversity. Our findings further suggest that microbial communities associated with different diets are linked to different levels of collembolan fitness. For example, the relative abundance of the genera of unclassified Thermogemmatisporaceae, Brevibacillus, and Novosphingobium were positively correlated with growth of the collembolans. Together, our work provides evidence that diet is a major force controlling the gut microbiome of collembolans, and is a good environmental predictor for collembolan growth, with implications for ecosystem functioning in terrestrial environments.

Growing evidences have demonstrated that heavy metal contamination can promote the proliferation of antibiotic resistance genes (ARGs) via co-selection. However, effects of nano-metal-materials on the occurrence and level of ARGs in the soil and plant, have not been fully explored. To gain insights into this impact, we conducted a pot experiment by adding nano‑silver particles (AgNPs) as a stimuli and Ag ion (AgNO3) and tetracycline as a comparison. By using high throughput quantitative PCR, our results indicated that application of AgNPs (~20 nm and ~50 nm) at a concentration of 100 ppm resulted in no significant changes in the abundance of ARGs in either soil or phyllosphere (P > 0.05). Nevertheless, the overall pattern of resistome, especially in soil, was shifted following AgNPs application, with a significance increase in the relative abundance of efflux pumps genes, which is an important mechanism for co-selection of ARGs by heavy metals. By comparison, Ag ion at an equivalent Ag mass of AgNPs markedly increased ARGs abundance and shifted ARGs profile in soil, indicating that free Ag ion had a stronger impact on ARGs than AgNPs. These findings provide new insights in assessing the risks of manufactured nanomaterials accumulated in the environment. Keywords: Nano-materials, Silver nanoparticles, Antibiotic resistance, Co-selection, Plant microbiome

Loss of biodiversity is a major threat to the ecosystem processes upon which society depends. Natural ecosystems differ in their resistance to invasion by alien species, and this resistance can depend on the diversity in the system. Little is known, however, about the barriers that microbial diversity provides against microbial invasion. The increasing prevalence of antibiotic-resistant bacteria is a serious threat to public health in the 21st century. We explored the consequences of the reduction in soil microbial diversity for the dissemination of antibiotic resistance. The relationship between this diversity and the invasion of antibiotic resistance was investigated using a dilution-to-extinction approach coupled with high-capacity quantitative PCR. Microbial diversity was negatively correlated with the abundance of antibiotic-resistance genes, and this correlation was maintained after accounting for other potential drivers such as incubation time and microbial abundance. Our results demonstrate that high microbial diversity can act as a biological barrier resist the spread of antibiotic resistance. These results fill a critical gap in our understanding of the role of soil microbial diversity in the health of ecosystems.

Growing evidence points to the pivotal role of the environmental factors in influencing the transmission of antibiotic resistance genes (ARGs) and the propagation of resistant human pathogens. However, our understanding of the ecological and evolutionary environmental factors that contribute to development and dissemination of antibiotic resistance is lacking. Here, we profiled a wide variety of ARGs using the high-throughput quantitative PCR analysis in 61 soil samples collected from ocean and river beaches, which are hotspots for human activities and platforms for potential transmission of environmental ARGs to human pathogens. We identified the dominant abiotic and biotic factors influencing the diversity, abundance and composition of ARGs in these ecosystems. A total of 110 ARGs conferring resistance to eight major categories of antibiotics were detected. The core resistome was mainly affiliated into β-lactam and multidrug resistance, accounting for 66.9% of the total abundance of ARGs. The oprJ gene conferring resistance to multidrug was the most widespread ARG subtype detected in all the samples. The relative abundances of total ARGs and core resistome were significantly correlated with salinity-related properties including electrical conductivity and concentrations of sodium and chloride. Random forest analysis and structural equation modelling revealed that salinity was the most important factor modulating the distribution patterns of beach soil ARGs after accounting for multiple drivers. These findings suggest that beach soil is a rich reservoir of ARGs and that salinity is a predominant factor shaping the distribution patterns of soil resistome.