Plant associated protists-Untapped promising candidates for agrifood tools.

The importance of host-associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the community structure and functions of plant-associated protists remain surprisingly underexplored. Harnessing plant-associated protists and other microbes can potentially enhance plant health and productivity and sustain healthy food and agriculture systems. In this review, we summarize the knowledge of multifunctionality of protists and their interactions with other microbes in plant hosts, and propose a future framework to study plant-associated protists and utilize protists as agrifood tools for benefiting agricultural production.

Community assembly of comammox Nitrospira in coastal wetlands across southeastern China.

Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.

Optimizing cropping systems to close the gap between economic profitability and environmental health.

Supporting food security while maintaining ecosystem sustainability is one of the most important global challenges for humanity. Optimization of cropping systems is expected to promote the ecosystem services of agroecosystems. Yet, how and why cropping system influences the trade-offs between economic profitability and multiple ecosystem services remain poorly understood. We investigate the influence of six cropping systems on trade-offs between economic profitability and multiple ecosystem services after considering 36 agricultural ecosystem properties using field experiment data from 2020 to 2022. We show that designing cropping system is a critical tool to closing the gap between ecosystem sustainability and commercial profitability. Cropping system with three harvests within 2 yr had higher performance in overall ecosystem multiple services through enhancement of supporting, regulating, and economic performance without compromising provisioning compared with four other systems. These systems diminished the trade-off among multiple services, resulting in a 'win-win' situation for economics and multiple services. By contrast, the monoculture and double cropping systems lead to a strong trade-off between pairwise services including ecosystem health and profitability. Our work illustrates the substantial potential of rotation systems with three harvests within 2 yr in enforcing ecosystem services and closing the trade-offs among multiple agricultural ecosystem services.

Full substitution of chemical fertilizer by organic manure decreases soil N2 O emissions driven by ammonia oxidizers and gross nitrogen transformations.

Replacing synthetic fertilizer by organic manure has been shown to reduce emissions of nitrous oxide (N2 O), but the specific roles of ammonia oxidizing microorganisms and gross nitrogen (N) transformation in regulating N2 O remain unclear. Here, we examined the effect of completely replacing chemical fertilizer with organic manure on N2 O emissions, ammonia oxidizers, gross N transformation rates using a 13-year field manipulation experiment. Our results showed that organic manure reduced cumulative N2 O emissions by 16.3%-210.3% compared to chemical fertilizer. The abundance of ammonia oxidizing bacteria (AOB) was significantly lower in organic manure compared with chemical fertilizer during three growth stages of maize. Organic manure also significantly decreased AOB alpha diversity and changed their community structure. However, organic manure substitution increased the abundance of ammonia oxidizing archaea and the alpha diversity of comammox Nitrospira compared to chemical fertilizer. Interestingly, organic manure decreased organic N mineralization by 23.2%-32.9%, and autotrophic nitrification rate by 10.5%-45.4%, when compared with chemical fertilizer. This study also found a positive correlation between AOB abundance, organic N mineralization and gross autotrophic nitrification rate with N2 O emission, and their contribution to N2 O emission was supported by random forest analysis. Our study highlights the key roles of ammonia oxidizers and N transformation rates in predicting cropland N2 O.

Plant Species-Driven Distribution of Individual Clades of Comammox Nitrospira in a Subtropical Estuarine Wetland.

Plant species play a crucial role in mediating the activity and community structure of soil microbiomes through differential inputs of litter and rhizosphere exudates, but we have a poor understanding of how plant species influence comammox Nitrospira, a newly discovered ammonia oxidizer with pivotal functionality. Here, we investigate the abundance, diversity, and community structure of comammox Nitrospira underneath five plant species and a bare tidal flat at three soil depths in a subtropical estuarine wetland. Plant species played a critical role in driving the distribution of individual clades of comammox Nitrospira, explaining 59.3% of the variation of community structure. Clade A.1 was widely detected in all samples, while clades A.2.1, A.2.2, A.3 and B showed plant species-dependent distribution patterns. Compared with the native species Cyperus malaccensis, the invasion of Spartina alterniflora increased the network complexity and changed the community structure of comammox Nitrospira, while the invasive effects from Kandelia obovata and Phragmites australis were relatively weak. Soil depths significantly influenced the community structure of comammox Nitrospira, but the effect was much weaker than that from plant species. Altogether, our results highlight the previously unrecognized critical role of plant species in driving the distribution of comammox Nitrospira in a subtropical estuarine wetland.

Non-native Plant Species Invasion Increases the Importance of Deterministic Processes in Fungal Community Assembly in a Coastal Wetland.

Fungal communities are essential to the maintenance of soil multifunctionality. Plant invasion represents a growing challenge for the conservation of soil biodiversity across the globe, but the impact of non-native species invasion on fungal diversity, community structure, and assembly processes remains largely unknown. Here, we examined the diversity, community composition, functional guilds, and assembly process of fungi at three soil depths underneath a native species, three non-native species, and a bare tidal flat from a coastal wetland. Plant species was more important than soil depth in regulating the diversity, community structure, and functional groups of fungi. Non-native species, especially Spartina alterniflora, increased fungal diversity, altered fungal community structure, and increased the relative abundance of saprotrophic and pathogenic fungi in coastal wetland soils. Stochastic processes played a predominant role in driving fungal community assembly, explaining more than 70% of the relative contributions. However, compared to a native species, non-native species, especially S. alterniflora, reduced the relative influence of stochastic processes in fungal community assembly. Collectively, our results provide novel evidence that non-native species can increase fungal diversity, the relative abundance of saprotrophic and pathogenic fungi, and deterministic processes in the assembly of fungi in coastal wetlands, which can expand our knowledge of the dynamics of fungal communities in subtropical coastal wetlands.

Aridity differentially alters the stability of soil bacterial and fungal networks in coastal and inland areas of Australia.

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.

Conversion of natural grassland to cropland alters microbial community assembly across northern China.

To feed the growing human population, natural grasslands are being converted to agricultural use at a massive scale. This conversion may have negative consequences for soil biodiversity, but its impact on the community assembly of differentially microbial groups remains largely unknown. Here, we investigated the diversity and community compositions of bacteria, archaea, fungi and protists, using a paired sampling of grassland and cropland soils across the agro-pastoral ecotone of northern China. Land-use conversion decreased α diversity of bacteria, fungi and protists, and altered the structures of the entire soil microbial community (archaea, bacteria, fungi and protists). The community assembly of archaea and bacteria was dominated by stochastic processes, and that of protists dominated by deterministic processes in both land-use types. By contrast, the fungal community was governed more strongly by stochastic processes in grassland soil, than by deterministic processes in cropland soil. Our findings support the 'size-plasticity' hypothesis that smaller body-sized microorganisms (archaea and bacteria) are more structured by stochastic processes, and larger one (protist) is more influenced by deterministic processes. Our study demonstrates that distinct ecological processes govern microbial community assembly, and land-use change regulates the balance between determinism and stochasticity.

Reduced pH is the primary factor promoting humic acid formation during hyperthermophilic pretreatment composting.

Hyperthermophilic pretreatment composting (HPC) has the advantages of enhanced composting efficiency and accelerated humic substance (HS) over conventional composting (CC). However, the mechanisms towards the accelerated humification process by HPC are still not clear. By means of sterilization technology, the roles of abiotic and biotic components on the formation of HS can be distinguished. The study investigated the humification degree and the succession of microbial community during HPC of pig manure. The mechanisms underlying the accelerated humification by HPC was identified using gamma sterilization. Results showed that HS content increased significantly by 13.72% in HPC and 29.93% in sterilized HPC inoculated with 1% CC (HPC_I), compared with 8.76% increase in CC and 7.12% increase in sterilized CC inoculated with 1% HPC during composting (CC_I). Compared with CC and CC_I, stronger intensities of HA-like and fulvic acid-like components were observed in HPC and HPC_I. Results showed that physicochemical properties, especially pH, were the key factors in accelerating the humification in HPC, while both physicochemical properties and microbial community contributed to the HA formation in CC. The study contributed to a better understanding of the mechanism towards the accelerated humification degree in HPC.

Semi-solid state promotes the methane production during anaerobic co-digestion of chicken manure with corn straw comparison to wet and high-solid state.

Total solid content (TS) is an important factor for biogas production during anaerobic digestion. In this study, we explored the influence of different TS (5% wet, 15% semi-solid and 25% solid state) on the relative cumulative methane production (RCMP) during anaerobic co-digestion of chicken manure with corn straw. Results showed that total ammonium nitrogen and free ammonia nitrogen concentration increased with the increase of TS. Ammonium nitrogen in treatments at 15% TS was 2.25-2.76 times as high as that at 5% TS, which was below 3 times. The highest chemical oxygen demand removal and RCMP were obtained in the treatment of 15% TS with a ratio of 2:1 chicken manure: corn straw (based on TS). The RCMP in the treatments of 15% TS were 3.63-4.59 times higher than that of 5% TS based on the volume of substrates. The abundance of Caldicoprobacter improving the degradation of corn straw was significantly positively correlated with the RCMP, and the average abundance of Caldicoprobacter at 15% TS was 8.33 and 7.02 times higher than that at 5% and 25% TS, respectively. Structural equation models analysis suggested that TS significantly impacted the RCMP by indirectly impacting free ammonia nitrogen and microbial abundance. These findings indicated semi-solid state (15% TS) decreased ammonia nitrogen releasing and improved the abundance of Caldicoprobacter, and increased RCMP during anaerobic co-digestion of chicken manure with corn straw.

Fertilization alters protistan consumers and parasites in crop-associated microbiomes.

Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8-year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant-soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top-down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop-associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.

Termite mound formation reduces the abundance and diversity of soil resistomes.

Termites are pivotal ecosystem engineers in tropical and subtropical habitats, where they construct massive nests ('mounds') that substantially modify soil properties and promote nutrient cycling. Yet, little is known about the roles of termite nesting activity in regulating the spread of antimicrobial resistance (AMR), one of the major Global Health challenges. Here, we conducted a large-scale (> 1500 km) investigation in northern Australia and found distinct resistome profiles in termite mounds and bulk soils. By profiling a wide spectrum of ARGs, we found that the abundance and diversity of antibiotic resistance genes (ARGs) were significantly lower in termite mounds than in bulk soils (P < 0.001). The proportion of efflux pump ARGs was significantly lower in termite mound resistome than in bulk soil resistome (P < 0.001). The differences in resistome profiles between termite mounds and bulk soils may result from the changes in microbial interactions owing to the substantial increase in pH and nutrient availability induced by termite nesting activities. These findings advance our understanding of the profile of ARGs in termite mounds, which is a crucial step to evaluate the roles of soil faunal activity in regulating soil resistome under global environmental change.

Precipitation increases the abundance of fungal plant pathogens in Eucalyptus phyllosphere.

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.

Termite mounds reduce soil microbial diversity by filtering rare microbial taxa.

Termites are ubiquitous insects in tropical and subtropical habitats, and some of them construct massive nests ('mounds'), which substantially promote substrate heterogeneity by altering soil properties. Yet, the role of termite nesting process in regulating the distribution and diversity of soil microbial communities remains poorly understood, which introduces uncertainty in predictions of ecosystem functions of termite mounds in a changing environment. Here, by using amplicon sequencing, we conducted a survey of 134 termite mounds across >1500 km in northern Australia and found that termite mounds significantly differed from bulk soils in the microbial diversity and community compositions. Compared with bulk soils, termite nesting process decreased the microbial diversity and the relative abundance of rare taxa. Rare taxa had a narrower habitat niche breadth than dominant taxa and might be easier to be filtered by the potential intensive microbial competition during the nesting processes. We further demonstrated that the shift in pH induced by termite nesting process was a major driver shaping the microbial community profiles in termite mounds. Together, our work provides novel evidence that termite nesting is an important process in regulating soil microbial diversity, which advances our understanding of the functioning of termite mounds.

Assembly processes lead to divergent soil fungal communities within and among 12 forest ecosystems along a latitudinal gradient.

Latitudinal gradients provide opportunities to better understand soil fungal community assembly and its relationship with vegetation, climate, soil and ecosystem function. Understanding the mechanisms underlying community assembly is essential for predicting compositional responses to changing environments. We quantified the relative importance of stochastic and deterministic processes in structuring soil fungal communities using patterns of community dissimilarity observed within and between 12 natural forests and related these to environmental variation within and among sites. The results revealed that whole fungal communities and communities of arbuscular and ectomycorrhizal fungi consistently exhibited divergent patterns but with less divergence for ectomycorrhizal fungi at most sites. Within those forests, no clear relationships were observed between the degree of divergence within fungal and plant communities. When comparing communities at larger spatial scales, among the 12 forests, we observed distinct separation in all three fungal groups among tropical, subtropical and temperate climatic zones. Soil fungal ß-diversity patterns between forests were also greater when comparing forests exhibiting high environmental heterogeneity. Taken together, although large-scale community turnover could be attributed to specific environmental drivers, the differences among fungal communities in soils within forests was high even at local scales.

Influence of Legacy Mercury on Antibiotic Resistomes: Evidence from Agricultural Soils with Different Cropping Systems.

Agricultural soils are important reservoirs for antibiotic resistance genes (ARGs), which have close linkage to human health via crop production. Metal stress in environments may function as a selection pressure for antibiotic resistomes. However, there is still a lack of field studies focusing on the effect of historical mercury (Hg) contamination on antibiotic resistomes in agricultural soils. Here, we explored the ARG profile in soils with different cropping systems (paddy and upland) and linked them to legacy Hg exposure. We found that ARG profiles were significantly different between paddy and upland soils. However, both paddy and upland soils with long-term field Hg contamination harbored higher diversity and abundance of ARGs than non-polluted soils. The co-occurrence network reveals significant associations among Hg, Hg resistance genes, mobile genetic elements (MGEs), and ARGs. Together with path analysis showing legacy Hg possibly affecting soil resistomes through the shifts of soil microbiota, Hg resistance genes, and MGEs, we suggest that legacy Hg-induced potential co-selection might elevate the ARG level. Redundancy analysis further supports that legacy Hg pollution had a significant association with ARG variations in the paddy and upland soils (P < 0.01). Collectively, our results highlight the underappreciated role of legacy Hg as a potential persistent selecting agent in contributing to soil ARGs in agroecosystems.

Manure Application Did Not Enrich Antibiotic Resistance Genes in Root Endophytic Bacterial Microbiota of Cherry Radish Plants.

Growing evidence suggests that livestock manure used as organic fertilizer in agriculture may lead to the potential propagation of antibiotic resistance genes (ARGs) from "farm to fork." However, little is known about the impacts of manure fertilization on the incidence of ARGs in the plant-associated microbiomes (including rhizosphere, endosphere, and phyllosphere), which hampers our ability to assess the dissemination of antibiotic resistance in the soil-plant system. Here, we constructed a pot experiment to explore the effects of poultry and cattle manure applications on the shifts in the resistome in the plant microbiome of harvested cherry radish. A total of 144 ARGs conferring resistance to eight major classes of antibiotics were detected among all the samples. Rhizosphere and phyllosphere microbiomes harbored significantly higher diversity and abundance of ARGs than did root endophytic microbiomes of cherry radish. Manure application significantly increased the abundance of ARGs in the rhizosphere and phyllosphere but not in the endophytes of the root, which is the edible part of cherry radish. Soil and plant microbiomes changed dramatically after manure applications and clustered separately according to different sample types and treatments. Structural equation modeling revealed that bacterial abundance was the most important factor modulating the distribution patterns of soil and plant resistomes after accounting for multiple drivers. Taken together, we provide evidence that enrichment of the resistome in the rhizosphere and phyllosphere of cherry radish is more obvious than with the endosphere after manure application, suggesting that manure amendment might not enhance the dissemination of ARGs into the root of vegetables in the pot experiment.IMPORTANCE Our study provides important evidence that manure application increased the occurrence of ARGs in the rhizosphere and phyllosphere of cherry radish, compared with that in the endophytic bacterial microbiota of root, which is the edible part of cherry radish. Our findings suggest that although manure amendment is a significant route of ARGs entering agricultural soils, these manure-derived ARGs may be at low risk of migrating into the endophytes of root vegetables.

Oxytetracycline and Ciprofloxacin Exposure Altered the Composition of Protistan Consumers in an Agricultural Soil.

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.

Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes.

Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected diverse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The diversity of ARGs was strongly and positively correlated with the diversity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance.