Search

Invasive plants disrupt native biodiversity and ecosystem functions and their distribution increase with ongoing global land-use changes. Clarifying plant nitrogen (N) uptake and use strategies mediated by rhizosphere microbes is key to understand the success of plant invasion. We used 15N labeling to assess the N uptake rate and N use efficiency (NUE) of four invasive species and their native congeners growing either alone (without competition) or pairwise (interspecific competition), and the abundance of functional genes and enzyme activities in the soil were linked to the richness and community composition of rhizosphere bacteria. Without competition, invasive plants have larger biomass (∼40%) and NUE (∼68%) than their natives, but the natives has a faster NO 3 − uptake rate (∼10%) than invasive plants. Interspecific competition decreases the plant biomass but increases the NUE of both invasive and native plants and increases the NH 4 + and NO 3 − uptake by invasive plants. Consequently, invasive plants produce more biomass due to their stronger competitive ability (higher relative competition index) and faster NH 4 + uptake rate than their natives. Invasive plants have a larger microbial biomass, higher activity of β-D-cellobiosidase, faster nitrification, denitrification, and nitrogenase activity, and higher abundances of nifH , nirS , and nosZ genes than their natives when growing pairwise. Competition leads to the enrichment in a set of OTUs in the rhizosphere of invasive and native plants compared with those grown alone, and the enrichment of another set in invasive compared with native plants grown together. The plant biomass, N uptake rate, and NUE are influenced by rhizosphere bacteria via the acceleration of N transformation in the soil. We conclude that the competitive advantage of invasive plants is achieved by fast NH 4 + uptake, rather than by strengthening NUE as would be the case in the absence of competition. These findings provide important insights into the critical mechanisms of plant N uptake during invasion by alien plants. [Display omitted] • Larger biomass and NUE of invaders are the main advantages compared to native plants. • Faster NH 4 + uptake rate of invaders allows to over compete the natives by N limitation. • Invaders achieved competitive advantages by strengthening NH 4 + uptake instead of NUE. • Rhizosphere functional bacteria mediated the competition via N mineralization for plant N uptake. [ABSTRACT FROM AUTHOR]

Land application of animal manure is a common agricultural practice potentially leading to dispersal and propagation of antibiotic resistance genes (ARGs) in environmental settings. However, the fate of resistome in agro-ecosystems over time following application of different manure sources has never been compared systematically. Here, soil microcosm incubation was conducted to compare effects of poultry, cattle and swine manures spiked with or without the antibiotic tylosin on the temporal changes of soil ARGs. The high-throughput quantitative PCR detected a total of 185 unique ARGs, with Macrolide-Lincosamide-Streptogramin B resistance as the most frequently encountered ARG type. The diversity and abundance of ARGs significantly increased following application of manure and manure spiked with tylosin, with more pronounced effects observed in the swine and poultry manure treatments than in the cattle manure treatment. The level of antibiotic resistance gradually decreased over time in all manured soils but was still significantly higher in the soils treated with swine and poultry manures than in the untreated soils after 130 days’ incubation. Tylosin-amended soils consistently showed higher abundances of ARGs than soils treated with manure only, suggesting a strong selection pressure of antibiotic-spiked manure on soil ARGs. The relative abundance of ARGs had significantly positive correlations with integrase and transposase genes, indicative of horizontal transfer potential of ARGs in manure and tylosin treated soils. Our findings provide evidence that application of swine and poultry manures might enrich more soil ARGs than cattle manure, which necessitates the appropriate treatment of raw animal manures prior to land application to minimise the spread of environmental ARGs. [ABSTRACT FROM AUTHOR]

Methylmercury (MeHg), a neurotoxin, is a global concern because of its potential risk to human and ecological health. Elevated mercury (Hg) concentrations were recently reported in the Tibetan Plateau (TP) due to increasing Hg input from distant regions, yet little is known about MeHg production and distribution in the terrestrial ecosystems of the TP. Here, we report longitudinal occurrence of MeHg and the factors regulating net MeHg production in 23 grassland sites from eastern to western TP. The soil MeHg content varied from 0.002 to 0.058 ng g −1 , with different distribution patterns between the eastern and western TP. There was a positive correlation between the MeHg concentration and the longitude after 90 °E, which is similar to the distribution patterns of the total mercury (THg), water and organic carbon in this region. Average MeHg concentration in topsoil is generally higher than that in subsoil. Our results show that MeHg concentration in soils of the TP is directly affected by soil water, potential microbial methylators and THg, while indirectly regulated by soil organic carbon through the microbial community and the longitude-dependent precipitation through soil water. Our study suggests that soil water is the most important driver regulating net MeHg production in the grasslands of the TP. These findings have important implications for unraveling the mechanism of net production of MeHg in high-altitude environments. [ABSTRACT FROM AUTHOR]

The effluents from wastewater treatment plants have been recognized as a significant environmental reservoir of antibiotics and antibiotic resistance genes (ARGs). Reclaimed water irrigation (RWI) is increasingly used as a practical solution for combating water scarcity in arid and semiarid regions, however, impacts of RWI on the patterns of ARGs and the soil bacterial community remain unclear. Here, we used high-throughput quantitative PCR and terminal restriction fragment length polymorphism techniques to compare the diversity, abundance and composition of a broad-spectrum of ARGs and total bacteria in 12 urban parks with and without RWI in Victoria, Australia. A total of 40 unique ARGs were detected across all park soils, with genes conferring resistance to β-lactam being the most prevalent ARG type. The total numbers and the fold changes of the detected ARGs were significantly increased by RWI, and marked shifts in ARG patterns were also observed in urban parks with RWI compared to those without RWI. The changes in ARG patterns were paralleled by a significant effect of RWI on the bacterial community structure and a co-occurrence pattern of the detected ARG types. There were significant and positive correlations between the fold changes of the integrase intI1 gene and two β-lactam resistance genes (KPC and IMP-2 groups), but no significant impacts of RWI on the abundances of intI1 and the transposase tnpA gene were found, indicating that RWI did not improve the potential for horizontal gene transfer of soil ARGs. Taken together, our findings suggested that irrigation of urban parks with reclaimed water could influence the abundance, diversity, and compositions of a wide variety of soil ARGs of clinical relevance. One-sentence summary Irrigation of urban parks with treated wastewater significantly increased the abundance and diversity of various antibiotic resistance genes, but did not significantly enhance their potential for horizontal gene transfer. [ABSTRACT FROM AUTHOR]

Currently, rice straw return in place of burning is becoming more intensive in China than observed previously. However, little is known on the effect of returned rice straw on mercury (Hg) methylation and microbial activity in contaminated paddy fields. Here, we conduct a microcosm experiment to evaluate the effect of rice straw amendment on the Hg methylation and potential nitrification in two paddy soils with distinct Hg levels. Our results show that amended rice straw enhanced Hg methylation for relatively high Hg content soil, but not for low Hg soil, spiking the same additional fresh Hg. methylmercury (MeHg) concentration was significantly correlated to the dissolved organic carbon (DOC) content and relative abundance of dominant microbes associated with Hg methylation. Similarly, amended rice straw was found to only enhance the potential nitrification rate in soil with relatively high Hg content. These findings provide evidence that amended rice straw differentially modulates Hg methylation and nitrification in Hg contaminated soils possibly resulting from different characteristics in the soil microbial community. This highlights that caution should be taken when returning rice straw to contaminated paddy fields, as this practice may increase the risk of more MeHg production. Main finding Rice straw amendment enhanced both Hg methylation and nitrification potential in the relatively high, but not low, Hg soil. [ABSTRACT FROM AUTHOR]

• Microbial residues and plant lignin contributed more to SOC in > 80-year forests. • N addition increased microbial residues and plant lignin in < 40-year forests. • P addition decreased muramic acid in the < 40-year forests. • Microbe and enzyme activity affect microbial residues and plant lignin retention. Soil microbial residues and plant-derived compounds are important components of the stable carbon (C) pool in forest soil. It is not well understood how microbial residues and plant lignin phenols respond to nutrient inputs in subtropical forests of different ages, especially in mature forest stands. Here, a 5-year nitrogen (N) and phosphorus (P) fertilization (addition) management experiment was conducted in two stages of subtropical forests (<40- and > 80-year). We found that the concentrations of amino sugars (i.e., microbial residues) and plant lignin phenols and their contributions to soil organic carbon (SOC) were significantly higher in the > 80-year forests than in the < 40-year forests. In the < 40-year forests, N addition increased amino sugars and lignin phenols and their contributions to SOC, whereas P addition decreased muramic acid (bacterial-derived) and its contribution to SOC. In the > 80-year forests, however, N and P addition had no significant effect on amino sugars and lignin phenols and their contributions to SOC. Overall, soil total amino sugars and lignin phenols could be directly and indirectly affected by forest age and N addition, and could be only indirectly impacted by P addition. Our results suggest that microbial residues and plant lignin phenols are sensitive to the nutrient additions in the young forests, which have a greater potential for the soil stable C sequestration in comparison with the mature forests. [ABSTRACT FROM AUTHOR]

Highlights: [•] We test the effects of super absorbent polymers on the soil–wheat system. [•] The SAPs were beneficial to the formation of larger aggregates. [•] The application of SAPs could potentially help to increase soil microbial activity. [•] The influence of SAPs on the wheat yield depended on the application methods. [•] This study represents a useful assessment of environmental effects of soil additives. [ABSTRACT FROM AUTHOR]

Abstract: Recent studies of ammonia-oxidizing archaea (AOA) suggested their significant contributions to global nitrogen cycling, and phylogenetic analysis categorized AOA into a novel archaeal phylum, the Thaumarchaeota. AOA are ubiquitous in terrestrial ecosystems, have unique mechanisms for nitrification, better adaptation to low-pH pressures, and strikingly lower ammonia requirements compared with ammonia-oxidizing bacteria (AOB). Previous perceptions that microbial ammonia oxidation in acidic soils was minimal, and entirely meditated by autotrophic bacteria and occasionally by heterotrophic nitrifiers have been dramatically challenged, and the dominant nitrifying groups urgently called for re-assessment. Controversially, the relative contributions of AOA and AOB to autotrophic ammonia oxidation have been reported to vary in different soils, but ammonia substrate availability, which was largely restricted under acidic conditions, seemed to be the key driver. Theoretically predicted ammonia concentrations in acidic soils below the substrate threshold of AOB and remarkably high ammonia affinity of AOA raised the supposition that thaumarchaea could represent the dominant ammonia-oxidizing group in ammonia-limited acidic environments. Recently, the functional dominance of thaumarchaea over its bacterial counterpart and autotrophic thaumarchaeal ammonia oxidation in acidic soils has been compellingly confirmed by DNA-stable isotope probing (SIP) experiments and the cultivation of an obligate acidophilic thaumarchaeon, Nitrosotalea devanaterra. Here, we review the currently available knowledge concerning the history and progress in our understanding of the ammonia-oxidizing microorganisms (AOB and AOA) and the mechanisms of nitrification in nutrient-depleted acidic soils, present the possible mechanisms shaping the distinct niches of AOA and AOB, and thus strengthen the assumption that AOA dominate over AOB in ammonia oxidation of acidic soils. [Copyright &y& Elsevier]

Abstract: Soil acidification can result in the release of heavy metals stabilized by soil components into soil solution, and therefore it causes ecological risk. The kinetics of Cd desorption from two Chinese soils (ultisol and oxisol) distributed in the acid rain sensitive areas of southern China, were studied using a flow-stirred method under simulated acid rain conditions. Cd desorption was well described by the first-order kinetic equation. Percentages of Cd desorbed were 80–99% in ultisol and 25–28% in oxisol, respectively. Cd desorption, regarded as a heterogeneous diffusion in soils, could be also fitted by the Elovich equation. The desorption process could be divided into a fast reaction and a slow reaction, which were corresponded to the exchangeable and the specific sorbed Cd, respectively. The obtained results are essential to understand the process of heavy metal release under acid deposition conditions and to evaluate the ecological risk of acid deposition in those acid rain sensitive areas of China. [Copyright &y& Elsevier]

Biogenic Mn oxides exert important controls on trace metal cycling in aquatic and soil environments. A Mn-oxidizing bacterium Bacillus sp. WH4 was isolated from Fe¿Mn nodules of an agrudalf in central China. The biogenic Mn oxides formed by mediation of this Mn oxidizing microorganism were identified as short-ranged and nano-sized Mn oxides. Cd adsorption isotherms, pH effect on adsorption and kinetics were investigated in comparison with an abiotic Mn oxide todorokite. Maximum adsorption of Cd to the biogenic Mn oxides and todorokite was 2.04 and 0.69mmol g¿1 sorbent, respectively. Thus, the biogenic Mn oxides were more effective Cd adsorbents than the abiotic Mn oxide in the aquatic environment. The findings could improve our knowledge of biogenic Mn oxides formation in the environment and their important roles in the biogeochemical cycles of heavy metals. [Copyright &y& Elsevier]

Several Mn oxide minerals commonly occurring in soils were synthesized by modified or optimized methods. The morphologies, structures, compositions and surface properties of the synthesized Mn oxide minerals were characterized. Adsorption and redox reactions of heavy metals on these minerals in relation to the mineral structures and surface properties were also investigated. The synthesized birnessite, todorokite, cryptomelane, and hausmannite were single-phased minerals and had the typical morphologies from analyses of XRD and TEM/ED. The PZCs of the synthesized birnessite, todorokite and cryptomelane were 1. 75, 3. 50 and 2. 10, respectively. The magnitude order of their surface variable negative charge was: birnessite≥cryptomelane>todorokite. The hausmannite had a much higher PZC than others with the least surface variable negative charge. Birnessite exhibited the largest adsorption capacity on heavy metals Pb2+, Cu2+, Co2+, Cd2+ and Zn2+, while hausmannite the smallest one. Birnessite, cryptomelane and todorokite showed the greatest adsorption capacity on Pb2+ among the tested heavy metals. Hydration tendency (pK 1) of the heavy metals and the surface variable charge of the Mn minerals had significant impacts on the adsorption. The ability in Cr(III) oxidation and concomitant release of Mn2+ varied greatly depending on the structure, composition, surface properties and crystallinity of the minerals. The maximum amounts of Cr(III) oxidized by the Mn oxide minerals in order were (mmol/kg): birnessite (1330. 0)>cryptomelane (422. 6)>todorokite (59. 7)>hausmannite (36. 6). [Copyright &y& Elsevier]

The soil microbiome determines crop production and drives nutrient cycling, functions that are altered by fertilization. Yet, we have only begun to understand the effects of fertilization on taxonomic changes on soil microorganisms, while impacts on functional groups across the microbiome and therefore potential soil functioning have never been assessed. Here, using a range of methods including high-throughput sequencing, we identified 77 functional parameters of the main microbiome groups including bacteria, fungi, and protists in three common agricultural soil types in China (black, fluvo-aquic, and red soil), which were fertilized in the same way over two years. We show that fertilization most strongly and generally throughout soil types reduced the relative abundance of the main microbial predators, phagotrophic protists, by 31%. Ten functional groups within the microbiome showed soil type-specific responses to fertilization. For example, ammonia-oxidizing bacteria, and predatory/exoparasitic bacteria were reduced by fertilization in the acidic black and the red soils, while, no other microbial functional group than phagotrophic protists was suppressed by fertilization in the alkaline fluvo-aquic soil. The significant reductions in microbial functional groups especially in acidic soils could be explained by nitrogen enrichment, increased soil acidification and potential biotic links between the functional groups within the microbiome. Together, we show that the fertilization-induced abiotic changes alter microbial functions that depend on the soil and environmental conditions. Particularly the most profound changes on the group of microbial predators might subsequently affect other soil functions performed by bacteria and fungi. • Microbiome functioning was affected by fertilization in a soil-specific manner. • Fertilization reduced AOB and predatory/exoparasitic bacteria in acidic soils. • Only phagotrophic protists were suppressed by fertilization across all soil types. • Fertilizer-induced changes on protists likely alter entire microbiome functioning. [ABSTRACT FROM AUTHOR]

Microbiota in urban green spaces underpin ecosystem services that are essential to environmental health and human wellbeing. However, the factors shaping the microbial communities in urban green spaces, especially those associated with turf grass phyllosphere, remain poorly understood. The lack of this knowledge greatly limits our ability to assess ecological, social and recreational benefits of urban green spaces in the context of global urbanization. In this study, we used amplicon sequencing to characterize soil and grass phyllosphere bacterial communities in 40 urban green spaces and three minimally disturbed national parks in Victoria, Australia. The results indicated that urbanization might have shown different impacts on soil and grass phyllosphere microbial communities. The bacterial diversity in soil but not in grass phyllosphere was significantly higher in urban green spaces than in national parks. Principal coordinate analysis revealed significant differences in the overall patterns of bacterial community composition between urban green spaces and national parks for both soil and grass phyllosphere. Industrial development, as represented by the number of industries in the region, was identified as a key driver shaping the bacterial community profiles in urban green spaces. Variation partitioning analysis suggested that industrial factors together with their interaction with other factors explained 20% and 28% of the variances in soil and grass phyllosphere bacterial communities, respectively. The findings highlight the importance of industrial development in driving the spatial patterns of urban microbiomes, and have important implication for the management of microbiomes in urban green spaces. Image 1 • Urbanization might differently impact soil and grass phyllosphere microbial communities in urban green spaces. • Industrial development was a key driver shaping the bacterial community profiles in urban green spaces. • The impact of urbanization on the bacterial communities might derive from increased environmental pollution. [ABSTRACT FROM AUTHOR]

Plant microbiome, as the second genome of plant, and the interface between human and environmental microbiome, represents a potential pathway of human exposure to environmental pathogens and resistomes. However, the impact of host identity on the profile of resistomes in plant phyllosphere is unclear and this knowledge is vital for establishing a framework to evaluate the dissemination of antibiotic resistance via the plant microbiome. Here, we explored the phyllosphere microbiome and resistomes in 12 selected plant species. By using High-throughput quantitative PCR, we identified a total of 172 unique resistance genes in plant phyllosphere microbiome, which was significantly divergent from the profile of resistomes in associated soils (Adonis, P < 0.01). Host identity had a significant effect on the plant resistome, which was mainly attributed to the dissimilarity of phyllosphere bacterial phylogeny across different plants. We identified a core set of plant resistomes shared in more than 80% of samples, which accounted for more than 64% of total resistance genes. These plant core resistomes conferred resistance to antibiotics that are commonly administered to humans and animals. Our findings extend our knowledge regarding the resistomes in plant phyllosphere microbiome and highlight the role of host identity in shaping the plant associated antibiotic resistance genes. Image 1 • Plant phyllosphere microbiome is an important reservoir of ARGs. • Host identities significantly affect the profile of plant resistomes. • A core plant associated resistomes was identified. Main finding : Plant phyllosphere microbiome is an important reservoir of ARGs and host identity had a significant effect on the plant associated resistome. [ABSTRACT FROM AUTHOR]

Abstract Dissimilatory nitrate reduction to ammonium (DNRA) and diazotrophic N 2 fixation contribute to nitrogen (N) supply in rice paddies, whereas denitrification contributes to N loss. Continuous N fertilization in rice paddies is known to increase denitrification and reduce N 2 fixation, however little is known about its effect on DNRA and the NO 3 − partitioning between DNRA and denitrification. Here, we investigated the rates of DNRA, denitrification and N 2 fixation, and their relevant microbial gene abundances, in long-term high and low N fertilized rice paddies using a 15NO 3 − tracer, an acetylene reduction assay and quantitative PCR analysis, in laboratory incubation studies. We observed that DNRA exceeded denitrification by a factor of eight in low N fertilized rice paddies, while DNRA was almost half of the denitrification rate in high N fertilized rice paddies. The nrfA gene abundance, related to DNRA, was significantly higher in the low N fertilized rice paddies and was positively correlated with DNRA rates. However, no clear difference in denitrifying gene (narG, nirK and nosZ) abundances was observed between the N fertilization regimes. The proportion of total NO 3 − reduced by DNRA had a significantly positive correlation with the soil organic carbon-to-NO 3 - ratio and negative correlation with the soil NO 3 − concentration. N 2 fixation added ten times more N in the low N input than in the high N input paddies. Our findings highlight the self-regulated microbial N cycling in low N input paddy systems which maintain long-term paddy soil N nutrition. Highlights • N 2 fixation added ten times more N to low N input than to high N input rice paddies. • DNRA retained the majority of nitrate in long-term low N input rice paddies. • Denitrification dominated nitrate reduction in long-term high N input rice paddies. • High SOC:NO 3 − ratio favours NO 3 − partitioning to DNRA in NO 3 − limited paddy soils. [ABSTRACT FROM AUTHOR]

15 N 2 has played a crucial role in fundamental studies of biological N 2 fixation. However, due to operational constraints, it has more often served as a qualitative rather than a quantitative tracer of biologically-fixed N (BFN). Therefore indirect methods based either on 15 N-enrichment or 15 N-natural abundance have assumed a dominant role in quantifying N cycle processes involving BFN. However, it is only through the direct 15 N 2 approach that biological N 2 fixation can be traced through the various components of the soil-plant system. Technological advances in the automated control of the chamber environment have made the 15 N 2 technique more attractive to long-term studies. Thus the need to enclose plants in a chamber and maintain conditions conducive to plant growth should no longer be seen as a major obstacle to the use of 15 N 2 . The way is now open to evaluate the efficacy of indirect methods used to estimate the contribution of BFN to the N economies of crop and pasture systems, and the dynamics of BFN in agroecosystems. In addition, new applications of 15 N 2 such as stable isotope probing are emerging, which have the potential to characterize non-cultivated diazotrophs in a range of environments. The role of biological N 2 fixation in the formation of reactive N in the environment and its relationship with the emission of the greenhouse gas N 2 O requires further investigation. [ABSTRACT FROM AUTHOR]

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. Arbuscular mycorrhizal fungi and soil invertebrates play critical roles in maintaining ecosystem primary productivity, nutrient cycling, soil health, and climate regulation. Soil invertebrates may affect the development of arbuscular mycorrhizal fungi through both direct (consumption, incidental damage, and dispersal vectors) and indirect effects (volatile organic compounds and nonvolatile secondary metabolites). Global environmental changes such as warming, drought, land use change, and microplastic pollution may affect the diversity and function of arbuscular mycorrhizal fungi and soil invertebrates. Unravelling the complex interactions between plants and soil biota will allow harnessing the potential of arbuscular mycorrhizal symbioses to improve plant resilience to biotic and abiotic stresses and to increase ecosystem sustainability in the changing environment. [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidation (anammox) is a globally important nitrogen-cycling process mediated by specialized microbes, and has been demonstrated to be ubiquitous in anoxic natural settings and bioreactors. However, our knowledge of its prevalence in different paddy soil types and along the depth profiles remains largely undocumented. Here, mesocosm incubations were constructed to investigate the activity and community compositions of anammox bacteria across different depth layers of three different paddy soils. 15 N tracer experiments showed that anammox rates were prevalent in almost all depth layers of an inceptisol (Binhai, BH) and an oxisol (Leizhou, LZ), but was absent in an ultisol (Taoyuan, TY). The functional gene hzsB of anammox bacteria was only detected in BH and LZ soil profiles with detected anammox activity. Anammox accounted for 0.4%–12.2% of the total N 2 production, and anammox rates were 0.02–0.77 nmol N g −1 dry soil h −1 and significantly correlated with soil pH and electric conductivity. Anammox activity and abundance of hzsB genes were significantly lower in the surface soil layers (0–5 cm) than in the sub-surface soil layers (20–60 cm). Candidatus Brocadia, Candidatus Kuenenia and Candidatus Jettenia were detected by cloning and sequencing, with Candidatus Brocadia being dominant in all the three soils and Candidatus Jettenia being more frequently detected in the LZ soil. The operational taxonomic unit number and diversity indices of anammox bacterial 16S rRNA gene increased with soil depth. Our results demonstrate that anammox is more common and active in alkaline soils than in acidic soils, in deep paddy soil layers than in surface soil layers, and that anammox activities are likely to be regulated by soil chemical properties such as pH, salinity and redox potential. [ABSTRACT FROM AUTHOR]

Denitrification by microorganisms in soil regulates ecosystem nitrogen availability and cycling. Although arbuscular mycorrhiza fungi (AMF) are best known as the key connectors between plant and microorganisms in below-ground soil, however, less knowledge is available about the interactive effects of AMF and vegetation community traits on soil denitrifiers. In this study, we manipulated experimental pots with or without AMF inoculation (AMF+ and AMF− treatments) under three plant richness levels and 27 different plant community compositions. Our results provided evidence that inoculation of AMF significantly increased the abundances of nirS -, nirK - and nosZ -type denitrifiers as revealed by quantitative PCR (qPCR), which inferred a positive role of AMF in N-cycling microorganisms. Plant community traits, including richness, community composition, biomass and species, were less important in influencing the abundances of soil denitrifiers, and no significant interactive effect was detected between AMF inoculation and plant richness or plant community compositions, indicating a weak direct relationship between plants and soil denitrifiers. Our study provided comprehensive insights into the roles of AMF-plant associate bio-system in driving the variation of soil denitrifiers. • AMF inoculation increased abundances of nirK , nirS and nosZ genes. • Plant traits were less important in influencing the abundances of soil denitrifiers. • The effect of AMF on denitrifiers' abundances was related with plant compositions. [ABSTRACT FROM AUTHOR]

Highlights: [•] Colloidal properties of Ferrihydrite humic acid coprecipitated are investigated. [•] Fe–HA coprecipitate increase in the size and negative charge compare with HA. [•] ξ-Potential measurements revealed a increment of negative charge for Fe–HA at pH 4–8. [•] At neutral alkaline pH the Fe–HA negative charge enhancing colloidal stability. [•] Ferrihydrite–HA coprecipitate could play an important role in the carbon stabilization. [ABSTRACT FROM AUTHOR]

Tardigrades, also known as 'water bear' or 'moss piglet', inhabit diverse environments ranging from marine to freshwater and terrestrial habitats. They occupy various trophic levels in the micro-food web attributed to their different feeding preferences and different predators, which also heralds the complexity of their ecological functions. Therefore, understanding the ecological preference of tardigrades and their interactions with other organisms is crucial for uncovering the changes in ecosystem functions performed by these organisms under future scenarios of climate change. Here, we investigated the diversity and community composition of tardigrades, and their driving factors from 194 soil samples across south and eastern Australia, based on amplicon sequencing of 18S rRNA gene. We further validated the presence or absence of tardigrades in selected soil samples using morphological detection. Eleven tardigrade genera were observed in 53 samples, predominantly from coastal soils, with Eremobiotus as the most dominant genus. Notably, mean annual temperature (MAT) was the most important factor influencing the presence of tardigrades, revealing a decreased relative abundance of tardigrades as MAT increased. Other abiotic factors, including soil pH, total nitrogen, and mean annual precipitation, as well as biotic factors, including bacteria, fungi, protists, algae and nematodes, were also critical to the distribution of tardigrades, as revealed by structural equation modelling. Morphological identification broadly aligned with our molecular findings; it also illustrated the sporadic distribution pattern of tardigrades. Taken together, our findings provide the first empirical evidence for the relationships between soil tardigrades and the environmental factors using environmental DNA and demonstrated the importance of both biotic and abiotic factors in shaping the large-scale distribution patterns of soil tardigrades. Additionally, our findings imply a certain degree of feasibility for soil tardigrade researches using environmental DNA, and highlight the potential risk of a decline in tardigrade communities in the face of increasing global temperatures. • Soil tardigrades were more prevalent in coastal areas rather than inland. • Temperature is an important factor influencing the presence or absence of soil tardigrades. • Lower temperature is more favourable for soil tardigrade existence. • Multiple biotic and abiotic factors affect the tardigrade community composition. • Morphological detection of tardigrade broadly aligned with molecular detection. [ABSTRACT FROM AUTHOR]

[Display omitted] • The diversity of fungal plant pathogens in the phyllosphere was higher than that in the rhizosphere. • Fungal pathogen diversity was significantly and negatively correlated with latitude in both phyllosphere and rhizosphere. • Climatic factors and soil properties were the most important factors influencing fungal pathogen diversity in phyllosphere and rhizosphere, respectively. • The phyllosphere fungal plant pathogen diversity plays a crucial role in sorghum yield. Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity. [ABSTRACT FROM AUTHOR]

Sequential extraction procedures were used to investigate the influence of the microbes on the distribution of arsenic in a Chinese paddy soil under different long-term fertilization treatments. The paddy soil with four long-term fertilization treatments (CK, M, NPK and NPK+M) and three levels of arsenate addition (0, 50, 100 mg As kg−1 dry soil), were selected to construct microcosms for laboratory incubation. After the incubation, soil samples were sequentially extracted to determine As in various fractions, i.e. water soluble (F0), exchangeable (F1), bound to carbonates (F2), bound to Fe and Mn oxides (F3), bound to organic matter and sulfides (F4), and residual (F5, mineral matrix). Results showed that most of the As was fixed by mineral matrix (F5, ratios ranging from 46.22% to 96.37%), followed by As bound to Fe and Mn oxides (F3, ratios ranging from 3.14% to 28.18%), and the ratios of the other four fractions (F0, F1, F2 and F4) were mostly less than 10%. The microbes in the paddy soil could make As transform from inactive fraction (F5) to relatively active fractions (F0, F1, F2 and F3) and thus increase its environmental risk. With the increase of the As addition levels and with the application of manure or chemical NPK fertilizers, As was distributed more in the relatively active fractions (F0, F1, F2, F3 and F4) in the paddy soil mediated by the microbes. In addition, Fe and Mn oxides could play an important role in decreasing the As leaching potential from the mineral matrix to soil solution and thus abate the As risk to human health. [Copyright &y& Elsevier]

• Manure application increases the alpha diversity of bacteria, but not fungi. • Manure application increases saprotrophic fungi while suppresses potential pathogenic fungi. • Microbial network complexity increases with increasing application rates of manure. • The complexity of microbial networks declines with increasing sizes of aggregates. • Manure application alters the number and community composition of keystone taxa. Soil aggregate fractions serve as functional units of a soil ecosystem, providing ecologically diverse microhabitats for microbial communities. Manure application has been previously reported to alter the abundance, diversity and structure of soil microbial communities. However, how manure application changes functional microbial groups and microbiome complexity in various soil aggregate fractions remains largely unclear. Here, we investigated the impact of 18-year pig manure application on microbial communities and their network complexity in soil aggregate fractions from an acidic Ultisol. Manure application significantly enhanced soil bacterial diversity rather than fungal diversity. Both manure application and aggregation had a significant impact on the bacterial and fungal community structure. Manure application reduced the relative abundance of Chloroflexi, AD3 and Basidiomycota phyla across all aggregate fractions, and enriched Proteobacteria and Ascomycota phyla in macroaggregates. As for functional microbial groups, the relative abundances of diazotrophs and bacterial nitrifiers were enhanced while bacterial denitrifiers were inhibited under manure application. Manure application increased the relative abundance of saprotrophic fungi while suppressed plant pathogens and parasites. Microbial network complexity, especially the number of positive links, increased with increasing application rates of manure. In contrast, the complexity of microbial networks declined with increasing aggregate sizes. Acidobacteria and Chloroflexi phyla comprised the majority of the potential keystone taxa in the low-rate and high-rate manure amended treatments, respectively. The importance of Chloroflexi phylum in microbial networks was promoted by manure application, despite of their reduced abundance. Together, these findings advance our understanding of the impacts of manure application on microbiome diversity, complexity and functional groups in soil aggregate fractions, with implications for managing agricultural ecosystem functioning in Ultisols. [ABSTRACT FROM AUTHOR]

The impacts of nitrogen (N) and phosphorus (P) additions on root-associated fungi (RAF) of mixed roots in forest soils remain poorly understood. We investigated how RAF communities respond to N and P inputs in a subtropical montane forest using a time-series sampling approach. Our results showed that sampling time had a significant effect on total fungal richness, while the N addition had significant impacts on symbiotrophic rather than saprotrophic fungal richness. RAF community composition was strongly influenced by P addition treatments regardless of sampling time. Furthermore, we found that RAF community structure was mainly affected by soil NO 3 –-N, C/N and N/P ratios. This influence could be ascribed to the direct control of fungal activities and the indirect effects of fertilization on soil properties. Together, our findings highlight the importance of considering temporal variation in RAF responses to fertilization for a more comprehensive understanding of fungal community dynamics. • Sampling time had a significant effect on total fungal OTU richness. • RAF community composition was strongly affected by P-related treatments. • Considering temporal variation in RAF responses to fertilization is critical. [ABSTRACT FROM AUTHOR]

The emergence, evolution and spread of antibiotic resistance genes (ARGs) in the environment represent a global threat to human health. Our knowledge of antibiotic resistance in human-impacted ecosystems is rapidly growing with antibiotic use, organic fertilization and wastewater irrigation identified as key selection pressures. However, the importance of biological interactions, especially predation and competition, as a potential driver of antibiotic resistance in the natural environment with limited anthropogenic disturbance remains largely overlooked. Stress-affected bacteria develop resistance to maximize competition and survival, and similarly bacteria may develop resistance to fight stress under the predation pressure of protists, an essential component of the soil microbiome. In this article, we summarized the major findings for the prevalence of natural ARGs on our planet and discussed the potential selection pressures driving the evolution and development of antibiotic resistance in natural settings. This is the first article that reviewed the potential links between protists and the antibiotic resistance of bacteria, and highlighted the importance of predation by protists as a crucial selection pressure of antibiotic resistance in the absence of anthropogenic disturbance. We conclude that an improved ecological understanding of the protists-bacteria interactions and other biological relationships would greatly expand our ability to predict and mitigate the environmental antibiotic resistance under the context of global change. Unlabelled Image • Antibiotic resistance is a natural phenomenon on Earth. • Biological interactions trigger antibiotic-resistant strategies of bacteria in nature. • Protists might be important factors for the origin and maintenance of antibiotic resistance. • Understandings of protist-bacteria interactions are important to mitigation of antibiotic resistance. [ABSTRACT FROM AUTHOR]

Abstract The new discovery of complete ammonia oxidizers (comammox), single organisms capable of oxidizing ammonia into nitrate, redefined the traditional view of nitrification. However, little is known about the relative contributions of comammox and other nitrifiers to nitrification, particularly in agricultural soils with long-term intensive input of nutrients. Herein, we investigated the communities of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and comammox Nitrospira in agricultural soils under nutrients input gradient of nitrogen (0–675 kg N ha−1 year−1), phosphorus (0–405 kg P 2 O 5 ha−1 year−1), and potassium (0–675 kg K 2 O ha−1 year−1) fertilizers for 19 years. The results showed that N and K fertilizers input significantly (P < 0.05) increased the AOB- amoA gene abundance, while AOA were not as sensitive as AOB. The comammox- amoA gene copies were increased in all fertilizer treatments and was significantly correlated (P < 0.05) with the amount of N fertilizer added. Terminal restriction fragment length polymorphism (T-RFLP) combined with clone-library assays of comammox- amoA gene showed that increasing gradient of nutrients input increased the relative abundance of 73 bp T-RF (assigned to Clade A) but decreased the relative abundance of 198 bp T-RF (representing Clade B). Correlation analyses and stepwise linear regression analyses demonstrated that AOB were the dominate contributors to soil potential nitrification, while comammox Nitrospira did not play a significant role (P > 0.05). This study provided insights into the adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations and their relative contributions to potential nitrification in arable soils. Graphical abstract Unlabelled Image Highlights • Long-term fertilizers inputs increased the abundance of comammox. • Specific comammox clades responded distinctly to fertilizers inputs. • Comammox played a less important role in soil nitrification than AOB. • The abundance of AOB increased with the gradients of fertilizers inputs. [ABSTRACT FROM AUTHOR]

Abstract 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. Graphical abstract Unlabelled Image Highlights • Ocean and river beach soils are important reservoirs of antibiotic resistance genes (ARGs). • The oprJ gene is the most widespread ARG in beach soils. • Beach soils in different geographical locations shared extensive core resistome. • The abundance of ARGs had a significantly positive correlation with soil salinity properties. • Salinity is the most important factor modulating the distribution patterns of beach soil ARGs. [ABSTRACT FROM AUTHOR]