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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]

Summary: Plants harbour highly diverse mycobiomes which sustain essential functions for host health and productivity. However, ecological processes that govern the plant–mycobiome assembly, interactions and their impact on ecosystem functions remain poorly known. Here we characterized the ecological role and community assembly of both abundant and rare fungal taxa along the soil–plant continuums (rhizosphere, phyllosphere and endosphere) in the maize–wheat/barley rotation system under different fertilization practices at two contrasting sites. Our results indicate that mycobiome assembly is shaped predominantly by compartment niche and host species rather than by environmental factors. Moreover, crop‐associated fungal communities are dominated by few abundant taxa mainly belonging to Sordariomycetes and Dothideomycetes, while the majority of diversity within mycobiomes are represented by rare taxa. For plant compartments, the abundant sub‐community is mainly determined by stochastic processes. In contrast, the rare sub‐community is more sensitive to host selection and mainly governed by deterministic processes. Furthermore, our results demonstrate that rare taxa play an important role in fungal co‐occurrence network and ecosystem functioning like crop yield and soil enzyme activities. These results significantly advance our understanding of crop mycobiome assembly and highlight the key role of rare taxa in sustaining the stability of crop mycobiomes and ecosystem functions. [ABSTRACT FROM AUTHOR]

Achieving the Sustainable Development Goal of climate change mitigation within this century will require adoption of new innovative technologies to control emissions of nitrous oxide (N2O), an important greenhouse gas leading to global warming. This is particularly important in the face of growing fertilizer consumption and continuous land degradation. Currently used tools to mitigate N2O emissions are based on agrochemical inputs and agronomic practices. Emerging technologies include plant breeding approaches to manipulate microbiome activities in agro-ecosystems, and microbial biotechnology approaches for in situ microbiome manipulation and engineering via use of biochemical, cellular and genome-editing methods. This article assessed the likely contribution of microbial biotechnology to the mitigation of N2O emissions and discussed how to facilitate the development of environmental-friendly microbiome-based biotechnology for sustainable climate change mitigation. [ABSTRACT FROM AUTHOR]

The bacterial abundance and community composition in four types of soils and their associated Fe-Mn nodules from Queyu (QY) in Shandong Province, Zaoyang (ZY), Wuhan (WH) in Hubei Province and Guiyang (GY) in Hunan Province, China were investigated using real-time PCR, cloning and sequencing approaches. It was found that the bacterial 16S rRNA gene copy numbers in the soils were almost 3 magnitudes greater than those in their corresponding nodules and positively correlated with OM. The bacterial diversity as indicated by Simpson and Shannon indices, were significantly lower in the nodules than in the soils. Remarkable divergence in bacterial community structure was observed between the soils and the nodules, and the difference was the mainly explained by OM. In contrast, the differences within the soils and within the nodules were minor, suggesting significant habitat filtering for the bacterial community composition in the nodules.Acidobacteriawas the most abundant group (accounting for 28.6%–51.6%) in soil bacterial community while nodule bacterial community was predominated byProteobacteria(accounting for 62.8%– 90.5%). A number of clones closely related to well-known Mn-oxidizing, Fe-oxidizing and Fe-reducing bacteria withinProteobacteriawere retrieved mainly from nodules. [ABSTRACT FROM PUBLISHER]

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]

Summary: 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. [ABSTRACT FROM AUTHOR]

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]

Soil microbial communities, key players of many crucial ecosystem functions, are susceptible to environmental disturbances, which might cause the loss of microbial diversity and functions. However, few ecological concepts and practices have been developed for rescuing stressed soil microbial communities. Here, we manipulated an experiment with or without arbuscular mycorrhizal fungi (AMF) inoculation and at three levels (one, three and six species) of plant diversity to disentangle how the AMF and vegetation rescue soil nitrogen (N) ‐cycling microbial loop from simulated degraded soil ecosystem. Our results showed that AMF inoculation improved the restoration of soil N‐cycling microbial communities. This improved restoration was related to the role of AMF in enhancing interactions within the N‐cycling microbial loop. Furthermore, increased plant diversity strengthened the role of AMF in rescuing N‐cycling microbial communities. Our findings provide novel insights into the roles of AMF and plant diversity in facilitating the rescue of microbial communities in degraded terrestrial ecosystems. [ABSTRACT FROM AUTHOR]

The impact of fire on above‐ground biomass has significant consequences on soil carbon (C) dynamics, which is essential in predicting the global C budget during the Anthropocene. However, there is considerable spatiotemporal variability in the directions and magnitudes of fire effects on soil respiration, and the drivers associated with these effects are not well understood.Here, we conducted a global meta‐analysis of 1327 individual observations from 170 studies to determine the extent to which fire influenced soil total respiration (Rs), heterotrophic respiration (Rh) and autotrophic respiration (Ra).We found fires reduced Rs, Rh and Ra, with an average effect of −11.0%, −17.5% and −40.6%, compared with unburnt sites. Specifically, wildfires significantly reduced Rs and Rh (−20.4% and −25.0%, respectively), and prescribed fire significantly decreased Ra (−74.8%). The influences of fire on Rs and its components were moderated by fire severity, season, type, climate zones and biomes. After several years from the time of the fire, the negative effects of fire on Rs diminished and then recovered to a state not significantly different from unburnt sites; Rh exhibited a similar but decayed temporal response. Similarly, the negative effects on Ra disappeared after 3 years following the latest fire. The magnitude of the effect on Rs was strongly associated with soil temperature, cation exchange capacity, total nitrogen (N) content and N‐acquiring enzyme activity. In contrast, the magnitude of the effect on Rh significantly changed with pH, bulk density, texture, soil C and nutrient contents, and C‐acquiring enzyme activity.Our findings advance the understanding of the inhibition and associated mechanisms of fire on Rs and its components, highlighting the need for new research efforts to predict the spatial‐temporal shifts in underground C‐cycling induced by fire. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Soil invertebrates contribute significantly to vital ecosystem functions such as the breakdown of organic matter and cycling of essential nutrients, but our knowledge of their large-scale distribution in agricultural systems is limited, which hinders our ability to robustly predict how they will respond to future global change scenarios. Here, we employed metabarcoding analysis of eukaryotic 18S rRNA genes to examine the diversity and community composition of invertebrates in 528 sorghum rhizosphere and bulk soils, collected from 53 experimental field sites across China. Our results revealed that Nematoda, Arthropoda and Annelida were the dominant soil invertebrate groups in agroecosystems. Among all the climatic and soil parameters we examined, precipitation seasonality (i.e. the irregular distribution of precipitation during a normal year) had the strongest relationship with the richness of soil invertebrates, with an increase in soil invertebrate richness predicted with increasing precipitation seasonality. Mean annual precipitation and soil pH were the most important predictors of soil invertebrate community structure, with numerous invertebrate phylotypes showing either significantly positive or negative relationships with these two variables. Our findings suggest that shifts in precipitation patterns and soil pH, induced by future climate change and agricultural practices, will have important consequences for the distribution of soil invertebrate communities, with implications for agricultural ecosystem sustainability. [ABSTRACT FROM AUTHOR]

Un-fertilized rice paddies have shown maintained soil nitrogen (N) status, stable N supply to the rice plant and sustained rice yields at moderate levels for hundreds of years. Microbial N2 fixation is known to contribute N to un-fertilized paddies, but it cannot fully explain the maintained N nutrition, where favourable conditions exist for N loss by denitrification. We used 15N tracer, 15N2 uptake, acetylene reduction assay and qPCR to simultaneously investigate N2 fixation, dissimilatory nitrate reduction to ammonium (DNRA), denitrification and related microbial gene abundances in long-term low (or no) and high N input rice paddies of Myanmar. We also determined how varying soil organic carbon-to-nitrate (SOC/NO3−) ratios affect nitrate partitioning between DNRA and denitrification by manipulating these ratios through labile organic carbon addition. We observed more than 2.5 times higher N2 fixation (1.49–2.08 μg N g−1 soil day−1) and significantly higher N2 fixing gene (nifH) abundance in low compared with high N input paddies. Up to 60% of the soil nitrate (1.51–2.67 μg NO3−-N g−1 soil day−1) was ammonified through DNRA, and only 15% was lost as N2 through denitrification in low N input paddies, whereas denitrification exceeded DNRA in high N input paddies. The microbial gene related to DNRA activity (nrfA) was also higher in low input than in high input rice paddies. We found that nitrate retention can be improved in high N input rice paddies by maintaining a higher soil organic carbon-to-nitrate ratio. Our findings highlight the unique microbial N-cycling strategies in resource-limited paddies which support maintained N nutrition of the paddy system. [ABSTRACT FROM AUTHOR]

Protists occupy multiple trophic positions in soil food webs and significantly contribute to organic matter decomposition and biogeochemical cycling. Protists can ingest bacteria and fungi as main food sources while being subjected to predation of invertebrates, but our understanding of how bottom‐up and top‐down regulations structure protists in natural soil habitats is limited. Here, we disentangle the effects of trophic regulations to the diversity and structure of soil protists in natural settings across northern and eastern Australia. Bacterial and invertebrate diversity were identified as important drivers of the diversity of functional groups of protists. Moreover, the compositions of protistan taxonomic and functional groups were better predicted by bacteria and fungi, than by soil invertebrates. There were strong trophic interconnections between protists and bacteria in multiple organismic network analysis. Altogether, the study provided new evidence that, bottom‐up control of bacteria played an important role in shaping the soil protist community structure, which can be derived from feeding preferences of protists on microbial prey, and their intimate relationships in soil functioning or environmental adaptation. Our findings advance our knowledge about the impacts of different trophic groups on key soil organismic communities, with implications for ecosystem functions and services. [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]

Abstract Long-term field fertilization trials have suggested that reduced chemical nitrogen (N) plus organic fertilization can effectively reduce N loss without sacrificing crop yield, while the knowledge of how organic fertilizers regulate soil microorganisms and their function in N transformation are limited. In this study, the response of net nitrification rate and the ammonia-oxidizer community within soil aggregates to long-term combined organic N and reduced chemical N fertilization was evaluated to understand the underlying mechanism of the practice in mitigating soil N loss. The fertilization experiment included an unfertilized control; chemical N fertilizer (N), superphosphate (P) and potassium sulfate (K) fertilizer (NPK); NPK plus straw (NPKS); and NPK plus manure (NPKM). The results showed that the large macro-aggregates mass (>2 mm) in soil significantly increased from 34.1% in NPK to 47.2% in NPKS (P < 0.05). NPKS and NPKM both had positive effects on soil moisture retention, total N (TN), soil organic carbon (SOC), ammonium (NH 4 +-N) and nitrate (NO 3 −-N) accumulation, particularly within micro- (<0.25 mm) and small macro-aggregates. Compared with the NPK treatment, soil net nitrification rate (NNR) and ammonia-oxidizing bacterial (AOB) abundance decreased by 67.1% and 40.7% respectively under NPKS (P < 0.05), and the decrease mainly appeared in large macro-aggregate and micro-aggregates. The net nitrification rate was significantly correlated with ammonia-oxidizing archaea (AOA) abundance only in small macro-aggregates (r = 0.642, n = 12, P < 0.05). In contrast, NRR was positively correlated with AOB abundance within small macro- and micro-aggregate size classes (r values ranged from 0.654 to 0.813, P < 0.05). The community structure of AOB varied among different fertilization treatments, while AOA community differentiation was mainly dependent on aggregate size. The shift of the AOA and AOB communities corresponded with high moisture and lower ammonia content in the large macro-aggregates and were potentially responsible for the suppressed nitrification activity in the NPKS treatment. These results indicated that reduced chemical N plus organic fertilization is beneficial for increasing N concentration in large macro-aggregates. Highlights • Long-term combined organic and reduced chemical fertilization (NPKS and NPKM) significantly improved soil aggregation. • Nitrification and AOB abundance were significantly suppressed in NPKS, particularly in its large macro-aggregates. • The shift of nitrifiers communities among three soil aggregates contributed to the suppressed nitrification activity. [ABSTRACT FROM AUTHOR]

Summary: Acid rain can cause severe effects on soil biota and nutrient biogeochemical cycles in the forest ecosystem, but how plant‐symbiotic ectomycorrhizal fungi will modulate the effects remains unknown. Here, we conducted a full factorial field experiment in a Masson pine forest by simultaneously controlling the acidity of the simulated rain (pH 5.6 vs. pH 3.5) and the ectomycorrhizal fungi Pisolithus tinctorius inoculation (non‐inoculation vs. inoculation), to investigate the effects on ammonia oxidizers and denitrifiers. After 10 months, compared with the control (rain pH 5.6, and non‐inoculation), simulated acid rain (pH 3.5) reduced soil nutrient content, decreased archaeal amoA gene abundance and inhibited denitrification enzyme activity. Also, simulated acid rain altered the community compositions of all the examined functional genes (archaeal amoA, bacterial amoA, nirK, nirS and nosZ). However, inoculation with ectomycorrhizal fungi under acid rain stress recovered soil nutrient content, archaeal amoA gene abundance and denitrification enzyme activity to levels comparable to the control, suggesting that ectomycorrhizal fungi inoculation ameliorates simulated acid rain effects. Taken together, ectomycorrhizal fungi inoculation – potentially through improving soil substrate availability – could alleviate the deleterious effects of acid rain on nitrogen cycling microbes in forest soils. [ABSTRACT FROM AUTHOR]

Deciphering the local diversity and community composition of plant-associated microorganisms is crucial to predict their ecological functions in forest ecosystems. The differences in microbial diversity and community composition between the aboveground and belowground tree compartments remain largely unknown. Here, we examined bacterial communities in the leaf surface (phyllosphere) and root-associated (root and rhizospheric soil) habitats of 13 tree species. Bacterial richness substantially differed across the three compartments, with the highest value observed in rhizospheric soil. Tree species exerted a significant effect on α-diversity of leaf- and soil- but not root-inhabiting bacteria. Bacterial communities were distinct across habitats and were significantly more divergent in leaf- than in root-associated habitats. Leaf nutrients and soil pH and NH4+-N were the main factors regulating leaf- and root-related community composition, respectively. This study highlights that host selection effects on bacterial community structure were more prominent in aboveground than in belowground habitats. Our findings contribute to a better understanding of the effect of compartments and subtropical tree species on microbial diversity, with crucial implications for sustainable forest plantation management. [ABSTRACT FROM AUTHOR]

The multidimensional dynamics of biodiversity and ecosystem function during the rewilding of Mediterranean forests remain poorly understood, limiting our capacity to predict how future restoration efforts may help mitigate climate change.Here, we investigated the changes in multiple dimensions of biodiversity and ecosystem services in a 120‐year forest succession after harvest to identify potential trade‐offs in multiple dimensions of ecosystem function, and further assess the link between above and below‐ground biodiversity and function.We found a positive influence of successional age on not only multiple dimensions of biodiversity and function but also some important trade‐offs. Two ecosystem axes of function explained nearly 75.4% of functional variation during ecosystem rewilding. However, while the first axis increased with successional age promoting plant productivity and element stocks, the second axis followed a hump‐shaped relationship with age supporting important reductions in nutrient availability and pathogen control in old forests. Our study further revealed a significant positive relationship between plant and soil biodiversity with multiple elements of multifunctionality as forests develop. Moreover, the influence of plant and soil biodiversity were especially important to support a high number of function working at high levels of functioning.Our work provides new insights on the patterns and functional trade‐offs in the multidimensional rewilding of forests and further highlights the importance of biodiversity for long‐term Mediterranean rewilding. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Globally, drylands represent the largest terrestrial biome and are projected to expand by 23% by the end of this century. Drylands are characterized by extremely low levels of water and nutrients and exhibit highly heterogeneous distribution in plants and biocrusts which make microbial processes shaping the dryland functioning rather unique compared with other terrestrial ecosystems. Nitrous oxide (N2O) is a powerful greenhouse gas with ozone depletion potential. Despite of the pivotal influences of microbial communities on the production and consumption of N2O, we have limited knowledge of the biological pathways and mechanisms underpinning N2O emissions from drylands, which are estimated to account for 30% of total gaseous nitrogen emissions on Earth. In this article, we describe the key microbial players and biological pathways regulating dryland N2O emissions, and discuss how these processes will respond to emerging global changes such as climate warming, extreme weather events and nitrogen deposition. We also provide a conceptual framework to precisely manipulate the dryland microbiome to mitigate N2O emissions in situ using emerging technologies with great specificity and efficacy. These cross-disciplinary efforts will enable the development of novel and environmental-friendly microbiome-based solutions to future mitigation strategies of climate change. [ABSTRACT FROM AUTHOR]

Increasing efforts have been devoted to exploring the impact of environmental stresses on soil bacterial communities, but the work on the archaeal community is seldom. Here, we constructed microcosm experiments to investigate the responses of archaeal communities to the subsequent dry-rewetting (DW) disturbance in two contrasting soils (fluvo-aquic and red soil) after 6 years of copper pollution. Ten DW cycles were exerted on the two soils with different copper levels, followed by a 6-week recovery period. In both soils, archaeal diversity (Shannon index) in the high copper-level treatments increased over the incubation period, and archaeal community structure changed remarkably as revealed by the non-metric multidimensional scaling ordinations. In both soils, copper pollution altered the response of dominant operational taxonomic units (OTUs) to the DW disturbance. Throughout the incubation and recovery period, the resistance of archaeal abundance to the DW disturbance was higher in the copper-polluted soils than soils without pollution. Taken together, copper pollution altered the response of soil archaeal diversity and community composition to the DW disturbance and increased the resistance of the archaeal abundance. These findings have important implications for understanding soil microbial responses to ongoing environmental change. [ABSTRACT FROM AUTHOR]

To characterize the archaeal community composition in soil originating iron-manganese nodules, four types of soils—brown soil, yellow-cinnamon soil, yellow brown soil and red soil—and their associated iron-manganese nodules were collected from Queyu (QY), Zaoyang (ZY), Wuhan (WH) and Guiyang (GY), China, respectively, and subjected to quantitative polymerase chain reaction, cloning and sequencing analyses. The results showed that the archaeal 16S rRNA gene copy numbers in nodules, ranging between 3.59 × 102and 4.17 × 103copies g−1dry nodule, were about 50–1000 times lower than those in their corresponding soils (1.87 × 105to 1.08 × 106copies g−1dry soil), correlating with the low organic matter in the nodules, while archaea accounted for a relatively higher proportion of total prokaryote in nodules than in soils. Community composition analysis suggested that the archaeal diversity in both soils and nodules were much lower than bacterial, but archaeal community structures were similar to each other among the soils and nodules from the same location but varied among four locations, converse to the previous observation that bacterial community shifted markedly between nodules and soils as the result of habitat filtering. The archaeal communities in both soils and nodules were predominated byThaumarchaeotaGroup I.1b with the relative abundance ranging between 73.88 and 94.17%, except thatEuryarchaeotadominated the archaeal community in one nodule sample (WHn) developed from lake sediment. The finding shed new light on the archaeal diversity and their ecophysiology in different habitats, and further supported the opinion that archaea are more adaptable to stress and unfavorable conditions. [ABSTRACT FROM PUBLISHER]

The discovery of complete ammonia oxidizers, comammox Nitrospira, represents a breakthrough in the history of nitrification research. Nitrospira inopinata, which was obtained from an aquatic ecosystem, is the only pure comammox bacterial isolate reported so far. Ammonia oxidation kinetics of N. inopinata indicated that they prefer an oligotrophic lifestyle and may directly compete with ammonia-oxidizing archaea (AOA), but representatives of comammox Nitrospira from terrestrial ecosystems are lacking. Current studies demonstrate that the functionally dominant comammox Nitrospira in terrestrial ecosystems are separated from most sequences obtained from aquatic and engineering systems. Clades A and B of comammox Nitrospira seemingly have different ecological preferences in soils, possibly due to their different ammonium uptake systems. Analyses of the evolutionary history indicate that some genes of comammox Nitrospira involved in ammonia oxidation could be laterally transferred from β-ammonia-oxidizing bacteria (AOB). Some comammox Nitrospira species may have similar ecological preferences with AOB and be functionally active in the niches where nitrification was previously considered to be dominated by AOB. Taken together, this review summarizes the recent findings of the biogeographical distribution and ecological preference of comammox Nitrospira in large-scale soil surveys, the responses of comammox Nitrospira to nitrogen application in soil, and the putative mechanisms underpinning the ecological niche of terrestrial comammox Nitrospira. These studies from terrestrial ecosystems suggest that comammox Nitrospira are not strictly oligotrophic but both oligotrophic and copiotrophic with a broader ecological niche breadth. Comammox Nitrospira in terrestrial ecosystems are abundant and active in both oligotrophic and copiotrophic environments. These findings have profoundly expanded our knowledge of the environmental niches of comammox Nitrospira and their relative contribution to nitrification in soils. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Not only do soils provide 98.7% of the calories consumed by humans, they also provide numerous other functions upon which planetary survivability closely depends. However, our continuously increasing focus on soils for biomass provision (food, fiber, and energy) through intensive agriculture is rapidly degrading soils and diminishing their capacity to deliver other vital functions. These tradeoffs in soil functionality – the increased provision of one function at the expense of other critical planetary functions – are the focus of this review. We examine how land-use change for biomass provision has decreased the ability of soils to regulate the carbon pool and thereby contribute profoundly to climate change, to cycle the nutrients that sustain plant growth and ecosystem health, to protect the soil biodiversity upon which many other functions depend, and to cycle the Earth's freshwater supplies. We also examine how this decreasing ability of soil to provide these other functions can be halted and reversed. Despite the complexity and the interconnectedness of soil functions, we show that soil organic carbon plays a central role and is a master indicator for soil functioning and that we require a better understanding of the factors controlling the behavior and persistence of C in soils. Given the threats facing humanity and their economies, it is imperative that we recognize that Soil Security is itself an existential challenge and that we need to increase our focus on the multiple functions of soils for long-term human welfare and survivability of the planet. [ABSTRACT FROM AUTHOR]

Grazing represents the most extensive use of land worldwide. Yet its impacts on ecosystem services remain uncertain because pervasive interactions between grazing pressure, climate, soil properties, and biodiversity may occur but have never been addressed simultaneously. Using a standardized survey at 98 sites across six continents, we show that interactions between grazing pressure, climate, soil, and biodiversity are critical to explain the delivery of fundamental ecosystem services across drylands worldwide. Increasing grazing pressure reduced ecosystem service delivery in warmer and species-poor drylands, whereas positive effects of grazing were observed in colder and species-rich areas. Considering interactions between grazing and local abiotic and biotic factors is key for understanding the fate of dryland ecosystems under climate change and increasing human pressure. [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]

Soil ecosystem multifunctionality (EMF), the ability of an ecosystem to perform multiple functions, remains uncertain in its contribution to crop production, especially in the context of long-term fertilization ecosystems. This study was carried out on a 40-year-old long-term fertilization experiment in black soil in China. Soil samples were collected from four treatments: control (CK); nitrogen (N) fertilizer; phosphorus (P) fertilizer; and a combination of nitrogen and phosphorus (NP) in both maize and wheat planting seasons. The results showed significant effects of N, P fertilizers and crop season on soil biotic and abiotic properties, especially on soil enzyme activities. Crop productivity and soil EMF showed a similar pattern across different treatments and both crop seasons, with significant higher values recorded in treatments with N addition (i.e. N and NP). Soil EMF was strongly associated with crop productivity in both maize and wheat seasons, while soil pH had a negative impact on crop yield. Random forest analysis revealed that microbial functional gene structure was significantly correlated with both soil ecosystem multifunctionality and crop yield. This suggested that fertilization leads to alterations in soil nutrients and the composition of functional microbial communities, subsequently impacting ecological functions and crop growth. These findings indicated that mineral fertilizers can enhance crop yield through soil EMF in the black soils, while exerted substantial impact on soil properties, raising concerns about the sustainability of soils under continuous chemical fertilization. • Long-term mineral fertilization improves soil ecosystem multifunctionality. • Soil ecosystem multifunctionality is strongly associated with crop productivity. • Soil pH and nitrate were the dominant variables in determining soil ecosystem multifunctionality. • Functional gene community structure had significant correlation with crop production. [ABSTRACT FROM AUTHOR]

Weeds reduce agricultural productivity by competing for resources intended for crops. Recently, the deactivation of weed seedbanks by microwave (MW) radiation has been developed as a chemical-free weed management practice. It is unknown, if these extreme heat disturbances permanently alter the soil microbiome of different farming systems. We performed a microcosm experiment to quantify the immediate and short-term effect of MW heating on the soil microbiome. We exposed three different soil types (representing dryland, temperate and irrigated farming systems) to MW heating, and monitored the fungal and bacterial communities over a month of recovery. Bacterial and fungal community composition were strongly dependent on the soil of origin. Following MW heating, bacterial and fungal richness decreased in all soils and did not recover during the period studied (four weeks). Notably, in all soils, bacterial communities became more dissimilar to each other following disturbance, but in fungi, this depended on the soil of origin. These results highlight the importance of considering the resistance and recovery of the resident soil microbiota in developing long-term sustainable MW-based weed management system. • Soils' resident microbiota were dependent on the origin of soil. • Soil heating intensities declined the richness of bacterial and fungal communities. • Four weeks appeared to be insufficient time for microbial recovery. • Heat disturbance led to changes in the abundance of bacterial and fungal taxa. • Heating induced an obvious difference in bacterial communities' composition. [ABSTRACT FROM AUTHOR]

A correction to the article "Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices ," in the previous issue.

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]

Background: Metal(loid)s can promote the spread and enrichment of antibiotic resistance genes (ARGs) in the environment through a co-selection effect. However, it remains unclear whether exposure of microorganisms to varying concentrations of selenium (Se), an essential but potentially deleterious metal(loid) to living organisms, can influence the migration and distribution of ARGs in forest soils. Results: Precisely 235 ARGs conferring resistance to seven classes of antibiotics were detected along a Se gradient (0.06–20.65 mg kg−1) across 24 forest soils. (flor)/(chlor)/(am)phenicol resistance genes were the most abundant in all samples. The total abundance of ARGs first increased and then decreased with an elevated available Se content threshold of 0.034 mg kg−1 (P = 2E−05). A structural equation model revealed that the dominant mechanism through which Se indirectly influences the vertical migration of ARGs is by regulating the abundance of the bacterial community. In addition, the methylation of Se (mediated by tehB) and the repairing of DNA damages (mediated by ruvB and recG) were the dominant mechanisms involved in Se resistance in the forest soils. The co-occurrence network analysis revealed a significant correlated cluster between Se-resistance genes, MGEs and ARGs, suggesting the co-transfer potential. Lelliottia amnigena YTB01 isolated from the soil was able to tolerate 50 μg mL−1 ampicillin and 1000 mg kg−1 sodium selenite, and harbored both Se resistant genes and ARGs in the genome. Conclusions: Our study demonstrated that the spread and enrichment of ARGs are enhanced under moderate Se pressure but inhibited under severe Se pressure in the forest soil (threshold at 0.034 mg kg−1 available Se content). The data generated in this pilot study points to the potential health risk associated with Se contamination and its associated influence on ARGs distribution in soil. [ABSTRACT FROM AUTHOR]

For many years after the discovery of the two stable isotopes of B (10B,11B) in 1920 it was not used routinely as a tracer in the biological sciences until the development of inductively coupled plasma mass spectrometry in the early 1980s. This development provided an impetus to the study of the role of B in plant nutrition, although many seminal discoveries were made beforehand without the aid of isotopes. Thus, much information on the mobility and physiological function of B in plants is post-1985. Boron is unusual in plant nutrition in that it is taken up by plants through roots or foliage as undissociated boric acid, unlike other essential elements that are taken up in ionic form. The within-plant mobility of B in species important in agriculture and horticulture is examined in the present review including the role of sugar alcohols in xylem to phloem transfer. The molecular basis of its movement at the cellular level via transporters as revealed through the strategic application of enriched 11B and 10B is addressed. Few studies have been carried out on B use efficiency by crops and results show great variability. Suggestions for future applications of tracing with 10B and 11B are provided. [ABSTRACT FROM AUTHOR]

Background: Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China. Results: Soil viral community were clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic composition and were mainly driven by geographic location and climate factors. A total of 972 viral populations (vOTUs) were detected spanning 23 viral families from the 19 viromes. Phylogenetic analyses of the phoH gene showed a remarkable diversity and the distribution of viral phoH genes was more dependent on the environment. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thymidylate synthase complementing protein (Thy1), and Ribonucleoside reductase (RNR), were mainly identified in agricultural soils. Conclusions: The present work revealed that soil viral communities were distributed across China according to geographical location and climate factors. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems. [ABSTRACT FROM AUTHOR]

Large-scale planting of Chinese fir (Cunninghamia lanceolata) can bring considerable economic benefits but also seriously alters soil properties, disrupting soil microbial survival patterns and giving rise to distinct microbial communities. Nitrous oxide (N 2 O) reduction is the sole recognized biological sink for N 2 O, thereby playing a critical role in forest nitrogen cycling. However, the distribution of N 2 O reducers in Chinese fir plantation soils and the underlying factors at a regional scale remain unclear. Here, we assessed the abundance, diversity, and community structure of nosZ I-type N 2 O reducers in soil samples collected from nine state-owned forest farms in Fujian Province, China. The abundance of nosZ I-type reducers exhibited significant variation across sites, with altitude exerting the greatest influence, positively influencing their abundance. Soil organic carbon (SOC) and dissolved organic carbon (DOC) were the strongest predictors of alpha-diversity. Interestingly, SOC and DOC exhibited a negative association with nosZ I-type reducer alpha-diversity. Additionally, DOC played a significant role in influencing community structure. All nosZ I sequences were associated with Alphaprotebacteria and Betaproteobacteria, with Alphaproteobacteria dominating nosZ I-type reducer communities in all soils, accounting for over 90 % of the total sequences. Moreover, the modified stochasticity ratio values exceeded 0.5 at all sampling sites except for one, characterized by the lowest pH and relatively lower nutrient content, indicating the predominance of stochastic processes in community assembly. Taken together, our results provide novel evidence that the augmentation of organic carbon content could potentially reduce diversity and alter the structure of nosZ I-type reducer communities, with potential implications for N 2 O emissions in Chinese fir plantations. • Soil N 2 O reduction rates were positively associated with nosZ I gene abundance. • SOC and DOC were negatively associated with nosZ I-type reducer alpha-diversity. • DOC was a critical factor influencing nosZ I-type reducer community structure. • Alphaproteobacteria accounting for >90 % of nosZ I-type reducer sequences. • Stochastic processes dominated the community assembly of nosZ I-type reducer. [ABSTRACT FROM AUTHOR]

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. [Display omitted] • Protists were highly responsive to livestock manure application. • Temporal changes were observed in protistan diversity and composition. • Poultry manures had stronger negative impacts on soil protists than cattle manures. • Greater effects on soil protists were observed in tylosin-spiked manure treatments. • Many functional taxa of protists were highly sensitive to manure treatments. [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]

Biofilters are the important source and sink of antibiotic resistance genes (ARGs) and antibiotic resistance bacteria (ARB) in the drinking water. Current studies generally ascribed the prevalence of BAR in biofilter from the perspective of gene behavior, i.e. horizontal gene transfer (HGT), little attentions have been paid on the ARGs carrier- ARB. In this study, we proposed the hypothesis that ARB participating in pollutant metabolism processes and becoming dominant is an important way for the enrichment of ARGs. To verify this, the antibiotic resistome and bacterial functional metabolic pathways of a sand filter was profiled using heterotrophic bacterial plate counting method (HPC), high-throughput qPCR, Illumina Hiseq sequencing and PICRUSt2 functional prediction. The results illustrated a significant leakage of ARB in the effluent of the sand filter with an average absolute abundance of approximately 102–103 CFU/mL. Further contribution analysis revealed that the dominant genera, such as Acinetobacter spp., Aeromonas spp., Elizabethkingia spp., and Bacillus spp., were primary ARGs hosts, conferring resistance to multiple antibiotics including sulfamethoxazole, tetracycline and β-lactams. Notably, these ARGs hosts were involved in nitrogen metabolism, including extracellular nitrate/nitrite transport and nitrite reduction, which are crucial in nitrification and denitrification in biofilters. For example, Acinetobacter spp., the dominant bacteria in the filter (relative abundance 69.97 %), contributed the majority of ARGs and 53.79 % of nitrite reduction function. That is, ARB can predominate by participating in the nitrogen metabolism pathways, facilitating the enrichment of ARGs. These findings provide insights into the stable presence of ARGs in biofilters from a functional metabolism perspective, offering a significant supplementary to the mechanisms of the emergence, maintenance, and transmission of BARin drinking water. • The Acinetobacter spp. were the main ARGs hosts in sand filters. • Efflux pump genes and FCA resistance genes were the primary ARGs in sand filters. • Glutamate dehydrogenase and nitrite reductase were the main nitrogen related enzymes. • ARGs hosts were main participants of denitrification/nitrification in the biofilter. • PICRUSt2 could predict metabolic pathways accurately in drinking water environment. [ABSTRACT FROM AUTHOR]

Addressing global warming necessitates innovative strategies in fossil fuel management. This study evaluates lignite, a low-rank coal with limited calorific value, exploring applications beyond its use as fuel. Utilizing Pt/TiO 2 catalytic oxidation, the research aims to enhance the cadmium adsorption capacity of lignite in wastewater. Lignite, treated with 0.5% Pt/TiO 2 at 125 °C for 2 h, demonstrated a threefold increase in cadmium adsorption capacity. Characterization using TGA-DSC confirmed the modification process as exothermic and self-sustainable. Spectroscopic analysis and Boehm titration revealed significant alterations in pore structure, surface area, and oxygen-containing functional groups, emphasizing the effectiveness of catalytic oxidation. Adsorption mechanisms such as complexation, cation exchange, and cation-π interactions were identified, enhancing Cd adsorption. Techniques, including the d-band model, H 2 -TPR, and O 2 -TPD, indicated that dissociative adsorption of molecular O 2 and the subsequent generation of reactive oxygen species introduced additional oxygen-containing functional groups on the lignite surface. These findings provide essential strategies for the alternative use of lignite in environmental remediation, promoting sustainable resource utilization and enhancing cost-effectiveness in remediation processes. This study innovates in using lignite to reduce cadmium (Cd) contamination in wastewater. Employing Pt/TiO 2 catalytic oxidation, lignite is transformed, enhancing its cadmium adsorption capacity. This process, being exothermic, contributes to decreased energy consumption. The approach not only mitigates the hazardous impacts of cadmium but also aligns with sustainability by reducing greenhouse gas emissions and energy use, showcasing a multifaceted environmental advancement. [Display omitted] ● Pt/TiO 2 catalytic oxidation triples lignite's cadmium adsorption capacity. ● The catalytic process is exothermic and self-sustaining, reducing energy use. ● Adsorption mechanisms include complexation, cation exchange, and cation-π interactions. ● O 2 - and O- species facilitate the generation of oxygen-containing groups on lignite. [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]

Abstract: Acid soils, extensively used for nitrogen-fertilized agriculture and agroforestry, have important roles in maintaining global biogeochemical cycling and ecosystem functions. Huge inputs of nitrogen-based fertilizers into terrestrial ecosystems accelerate soil acidification, concomitantly altering the nitrogen transformation processes. Nitrification, as a critical component of the nitrogen cycle, is a microbially mediated process from ammonia to nitrate via nitrite, contributing to enormous losses of fertilizers through atmospheric emissions of greenhouse gas N2O and nitrate leaching to groundwater. However, the functionally dominant nitrifiers and underlying mechanisms for the acid soil nitrification are a long-standing mystery, which have confused scientists for more than 100 years. This century-long paradox originated from the early observations of active nitrification activity in acid soils, intensified by the failure of ammonia-oxidizing bacteria (AOB) cultures to sustain the nitrification in liquid batch under acid conditions, might be resolved by the recent progress in metagenomic, isotopic probing studies, and isolation of acidophilic ammonia-oxidizing archaea (AOA). Emerging evidence led to the supposition of the predominant role of AOA in controlling the autotrophic ammonia oxidation of acid soils, which has radically revised the previous perception that this oxidative reaction was exclusively regulated by autotrophic AOB and occasionally by heterotrophic nitrifiers. In this chapter, we review the recent progress in our understanding of the pH-impacted distribution of ammonia oxidizers, the niche differentiation of AOA and AOB shaped by acid stress, and the possible mechanisms of autotrophic nitrification in acid soils. The unveiling of this key process in widely distributed acid soils would help to identify effective biological strategies for better management of terrestrial nitrogen turnover and balance. [Copyright &y& Elsevier]

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]

Summary: 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. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

Summary: 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 β‐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. [ABSTRACT FROM AUTHOR]

To assess the effects of long-term fertilization on arsenic (As) accumulation in soils and crops with different agricultural practices, five experimental stations (Changshu, Taoyuan, Hailun, Fengqiu, and Qiyang) with long-term fertilization practices, representing five typical soils of China, were selected to investigate the soil As concentrations. Results indicated that the geological source, that is, parent materials, played a dominant role in determining the soil As concentrations. Long-term application of manure and phosphorus fertilizers led to a decrease of As concentration in the surface paddy soil at Taoyuan, while the effects of fertilization on As concentration in other samples were minimal. In addition, other agricultural practices, such as the removal of crop biomass, reduced the As concentrations in the surface soils with low levels of soil As (Fengqiu, Changshu, and Taoyuan). In the upland soils with higher As concentrations, wheat may have risk to human health through food-chain and maize can be considered as a favorable crop. [ABSTRACT FROM AUTHOR]