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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]

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]

Purpose: Nitrogen (N) and phosphorus (P) amendments considerably influence fungal diversity and community composition in various ecosystems. Nevertheless, how N and P additions would change arbuscular mycorrhizal (AM) fungal community and functional guilds in forest soil remains largely unclear. Materials and methods: A 5-year N and P addition experiment was conducted in a subtropical forest of southeastern China. Soil AM fungal communities were detected by the high throughput sequencing of 18S rRNA gene-fragments. We investigated the six-seasonal responses of AM fungal diversity, community assembly pattern and functional guild composition to N and/or P amendments. Results and discussion: The AM fungal Shannon index changed from a positive (3–4 years) to a nonsignificant (4–5 years) effect under P and NP additions as the duration of fertilization increased. P addition, but not N addition, changed the AM fungal community assembly pattern from stochastic- to deterministic-dominant processes. In contrast, P and NP additions significantly influenced AM fungal functional guild components, and the relative abundances of ancestral and edaphophilic guilds increased with increasing years of fertilization. Additionally, the AM fungal guild structure was significantly affected by soil P-related parameters. Conclusions: Our results emphasize the substantial impacts of P amendment on soil AM community assembly pattern and functional guild composition. This study contributes to a better understanding of the temporal dynamics and potential ecological functioning of AM fungi under global environmental changes. [ABSTRACT FROM AUTHOR]

Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing. Liu et al. demonstrate that human-driven soil contamination in natural areas mirrors that in nearby urban greenspaces globally, and highlight the potential influence that soil contaminants have on ecosystem functions. [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]

Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing. Liu et al. demonstrate that human-driven soil contamination in natural areas mirrors that in nearby urban greenspaces globally, and highlight the potential influence that soil contaminants have on ecosystem functions. [ABSTRACT FROM AUTHOR]

Globally, tomato is the second most cultivated vegetable crop next to potato, preferentially grown in temperate climates. Processing tomatoes are generally produced in field conditions, in which soilborne pathogens have serious impacts on tomato yield and quality by causing diseases of the tomato root system. Major processing tomato-producing countries have documented soilborne diseases caused by a variety of pathogens including bacteria, fungi, nematodes, and oomycetes, which are of economic importance and may threaten food security. Recent field surveys in the Australian processing tomato industry showed that plant growth and yield were significantly affected by soilborne pathogens, especially Fusarium oxysporum and Pythium species. Globally, different management methods have been used to control diseases such as the use of resistant tomato cultivars, the application of fungicides, and biological control. Among these methods, biocontrol has received increasing attention due to its high efficiency, target-specificity, sustainability and public acceptance. The application of biocontrol is a mix of different strategies, such as applying antagonistic microorganisms to the field, and using the beneficial metabolites synthesized by these microorganisms. This review provides a broad review of the major soilborne fungal/oomycete pathogens of the field processing tomato industry affecting major global producers, the traditional and biological management practices for the control of the pathogens, and the various strategies of the biological control for tomato soilborne diseases. The advantages and disadvantages of the management strategies are discussed, and highlighted is the importance of biological control in managing the diseases in field processing tomatoes under the pressure of global climate change. [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]

Purpose: The compounds 1-octyne and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) are frequently used as nitrification inhibitors for ammonia-oxidizing bacteria (AOB) and archaea (AOA), respectively, but their influence on comammox Nitrospira remains unclear. In this study, we examine how will 1-octyne and PTIO influence AOA, AOB, and comammox Nitrospira in an acidic Ultisol. The results will provide guidance for the nitrification inhibitor selections in the relevant research and field management practices. Materials and methods: We carried out a microcosm experiment using acetylene, 1-octyne, and PTIO as nitrification inhibitors to investigate their effects on ammonia oxidizers, especially comammox Nitrospira. The abundance of ammonia oxidizers was determined by real-time quantitative PCR while the community structure of comammox Nitrospira was examined by Illumina MiSeq sequencing. Results and discussion: Acetylene, 1-octyne, and PTIO significantly reduced the net nitrification rate, with a more pronounced effect observed for acetylene and 1-octyne amendments. The addition of 1-octyne suppressed the growth of comammox Nitrospira clade A, indicating that 1-octyne was not an exclusive inhibitor for AOB in the acidic Ultisols. Moreover, PTIO reduced the abundance of AOB and comammox Nitrospira clade A, rather than that of AOA, suggesting that AOB and comammox Nitrospira were more sensitive than AOA to the PTIO inhibition in the tested soils. Acetylene, 1-octyne, and PTIO did not show observed changes to comammox Nitrospira community structure. Conclusions: We provide novel evidence that 1-octyne and PTIO can significantly inhibit the growth of comammox Nitrospira, but have no significant effects on their community structure in the acidic Ultisols. Our findings have implications for proper selection of nitrification inhibitors 1-octyne and PTIO in both laboratory experiments and field practices. [ABSTRACT FROM AUTHOR]

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]

Soil fungi play a critical role in the carbon and nutrient cycling of forest ecosystems. Identifying the composition of soil fungi in response to the broadleaf restoration of Pinus massoniana plantation is essential for exploring the mechanistic linkages between tree species and ecological processes, but remains unexplored. We compared the shifts in soil fungal diversity and guilds by high–throughput sequencing between two P. massoniana plantations at different stand ages, two modes of restoration with broadleaf trees, and a secondary forest in subtropical China. We found that soil fungal taxonomic and functional compositions significantly differed among forests. The highest Chao 1, Shannon, and phylogenetic diversity indices were consistently observed in the two P. massoniana monocultures, followed by the two modes of broadleaf mixing, and the secondary forests. Fungal communities transitioned from Ascomycota-dominated at P. massoniana plantations to Basidiomycota-dominated at other forests in the topsoil. Furthermore, saprotrophs and symbiotrophs were favoured in plantations and secondary forests, respectively. Soil pH exerted the most significant effect on the relative abundance of Ascomycota and Rozellomycota, as well as the saprotrophs. Moreover, the dominant phyla of Ascomycota, Mucoromycota, and Rozellomycota were negatively related to soil microbial biomass nitrogen, ammonium nitrogen, and total nitrogen contents; however, Mortierellomycota benefited from the elevated soil ammonium nitrogen content. On the other hand, soil nitrate nitrogen and available phosphorus contents strongly and negatively influenced the ectomycorrhizal fungi, while the other fungal guilds were mainly affected by soil pH. Our findings guide an evaluation of the consequences of forest restoration and contribute to an improved understanding of the mechanisms behind soil biogeochemical cycling in subtropical forest ecosystems. [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]

Purpose: Temperature is a key factor influencing the growth and activities of microorganisms and their associated biogeochemical processes including nitrification. However, limited studies have been performed to evaluate the response of the newly discovered comammox Nitrospira to temperature change and nitrogen (N) addition in agroecosystems, which has hindered our understanding of the ecophysiology and environmental adaption of comammox Nitrospira in agroecosystems. Materials and methods: We set up a microcosm experiment with 3 temperature treatments (15 °C, 25 °C, and 35 °C) × 3 levels of N addition (0 mg kg−1, 25 mg kg−1, and 50 mg kg−1) in an acidic Ultisol. We explored the impact of temperature and N addition on the abundance and community structure of comammox Nitrospira. Results and discussion: The addition of N and increasing temperature generally increased the net nitrification rate. The comammox Nitrospira clade A abundance decreased with the increase of temperature, indicating that clade A might favor environments with relatively lower temperature. However, the addition of N did not significantly influence the abundance of comammox Nitrospira clade A. Moreover, temperature had a stronger effect than N addition on the community structure of comammox Nitrospira. Clade A.2.1 were the exclusively dominant comammox Nitrospira phylotype in the tested soils, and were not affected by temperature and N addition, suggesting that temperature influenced comammox Nitrospira mainly through regulating the internal subclades of clade A.2.1. Conclusions: Our findings provide novel evidence that temperature had a stronger effect than N addition on the abundance and community structure of comammox Nitrospira and suggest that comammox Nitrospira are temperature sensitive and favor relatively lower temperature in the acidic Ultisols. [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]

Viruses are extremely abundant in the soil environment and have potential roles in impacting on microbial population, evolution, and nutrient biogeochemical cycles. However, how environment and climate changes affect soil viruses is still poorly understood. Here, a metagenomic approach was used to investigate the distribution, diversity, and potential biogeochemical impacts of DNA viruses in 12 grassland soils under three precipitation gradients on the Qinghai-Tibet Plateau, which is one of the most sensitive areas to climate change. A total of 557 viral operational taxonomic units were obtained, spanning 152 viral families from the 30 metagenomes. Both virus-like particles (VLPs) and microbial abundance increased with average annual precipitation. A significant positive correlation of VLP counts was observed with soil water content, total carbon, total nitrogen, soil organic matter, and total phosphorus. Among these biological and abiotic factors, SWC mainly contributed to the variability in VLP abundance. The order Caudovirales (70.1% of the identified viral order) was the predominant viral type in soils from the Qinghai-Tibet Plateau, with the Siphoviridae family being the most abundant. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes represented by glycoside hydrolases were identified, indicating that soil viruses may play a potential role in the carbon cycle on the Qinghai-Tibet Plateau. There were more diverse hosts and abundant CAZyme genes in soil with moderate precipitation. Our study provides a strong evidence that changes in precipitation impact not only viral abundance and virus–host interactions in soil but also the viral functional potential, especially carbon cycling. [ABSTRACT FROM AUTHOR]

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]

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]

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]

Purpose: Protists play important roles in soils by regulating organic matter decomposition, catalysing biogeochemical nutrient cycling processes and maintaining soil fertility and plant productivity, but they remain poorly characterized in the plant-soil system under long-term intensive agricultural management. Methods: We investigated the impacts of multiple inorganic fertilization regimes on the diversity, composition and potential functions of protists and their interactions with bacteria and fungi in the rhizosphere and bulk soils of sorghum plants in a long-term field experiment. Results: Protists were dominated by the supergroups Rhizaria, Stramenopiles, Alveolata, Amoebozoa and Archaeplastida in both rhizosphere and bulk soils. The diversity of protists was significantly lower in rhizosphere than bulk soils, and the community compositions of total protists were remarkably different in the two compartments. Inorganic fertilization had no significant impacts on the total protistan diversity or compositions but significantly changed the relative abundances of specific taxa of consumers and parasites. Protists were significantly correlated with bacteria and fungi as revealed by the co-occurrence network analysis, indicating their intensive trophic interactions with bacteria and fungi in soil food webs. Soil properties and the community compositions of bacteria and fungi were important factors shaping the variation in the protistan communities, as revealed by variation partitioning modelling analysis. Conclusion: Altogether, we provide new information for the impacts of fertilization on the protist communities in rhizosphere and bulk soils and identified specific functional groups of protists that are most responsive to long-term agricultural management. [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]

Background: Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics. Results: Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage. Conclusions: Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. 2NpR2QgL41qVHhBsXo3pXw Video Abstract [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]

Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems. [ABSTRACT FROM AUTHOR]

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

Nitrogen (N) fertilization has boosted grain production during the past century, while excess N fertilization with declining N use efficiency (NUE) has led to severe pollution in many regions. To achieve the goal of sustainable food production, Technologies and Management Practices (TMPs, e.g., optimum N application rate and methods, N‐transformation inhibitors) have been developed to improve crop yield and NUE and to reduce N losses. However, it remains unclear how N fate has been changed by environmental factors and TMPs. Here, we compiled a dataset of 366 field 15N tracer observations from 74 publications worldwide and conducted a meta‐analysis to examine how environmental conditions and management practices influence the fertilizer‐N fate one growing season after the fertilization of maize. We show that the proportion of 15N taken up by aboveground biomass (NUE15N), was significantly lower in China (33%) than that in North America (42%) and the European Union (54%). Soil organic carbon was the most critical environmental factor positively correlated with NUE15N. Among the nine selected categories of TMPs, deep placement of fertilizer and split application increased the grain yield and decreased the fertilizer‐N loss consistently among studies. Reducing the fertilizer‐N rate could increase the NUE15N but presents risks of yield reduction in some regions. This study demonstrates the importance of SOC and varying impacts of TMPs on the efficiency of fertilizer use in cropping systems globally and provides critical information for farmers and policymakers to improve N management for higher productivity and less pollution. Plain Language Summary: The efficient use of Nitrogen (N) fertilizer benefits both food security and environmental quality. To characterize the fate and the efficiency of fertilizer‐N in maize production, we conducted a comprehensive meta‐analysis with existing field 15N‐tracer trials. Our results show that higher organic carbon content in the soil is associated with higher 15N recovery under conventional management practices. Among nine N management practices developed for more efficient use of N, deep placement in the soil (rather than surface application) and split application of N fertilizer (dividing annual fertilization into two or more smaller applications) improved yield, 15N recovery, and environmental impacts. This study improves our understanding of management practices on the fate of fertilizer‐N and provides guidance for farmers and policymakers to improve N fertilizer management. Key Points: Globally, 41 ± 14%, 31 ± 14%, and 28 ± 19% of N fertilizer was taken up by maize, retained in the soil and lost one season after its applicationThe nitrogen use efficiency measured with 15N approach is low in Chinese maize cropping system mainly due to low soil organic carbonDeep placement of N fertilizer and split fertilization can improve yield and reduce N loss [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]

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

Summary: Viruses can affect microbial dynamics, metabolism and biogeochemical cycles in aquatic ecosystems. However, viral diversity and functions in agricultural soils are poorly known, especially in the rhizosphere. We used virome analysis of eight rhizosphere and bulk soils to study viral diversity and potential biogeochemical impacts in an agro‐ecosystem. The order Caudovirales was the predominant viral type in agricultural soils, with Siphoviridae being the most abundant family. Phylogenetic analysis of the terminase large subunit of Caudovirales identified high viral diversity and three novel groups. Viral community composition differed significantly between bulk and rhizosphere soils. Soil pH was the main environmental driver of the viral community structure. Remarkably, abundant auxiliary carbohydrate‐active enzyme (CAZyme) genes were detected in viromes, including glycoside hydrolases, carbohydrate esterases and carbohydrate‐binding modules. These results demonstrate that virus‐encoded putative auxiliary metabolic genes or metabolic genes that may change bacterial metabolism and indirectly contribute to biogeochemical cycling, especially carbon cycling, in agricultural soil. [ABSTRACT FROM AUTHOR]

Summary: Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known.Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)‐wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites.Our results demonstrate that microbiome assembly along the soil‐plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize.Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture. [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]

Purpose: Intensified livestock system produced large amount of bio-waste, and improper disposal of livestock manure has led to severe environmental consequences. However, knowledge about the time-dependent changes of manure-derived nitrate and soil bacterial diversity along the soil profiles is limited. Materials and methods: Vertical variation of soil bacterial diversity and composition in a manure-amended maize field and adjacent non-manured woodland was investigated using high-throughput sequencing technique in spring and autumn along a 1-m profile depth. The soil is classified as aquic inceptisol with a bulk density of 1.31 g cm−3, and a sandy loam texture. Results: The results showed that significant higher amount of nitrate (up to 172.13 mg kg−1) was detected along the soil profile loaded with cattle manure compared with the adjacent non-manured woodland. Soil δ15N-NO3− composition from maize field fall between + 5 and 25‰, while those from woodland fall between − 5 and 15‰. No significant difference in bacterial richness between the two land uses was found, while clear separation of bacterial structure was detected even to the deep soil layers. Canonical correspondence analysis showed that soil organic matter, C/N ratio, nitrate content, pH, and moisture were the major factors influencing the variance of bacterial community composition. Bacterial networks in the maize field harbor more modules than those in the adjacent woodland. Negative standardized effect size measure of mean nearest taxon distance in the soils tended to be more phylogenetically clustered than expected by chance, and was more likely to be clustered along the depth. Conclusions: These findings suggested that soil bacterial β diversity was strongly affected by multi-nutrient properties in terms of high livestock manure load, and had important implications for assessing the environmental impacts on belowground biodiversity in sandy loam soils. [ABSTRACT FROM AUTHOR]

Most current microbial studies in paddy soils have focused on the top (0–20 cm) layer where rice roots are concentrated. To better understand the vertical distribution of microorganisms in paddy soils, we investigated the abundances, diversities and community compositions of archaea, bacteria and fungi in six geographically and climatically distinct paddy soil profiles from 0–80‐cm depth. Although microbial abundances and operational taxonomic unit (OTU) diversities largely decreased with soil depth, only the community composition of archaea (not bacteria or fungi) was associated with soil depth, echoing that only one archaeal OTU, but no bacterial or fungal OTUs, differed significantly in relative abundance between depth intervals. Mean annual temperature, precipitation and soil iron and manganese concentrations were significantly correlated with the ordinations of microbial communities for all three domains. Besides these common environmental factors, bacterial and archaeal community structures were also influenced by soil chloride and sulphate concentrations, whereas the concentrations of organic matter and total nitrogen were important explanatory factors for the variation in fungal community composition. Further analyses on putative bacterial functions showed significant differences between sampling sites rather than depth intervals, and suggested that bacterial OTUs that significantly varied in relative abundance across sampling sites might be functionally related to organic matter decomposition, sulphur oxidation and reduction, as well as nitrate reduction. Altogether, in the studied paddy soil profiles, the community composition and putative functions of bacteria were largely the same between different vertical layers, each with a thickness of 20 cm. This study suggests that the community compositions of archaea, bacteria and fungi are mainly driven by different soil chemical properties rather than soil depth, which could be linked to the ecological traits of the three microbial domains. Highlights: Communities of archaea, bacteria and fungi were investigated in six paddy soil profiles.Soil depth was only correlated with archaeal community structureEnvironmental factors influenced community composition differently for different domains.Bacterial OTUs contributing to variation in community composition among sites were functionally linked to C, N and S cycling. [ABSTRACT FROM AUTHOR]

Summary: Microbial elevational diversity patterns have been extensively studied, but their shaping mechanisms remain to be explored. Here, we examined soil bacterial and fungal diversity and community compositions across a 3.4 km elevational gradient (consists of five elevations) on Mt. Kilimanjaro located in East Africa. Bacteria and fungi had different diversity patterns across this extensive mountain gradient—bacterial diversity had a U shaped pattern while fungal diversity monotonically decreased. Random forest analysis revealed that pH (12.61% importance) was the most important factor affecting bacterial diversity, whereas mean annual temperature (9.84% importance) had the largest impact on fungal diversity, which was consistent with results obtained from mixed‐effects model. Meanwhile, the diversity patterns and drivers of those diversity patterns differ among taxonomic groups (phyla/classes) within bacterial or fungal communities. Taken together, our study demonstrated that bacterial and fungal diversity and community composition responded differently to climate and edaphic properties along an extensive mountain gradient, and suggests that the elevational diversity patterns across microbial groups are determined by distinct environmental variables. These findings enhanced our understanding of the formation and maintenance of microbial diversity along elevation, as well as microbial responses to climate change in montane ecosystems. [ABSTRACT FROM AUTHOR]

The abundance, community composition and activity of key nitrogen (N)-cycling functional guilds were monitored at a site where coniferous Cunninghamia lanceolate and broadleaved Mytilaria laosensis were planted in 1993. Leaf cellulose, litter C/N ratio, leaf dry matter content, soil inorganic N content were significantly higher under C. lanceolata, while specific leaf area, litter production, litter magnesium, soil C and soil C/NO3− ratio were higher under M. laosensis. The 15N tracing experiment together with quantitative PCR revealed that autotrophic nitrification rates, as well as the abundances of ammonia-oxidizing archaea and comammox Nitrospira were significantly higher under C. lanceolate than M. laosensis. However, M. laosensis exhibited substantially higher nitrate retention capacity via dissimilatory nitrate reduction to ammonium (DNRA), accompanied by a significantly higher abundance of nrfA gene than C. lanceolate. The Illumina sequencing indicated that tree species markedly affected soil bacterial community composition regardless of the soil layers. Redundancy analysis suggested that litter C/N ratio was the most influential factor explaining functional gene abundances and bacterial communities. Taken together, our findings showed that M. laosensis improved soil N retention capacity mainly through inhibiting autotrophic nitrification while enhancing DNRA activity. This study highlights the importance of tree species identity in influencing the microbially-mediated N cycling and bacterial community composition. [ABSTRACT FROM AUTHOR]

Bioremediation is one of the most effective ways for removal of heavy metals and restoration of contaminated sites. This study investigated the copper (Cu) resistance mechanism and bioremediation potential of an Acinetobacter calcoaceticus strain KW3 isolated from sludge of Cu mine. The effect of Cu concentrations on the bacterial growth, biomass, and adsorption capacity, as well as the effect of contact time on the adsorption process was evaluated in a batch biosorption test. The strain exhibited strong tolerance of Cu, and the minimal inhibitory concentration was around 400 mg Cu2+ L−1, at which the maximum adsorption capacity was 14.1 mg g−1 dry cell mass. Cell walls and intracellular soluble components adsorbed 51.2% and 46.6% of Cu2+, respectively, suggesting that the strain not only adsorbed Cu2+ on the surface but also metastasized ions into cells. The adsorption and kinetic data were well fitted with Freundlich isotherm and Pseudo-second-order models, suggesting that cell surface had a high affinity for Cu2+ and the chemisorption could be the main adsorption mechanism. Scanning electron microscope and Fourier transform infrared spectroscopy analysis revealed that hydroxyl, carboxylic, amide, sulfate, and phosphate on cell walls might be involved in the biosorption process. Two-dimensional gel electrophoresis and MALDI-TOF/TOF mass spectrometry revealed that some oxidoreductases, in particular Cu resistance protein A (CopA) expression levels, were upregulated. Antioxidant defense and P1B-type ATPases CopA efflux might play a crucial role in maintaining cellular homeostasis and intracellular detoxification. To our knowledge, this is the first time that Cu resistance mechanisms, especially intracellular enzymatic mechanisms, were identified in an A. calcoaceticus KW3 strain. [ABSTRACT FROM AUTHOR]

Purpose: Urease inhibitors (UIs) such as N-(n-butyl)thiophosphoric triamide (NBPT) and nitrification inhibitors (NIs) such as 3,4-dimethylpyrazole phosphate (DMPP) have been reported to improve the efficiency of nitrogen (N) fertilizers. However, their effects on the ureolytic and ammonia-oxidizing microbes in agricultural soils are uncertain. This study aimed to investigate the effects of DMPP and NBPT on the abundance and community composition of ureolytic and nitrifying microbes in selected agricultural soils in Australia. Materials and methods: Soil was collected from five agricultural farms and used to establish an incubation experiment. Urea, urea + NBPT, urea + DMPP, and urea + NBPT + DMPP were applied on the soils which were incubated under 25 °C and 60% water-filled pore space for 28 days. Sampling was done on different days for DNA extraction and measurement of ammonium (NH4+) and nitrate (NO3−) concentration. Results and discussion: NBPT inhibited NH4+ accumulation in all the soils but had no significant effect on nitrification in any soil. DMPP alone or DMPP + NBPT significantly inhibited nitrification. The abundances of ammonia-oxidizing bacteria (AOB) and complete ammonia oxidizers (comammox Nitrospira), but not ammonia-oxidizing archaea (AOA), were significantly influenced by the application of NBPT, DMPP, or DMPP + NBPT. AOA, AOB, and comammox Nitrospira clade B might be significant contributors to nitrification in the studied soils. Conclusions: These findings suggest that NBPT and DMPP can reduce N losses and improve N fertilizer efficiency by directly inhibiting the growth of AOB and comammox organisms in the soils, with implications for our mechanistic understanding of the molecular mechanisms of urease and nitrification inhibitors. [ABSTRACT FROM AUTHOR]

Purpose: The recently discovered complete ammonia oxidizers (comammox Nitrospira) challenged our concept of the whole nitrification process, i.e., ammonia oxidation catalyzed by autotrophic ammonia-oxidizing archaea (AOA) and bacteria (AOB), followed by the oxidation of nitrite to nitrate. However, the relative contributions of different ammonia oxidizers to soil nitrification are poorly understood. Materials and methods: Soil samples were collected from five land use types (i.e., cropland, grassland, bushland, transition land, and forest land) from a subtropical soil in Yunnan Province, Southwest China. The quantitative distribution of comammox Nitrospira, AOA and AOB in soils was firstly investigated using the QPCR approach and three of which (cropland, transition land and forest land) with pH below 6 were further examined using DNA stable isotope probing approach with 13CO2. Clone library combined with sequencing was applied to detect the phylogenetic information of active microbial groups. Results and discussion: The results showed that the amoA gene abundance of ammonia oxidizers except AOB was significantly lower in croplands than other land uses. Based on the 13CO2 labeling method, AOA, rather than AOB or comammox Nitrospira, was found to incorporate 13CO2 into their genomes during the incubation in cropland and transition land but not in forest land, suggesting the dominant role of AOA in ammonia oxidation. Phylogenetic analysis of the active AOA group revealed that autotrophic AOA community was mainly affiliated with the cluster of Nitrososphaera in transition land, whereas Nitrososphaera, Nitrosopumilus, and Nitrosotalea in cropland. Conclusions: These findings suggested niche differentiation of AOB, AOA, and comammox Nitrospira in the subtropical acid soil with different land uses, and AOA played a more important role in nitrification process of this acid soil. [ABSTRACT FROM AUTHOR]

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

Primary succession of plant and microbial communities in the glacier retreating foreland has been extensively studied, but shifts of antibiotic resistance genes (ARGs) with the glacier retreating due to global warming remain elusive. Unraveling the diversity and succession features of ARGs in pristine soil during glacier retreating could contribute to a mechanistic understanding of the evolution and development of soil resistome. In this study, we quantified the abundance and diversity of ARGs along a 50-year soil development chronosequence by using a high-throughput quantitative PCR (HT-qPCR) technique. A total of 24 ARGs and two mobile genetic elements (MGEs) were detected from all the glacier samples, and the numbers of detected ARGs showed a unimodal pattern with an increasing trend at the early stage (0∼8 years) but no significant change at later stages (17∼50 years). The opr J and mex F genes encoding multidrug resistance were the only two ARGs that were detected across all the succession ages, and the mex F gene showed an increasing trend along the succession time. Structural equation models indicated the predominant role of the intI1 gene encoding the Class 1 integron-integrase in shaping the variation of ARG profiles. These findings suggested the presence of ARGs in pristine soils devoid of anthropogenic impacts, and horizontal gene transfer mediated by MGEs may contribute to the succession patterns of ARGs during the initial soil formation stage along the chronosequence. [ABSTRACT FROM AUTHOR]