Pesticide residues alter taxonomic and functional biodiversity in soils.

Ammonia oxidation is an essential part of the global nitrogen cycling and was long thought to be driven only by bacteria. Recent findings expanded this pathway also to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing archaea, such as ammonia oxidation and potential CO(2) fixation, remain open, especially for terrestrial environments. Here, we investigated the activity of ammonia-oxidizing archaea and bacteria in an agricultural soil by comparison of RNA- and DNA-stable isotope probing (SIP). RNA-SIP demonstrated a highly dynamic and diverse community involved in CO(2) fixation and carbon assimilation coupled to ammonia oxidation. DNA-SIP showed growth of the ammonia-oxidizing bacteria but not of archaea. Furthermore, the analysis of labeled RNA found transcripts of the archaeal acetyl-CoA/propionyl-CoA carboxylase (accA/pccB) to be expressed and labeled. These findings strongly suggest that ammonia-oxidizing archaeal groups in soil autotrophically fix CO(2) using the 3-hydroxypropionate-4-hydroxybutyrate cycle, one of the two pathways recently identified for CO(2) fixation in Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH targeting the gene encoding subunit A of ammonia monooxygenase (amoA) mRNA and 16S rRNA of archaea also revealed ammonia-oxidizing archaea to be numerically relevant among the archaea in this soil. Our results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO(2) assimilation and that their importance to the overall archaeal community might be larger than previously thought.

The relative contribution of different soil organism groups to nutrient cycling has been quantified for a number of ecosystems. Some functions, particularly within the N‐cycle, are carried out by very specific organisms. Others, including those of decomposition and nutrient release from organic inputs are, however, mediated by a diverse group of bacteria, protozoa, fungi and invertebrate animals. Many authors have hypothesized that there is a high degree of equivalence and flexibility in function within this decomposer community and thence a substantial extent of redundancy in species richness and resilience in functional capacity. Three case studies are presented to examine the relationship between soil biodiversity and nitrogen cycling under global change in ecosystem types from three latitudes, i.e. tundra, temperate grassland and tropical rainforest.In all three ecosystems evidence exists for the potential impact of global change factors (temperature change, CO2enrichment, land‐use‐change) on the composition and diversity of the soil community as well as on various aspects of the nitrogen and other cycles. There is, however, very little unequivocal evidence of direct causal linkage between species richness and nutrient cycling efficiency. Most of the changes detected are shifts in the influence of major functional groups of the soil biota (e.g. between microflora and fauna in decomposition). There seem to be few data, however, from which to judge the significance of changes in diversity within functional groups. Nonetheless the soil biota are hypothesized to be a sensitive link between plant detritus and the availability of nutrients to plant uptake. Any factors affecting the quantity or quality of plant detritus is likely to change this link. Rigorous experimentation on the relationships between soil species richness and the regulation or resilience of nutrient cycles under global change thus remains a high priority.

The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.

CONTEXTIn the European Union (EU-27) and UK, animal farming generated annually more than 1.4 billion tonnes of manure during the period 2016–2019. Of this, more than 90% is directly re-applied to soils as organic fertiliser. Manure promotes plant growth, provides nutritious food to soil organisms, adds genetic and functional diversity to soils and improves the chemical and physical soil properties. However, it can also cause pollution by introducing toxic elements (i.e., heavy metals, antibiotics, pathogens) and contribute to nutrient losses. Soil organisms play an essential role in manure transformation into the soil and the degradation of any potential toxic constitutes; however, manure management practices often neglect soil biodiversity. OBJECTIVEIn this review, we explored the impact of manure from farmed animals on soil biodiversity by considering factors that determine the effects of manure and vice versa. By evaluating manure's potential to enhance soil biodiversity, but also its environmental risks, we assessed current and future EU policy and legislations with the ultimate aim of providing recommendations that can enable a more sustainable management of farm manures. METHODSThis review explored the relationship between manure and soil biodiversity by considering 407 published papers and relevant legislative provisions. In addition, we evaluated whether benefits and risks on soil biodiversity are considered in manure management. Thereafter, we analysed the current legislation in the European Union relevant to manure, an important driver for its treatment, application and storage. RESULTS AND CONCLUSIONSThis review found that coupling manure management with soil biodiversity can mitigate present and future environmental risks. Our analyses showed that manure quality is more important to soil biodiversity than manure quantity and therefore, agricultural practices that protect and promote soil biodiversity with the application of appropriate, high-quality manure or biostimulant preparations based on manure, could accelerate the move towards more sustainable food production systems. Soil biodiversity needs to be appropriately factored in when assessing manure amendments to provide better guidelines on the use of manure and to reduce costs and environmental risks. However, radical changes in current philosophies and practices are needed so that soil biodiversity can be enhanced by manure management. SIGNIFICANCEManure quality in the EU requires greater attention, calling for more targeted policies. Our proposed approach could be applied by European Union Member States to include soil protection measures in national legislation, and at the EU level, can enable the implementation of strategic goals.

Effects of plastispheres and pristine microplastics on sediment microbial communities and nitrogen cycling under global warming.

Some microbes enhance stress tolerance in plants by minimizing plant ethylene levels via degradation of its immediate precursor, 1-aminocyclopropane-1-carboxylate (ACC), in the rhizosphere. In return, ACC is used by these microbes as a source of nitrogen. This mutualistic relationship between plants and microbes may be used to promote soil properties in stressful environments. In this study, we tested the hypothesis that amendments of ACC in soils reshape the structure of soil microbiome and alleviate the negative impacts of salinity on soil properties. We treated non-saline and artificially-developed saline soils with ACC in different concentrations for 14 days. The structure of soil microbiome, soil microbial properties and productivity were examined. Our results revealed that microbial composition of bacteria, archaea and fungi in saline soils was affected by ACC amendments; whereas community composition in non-saline soils was not affected. The amendments of ACC could not fully counteract the negative effects of salinity on soil microbial activities and productivity, but increased the abundance of ACC deaminase-encoding gene (acdS), enhanced soil microbial respiration, enzymatic activity, nitrogen and carbon cycling potentials and Arabidopsis biomass in saline soils. Collectively, our study indicates that ACC amendments in soils could efficiently ameliorate salinity impacts on soil properties and plant biomass production.

Solar park (SP) is rapidly growing throughout the planet due to the increasing demand for low-carbon energy, which represents a remarkable global land-use change with implications for the hosting ecosystems. Despite dozens of studies estimating the environmental impacts of SP based on local microclimate and vegetation, responses of soil microbial interactions and nutrient cycle potentials remain poorly understood. To bridge this gap, we investigated the diversity, community structure, complexity, and stability of co-occurrence network and soil enzyme activities of soil prokaryotes and fungi in habitats of ambient, the first, and sixth year since solar park establishment. Results revealed different response patterns of prokaryotes and fungi. SP led to significant differences in both prokaryotic and fungal community structures but only reduced prokaryotic alpha diversity significantly. Co-occurrence network analysis revealed a unimodal pattern of prokaryotic network features and more resistance of fungal networks to environmental variations. Microbial nitrogen and phosphorus cycle potentials were higher in SP and their variances were more explained by network features than by diversity and environmental characteristics. Our findings revealed for the first time the significant impacts of SP on soil prokaryotic and fungal stability and functional potentials, which provides a microbial insight for impact evaluation and evidence for the optimization of solar park management to maximize the delivery of ecosystem services from this growing land use.

Identifying soil microbial responses to anthropogenically driven environmental changes is critically important as concerns intensify over the potential degradation of ecosystem function. We assessed the effects of elevated atmospheric CO2 on microbial carbon (C) and nitrogen (N) cycling in Mojave Desert soils using extracellular enzyme activities (EEAs), community‐level physiological profiles (CLPPs), and gross N transformation rates. Soils were collected from unvegetated interspaces between plants and under the dominant shrub (Larrea tridentata) during the 2004–2005 growing season, an above‐average rainfall year. Because most measured variables responded strongly to soil water availability, all significant effects of soil water content were used as covariates to remove potential confounding effects of water availability on microbial responses to experimental treatment effects of cover type, CO2, and sampling date. Microbial C and N activities were lower in interspace soils compared with soils under Larrea, and responses to date and CO2 treatments were cover specific. Over the growing season, EEAs involved in cellulose (cellobiohydrolase) and orthophosphate (alkaline phosphatase) degradation decreased under ambient CO2, but increased under elevated CO2. Microbial C use and substrate use diversity in CLPPs decreased over time, and elevated CO2 positively affected both. Elevated CO2 also altered microbial C use patterns, suggesting changes in the quantity and/or quality of soil C inputs. In contrast, microbial biomass N was higher in interspace soils than soils under Larrea, and was lower in soils exposed to elevated CO2. Gross rates of NH4+ transformations increased over the growing season, and late‐season NH4+ fluxes were negatively affected by elevated CO2. Gross NO3− fluxes decreased over time, with early season interspace soils positively affected by elevated CO2. General increases in microbial activities under elevated CO2 are likely attributable to greater microbial biomass in interspace soils, and to increased microbial turnover rates and/or metabolic levels rather than pool size in soils under Larrea. Because soil water content and plant cover type dominates microbial C and N responses to CO2, the ability of desert landscapes to mitigate or intensify the impacts of global change will ultimately depend on how changes in precipitation and increasing atmospheric CO2 shift the spatial distribution of Mojave Desert plant communities.

Salinization damages soil system health and influences microbial communities structure and function. The response of microbial functions involved in the nutrient cycle to soil salinization is a valuable scientific question. However, our knowledge of the microbial metabolism functions in salinized soil and their response to salinity in arid desert environments is inadequate. Here, we applied metagenomics technology to investigate the response of microbial carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling and the key genes to salinity, and discuss the effects of edaphic variables on microbial functions. We found that carbon fixation dominated the carbon cycle. Nitrogen fixation, denitrification, assimilatory nitrate reduction (ANRA), and nitrogen degradation were commonly identified as the most abundant processes in the nitrogen cycle. Organic phosphorus dissolution and phosphorus absorption/transport were the most enriched P metabolic functions, while sulfur metabolism was dominated by assimilatory sulfate reduction (ASR), organic sulfur transformation, and linkages between inorganic and organic sulfur transformation. Increasing salinity inhibited carbon degradation, nitrogen fixation, nitrogen degradation, anammox, ANRA, phosphorus absorption and transport, and the majority of processes in sulfur metabolism. However, some of the metabolic pathway and key genes showed a positive response to salinization, such as carbon fixation (facA, pccA, korAB), denitrification (narG, nirK, norBC, nosZ), ANRA (nasA, nirA), and organic phosphorus dissolution processes (pstABCS, phnCD, ugpAB). High salinity reduced the network complexity in the soil communities. Even so, the saline microbial community presented highly cooperative interactions. The soil water content had significantly correlations with C metabolic genes. The SOC, N, and P contents were significantly correlated with C, N, P, and S network complexity and functional genes. AP, NH4+, and NO3- directly promote carbon fixation, denitrification, nitrogen degradation, organic P solubilization and mineralization, P uptake and transport, ASR, and organic sulfur transformation processes. Soil salinity in arid region inhibited multiple metabolic functions, but prompted the function of carbon fixation, denitrification, ANRA, and organic phosphorus dissolution. Soil salinity was the most important factor driving microbial functions, and nutrient availability also played important roles in regulating nutrient cycling.

The effects of agricultural wastes on degradation of polycyclic aromatic hydrocarbons(PAHs) and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in PAH-polluted soils were determined by liquid chromatography and real-time quantitative PCR. The results showed that addition of agricultural wastes didn't improve the degradation of PAHs, in the contrary, the degradation of PAHs decreased in the soil added with wheat straw. And the degradation rate of PAHs decreased with increased molecular weight of PAHs. Furthermore, the abundance of AOA and AOB was enhanced in PAH-polluted soils after adding agricultural wastes, the content of pyrene and benzo(a)pyrene has significant negative correlation with the abundance of AOA. These results suggested that the degradation of PAHs can not be promoted through applying agricultural wastes into the soils freshly polluted by PAHs. Pyrene and benzo(a)pyrene would reduce the abundance of AOA, while addition of agricultural wastes could improve the ammonia oxidation function in PAH-polluted soils. This study provided some insights for the remediation and risk assessment of PAH-polluted soils.

Metagenomics reveals taxon-specific responses of soil nitrogen cycling under different fertilization regimes in heavy metal contaminated soil

The increasing frequency and intensity of wildfires pose significant threats to forest ecosystems, particularly in Chinas diverse climatic regions. This review focuses on the impacts of wildfires on forest soil properties in China, highlighting changes in soil physiochemical properties, nutrient cycles, enzyme activities, and microbial communities. Wildfires often lead to the loss of soil organic matter, disruptions in nutrient availability, and alterations in microbial dynamics, which are essential for nutrient cycling and ecosystem recovery. The severity of these impacts is closely linked to fire intensity, soil depth, and post-fire management practices. While short-term recovery of soil properties is possible, long-term effects on soil health, especially on microbial diversity and nitrogen cycling can persist for years. This review underscores the importance of region-specific research and long-term monitoring to better understand the complex interactions between soil and vegetation post-fire. Future research should focus on the influence of climate change on wildfire patterns, the role of innovative restoration techniques, and the development of comprehensive management strategies tailored to Chinas unique forest ecosystems

Linking nematode trophic diversity to plantation identity and soil nutrient cycling

Land‐use change and habitat degradation are among the biggest drivers of aboveground biodiversity worldwide but their effects on soil biodiversity are less well known, despite the importance of soil organisms in developing soil structure, nutrient cycling and water drainage. Combining a global compilation of biodiversity data from soil assemblages collated as part of the PREDICTS project with global data on soil characteristics, we modelled how taxon richness and total abundance of soil organisms have responded to land use. We also estimated the global Biodiversity Intactness Index (BII)—the average abundance and compositional similarity of taxa that remain in an area, compared to a minimally impacted baseline, for soil biodiversity. This is the first time the BII has been calculated for soil biodiversity. Relative to undisturbed vegetation, soil organism total abundance and taxon richness were reduced in all land uses except pasture. Soil properties mediated the response of soil biota, but not in a consistent way across land uses. The global soil BII in cropland is, on average, a third of that originally present. However, in grazed sites the decline is less severe. The BII of secondary vegetation depends on age, with sites with younger growth showing a lower BII than mature vegetation. We conclude that land‐use change has reduced local soil biodiversity worldwide, and this further supports the proposition that soil biota should be considered explicitly when using global models to estimate the state of biodiversity.

Bacteria play determining roles in forest soil environment and contribute to essential functions in the cycling of nitrogen (N) and phosphorus (P). Understanding the effects of different fertilizer applications, especially successive fertilization, on soil properties and bacterial community could reveal the impacts of fertilization on forest soil ecology and shed light on the nutrient cycling in forest system. This study aimed to evaluate the impacts of successive mineral N (NH4NO3) and P (NaH2PO4) fertilization at different rates, alone or together, on soil bacterial biomass and communities at 0-5, 5-10, and 10-20cm. Compared with the control, N fertilization decreased soil pH, but P alone or with N fertilization had negligibly negative impacts on soil pH. Different mineral fertilizer applications, alone or together, showed no significant effects on soil organic matter contents, relative to the control treatment. Bacterial biomass remained stable to different fertilizations but decreased with sampling depths. Sole N or P fertilization, rather than combined fertilizations, significantly changed soil bacterial community structures. Our results demonstrated that mineral N or P fertilization alone significantly affected bacterial community structures rather than biomass in the plantation soils. KEY POINTS: • Impacts of successive mineral fertilization on soil bacteria were determined. • Mineral fertilization showed negligible impacts on bacterial biomass. • N additions stimulated Chloroflexi relative abundances. • Mineral N or P fertilization significantly altered bacterial community structure.