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Efficient remediation of soil contaminated by polycyclic aromatic hydrocarbons (PAHs) is challenging. To determine whether soil ecoenzyme stoichiometry influences PAH degradation under biostimulation and bioaugmentation, this study initially characterized soil ecoenzyme stoichiometry via a PAH degradation experiment and subsequently designed a validation experiment to answer this question. The results showed that inoculation of PAH degradation consortia ZY-PHE plus vanillate efficiently degraded phenanthrene with a K value of 0.471 (depending on first-order kinetics), followed by treatment with ZY-PHE and control. Ecoenzyme stoichiometry data revealed that the EEA C:N , vector length and angle increased before day five and decreased during the degradation process. In contrast, EEA N:P decreased and then increased. These results indicated that the rapid PAH degradation period induced more C limitation and organic P mineralization. Correlation analysis indicated that the degradation rate K was negatively correlated with vector length, EEA C:P , and EEA N:P , suggesting that C limitation and relatively less efficient P mineralization could inhibit biodegradation. Therefore, incorporating liable carbon and acid phosphatase or soluble P promoted PAH degradation in soils with ZY-PHE. This study provides novel insights into the relationship between soil ecoenzyme stoichiometry and PAH degradation. It is suggested that soil ecoenzyme stoichiometry be evaluated before designing bioremeiation stragtegies for PAH contanminated soils., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The preservation of soil organic carbon (OC) is an effective way to decelerate the emission of CO 2 emission. However, the coregulation of pore structure and mineral composition in OC stabilization remains elusive. We employed the in situ nondestructive oxidation of OC by low-temperature ashing (LTA) combined with near edge X-ray absorption fine structure (NEXAFS), high-resolution microtomography (μ-CT), field emission electron probe microanalysis (FE-EPMA) with C-free embedding, and novel Cosine similarity measurement to investigate the C retention in different aggregate fractions of contrasting soils. Pore structure and minerals contributed equally ( ca . 50%) to OC accumulation in macroaggregates, while chemical protection played a leading role in C retention with 53.4%-59.2% of residual C associated with minerals in microaggregates. Phyllosilicates were discovered to be more prominent than Fe (hydr)oxides in C stabilization. The proportion of phyllosilicates-associated C (52.0%-61.9%) was higher than that bound with Fe (hydr)oxides (45.6%-55.3%) in all aggregate fractions tested. This study disentangled quantitatively for the first time a trade-off between physical and chemical protection of OC varying with aggregate size and the different contributions of minerals to OC preservation. Incorporating pore structure and mineral composition into C modeling would optimize the C models and improve the soil C content prediction.

Soil biodiversity contains the metabolic toolbox supporting organic matter decomposition and nutrient cycling in the soil. However, as soil develops over millions of years, the buildup of plant cover, soil carbon and microbial biomass may relax the dependence of soil functions on soil biodiversity. To test this hypothesis, we evaluate the within-site soil biodiversity and function relationships across 87 globally distributed ecosystems ranging in soil age from centuries to millennia. We found that within-site soil biodiversity and function relationship is negatively correlated with soil age, suggesting a stronger dependence of ecosystem functioning on soil biodiversity in geologically younger than older ecosystems. We further show that increases in plant cover, soil carbon and microbial biomass as ecosystems develop, particularly in wetter conditions, lessen the critical need of soil biodiversity to sustain function. Our work highlights the importance of soil biodiversity for supporting function in drier and geologically younger ecosystems with low microbial biomass., (© 2024. The Author(s).)

Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH 4 ) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH 4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and 13 CH 4 -DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH 4 oxidation in supporting denitrification. Our results reveal positive relationships between CH 4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH 4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, 13 CH 4 -DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating 13 C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of 13 C-metagenome-assembled genomes and 13 C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH 4 oxidation, for the coupling of CH 4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH 4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems., (© 2024. The Author(s).)

Soil protists, the major predator of bacteria and fungi, shape the taxonomic and functional structure of soil microbiome via trophic regulation. However, how trophic interactions between protists and their prey influence microbially mediated soil organic carbon turnover remains largely unknown. Here, we investigated the protistan communities and microbial trophic interactions across different aggregates-size fractions in agricultural soil with long-term fertilization regimes. Our results showed that aggregate sizes significantly influenced the protistan community and microbial hierarchical interactions. Bacterivores were the predominant protistan functional group and were more abundant in macroaggregates and silt + clay than in microaggregates, while omnivores showed an opposite distribution pattern. Furthermore, partial least square path modeling revealed positive impacts of omnivores on the C-decomposition genes and soil organic matter (SOM) contents, while bacterivores displayed negative impacts. Microbial trophic interactions were intensive in macroaggregates and silt + clay but were restricted in microaggregates, as indicated by the intensity of protistan-bacterial associations and network complexity and connectivity. Cercozoan taxa were consistently identified as the keystone species in SOM degradation-related ecological clusters in macroaggregates and silt + clay, indicating the critical roles of protists in SOM degradation by regulating bacterial and fungal taxa. Chemical fertilization had a positive effect on soil C sequestration through suppressing SOM degradation-related ecological clusters in macroaggregate and silt + clay. Conversely, the associations between the trophic interactions and SOM contents were decoupled in microaggregates, suggesting limited microbial contributions to SOM turnovers. Our study demonstrates the importance of protists-driven trophic interactions on soil C cycling in agricultural ecosystems., (© 2023 John Wiley & Sons Ltd.)

Organo-mineral interactions have been regarded as the primary mechanism for the stabilization of soil organic carbon (SOC) over decadal to millennial timescales, and the capacity for soil carbon (C) storage has commonly been assessed based on soil mineralogical attributes, particularly mineral surface availability. However, it remains contentious whether soil C sequestration is exclusively governed by mineral vacancies, making it challenging to accurately predict SOC dynamics. Here, through a 400-day incubation experiment using 13 C-labeled organic materials in two contrasting soils (i.e., Mollisol and Ultisol), we show that despite the unsaturation of mineral surfaces in both soils, the newly incorporated C predominantly adheres to "dirty" mineral surfaces coated with native organic matter (OM), demonstrating the crucial role of organo-organic interactions in exogenous C sequestration. Such interactions lead to multilayered C accumulation that is not constrained by mineral vacancies, a process distinct from direct organo-mineral contacts. The coverage of native OM by new C, representing the degree of organo-organic interactions, is noticeably larger in Ultisol (~14.2%) than in Mollisol (~5.8%), amounting to the net retention of exogenous C in Ultisol by 0.2-1.3 g kg -1 and in Mollisol by 0.1-1.0 g kg -1 . Additionally, organo-organic interactions are primarily mediated by polysaccharide-rich microbial necromass. Further evidence indicates that iron oxides can selectively preserve polysaccharide compounds, thereby promoting the organo-organic interactions. Overall, our findings provide direct empirical evidence for an overlooked but critically important pathway of C accumulation, challenging the prevailing "C saturation" concept that emphasizes the overriding role of mineral vacancies. It is estimated that, through organo-organic interactions, global Mollisols and Ultisols might sequester ~0.1-1.0 and ~0.3-1.7 Pg C per year, respectively, corresponding to the neutralization of ca. 0.5%-3.0% of soil C emissions or 5%-30% of fossil fuel combustion globally., (© 2024 John Wiley & Sons Ltd.)

Competing Interests: Conflict of interest The authors declare that they have no conflict of interest.

Microbial residues contribute to the long-term stabilization of carbon in the entire soil profile, helping to regulate the climate of the planet; however, how sensitive these residues are to climatic seasonality remains virtually unknown, especially for deep soils across environmental gradients. Here, we investigated the changes of microbial residues along soil profiles (0-100 cm) from 44 typical ecosystems with a wide range of climates (~3100 km transects across China). Our results showed that microbial residues account for a larger portion of soil carbon in deeper (60-100 cm) vs. shallower (0-30 and 30-60 cm) soils. Moreover, we find that climate especially challenges the accumulation of microbial residues in deep soils, while soil properties and climate share their roles in controlling the residue accumulation in surface soils. Climatic seasonality, including positive correlations with summer precipitation and maximum monthly precipitation, as well as negative correlations with temperature annual range, are important factors explaining microbial residue accumulation in deep soils across China. In particular, summer precipitation is the key regulator of microbial-driven carbon stability in deep soils, which has 37.2% of relative independent effects on deep-soil microbial residue accumulation. Our work provides novel insights into the importance of climatic seasonality in driving the stabilization of microbial residues in deep soils, challenging the idea that deep soils as long-term carbon reservoirs can buffer climate change., (© 2023 John Wiley & Sons Ltd.)

Agricultural ecosystems contribute significantly to atmospheric emissions of soil nitrous oxide (N 2 O), which exacerbate environmental pollution and contribute to global warming. Glomalin-related soil protein (GRSP) stabilizes soil aggregates and enhances soil carbon and nitrogen storage in agricultural ecosystems. However, the underlying mechanisms and relative importance of GRSP on N 2 O fluxes within soil aggregate fraction remain largely unclear. We examined the GRSP content, denitrifying bacterial community composition, and potential N 2 O fluxes across three aggregate-size fractions (2000-250 μm, 250-53 μm, and <53 μm) under a long-term fertilization agricultural ecosystem, subjected to mineral fertilizer or manure and their combination. Our findings indicated that various fertilization treatments have no discernible impact on the size distribution of soil aggregates, paving the way to further research into the impact of soil aggregates on GRSP content, the denitrifying bacterial community composition, and potential N 2 O fluxes. GRSP content increased with the increase in soil aggregate size. Potential N 2 O fluxes (including gross N 2 O production and N 2 O reduction and net N 2 O production) among aggregates were highest in microaggregates (250-53 μm), followed by macroaggregates (2000-250 μm) and lowest in silt + clay (<53 μm) fractions. Potential N 2 O fluxes had a positive response to soil aggregate GRSP fractions. The non-metric multidimensional scaling analysis revealed that soil aggregate size could drive the denitrifying functional microbial community composition, and deterministic processes play more critical roles than stochasticity processes in driving denitrifying functional composition under soil aggregate fractions. Procrustes analysis revealed a significant correlation between denitrifying microbial community, soil aggregate GRSP fractions, and potential N 2 O fluxes. Our study suggests that soil aggregate GRSP fractions influence potential nitrous oxide fluxes by affecting denitrifying microbial functional composition within soil aggregate., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

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., (© 2023. The Author(s).)

Protist predation is a crucial biotic driver modulating bacterial populations and functional traits. Previous studies using pure cultures have demonstrated that bacteria with copper (Cu) resistance exhibited fitness advantages over Cu-sensitive bacteria under the pressure of protist predation. However, the impact of diverse natural communities of protist grazers on bacterial Cu resistance in natural environments remains unknown. Here, we characterized the communities of phagotrophic protists in long-term Cu-contaminated soils and deciphered their potential ecological impacts on bacterial Cu resistance. Long-term field Cu pollution increased the relative abundances of most of the phagotrophic lineages in Cercozoa and Amoebozoa but reduced the relative abundance of Ciliophora. After accounting for soil properties and Cu pollution, phagotrophs were consistently identified as the most important predictor of the Cu-resistant (Cu R ) bacterial community. Phagotrophs positively contributed to the abundance of a Cu resistance gene ( copA ) through influencing the cumulative relative abundance of Cu-resistant and -sensitive ecological clusters. Microcosm experiments further confirmed the promotion effect of protist predation on bacterial Cu resistance. Our results indicate that the selection by protist predation can have a strong impact on the Cu R bacterial community, which broadens our understanding of the ecological function of soil phagotrophic protists.

Rice-crayfish co-culture (RC) has been widely and rapidly promoted as a sustainable agricultural system in many countries. The accumulation of crayfish residues could enhance soil organic matters; however, impacts of this integrated farming model on the dissemination and pathogenicity of resistance and virulence genes remain poorly understood. Here, we characterized antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence factor genes (VFGs) using metagenomic methods in paired RC and rice monoculture (RM) systems across China. The RC model did not increase the abundance of soil ARGs, BRGs, MRGs, or VFGs in comparison to the RM model, but selectively enriched 35 subtypes of these potential resistance and virulence genes. Network analysis revealed that resistance and virulence genes had a higher number of connections with mobile genetic elements (MGEs) in the RC system than that in the RM system, suggesting a higher horizontal transfer potential of these genes. Moreover, the RC model had a higher abundance of human opportunistic pathogens such as Salmonella enterica, Vibrio cholerae, and Shigella dysenteriae which were potential hosts of VFGs such as phoP, fleS, and gspE, suggesting a potential threat to human health. We further unraveled that stochastic process was the main driver of the assembly of resistance and virulence genes in the RC system. The abundance of ARGs and VFGs were primarily associated with microbial community compositions, while the abundance of BRGs and MRGs were mainly associated with that of MGEs. Taken together, our results suggest that the RC model has potential to cause the dissemination and pathogenicity of resistance and virulence genes, which has important implications for the control of soil-borne biological risks and the strategic management of sustainable agriculture., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The rice-crayfish co-culture (RC) is a putative sustainable agricultural system. However, studies on the ecological effects of long-term RC systems were still lacking. Here, we compare enzymatic stoichiometry, microbial necromass, and microbial community between the RC and rice monoculture systems (RM). Soil enzymatic stoichiometry analysis showed that after transformation from RM to RC for about three years, ammonium nitrogen (NH 4 -N) availability increased to depress relative N-acquiring enzyme production, especially for leucine aminopeptidase. The contents of microbial necromass increased approximately onefold in the RC system, making microbial necromass' contribution to the soil nitrogen (N) reach up to 46.72%. Elevation in NH + decreased N-acquiring enzyme, and a relatively more effective C acquisition likely benefited microbial necromass retention and production in the RC system. This study highlights that the rice-crayfish co-culture could modify the N pool of the surface paddy soil.4 + decreased N-acquiring enzyme, and a relatively more effective C acquisition likely benefited microbial necromass retention and production in the RC system. This study highlights that the rice-crayfish co-culture could modify the N pool of the surface paddy soil., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Microbial communities play critical roles in fixing carbon from the atmosphere and fixing it in the soils. However, the large-scale variations and drivers of these microbial communities remain poorly understood. Here, we conducted a large-scale survey across China and found that soil autotrophic organisms are critical for explaining CO 2 fluxes from the atmosphere to soils. In particular, we showed that large-scale variations in CO 2 fixation rates are highly correlated to those in autotrophic bacteria and phototrophic protists. Paddy soils, supporting a larger proportion of obligate bacterial and protist autotrophs, display four-fold of CO 2 fixation rates over upland and forest soils. Precipitation and pH, together with key ecological clusters of autotrophic microbes, also played important roles in controlling CO 2 fixation. Our work provides a novel quantification on the contribution of terrestrial autotrophic microbes to soil CO 2 fixation processes at a large scale, with implications for global carbon regulation under climate change., (© 2022 John Wiley & Sons Ltd.)

Warming is known to reduce soil carbon (C) stocks by promoting microbial respiration, which is associated with the decomposition of microbial residue carbon (MRC). However, the relative contribution of MRC to soil organic carbon (SOC) across temperature gradients is poorly understood. Here, we investigated the contribution of MRC to SOC along two independent elevation gradients of our model system (i.e., the Tibetan Plateau and Shennongjia Mountain in China). Our results showed that local temperature increases were negatively correlated with MRC and SOC. Further analyses revealed that rising temperature reduced SOC via decreasing MRC, which helps to explain future reductions in SOC under climate warming. Our findings demonstrate that climate warming has the potential to reduce C sequestration by increasing the decomposition of MRC, exacerbating the positive feedback between rising temperature and CO 2 efflux. Our study also considered the influence of multiple environmental factors such as soil pH and moisture, which were more important in controlling SOC than microbial traits such as microbial life-style strategies and metabolic efficiency. Together, our work suggests an important mechanism underlying long-term soil C sequestration, which has important implications for the microbial-mediated C process in the face of global climate change., (© 2022 John Wiley & Sons Ltd.)

Identifying the drivers of the response of soil microbial respiration to warming is integral to accurately forecasting the carbon-climate feedbacks in terrestrial ecosystems. Microorganisms are the fundamental drivers of soil microbial respiration and its response to warming; however, the specific microbial communities and properties involved in the process remain largely undetermined. Here, we identified the associations between microbial community and temperature sensitivity (Q 10 ) of soil microbial respiration in alpine forests along an altitudinal gradient (from 2974 to 3558 m) from the climate-sensitive Tibetan Plateau. Our results showed that changes in microbial community composition accounted for more variations of Q 10 values than a wide range of other factors, including soil pH, moisture, substrate quantity and quality, microbial biomass, diversity and enzyme activities. Specifically, co-occurring microbial assemblies (i.e., ecological clusters or modules) targeting labile carbon consumption were negatively correlated with Q 10 of soil microbial respiration, whereas microbial assemblies associated with recalcitrant carbon decomposition were positively correlated with Q 10 of soil microbial respiration. Furthermore, there were progressive shifts of microbial assemblies from labile to recalcitrant carbon consumption along the altitudinal gradient, supporting relatively high Q 10 values in high-altitude regions. Our results provide new insights into the link between changes in major microbial assemblies with different trophic strategies and Q 10 of soil microbial respiration along an altitudinal gradient, highlighting that warming could have stronger effects on microbially-mediated soil organic matter decomposition in high-altitude regions than previously thought., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Bacterial interactions play significant roles in ecological functions in responding to anthropogenic interference and soil structure changes. However, it remains largely unknown how fertilizer regimes and soil particle sizes drive bacterial interactions. To evaluate bacterial interaction patterns in soil aggregates under long-term fertilizer treatments, we sampled nine bacterial co-occurrence communities and compared the difference between interspecies resource consumption patterns and network structure. Despite the differences between fertilizer treatments, the negative correlation ratios of interaction networks in soil aggregates were macroaggregates > microaggregates > silt + clays. Likewise, NPK-supplement (chemical fertilizer) had also decreased the number of positive correlations of the interaction network than M-supplement (organic fertilizer), regardless of the size of soil aggregates. Linear model analysis revealed that interspecies trophic patterns, including niche overlap and nestedness, drove bacterial competition in the interaction networks. Most importantly, interspecies niche overlap may be the intrinsic factor in the effects of fertilizer treatments and soil aggregates on bacterial interactions. This study enhances our understanding of the potential for changes in species trophic patterns and might guide the promotion of land management. IMPORTANCE Despite that the influence of soil structure and fertilizer treatments on the bacterial community has been widely studied, how they drive interspecies interactions has not been largely explored. Connectance and nestedness were significantly correlated with bacterial interactions, but no differences were found in different soil aggregates and fertilizer treatments. However, interspecies niche overlap could respond to soil aggregates and fertilizer treatments and ultimately drive the bacterial interactions. This study enhances our understanding of the mechanism of microbial interactions and highlights the importance of trophic patterns in the bacterial community. Our findings extend knowledge for nutrient availability on interspecific interactions.

Soil-borne fungal phytopathogens are important threats to soil and crop health. However, their community composition and environmental determinants remain unclear. Here, we explored the effects of agricultural fertilization regime (i.e., organic material application) on soil fungal phytopathogens, using data sets from a combination of field survey and long-term experiment. We found that soil organic carbon was the key factor that affected the diversity and relative abundance of fungal phytopathogens in agricultural soils. The dominant genera of phytopathogens including Monographella was also strongly associated with soil organic carbon. In addition, the elevated soil organic carbon enhanced the node proportion of phytopathogens and the positive interactions within the fungal community in the network. Results of the long-term experiment revealed that applications of crop straw and fresh livestock manure significantly increased the proportion of phytopathogens, which were associated with the elevated soil organic carbon. This work offers new insights into the occurrence and environmental factors of fungal phytopathogens in agricultural soils, which are fundamental to control their impacts on the soil and crop systems. IMPORTANCE Fungal phytopathogens are important threats to soil and crop health, but their community composition and environmental determinants remain unclear. We found that soil organic carbon is the key factor of the prevalence of fungal phytopathogens through a field survey, which is also supported by our long-term (6-year) experiment showing the applications of crop straw and fresh livestock manure significantly increased the proportion of fungal phytopathogens. These findings advance our understanding of the occurrence and environmental drivers of soil-borne fungal phytopathogens under agricultural fertilization regime and have important implications for the control of soil-borne pathogens.

Microbial diversities are key drivers of soil multifunctionality in terrestrial ecosystems and are important for stability and productivity of ecosystems. However, the relationships among microbial diversity, community assembly and soil multifunctionality in forest ecosystems remained unclear. Here, soil samples were collected from a subtropical forest ecosystem, Lushan Mountain, China. High-throughput sequencing was employed to reveal the bacterial/fungal community assembly and biodiversity, as well as 10 enzyme activities were measured to assess soil multifunctionality. We found that soil multifunctionality was negatively regulated by bacterial and fungal alpha diversity, implying a higher potential functional redundancy in this forest soil. The null model indicated that deterministic processes (variable selection) and stochastic processes (dispersal limitation) govern bacterial and fungal phylogenetic turnover, respectively. Correlation analysis revealed that bacterial rather than fungal community assembly processes have a significant linkage to soil multifunctionality. These observations projected that soil variables could regulate multifunctionality by shaping the phylogenetic and taxonomic turnover of bacteria rather than fungi. In summary, our study highlighted that soil multifunctionality is mainly driven by bacterial diversity and community assembly processes while not fungal, presenting different views and knowledge of microbial diversity and community assembly processes in ecosystem functioning., (© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Dissolved organic matter (DOM) represents the most mobile and reactive pool of soil organic matter (SOM). Climate changes, such as global warming and altered precipitation exert considerable influences on the quality and quantity of soil DOM. However, rare reports have focused on the interactive effects of soil warming and increased precipitation. In the present study, we conducted a 90-day incubation experiment to investigate how the concentration, source and chemical composition of DOM from an Alfisol respond to the variations of temperatures (15, 30 and 45 °C) and moistures (40%, 60%, and 80% of saturated soil water content). Four DOM components were identified through fluorescence excitation emission matrix (EEM)-parallel factor analysis (PARAFAC). Increased temperature alone aggravated the decomposition of plant-derived aromatic components (C2 and C4) but promoted the accumulation of microbial-derived aliphatic carbon (C1) and tryptophan-like component (C3). Increased fungi/bacteria ratio with warming was responsible for the decomposition of plant-derived components. Warming-induced disassociation of Ca-bearing mineral to colloidal Ca facilitated the accrual of microbial-derived aliphatic DOM. Humidification alone and humidification + warming significantly increased the concentration of DOM and the percentage of plant-derived aromatic carbon (C2, C4), which was attributed to the release of Fe-bearing mineral-OC. Based on the above findings along with the results of two-way ANOVA and Variation partition analysis, we infer that moisture will play a dominant role in regulating the chemical composition of DOM in Alfisols under both warming and humidification which in turn impact global C cycling and the ultimate climate., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The mineralization of soil organic matter (SOM) is closely related to the emission of greenhouse gas into atmosphere and the stability of organic carbon in soil. The influence of minerals on SOM mineralization in the specific soil received very few attentions. The influence characteristics and potential mechanisms of oxides on the mineralization of SOM in the paddy soil were observed in this study by incubating soil with the addition (dosage: 10 g kg -1 ) of prepared gibbsite, goethite, ferrihydrite or birnessite for 60 days. A sequence control treatment (753 mg CO 2 -C kg -1 ) > goethite treatment (656 mg CO 2 -C kg -1 ) ≈ gibbsite treatment (649 mg CO 2 -C kg -1 ) > birnessite treatment (529 mg CO 2 -C kg -1 ) > ferrihydrite treatment (441 mg CO 2 -C kg -1 ) was found in the cumulative amount of released CO 2 in 60 days of incubation. Oxides especially ferrihydrite significantly decreased the content of dissolved organic matter (DOM) but tended to increase the content of microbial biomass carbon (MBC). The molecular structure of DOM in the paddy soil was simplified by gibbsite, ferrihydrite and birnessite after the incubation. Oxides especially birnessite and ferrihydrite reduced soil pH and the content of soil available N but increased soil redox potential (Eh). All examined oxides especially Fe oxides enhanced soil bacterial abundance but only birnessite significantly affected bacterial composition at phyla level. The stimulation on the immobilization and/or microbial assimilation of labile organic carbon, the modulation on soil basic properties (available N, pH, Eh), and the decrease of the relative abundance of some decomposing bacteria phyla such as Actinobacteria were the potential pathways of oxides in decreasing SOM mineralization., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Salinization is considered a major threat to soil fertility and agricultural productivity throughout the world. Soil microbes play a crucial role in maintaining ecosystem stability and function (e.g., nitrogen cycling). However, the response of bacterial community composition and community-level function to soil salinity remains uncertain. Here, we used multiple statistical analyses to assess the effect of high salinity on bacterial community composition and potential metabolism function in the agricultural ecosystem. Results showed that high salinity significantly altered both bacterial alpha (Shannon-Wiener index and phylogenetic diversity) and beta diversity. Salinity, total nitrogen (TN), and soil organic matter (SOM) were the vital environmental factors shaping bacterial community composition. The relative abundance of Actinobacteria , Chloroflexi , Acidobacteria , and Planctomycetes decreased with salinity, whereas Proteobacteria and Bacteroidetes increased with salinity. The modularity and the ratio of negative to positive links remarkedly decreased, indicating that high salinity destabilized bacterial networks. Variable selection, which belongs to deterministic processes, mediated bacterial community assembly within the saline soils. Function prediction results showed that the key nitrogen metabolism (e.g., ammonification, nitrogen fixation, nitrification, and denitrification processes) was inhibited in high salinity habitats. MiSeq sequencing of 16S rRNA genes revealed that the abundance and composition of the nitrifying community were influenced by high salinity. The consistency of function prediction and experimental verification demonstrated that high salinity inhibited soil bacterial community mediating nitrogen cycling. Our study provides strong evidence for a salinity effect on the bacterial community composition and key metabolism function, which could help us understand how soil microbes respond to ongoing environment perturbation. IMPORTANCE Revealing the response of the soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated the effect of high salinity on the bacterial community composition and key biogeochemical processes in salinized agricultural soils (0.22 to 19.98 dS m -1 ). Our results showed that high salinity significantly decreased bacterial diversity, altered bacterial community composition, and destabilized the bacterial network. Moreover, variable selection (61% to 66%) mediated bacterial community assembly within the saline soils. Functional prediction combined with microbiological verification proved that high salinity inhibited soil bacterial community mediating nitrogen turnover. Understanding the impact of salinity on soil bacterial community is of great significance for managing saline soils and maintaining a healthy ecosystem.

As one of the horizontal gene transfer processes, transformation provides bacteria flexible adaptation to changing environmental conditions. Soil minerals have been shown to inhibit bacterial transformation efficiency due to their high adsorption affinity for DNA molecules. However, the intrinsic mechanisms in regulating genetic transformation by soil components remain elusive. Little is known whether bacterial exposure to minerals may influence competence development which is regarded as a prerequisite of bacterial transformation. In this study, we examined the effects of kaolinite, montmorillonite, and goethite on the transformation of B. subtilis via chemical adsorption, Live-Dead staining, β-galactosidase assay, and qPCR. Results showed that kaolinite and montmorillonite reduced the transformability of B. subtilis by strong adsorption of CSF (competence-stimulating factor), a signaling molecule of cell competence, and the down-regulated transcriptional genes resulting from suppressed competence development. Conversely, goethite depressed bacterial transformation only at low mineral content by DNA adsorption. The striking membrane damage on B. subtilis in presence of high content of goethite yielded a marked increase of bacterial transformation. This finding subverted our previous view regarding the impact of soil minerals on bacterial transformation. Three mechanisms were thus proposed governing bacterial transformation in mineral systems: adsorption of CSF, gene expression and membrane damage. This work has advanced our understanding on the genetic transformation of bacteria as influenced by minerals in a wide range of soils and associated environments., Competing Interests: Declaration of competing interest All of the reported work is original and has not been published previously. All authors listed have approved of the manuscript and declare no conflict of interest., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Soil aggregates are integral parts of soil structure and play paramount roles in supporting microbial diversity, nutrient cycling and water retention. The formation of multispecies biofilms is a survival strategy for bacterial adaptation to the environment and help microorganisms access more complex nutrient sources via labor sharing, especially in soil aggregates. However, very little is known about the effect of species richness and composition on bacterial multispecies biofilms formation in different size soil aggregates. A random partition design strategy was used to identify the relative importance of bacterial richness and composition in driving multispecies biofilms. The strategy can separate the effects of species richness and composition from the soil aggregates occurring bacterial assemblage. Increasing species richness was found to be always positively correlated with multispecies biofilms productivity for bacteria from the same aggregate fractions. General linear model analysis revealed that species composition contributed more than species richness to forming multispecies biofilms, suggesting that "selection mechanism" plays a more important role than "complementarity mechanism". This "selection mechanism" relies mainly on culturable keystone species that can significantly enhance the formation of multispecies biofilms. The co-occurrence network was investigated to explore whether the culturable keystone species from the random partitions experiment are consistent with the keystone taxa. Four out of 10 culturable keystone species isolated from soil aggregates were matched the keystone taxa. It is concluded that the culturable keystone species determine the multispecies biofilms formation for bacteria residing in soil aggregates. This study provides insights into the role of culturable keystone species in multispecies biofilms. Understanding the formation of multispecies biofilms is fundamental to decipher how microbes interact with each other in soil aggregates. Meanwhile, it will enhance our knowledge of the quorum behavior of complex bacterial communities., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification by oxidizing nitrite to nitrate, which is a key process in the biogeochemical nitrogen cycling. However, little is known about the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. Here, we explored the effects of salinity on Nitrobacter and Nitrospira community using high-throughput sequencing and multivariate statistical analyses. Our results showed that high salinity significantly inhibited the nitrite oxidation rates and decreased the abundance of Nitrobacter and Nitrospira. Extreme salty conditions significantly altered the diversity and composition of Nitrospira community but had little effect on Nitrobacter community. Nitrobacter network in high salinity soils was more closely connected while the connectivity of Nitrospira network became weak. Nitrobacter and Nitrospira community exhibited distinct assembly processes at different salinity levels. Stochastic processes were dominant in the Nitrobacter community assembly in both low and high salinity soils. Interestingly, the assembly of Nitrospira community was governed by stochastic and deterministic processes in low and high salinity soils, respectively. To our knowledge, our study provides the first description of the co-occurrence patterns and assembly processes of NOB communities in agricultural soils with different salinities. These results can help us understand the NOB ecological roles and improve the nitrite oxidation activity in a high salinity environment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Published by Elsevier B.V.)

The mineralization of soil organic matter is closely related to climate change. Labile organic matter and microbial community are vital intrinsic factors in controlling the mineralization of soil organic matter. Regulation of soil aggregate size on dissolved organic matter (DOM), the cellobiose hydrolyzing microbial community, and their roles in organic matter mineralization remains unclear. The mineralization of organic matter in large macroaggregates (LMA, >2 mm), small macroaggregates (SMA, 0.25-2 mm), and microaggregates (MI, <0.25 mm) from an Ultisol treated with long-term non-fertilizers (Ck), chemical fertilizers (NPK) and animal manure (AM) was observed in this study. The concentration and structure of DOM, activity of β-glucosidase, and the abundance, diversity, and community composition of GH1 (glycoside hydrolase family 1) microbial β-glucosidase encoding genes were investigated. The cumulative CO 2 -C emissions occurred in the order LMA < SMA < MI in each fertilization treatment and followed the sequence Ck < NPK < AM in each size of aggregate. The concentration of DOM in the soil aggregates increased as the aggregate size decreased, while the structural complexity of DOM followed the opposite trend. The activity of β-glucosidase in the smaller aggregates was higher than that in the larger aggregates, and the abundance and diversity of the GH1 microbial β-glucosidase genes generally echoed the same trend. The dominant microbial classes harboring GH1 β-glucosidase genes in the soil aggregates were Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, Flavobacteria, Eurotiomycetes, and Sordariomycetes. The relative abundance of Actinobacteria, Sordariomycetes, and Eurotiomycetes revealed significant differences among the aggregates. Redundancy analysis confirmed that microbial GH1 β-glucosidase community in the soil aggregates was primarily regulated by DOM concentration and pH. Structural equation modelling revealed that soil aggregates mainly regulated the β-glucosidase activity and DOM concentration and then the abundance and diversity of the GH1 microbial β-glucosidase genes in controlling organic matter mineralization., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Elucidating the association between the phoD-harboring bacterial community and soil ecosystem multifunctionality, which is crucial for the comprehension of the phoD-harboring bacterial role and contribution in agro-ecosystems, is an essential but rarely investigated subject. Here, we explored the phoD-harboring bacterial community in long-term fertilized soils using amplicon sequencing and multiple analysis methods including the null, neutral, and niche breadth models. We found distance-decay relationships of community similarities against geographical distance on a large spatial scale. Community dissimilarity was significantly lower in the organic fertilization treatment (M) than that in the no (CK) and mineral (NPK) fertilizer treatments. Dispersal limitation governed community assembly in CK, M, NPK, and whole samples, with corresponding relative contributions of 58.2%, 58.3%, 52.8%, and 54.4%, respectively. Electrical conductivity, total carbon, total nitrogen, total phosphorus, organic phosphorus, and available phosphorus were responsible for the community assembly of phoD-harboring bacteria. Multiple model analysis revealed that the phoD-harboring bacterial community was less constrained by the environment and presented flexible metabolism in soils with the M fertilization treatment. phoD-harboring bacteria presented more conflicting interaction and exhibited significantly higher ecosystem multifunctionality in soils with the M fertilization treatment than that in the CK and NPK fertilization treatments. To our knowledge, this is the first study to report a less environment-constrained phoD-harboring bacterial community might lead to a larger difference in ecosystem multifunctionality in fertilized soils. Therefore, we suggest phoD-harboring bacterial community assembly could be a biotic indicator for evaluating soil ecosystem multifunctionality., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Soil is the largest C pool in the terrestrial ecosystem. Numerous studies have been devoted to the decomposition of soil organic C as influenced by agricultural management. However, little is known about the effect of fertilization on the microbial CO 2 fixation potential. Here, we examined the atmospheric CO 2 fixation rates and structure of autotrophic cbbL-containing bacterial communities and accA-containing archaeal communities in response to 38 years of chemical and/or organic fertilizer application in a Mollisol. The autotrophic microbial abundance and community composition were analyzed by quantitative polymerase chain reaction and high throughput sequencing, respectively. Our results showed that chemical fertilization additions significantly decreased CO 2 fixation rates by 57%, but organic manure use resulted in no notable differences compared to no fertilizer regimes (0.38 mg CO 2 kg -1 soil d -1 ) through stable isotope methods. The declining soil pH and increasing Olsen-phosphorus in soils with chemical fertilization dramatically reduced the cbbL gene diversity and accA gene abundances and altered both the autotrophic bacterial and archaeal community compositions. The changes in CO 2 -fixation rate were more greatly attributed to the shifts in autotrophic bacterial community composition than to the diversity and abundance. The C fixation potentials were positively correlated with the relative abundances of Acidiphilium and Methylibium but were negatively related to those of Azospirillum and Nitrosospira. Both composition and abundance of the autotrophic archaeal community contributed together to the CO 2 fixation activities. Our finding suggests that long-term chemical fertilization has a strong impact on the soil microbial CO 2 fixation activity and autotrophic microorganisms in upland soils and highlight the important roles of the CO 2 fixing process in soil organic carbon sequestration., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

The use of biochar to amend soil has been gaining increasing attention in recent years. In this study, the 15 N tracer technique was used together with elemental analysis-stable isotope ratio analysis and gas isotope mass spectrometry to characterise biochar, soil, plant, and gas samples in order to explore the nitrogen transport mechanisms in the biochar-soil-plant-atmosphere system during the process of returning biochar to the soil (RBS). The results showed that the nitrogen retention rate of biochar was negatively correlated with the pyrolysis temperature during the preparation process, but was less affected by the pyrolysis atmosphere. In the RBS process, the migration of biochar nitrogen to plants was significantly greater than that of straw nitrogen, and it showed an overall decreasing trend with the increase in pyrolysis temperature, but was less influenced by the pyrolysis atmosphere. At temperatures of 300-500 °C, the pyrolysis atmosphere had a slightly smaller effect on the migration of biochar nitrogen to the air, plant, and soil system, and the pyrolysis temperature was much more important. However, the activation with CO 2 gas at a higher temperature (600 °C) significantly enhanced the pore structure of biochar, particularly the structure of small pores; therefore, biochar prepared under a CO 2 atmosphere at 600 °C reduces gaseous nitrogen emissions better than that under a N 2 atmosphere. In the future, more pyrolysis conditions should be examined and their optimal combination should be further explored to reduce gaseous nitrogen emissions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

The studies of the mechanism of Cd fixation by biochar have mainly focused on the pore size, pH, and oxygen-containing functional groups, and few researches have paid close attention to the effect of the negative charge in biochar surface. In this paper, biochar was produced in the CO 2 atmosphere at different pyrolysis temperatures, and the influence of the pyrolysis temperature on biochar surface charge were explored. The cause of the negative charge on the biochar surface has been analysed, and the optimal preparing temperature for the biochar with the best effect of cadmium immobilization from soil has been found. The results show that with the increasing temperature from 300 to 700 °C, the negative surface charge on biochar surface gradually decreases, while the fixed amount of Cd increases. The factors affecting the surface charge of biochar are ash content, pH, oxygen-containing functional groups, polar groups, and hydrogen bonds. Among them, the pH, oxygen-containing functional groups and polar groups have positive effects on the surface negative charge, whereas the hydrogen bond has a negative effect. The determinant of surface charge is the hydroxyl group, the content of hydroxyl group decreases as increasing temperature, resulting in a decrease in surface negative charge., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Ureolytic microbes play a pivotal role in the maintenance of soil fertility. Soil aggregates are supposed to provide heterogeneous habitats for microorganisms, which may result in distinct metabolic functions. However, limited information is available regarding the distribution patterns, driving factors, and activity of ureolytic microbiota at the aggregate scale. In this study, we characterized the ureolytic microbiota and urease activity of three soil aggregate fractions from an Inceptisol subjected to 5 years of different fertilization regimes. Correlations between soil chemical characteristics and ureolytic microbial communities were analyzed. The results showed that the total abundance as well as the relative abundance of copiotrophic ureolytic microbes generally increased with the increasing soil aggregate size. This trend was in line with the nutrient distribution patterns, including labile carbon, NH 4 , total carbon, nitrogen, and phosphorus. Soil urease activity also increased significantly with the increasing soil aggregate size and was positively correlated with copiotrophic ureolyric microbes, such as Betaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria. Thus, we speculated that larger size soil aggregates with greater availability of labile carbon support more copiotrophic ureolyric microbes with a high growth rate, leading to a high density of total ureolytic microbes and higher urease activity. Smaller aggregates with less available carbon were associated with more oligotrophs, higher abundances of total ureolytic microbes, and higher urease activity. Our results suggest that larger soil aggregates and associated ureolyric microbes play a more important role in nutrient cycling for crop growth in this Inceptisol ecosystem.+ , total carbon, nitrogen, and phosphorus. Soil urease activity also increased significantly with the increasing soil aggregate size and was positively correlated with copiotrophic ureolyric microbes, such as Betaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria. Thus, we speculated that larger size soil aggregates with greater availability of labile carbon support more copiotrophic ureolyric microbes with a high growth rate, leading to a high density of total ureolytic microbes and higher urease activity. Smaller aggregates with less available carbon were associated with more oligotrophs, higher abundances of total ureolytic microbes, and higher urease activity. Our results suggest that larger soil aggregates and associated ureolyric microbes play a more important role in nutrient cycling for crop growth in this Inceptisol ecosystem.

In situ passivation of heavy metals by biochar mainly focuses on the effect of biochar's pH, surface oxygen-containing functional groups (OCFGs), and ash content. In this paper, starting with the measurement of biochar's electrical properties under different pyrolysis atmospheres and temperatures, the changes in the zeta potential of biochar and the consequent effects on cadmium immobilization in soil are studied. The results show that the zeta potential of biochar from the pyrolysis of high temperature (800 °C) is higher than that of biochar at low temperatures, so its electronegativity is weaker than that of biochar at low temperatures, but the protective effect on wheat is stronger than that of biochar obtained at low temperatures. The zeta potential of biochar obtained under a CO 2 atmosphere was higher than that of biochar prepared under a N 2 atmosphere, so its protective effect on wheat was stronger than that of biochar under N 2 . The reason is that biochar particles with a high zeta potential and weak electronegativity have higher cohesion and are better at in situ passivation of Cd in soils. Namely, biochar obtained at high pyrolysis temperatures (800 °C) and prepared under a CO 2 atmosphere has better effect on Cd immobilization.

Soil contamination poses a serious threat to ecosystem and human well-being. Compared to conventional physical and chemical treatment, the microbial electrochemical system (MES) offers a sustainable and environment-friendly solution for soil bioremediation. In principle, soil microbe degrades organic substrate and releases electron in anode region. The electron flows through electric circuit to the cathode and finally is accepted by oxygen or oxidized metals. With various inherent advantages, MES has been applied in petroleum hydrocarbon, chlorinated organics and heavy metals bioremediation in soils. This paper aims to review the recent advances of MES in soil bioremediation, including main mechanisms of contaminant removal with MES, configurations of soil MES and current development in bioremediation of soil contaminated by organic and inorganic pollutants. Moreover, challenges and future prospects of soil MES are discussed., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Copper contamination of soils is a global environmental problem. Soil components (organic matter, clay minerals, and microorganisms) and retention time can govern the adsorption, fixation, and distribution of copper. This study evaluated the interaction effects of soil components and aging on the distribution of exogenous copper. Three typical Chinese soils (Ultisol, Alfisol, and Histosol) were collected from Hunan, Henan, and Heilongjiang Provinces. Soils were incubated with rice straw (RS) and engineered bacteria (Pseudomonas putida X4/pIME) in the presence of exogenous copper for 12 months. Sequential extraction was employed to obtain the distribution of Cu species in soils, and the mobility factors of Cu were calculated. The relationships between soil properties and Cu fractions were analyzed with stepwise multiple linear regression. The results show that organic carbon plays a more important role in shaping the distribution of relatively mobile Cu, and iron oxides can be more critical in stabilizing Cu species in soils. Our results suggest that organic matter is the most important factor influencing copper partitioning in Ultisols, while iron oxides are more significant in Alfisols. The mobility of exogenous Cu in soils depends largely on organic carbon, amorphous Fe, and aging. The introduction of both rice straw and rice straw + engineered bacteria enhanced the stabilization of Cu in all the three soils during aging process. The introduction of bacteria could reduce copper mobility, which was indicated by the lowest mobility factors of Cu for the treatment with bacteria in Black, Red, and Cinnamon soils at the first 4, 8, and 8 months, respectively. Different measures should be taken into account regarding the content of organic matter and iron oxides depending on soil types for the risk assessment and remediation of Cu-contaminated soils.

A field experiment was conducted to investigate the effect of chicken manure compost on the fractionation of cadmium (Cd), soil biological properties and Cd uptake by wheat in a soil affected by mining activities in Hubei province, China. Compost was applied at five levels (0, 27, 54, 108, 216 t ha(-1)), and winter wheat (Triticum aestivum L.) was chosen as an indicator plant. Results showed that the application of compost increased soil pH and the content of total phosphorus and organic matter. Soil biological properties such as microbial biomass carbon, invertase, protease, urease and catalase activities were significantly enhanced by 0.24-3.47 times after compost application. Sequential extraction indicated that compost amendments decreased the acid-extractable Cd by 8.2-37.6 %, while increased the reducible and oxidisable Cd by 9.2-39.5 and 8.2-60.4 %, respectively. The addition of 27-54 t ha(-1) compost reduced Cd content in wheat stems and seeds by 69.6-75.0 % and 10.3-18.4 %, respectively. However, only 25.5-26.5 % reductions in Cd content in wheat stems were observed in 108-216 t ha(-1) compost amendments, and no significant decrease was detected for seeds. This study suggests that although compost is a suitable organic amendment to improve soil fertility and biological activities, the addition of compost should be moderated by an appropriate rate to optimize the use of compost for the reclamation of metal-contaminated soils at field scale.

We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production.

The adsorption of extracellular polymeric substances (EPS) from Pseudomonas putida on montmorillonite, kaolinite and goethite was investigated as a function of pH using batch studies coupled with confocal laser scanning microscopy (CLSM) and isothermal titration calorimetry (ITC). Characterization by Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy showed that the extracted EPS contained carboxyl, phosphoryl, amino, and hydroxyl on functional groups as well as polysaccharides, protein and nucleic acid on components. The mass fraction of EPS adsorption on minerals decreased with the final pH increased from 3.0 to 9.0. The mass fraction of EPS-N adsorption varied with pH values and was higher than that of EPS-C or EPS-P on montmorillonite and kaolinite, while the mass fraction of EPS-P adsorption was the highest on goethite. CLSM results further demonstrated that proteins were predominantly distributed on the montmorillonite and kaolinite surfaces, while nucleic acids were mainly on the goethite surface. ITC results revealed that the adsorption process in all mineral systems was exothermic, and pH altered the heat effect of EPS-mineral reactions. The data obtained in this study would facilitate a better understanding of the adsorption mechanisms of EPS on minerals., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Understanding pathogen sorption on natural soil particles is crucial to protect public health from soilborne and waterborne diseases. Sorption of pathogen Streptococcus suis on 10 agricultural soils was examined, and its correlations with soil physico-chemical properties were also elucidated. S. suis sorption isotherms conformed to the linear equation, with partition coefficients (Ks) ranging from 12.7 mL g(-1) to 100.1 mL g(-1). Bacteria were observed to sorb on the external surfaces of soil aggregates by scanning electron microscopy. Using Pearson correlation and linear regression analysis, solution pH was found to have significant negative correlations with Ks. Stepwise multiple regression and path analysis revealed that pH and cation exchange capacity (CEC) were the main factors influencing sorption behaviors. The obtained overall model (Ks=389.6-45.9×pH-1.3×CEC, R(2)=0.943, P<0.001) can accurately predict Ks values. However, the variability in Ks was less dependent on soil organic matter, specific surface area, soil texture and zeta potential, probably due to the internal-surface shielding phenomenon of soil aggregates. Additionally, the sorption trends cannot be interpreted by interaction energy barriers calculated using the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, suggesting the limits of DLVO theory in describing pathogen sorption on natural soils. Our results also indicated soil pH and CEC should be preferentially considered when modeling S. suis sorption process., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

Microcalorimetry, plate count and PCR-denaturing gradient gel electrophoresis (DGGE) were employed to investigate microbial diversity and activity in soils from the Red Soil Experimental Station of the Chinese Academy of Agricultural Sciences, Hunan Province, China, where a wheat-corn rotation with 12 fertilization treatments was established in 1990. Fertilization greatly increased microbial biomass carbon (C) and nitrogen (N) (C(mic) and N(mic)) as well as the activities of phosphatase, urease, invertase, protease, catalase and dehydrogenase. Manure alone (M) enhanced the number of denitrifying and aerobic bacteria by 54.4% and 20.5%, respectively, whereas fallow (H) increased the number of aerobic cellulose decomposing bacteria by 31.4%. Fallow and soils amended with mineral fertilizers plus pig manure or straw increased both the DGGE band patterns and the Shannon index compared with mineral fertilizers or the control. Mineral treatments with lower bacterial numbers enhanced the values of the peak time (t(max)) more than did organic treatments. The peak height (P(max)) was positively correlated (P<0.01), with soil enzymes, C(mic) and N(mic), and the number of microorganisms, whereas the peak time (t(max)) was negatively connected (P<0.01) with these parameters. The microbial growth rate constant (k) was linked to bacteria (P<0.01), actinomycetes (P<0.05) and catalase (P<0.05). The total heat evolution (Q) had no relationships with any soil microbial properties (except for catalase). We propose that P(max) and t(max) could be used as indices of soil microbial activity, while the values of k and Q are poor indicators.

The present study was carried out to investigate the conformation, enzymatic activity and proteolytic stability of acid phosphatase on montmorillonite, kaolinite and soil colloids from an Alfisol by means of circular dichroism (CD) spectroscopy, isothermal titration microcalorimetry (ITC) and biochemical assay, respectively. The results showed that the secondary structure of phosphatase was changed from disordered type to ordered form during adsorption/desorption cycle, organic substance and 2:1-clay mineral in Brown Soil benefited the formation of ordered structure. Enzymatic activity of phosphatase was inhibited while the proteolytic stability was promoted after the interaction with active particles from permanent charge soil. The decrease of enzymatic activity and the increase of proteolytic stability resulted by montmorillonite and organic colloid were both greater than that by kaolinite and inorganic colloid, which was in consistent with the extent of structural change induced by different colloid particles. Thus, one of the most significant factors responsible for the variation of enzymatic activity and proteolytic stability might be the hiding or even damage of active sites and the irrecognition of cleavage sites in enzyme molecules induced by the formation of ordered structure. The information obtained in this study is of crucial significance for the understanding of the behavior and fate of extracellular enzymes in soils with permanent charges.

Adsorption and desorption of salmon sperm DNA on bacteria (Bacillus thuringiensis, Pseudomonas putida), two different colloidal fractions (organic and inorganic clay) from an Alfisol, minerals (montmorillonite, kaolinite and goethite) and colloid-bacteria composites were studied. Similar adsorption capacity and affinity of DNA were observed on two bacterial cells. However, the two bacterial strains played different roles in affecting the adsorption of DNA on the composites of soil colloidal particles with bacteria. The introduction of B. thuringiensis in soil colloids and minerals systems dramatically promoted DNA adsorption on colloidal particles especially organic clay, while P. putida decreased the adsorption of DNA on kaolinite and goethite. Electrostatic force and ligand exchange are regarded to be the major driving forces involved in the adsorption of DNA on bacterial cells, montmorillonite, soil colloids and goethite. Presence of bacteria enhanced the proportion of DNA adsorption on soil colloidal particles by electrostatic force and depressed that by ligand exchange process. Information obtained in this study is of fundamental significance for the understanding of the ultimate fate of extracellular DNA in soil systems.

Adsorption of DNA on montmorillonite, kaolinite, goethite and soil clays from an Alfisol in the presence of citrate, tartrate and phosphate was studied. A marked decrease in DNA adsorption was observed on montmorillonite and kaolinite with increasing anion concentrations from 0 to 5 mM. However, the amount of DNA adsorbed by montmorillonite and kaolinite was enhanced when ligand concentration was higher than 5 mM. In the system of soil colloids and goethite, with the increase of anion concentrations, a steady decrease was found and the ability of ligands in depressing DNA adsorption followed the sequence: phosphate > citrate > tartrate. Compared to H2O2-treated clays (inorganic clays), a sharp decrease in DNA adsorption was observed on goethite and organo-mineral complexes (organic clays) with increasing ligand concentrations. The results suggest that the influence of anions on DNA adsorption varies with the type and concentration of anion as well as the surface properties of soil components. Introduction of DNA into the system before the addition of ligands had the greatest amount of DNA adsorption on soil colloids and goethite. Organic and inorganic ligands promoted DNA adsorption on montmorillonite and kaolinite when ligands were introduced into the system before the addition of DNA. The results obtained in this study have important implications for the understanding of the persistence and fate of DNA in soil environments especially rhizosphere soil where various organic and inorganic ligands are active.

This study applied TAM air isothermal calorimeter to measure the adsorption enthalpies of DNA on eight colloidal fractions from permanent-charge and variable-charge soils. The adsorption of DNA on soil colloids was also examined by equilibrium adsorption analysis. The data evaluated from isotherms fitted by Langmuirean model revealed that the affinity of DNA for variable-charge soil colloids was higher than that for permanent-charge soil colloids. More tightly bound DNA molecules were observed on coarse clays and inorganic clays than on fine clays and organic clays, respectively. The adsorption enthalpies of DNA on permanent-charge soil colloids were higher than those on variable-charge soil colloids. DNA adsorption on organic clays is endothermic, whereas that on inorganic clays is exothermic. Dehydration and electrostatic repulsion were considered to cause the higher adsorption enthalpies of DNA with organic clays, while hydrogen bonding, ligand exchange and electrostatic attraction result in the lower DNA adsorption enthalpies on inorganic clays. The thermodynamic parameters presented in this study have important implication for providing further insight into mechanisms of the adsorption of DNA on soil particles.

In this paper, an on-the-spot sampling and survey method for studying the soil nutrient cycling in a regional scale was discussed, with considering the principles of representation, reproducibility, randomness and timeliness. Firstly, some representative sampling areas in a definite region should be selected, based on the relevant hypsographic maps and airscapes. During the course of sampling soil and plant, a field survey related to the sampling sites should be carried out to understand the natural affecting factors on the soil nutrient cycling in a regional agro-ecosystem scale. Moreover, the farmers' basic status, crop production, and applied amount of fertilizers and their allotment should be also investigated. A case study of nutrient cycling in subtropical regions of China was carried out to approach the application of the method in the study of soil nutrient cycling in some regions.

By a batch method, this paper studied the effects of different concentration and pH of oxalate, an important root exudate, on the adsorption of acid phosphatase and its activity on < 2 microm colloids of yellow brown soil and latosol, and on minerals goethite and kaolinite. The results showed that the acid phosphatase adsorption by goethite was less affected by the concentration of oxalate; while the adsorbed amount of this enzyme by the other test colloids and kaolinite was sharply decreased with the increasing oxalate concentration (0-5 mmol x L(-1)) first, and then gradually increased to the level equal to or less than the blank, which may be related to the coordination type of oxalate on soil colloids and minerals, and their surface charge change and dissolution. In the systems oxalate existed, the adsorbed amount of acid phosphatase by soil colloids and minerals decreased in order of goethite >> yellow brown soil > kaolinite > latosol. The pH value for the maximum adsorption of acid phosphatase was between the IEP of the enzyme and the PZC of test colloids and minerals. After the enzyme was immobilized on colloids and minerals, the pH of its maximum specific activity had no change, or shifted to a higher value.

This paper studied the effect of acetic acid with different concentrations and pH values on the adsorption of acid phosphatase by some soil colloids and clay minerals (SCCM). The results showed that the pH values for the maximum adsorption of the enzyme were between the IEP of the enzyme and the PZC of SCCM. In the acetic acid systems, the amount of the enzyme adsorbed by SCCM was in the order of goethite >> yellow brown soil > latosol > kaolinite > delta-MnO2. A remarkable influence of acetic acid concentration on the adsorption amount and the binding energy of the enzyme was observed. With the increase of the concentration from 0 to 200 mmol.L-1 in the system, acetic acid exhibited an enhanced effect, followed by an inhibition action on the adsorption of the enzyme on SCCM. The changes of the binding energy (K value) for the enzyme on SCCM were on the contrary to those of the maximum adsorption. The possible mechanisms for the influence of acetic acid on the adsorption of enzyme by SCCM were also discussed.

Red soil from Chenzhou of Hunan and brown soil from Gongyi of Henan were collected and treated with Cu (NO3)2, Zn(NO3)2 or Cd(NO3)2, respectively for 2 weeks, and Rhizobium fredii strain HN01 was inoculated. Sequential extraction method was employed to investigate the forms of Cu, Zn and Cd in the examined soils with the absence and presence of rhizobia. The results showed that after inoculation, the total amount of solid-bound Zn decreased 10%, and the amount of Zn associated with carbonate, Mn oxides, and organic matter fraction decreased 9-26%. No significant change was observed for the total amount of Zn combined with the solid phase of red soil in the presence of rhizobia. However, the amount of specifically adsorbed and Mn oxides bound Zn decreased, while the amount of exchangeable Zn increased. Inoculation of rhizobia depressed the release of Cu to the soil solution, and increased the total amount of Cu associated with the solid phase of brown soil. The increase of the amount of exchangeable Cu and of the Cu in fractions of carbonate, Mn oxides and organic matter ranged from 20% to 54%. There was no significant change for the level of Cd in the solution in both soils after rhizobia inoculation. The amount of exchangeable and organic Cd increased 22% and 11%, while the specifically adsorbed, and Mn oxides bound Mn decreased 14% and 29%, respectively. The different influence of rhizobia on the morphological distribution of test heavy metals in two soils was mainly ascribed to the soil pH changes.

Adsorption of acid phosphatase on goethite, kaolinite and two colloids from the soils in central and south China in the presence of organic acids and phosphate was studied. With the increase of anion concentration, the ability in decreasing enzyme adsorption followed the sequence: phosphate>tartrate>oxalate>acetate. Acetate showed promotive effect on enzyme adsorption at lower anion concentrations whereas oxalate, tartrate and phosphate compete effectively with enzyme in a broad range of anion concentration. The adsorption isotherms of enzyme in most of the anionic systems studied conformed to the Langmuir equation. Phosphate reduced the affinity of enzyme on goethite more significantly than the other anions. However, tartrate decreased the affinity of enzyme on soil colloids and kaolinite to a greater extent than phosphate, oxalate and acetate. This observation suggested that the impact of anions on enzyme adsorption varies with anionic type and the surface characteristics of soil components. The influence of the addition order of ligand on enzyme adsorption was found greater in tartrate and phosphate systems. In general, simultaneous introduction of ligand and enzyme into the system had the lowest enzyme adsorption, showing more competition between ligand and enzyme molecules in this system. Data from this work indicated that the status and activity of enzyme in certain soil microenvironments especially the rhizosphere where various organic and inorganic ligands are active can be altered and may be completely different from the bulk soil.

Heavy metal contamination of soils has been a global environmental issue over the past decades, threatening food security and human health. Understanding the migration and transformation of heavy metals in soils is critical for restoring an impaired environment and developing sustainable agriculture, particularly in the face of global warming. However, little effort has been devoted to investigating the impact of elevated temperatures on the migration and distribution of exogenous heavy metals in soils. This study experimented with a 180-day incubation at 15 °C, 30 °C, and 45 °C with an arable soil (Alfisol) of Huang-Huai-Hai River Basin, China, which was initially spiked with copper (Cu). A comparison of the results revealed that the percentage of soil water-soluble Cu doubled at 45 °C compared with 15 °C. The percentage of protein-like substances in dissolved organic matter (DOM) was the highest at 45 °C, suggesting that proteinaceous components play a more significant role in controlling the dissolution of Cu into DOM. Moreover, by sequential extraction and micro-X-ray fluorescence (μ-XRF), Cu was facilitatively transformed from exchangeable, and specifically adsorbed fractions, to iron (Fe)/manganese (Mn) oxides bound species by 7.75% 23.63% with the elevation of temperature from 15 °C to 45 °C. The conversion of Cu speciation is attributed to the significant release of organic carbon from Fe/Mn oxides, especially the Mn oxide components, which are available for Cu binding. The findings of this work will provide an in-depth understanding of the fate of Cu in soils, which is fundamental for the risk assessment and remediation of Cu-polluted soils in the Huang-Huai-Hai River Basin under the context of global warming. [Display omitted] • Warming enhanced Cu transformation to soil solution and solid phases. • The proteinaceous components control the binding of Cu with soil DOM. • The release of OC from Fe/Mn oxides offered the binding sites for Cu. • The μ-XRF provided direct evidence for the formation of stable Cu in soil. [ABSTRACT FROM AUTHOR]

Pot experiments were conducted to investigate the effects of γ-polyglutamic acid (γ-PGA), phosphate rock (PR), and γ-PGA-activated PR (γ-PGA-PR) on the immobilization and phytotoxicity of Pb in a contaminated soil. The proportion of residual Pb (Re-Pb) in soil was reduced by the addition of γ-PGA but was increased by the application of PR and γ-PGA-PR. The addition of γ-PGA in soil improved the accumulation of Pb in pak choi and decreased the growth of pak choi, suggesting the intensification of Pb phytotoxicity to pak choi. However, opposite effects of PR and γ-PGA-PR on the phytotoxicity of Pb to pak choi in soil were observed. Moreover, in the examined range, γ-PGA-PR activated by a higher amount of γ-PGA resulted in a greater proportion of Re-Pb in soil and weaker phytotoxicity of Pb to pak choi. The predominance of γ-PGA-PR in relieving the phytotoxicity of Pb was ascribed mainly to the increase of soil pH and available phosphate after the amendment, which could facilitate the precipitation of Pb in soil and provide pak choi with more phosphorus nutrient. [ABSTRACT FROM AUTHOR]