Communities In Agricultural Soils Research Articles

The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil.

Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices.

Impacts of the coexistence of polystyrene microplastics and pesticide imidacloprid on soil nitrogen transformations and microbial communities

The pollution of agricultural soils by microplastics (MPs) and pesticides has attracted significant attention. However, the combined impact of MPs and pesticides on soil nitrogen transformation and microbial communities remains unclear. In this study, we conducted a 28-day soil incubation experiment, introducing polystyrene microplastics (PS-MPs) at concentrations of 0.1% and 10% (w/w) and pesticide imidacloprid at concentrations of 0.1 mg/kg and 1.0 mg/kg. Our aim was to investigate the individual and combined effects of these pollutants on nitrogen transformations and microbial communities in agricultural soils. Imidacloprid accelerated the decline in soil pH, while PS-MPs slowed the process. Imidacloprid hindered soil nitrification and denitrification processes, however, the presence of PS-MPs mitigated the inhibitory effects of imidacloprid. Based on microbial community and functional annotation analyses, this is mainly attributed to the different effects of PS-MPs and imidacloprid on soil microbial communities and the expression of key nitrogen transformation-related genes. Variance partitioning analysis and partial least squares path modeling analyses revealed that PS-MPs and imidacloprid indirectly influenced the microbial community structure, primarily through changes in soil pH. This study elucidates the mechanism through which the combined stress of MPs and pesticides in agricultural soils influence soil nitrogen transformation and microbial communities. The findings offer valuable insights for the systematic evaluation of the ecological risks posed by the coexistence of these pollutants.

Increases in the soil ammonia oxidizing phylotypes and their rechange due to long-term irrigation with wastewater.

Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.

Heavy metal contamination impacts the structure and co-occurrence patterns of bacterial communities in agricultural soils.

Heavy metal (HM) contamination caused by mining and smelting activities can be harmful to soil microbiota, which are highly sensitive to HM stress. Here, we explore the effects of HM contamination on the taxonomic composition, predicted function, and co-occurrence patterns of soil bacterial communities in two agricultural fields with contrasting levels of soil HMs (i.e., contaminated and uncontaminated natural areas). Our results indicate that HM contamination does not significantly influence soil bacterial α diversity but changes the bacterial community composition by enriching the phyla Gemmatimonadetes, Planctomycetes, and Parcubacteria and reducing the relative abundance of Actinobacteria. Our results further demonstrate that HM contamination can strengthen the complexity and modularity of the bacterial co-occurrence network but weaken positive interactions between keystone taxa, leading to the gradual disappearance of some taxa that originally played an important role in healthy soil, thereby possibly reducing the resistance of bacterial communities to HM toxicity. The predicted functions of bacterial communities are related to membrane transport, amino acid metabolism, energy metabolism, and carbohydrate metabolism. Among these, functions related to HM detoxification and antioxidation are enriched in uncontaminated soils, while HM contamination enriches functions related to metal resistance. This study demonstrated that microorganisms adapt to the stress of HM pollution by adjusting their composition and enhancing their network complexity and potential ecological functions.

Low-density polyethylene microplastics alter chemical properties and microbial communities in agricultural soil

Microplastic (MP) pollution in agricultural soils, resulting from the use of plastic mulch, compost, and sewage sludge, jeopardizes the soil microbial populations. However, the effects of MPs on soil chemical properties and microbial communities remain largely unknown. Here, we investigated the effects of different concentration levels (0, 0.1, 1, 3, 5, and 7%; w:w) of low-density polyethylene (LDPE) MPs on the chemical properties and bacterial communities of agricultural soil in an incubation study. The addition of LDPE MPs did not drastically change soil pH (ranging from 8.22 to 8.42). Electrical conductivity increased significantly when the LDPE MP concentrations were between 1 and 7%, whereas the total exchangeable cations (Na+, K+, Mg2+, and Ca2+) decreased significantly at higher LDPE MP concentrations (3–7%). The highest available phosphorus content (2.13 mg kg−1) was observed in 0.1% LDPE MP. Bacterial richness (Chao1 and Ace indices) was the lowest at 0.1% LDPE MP, and diversity indices (Shannon and Invsimpson) were higher at 0 and 1% LDPE MP than at other concentrations. The effect of LDPE MP concentrations on bacterial phyla remained unchanged, but the bacterial abundance varied. The relative abundance of Proteobacteria (25.8–33.0%) was the highest in all treatments. The abundance of Acidobacteria (15.8–17.2%) was also high, particularly in the 0, 0.1, and 1% LDPE MPs. With the increase in LDPE MP concentration, the abundance of Actinobacteria gradually increased from 7.80 to 31.8%. Our findings suggest that different MP concentration levels considerably alter soil chemical properties and microbial composition, which may potentially change the ecological functions of soil ecosystems.

Antibiotic resistome and associated bacterial communities in agricultural soil following the amendments of swine manure-derived fermentation bed waste.

The practice of utilizing animal manures on land is widespread in agriculture, but it has raised concerns about the possible spread of antibiotic resistance genes (ARGs) and thepotential risk it poses to public health through food production. Fermentation bed culture is an effective circular agricultural practice commonly utilized in pig farming that minimizes the environmental impact of livestock farming. However, this method generates a significant amount of fermentation bed waste (FBW), which can be turned into organic fertilizer for land application. The objective of this research was to examine the impacts of amending agricultural soil samples with swine manure-derived FBW on microbial communities, mobile genetic elements (MGEs), and ARG profiles over different periods. The study findings indicated that the amendment of swine manure-derived FBW significantly increased the diversity and abundance of ARGs and MGEs during the early stages of amendment, but this effect diminished over time, and after 12months of FBW amendments, the levels returned to those comparable to control samples. The shift in the bacterial communities played a significant role in shaping the patterns of ARGs. Actinobacteriota, Proteobacteria, and Bacteroidetes were identified as the primary potential hosts of ARGs through metagenomic binning analysis. Furthermore, thepH of soil samples was identified as the most important property in driving the composition of the bacterial community and soil resistome. These findings provided valuable insights into the temporal patterns and dissemination risks of ARGs in FBW-amended agriculture soil, which could contribute to the development of effective strategies to manage the dissemination risks of FBW-derived ARGs.

Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties

Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.

The role of inherited characteristics from parent materials in shaping bacterial communities in agricultural soils

Parent materials are crucial in soil formation and development, but their importance in shaping soil bacterial communities after thousands of years of soil formation remains unknown, especially in agricultural soils. To resolve the influence of underlying features inherited from parent materials on soil microbiome, the microbial community in 197 agricultural soils with long-term crop cultivation history and nonagricultural reference soils from four major types of soils in China, i.e., quaternary red clay soils, tertiary red sandstone soils, alluvial soils and black soils, were analyzed and compared. We found that different types of soils supported distinct bacterial communities. The characteristics inherited from parent materials explained more of the variation (31.47%) in bacterial community structure than the selected variables regulated by soil management (1.63%) and the climate condition (1.10%). Only 9.0% of total bacterial amplicon sequence variants (ASVs) which contributed, on average, 47% of the total bacterial abundances in a given agricultural soil, were shared by all soil types. These abundant common ASVs were closely related to agricultural practices, suggesting a strong enrichment effect of a small number of core taxa by long-term crop cultivation. In contrast, approximately 55.6% of ASVs with low relative abundance were specific to soil type. These specific groups were closely associated with the distinctive features of soil type, implying that they represent unique populations selected by the parent material features during pedogenesis. Collectively, soil type may have a strong selective pressure on the bacterial communities in matured agricultural soils, leading to a large pool of specific taxa with limited environmental occurrence. Whilst a small number of core taxa achieve high abundances by responding to long-term crop cultivation.

Moderate Nitrogen Reduction Increases Nitrogen Use Efficiency and Positively Affects Microbial Communities in Agricultural Soils

Excessive nitrogen fertilizer usage in agricultural often leads to negative ecological and production gains. Alterations in the physical and chemical properties and microbial community structure of agricultural soils are both the cause and consequence of this process. This study explored the perturbation of soil properties and microorganisms in agricultural soils by different nitrogen levels. Soil total nitrogen, total phosphorus, and total potassium decreased in the shallow soil layer with decreasing nitrogen. Changes in nitrogen affected soil organic matter, pH, bulk density, and water content. However, a moderate reduction in nitrogen did not cause significant yield loss; the increased nitrogen use efficiency was the main reason, attributed to the available phosphorus and potassium. Short-term changes in nitrogen had limited effects on soil microbial community structure. Bacteria were more susceptible to perturbation by nitrogen changes. Nitrogen reduction increased the relative abundance of MND1 (1.21%), RB41 (1.96%), and Sphingomonas (0.72%) and decreased Dongia (0.3%), Chaetomium (0.41%), and Penicillium (0.5%). Nitrogen reduction significantly increased the bacteria functional composition of aerobic ammonia oxidation (4.20%) and nitrification (4.10%) and reduced chemoheterotrophy (2.70%) and fermentation (4.08%). Available phosphorus specifically drove bacterial community structure variation in the shallow soil layers of moderate nitrogen reduction treatments. Steroidobacter, RB41, Gemmatimonas, Ellin6067, Haliangium, and Sphingomonas were the main component nodes in this community structure. These results provide insights into the study of nitrogen and microorganisms in agricultural soils.

Climate-smart agricultural practices influence the fungal communities and soil properties under major agri-food systems.

Fungal communities in agricultural soils are assumed to be affected by climate, weather, and anthropogenic activities, and magnitude of their effect depends on the agricultural activities. Therefore, a study was conducted to investigate the impact of the portfolio of management practices on fungal communities and soil physical-chemical properties. The study comprised different climate-smart agriculture (CSA)-based management scenarios (Sc) established on the principles of conservation agriculture (CA), namely, ScI is conventional tillage-based rice-wheat rotation, ScII is partial CA-based rice-wheat-mungbean, ScIII is partial CSA-based rice-wheat-mungbean, ScIV is partial CSA-based maize-wheat-mungbean, and ScV and ScVI are CSA-based scenarios and similar to ScIII and ScIV, respectively, except for fertigation method. All the scenarios were flood irrigated except the ScV and ScVI where water and nitrogen were given through subsurface drip irrigation. Soils of these scenarios were collected from 0 to 15 cm depth and analyzed by Illumina paired-end sequencing of Internal Transcribed Spacer regions (ITS1 and ITS2) for the study of fungal community composition. Analysis of 5 million processed sequences showed a higher Shannon diversity index of 1.47 times and a Simpson index of 1.12 times in maize-based CSA scenarios (ScIV and ScVI) compared with rice-based CSA scenarios (ScIII and ScV). Seven phyla were present in all the scenarios, where Ascomycota was the most abundant phyla and it was followed by Basidiomycota and Zygomycota. Ascomycota was found more abundant in rice-based CSA scenarios as compared to maize-based CSA scenarios. Soil organic carbon and nitrogen were found to be 1.62 and 1.25 times higher in CSA scenarios compared with other scenarios. Bulk density was found highest in farmers' practice (Sc1); however, mean weight diameter and water-stable aggregates were found lowest in ScI. Soil physical, chemical, and biological properties were found better under CSA-based practices, which also increased the wheat grain yield by 12.5% and system yield by 18.8%. These results indicate that bundling/layering of smart agricultural practices over farmers' practices has tremendous effects on soil properties, and hence play an important role in sustaining soil quality/health.

Stronger responses of soil protistan communities to legacy mercury pollution than bacterial and fungal communities in agricultural systems

Soil pollution is an important stressor affecting biodiversity and ecosystem functioning. However, we lack a holistic understanding of how soil microbial communities respond to heavy metal pollution in agricultural ecosystems. Here, we explored the distribution patterns and inter-kingdom interactions of entire soil microbiome (including bacteria, fungi, and protists) in 47 paired paddy and upland fields along a gradient of legacy mercury (Hg) pollution. We found that the richness and composition of protistan community had stronger responses to Hg pollution than those of bacterial and fungal communities in both paddy and upland soils. Mercury polluted soils harbored less protistan phototrophs but more protistan consumers. We further revealed that long-term Hg pollution greatly increased network complexity of protistan community than that of bacterial and fungal communities, as well as intensified the interactions between protists and the other microorganisms. Moreover, our results consistently indicated that protistan communities had stronger responses to long-term Hg pollution than bacterial and fungal communities in agricultural soils based on structural equation models and random forest analyses. Our study highlights that soil protists can be used as bioindicators of Hg pollution, with important implications for the assessment of contaminated farmlands and the sustainable management of agricultural ecosystems.

Patterns of denitrifier communities assembly and co-occurrence network regulate N2O emissions in soils with long-term contrasting tillage histories

Denitrification is reducing nitrate to nitrous oxide (N2O) and nitrogen (N2) under the action of denitrifying microorganisms, which are the main source of soil N2O emissions. However, the co-occurrence pattern and community assembly process of denitrifier communities have not been studied in agricultural soils with long-term contrasting tillage histories. Based on a continuous (> 11 yr) conservation experiment, we aimed to understand the community assembly process and co-occurrence network of nirK-, nirS-, nosZI- and nosZII-type denitrifier communities under conservation tillage (i.e., zero tillage (ZT) and chisel plough tillage (CPT)) and conventional tillage (i.e., plow tillage (PT)). Continuous in situ measurements showed that long-term conservation tillage significantly decreased the denitrification potential and N2O emission fluxes. CPT and ZT significantly increased the taxonomic and phylogenetic diversity of nirK, nosZI, and nosZII type communities, whereas consistently decreased the diversity of nirS-type communities, compared with PT. Although the assembly of nirK, nirS, nosZI, and nosZII type denitrifier communities were dominated by stochastic processes, the relative importance of stochastic assembly of denitrifying microbial communities was higher in conservation tillage soil. The co-occurrence network analyses further revealed clear tillage-induced ecological functions of N2O emissions, as evidenced by lower key nodes abundance and robustness of nirS and nirK communities network and higher key nodes abundance and robustness of nosZI and nosZII communities in conservation tillage soils. Variation partitioning analysis further indicated that the assembly processes significantly changed soil N2O emission intensity by regulating α-diversity and the key species abundances in the co-occurrence network of denitrifying communities. Overall, conservation tillage practices increased the diversity and the key nodes abundance of nosZI- and nosZII-type communities and decreased the diversity and the key nodes abundance of nirS- and nirK-type communities by regulating the relative importance of the stochastic assembly process of denitrifier communities, which is eventually likely to curb N2O emissions by strengthening the capacity of the N2O sink and weakening the capacity of the N2O source. These findings provide new insights into the formation of dryland microbial communities in agricultural soils with long-term contrasting tillage histories. Especially considering future climate change, this knowledge would prove useful in improving agroecosystem productivity and curbing greenhouse gas emissions.

Distinct and Temporally Stable Assembly Mechanisms Shape Bacterial and Fungal Communities in Vineyard Soils

Microbial communities in agricultural soils are fundamental for plant growth and in vineyard ecosystems contribute to defining regional wine quality. Managing soil microbes towards beneficial outcomes requires knowledge of how community assembly processes vary across taxonomic groups, spatial scales, and through time. However, our understanding of microbial assembly remains limited. To quantify the contributions of stochastic and deterministic processes to bacterial and fungal assembly across spatial scales and through time, we used 16 s rRNA gene and ITS sequencing in the soil of an emblematic wine-growing region of Italy.Combining null- and neutral-modelling, we found that assembly processes were consistent through time, but bacteria and fungi were governed by different processes. At the within-vineyard scale, deterministic selection and homogenising dispersal dominated bacterial assembly, while neither selection nor dispersal had clear influence over fungal assembly. At the among-vineyard scale, the influence of dispersal limitation increased for both taxonomic groups, but its contribution was much larger for fungal communities. These null-model-based inferences were supported by neutral modelling, which estimated a dispersal rate almost two orders-of-magnitude lower for fungi than bacteria.This indicates that while stochastic processes are important for fungal assembly, bacteria were more influenced by deterministic selection imposed by the biotic and/or abiotic environment. Managing microbes in vineyard soils could thus benefit from strategies that account for dispersal limitation of fungi and the importance of environmental conditions for bacteria. Our results are consistent with theoretical expectations whereby larger individual size and smaller populations can lead to higher levels of stochasticity.

Microbial Community Compositional Stability in Agricultural Soils During Freeze-Thaw and Fertilizer Stress

Microbial activity persists in cold region agricultural soils during the fall, winter, and spring (i.e., non-growing season) and frozen condition, with peak activity during thaw events. Climate change is expected to change the frequency of freeze-thaw cycles (FTC) and extreme temperature events (i.e, altered timing, extreme heat/cold events) in temperate cold regions, which may hasten microbial consumption of fall-amended fertilizers, decreasing potency come the growing season. We conducted a high-resolution temporal examination of the impacts of freeze-thaw and nutrient stress on microbial communities in agricultural soils across both soil depth and time. Four soil columns were incubated under a climate model of a non-growing season including precipitation, temperature, and thermal gradient with depth over 60 days. Two columns were amended with fertilizer, and two incubated as unamended soil. The impacts of repeated FTC and nutrient stress on bacterial, archaeal, and fungal soil community members were determined, providing a deeply sampled longitudinal view of soil microbial response to non-growing season conditions. Geochemical changes from flow-through leachate and amplicon sequencing of 16S and ITS rRNA genes were used to assess community response. Despite nitrification observed in fertilized columns, there were no significant microbial diversity, core community, or nitrogen cycling population trends in response to nutrient stress. FTC impacts were observable as an increase in alpha diversity during FTC. Community compositions shifted across a longer time frame than individual FTC, with bulk changes to the community in each phase of the experiment. Our results demonstrate microbial community composition remains relatively stable for archaea, bacteria, and fungi through a non-growing season, independent of nutrient availability. This observation contrasts canonical thinking that FTC have significant and prolonged effects on microbial communities. In contrast to permafrost and other soils experiencing rare FTC, in temperate agricultural soils regularly experiencing such perturbations, the response to freeze-thaw and fertilizer stress may be muted by a more resilient community or be controlled at the level of gene expression rather than population turn-over. These results clarify the impacts of winter FTC on fertilizer consumption, with implications for agricultural best practices and modeling of biogeochemical cycling in agroecosystems.

Response of Nitrifier and Denitrifier Abundance to Salinity Gradients in Agricultural Soils at the Yellow River Estuary

Salinization is considered a threat to agricultural soil and decreases crop yield worldwide. Nitrification and denitrification are the core processes of soil N-cycle. However, the response of nitrifiers and denitrifiers to salinity in agricultural soils remains ambiguous. The study aimed to explore the effect of salinity on nitrifiers and denitrifiers communities in agricultural soils along a naturally occurring salinity gradient. The effects of salinity on the abundance, composition, and interactions of nitrifiers and denitrifiers in surface soils were investigated. The abundance of nitrifiers significantly decreased in response to the increase in salinity. Ammonia-oxidizing archaea (AOA) were more susceptible to salinity elevation than ammonia-oxidizing bacteria (AOB). Nitrospira and Nitrobacter showed a similar trend to the salinity gradient, but the relative abundance of Nitrobacter was increased in the saline soils. High salinity decreased the abundance of napA and nirK, but had no significant effect on other marker genes for denitrification. Besides electrical conductivity, total sulfur (TS)+available potassium (AK) and TN+TS+C/N+total phosphorus (TP)+AK significantly explained the variation in denitrifier and nitrifier communities. We also found that high salinity decreased the connections between different N functional genes. These results implied the alteration of the nitrogen cycling community by high salinity mainly through decreasing AOA, NOB, and some denitrifiers with nitrate or nitrite reduction potentials and weakening the connectivity between nitrogen cycling drivers.

Tolerance of soil bacterial community to tetracycline antibiotics induced by As, Cd, Zn, Cu, Ni, Cr, and Pb pollution

Abstract. The widespread use of both heavy metals and antibiotics in livestock farming, followed by their subsequent arrival on agricultural soils through manure and slurry spreading, has become a problem of vital importance for human health and the environment. In the current research, a laboratory experiment was carried out for 42 d to study tolerance and co-tolerance of three tetracycline antibiotics (tetracycline, TC; oxytetracycline, OTC; chlortetracycline, CTC) in soils polluted with heavy metals (As, Cd, Zn, Cu, Ni, Cr, and Pb) at high concentrations (1000 mg kg−1 of each one, separately). Pollution induced community tolerance (PICT) of the bacterial community was estimated using the leucine incorporation technique. The log IC50 (logarithm of the concentration causing 50 % inhibition in bacterial community growth) values obtained in uncontaminated soil samples for all the heavy metals tested showed the following toxicity sequence: Cu > As > Cr ≥ Pb ≥ Cd > Zn > Ni. However, in polluted soil samples the toxicity sequence was Cu > Pb ≥ As ≥ Cd ≥ Cr ≥ Ni ≥ Zn. Moreover, at high heavy metal concentrations, the bacterial communities showed tolerance to the metal itself, this taking place in the long term for all the metals tested. The bacterial communities of the soil polluted with heavy metals showed also long-term co-tolerance to TC, OTC, and CTC. This kind of study, focusing on the eventual increases of tolerance and co-tolerance of bacterial communities in agricultural soil, favored by the presence of different kinds of pollutants, is of crucial importance, mostly bearing in mind that the appearance of antibiotic resistance genes in soil bacteria could be transmitted to human pathogens.

Bacterial and archaeal communities in saline soils from a Los Negritos geothermal area in Mexico

In recent years, there has been a growing need to understand how salinity affects microbial communities in agricultural soils. The archaeal and bacterial community diversity and structure were investigated through high-throughput sequencing analysis of their 16S rRNA in two arable soils with low electrolytic conductivity (EC) (arable 1 soil 2.3 dS m -1 and arable 2 soil 2.6 dS m -1 ) and a saline soil (EC = 17.6 dS m -1 ). The dominant bacterial phyla in the soils were Proteobacteria (relative abundance 46.2±8.9%), followed by Acidobacteria (13.1±9.1%) and Actinobacteria (10.0±4.8%), while Serratia (6.0±5.8%) and Bacillus (4.0±3.6%) were the dominant bacterial genera. Candidatus Nitrososphaera (53.5±46.8%) was the dominant archaeal phylotype in the arable soils, whereas Nitrosopumilus (0.4±0.01%) in the saline soil. The archaeal and bacterial community structure was different between the soils and the sand, As, Ba and Sb content had a significant effect on bacterial and archaeal community structure in the soils of this study, but not soil salinity.

Effect of different washing solutions on soil enzyme activity and microbial community in agricultural soil severely contaminated with cadmium.

Soil enzyme activities and microbial communities have a good response to the remediation effect of heavy metal-contaminated soils. To evaluate the effect of three commonly used washing agents, ferric chloride (FC), ethylenediaminetetraacetic acid (EDTA) and ethylenediamine-tetra-methylenephosphonic acid (EDTMP) on soil enzyme activities and microbial community in cadmium (Cd)-contaminated agricultural soil were collected from farmland near a non-ferrous metal smelter. The soil enzyme activities, microbial community, chemical forms of Cd and some physicochemical properties of the soil washed with different washing solutions were determined. The results showed that the three washing solutions had moderate removal efficiencies for Cd in the tested soil and the breakdown product of EDTMP has a certain stabilizing effect on Cd. The geometric mean and the integrated total enzyme activity index showed that soil washing with FC and EDTA was more beneficial to the restoration of biochemical functions than that with EDTMP. After soil washing, the Chao1 index of bacteria increased, and the microbial community structure changed. Pearson correlation analysis and redundancy analysis (RDA) indicated that the three washing solutions affected soil enzyme activities and microbial community by altering soil nutrient, total Cd concentration and Cd fractions in soils.

The long-term effects of microplastics on soil organomineral complexes and bacterial communities from controlled-release fertilizer residual coating

Controlled-release fertilizer (CRF) was applied widely in China as an efficient utilization strategy for improving grain yield and reducing the nitrogen contamination. However, it was indeterminate to know the impacts of inevitably imported plastic into the soil on sustainable development. After ten-year fixed-site experiment, the visible residual coating microplastics were separated from the soil to measure their changes, then the long-term effects of CRF application (theoretical microplastic content 0.018–0.151 g kg−1 soil) on soil architecture and bacterial communities were evaluated. Based on soil organomineral complexes (OMC) distribution experiments and soil 16S rRNA sequence analysis, residual coating microplastics had no significant impact on soil architecture and limited effects on soil bacteria, but became the specific microbial habitat. The nitrogen rate and nitrogen release mode affected sand- and silt-grade OMC, and nitrogen rate impacted soil bacteria communities. The residual coating, small inert particles, is safe for soil OMC and bacterial communities in agricultural soil. Due to the effectiveness of CRF on reducing environmental pollution, CRF is considered as a favorable measure to the sustainable agricultural development in Shandong Province, China.

Metagenomic Analysis of Bacterial Communities in Agricultural Soils from Vietnam with Special Attention to Phosphate Solubilizing Bacteria.

Bacterial communities can promote increased phosphorus (P) availability for plants and microbes in soil via various mechanisms of phosphate solubilization. The production of extracellular phosphatases releases available P through the hydrolysis of organic P. Examining the abundance and diversity of the bacterial community, including phosphate solubilizing bacteria in soil, may provide valuable information to overcome P scarcity in soil ecosystems. Here, the diversity and relative abundance of bacterial phyla and genera of six agricultural soil samples from Vietnam were analysed by next generation sequencing of the 16S rRNA gene. Phosphatase activities of each soil were compared with physico-chemical parameters and the abundance of the alkaline phosphatase gene phoD. We showed the dominance of Chloroflexi, Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes. Total nitrogen positively correlated with phyla Proteobacteria, Acidobacteria, Firmicutes and Planctomycetes. The abundance of several genera of Proteobacteria showed positive relationship with the copy number of the phoD gene. The abundance of several taxa positively correlated with silt content, while a negative relationship of Proteobacteria was found with sand content. Our results demonstrated the clear influence of soil physico-chemical properties on the abundance of various bacterial taxa including those potentially involved in phosphate solubilization.