Microorganisms were reported to be the indicators and drivers of metal(loid)s-contaminated soils. Chloroflexota is a widely-distributed phylum in arsenic (As) and antimony (Sb) contaminated soils, but the diversity and functional potential of its genomes remain largely unknown. In this study, we collected As and Sb contaminated soils from smelting-affected agricultural soils and mining soils, with the latter exhibiting much higher concentrations of As (mean 19421.2 mg kg⁻¹) and Sb (mean 4953.5 mg kg⁻¹) as well as lower carbon and nitrogen levels. We reconstructed 170 medium- to high-quality metagenome-assembled genomes (MAGs) of Chloroflexota from these soils. A total of 11 MAGs were proposed as novel candidate species, including 3 novel candidate genera affiliated with the classes Ktedonobacteria, Limnocylindria, and Dormibacteria. Functional annotation reveals that many MAGs from Ktedonobacteria and Dormibacteria may have novel potential for carbon fixation through the Calvin–Benson–Bassham cycle. Additionally, many Chloroflexota MAGs harbored essential genes involved in enhancing soil phosphorus (P) availability. In Chloroflexota MAGs, the gene responsible for extracellular oxidation, dldH, rather than the intracellular oxidation gene arsO, was widespread for Sb(III) oxidation. Under heavy As and Sb contamination and nutrient limitation, Chloroflexota MAGs exhibited higher guanine-cytosine contents and smaller genome sizes. Moreover, MAGs derived from these conditions were enriched with a higher proportion of genes related to Sb oxidation, As/P transport, As reduction and methylation, as well as pathways involved in carbohydrate degradation and bioavailable nitrogen biosynthesis. These findings might be helpful for developing bioremediation strategy for Chloroflexota in As/Sb contaminated soils.

Climate change has caused high weather variability, affecting crop production in arid and semi-arid regions. Circular buffer strips (CBS) of perennial native grasses can produce crops with less irrigation water while providing other ecological services. This study investigated the impact of CBS grasses on microbial abundances and soil health in water-limited semi-arid agroecosystems over five years (2017−2021). Experimental plots included corn (Zea mays L.) with and without buffer strips grass (BSG) in two adjoining center pivots. Soil samples were collected from 0−20, 20−40, 40−60, and 60−80 cm depths and analyzed for microbial community composition using phospholipid fatty acid (PLFA) indicators. Soils under BSG had greater biomass after the third year (37%), and this increase in microbial biomass was particularly mycorrhizal fungi. A significant decrease in microbial biomass with soil depths was also observed. Microbial biomass growth was strongly associated with annual precipitation, with water availability influencing the upper layers (0−20 and 20−40 cm) and soil nutrients, mainly nitrogen ({\text{NO}}_{\text{3}}^{-}-N) and pH, affecting the deeper layers (40−60 and 60−80 cm). Incorporating BSG in cropping systems modifies soil microbial communities, primarily the fungal component while increasing soil health and boosting plant-soil microbial interactions.

● Benzonase removes relic DNA twice as efficiently as PMA and is adaptable across more types of soil than DNase I.

Microbes play a crucial ecological role in soils, but the presence of relic DNA left by previous microorganisms can lead to inaccurate estimations of viable microbial function and diversity. To address this, we proposed a new method for removing relic DNA in soil using Benzonase endonuclease and compared it with propidium monoazide (PMA) and DNase I, which have been widely applied in viable microbiome studies. Unlike PMA, Benzonase does not require light activation and is suitable for use in opaque media such as soil. Therefore, its efficiency (40%−60%) in removing soil relic DNA was twice that of PMA (0−30%). Moreover, our results showed that Benzonase outperformed DNase I in most soils, probably due to its broader range of operating conditions compared to DNase I. In addition to higher relic DNA removal efficiency, Benzonase exhibited a weak impact on soil viable microbial communities. Subsequently, Benzonase was used to remove relic DNA in natural soils, and the results showed that relic DNA removal led to an approximately 10% reduction in microbial diversity and richness on average. Notably, it caused significant changes in the relative abundance of specific taxa, such as Bacillus and Sphingomonas. These findings reveal disparities between total and viable microbiomes in soils. Our study not only provides a reliable method for soil relic DNA removal but also highlights the necessity of relic DNA removal for viable soil microbiome assessments, laying the methodological foundation for advancing soil microbial ecology research.

● Impacts of soil moisture levels from 10% to 100% on two soil invertebrates.

Knowledge on impacts of climate change on soil invertebrate communities is scarce. Amongst the biggest challenges are the increase in temperature and arid regions, while at the same time, in other parts of the planet, extreme precipitation events and flooding occur. The aim of the present study was to investigate the impacts of drought and flooding in soil invertebrates. Enchytraeus crypticus and Folsomia candida, model ecotoxicology test-species (OECD) were used to assess performance (survival, reproduction, size) in LUFA 2.2 soil moistened to 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% of the soil water holding capacity (WHC). Overall, both species had high tolerance for drought and flooding scenarios, with survival threshold for E. crypticus being between 10% and 90% moisture and for F. candida being between 10% and 100% moisture. Reproduction decreased from moisture ≤30% and >70% moisture. In drought there was a decrease on adults’ size, for both species from ≤30% moisture. The morphological adaptations observed support evidence of adaptative phenotypic plasticity for both species, but highest for F. candida. A redistribution of soil invertebrate species can be expected to occur, this under the present and future climate change scenarios, with new and more tolerant species to prevail in different habitats. This will impact not only soil biodiversity structure, but also its function.

● Straw return lowered the abundances of nirS and nosZ genes in low nitrogen soil.

Rhizosphere denitrification is affected by straw return. However, the roles of root exudates and soil metabolites in shaping denitrifying bacteria under wheat straw return are relatively unexplored. Here, wheat straw was amended at 2% (w/w) to two paddy soils with different levels of nitrogen for rice cultivation, which altered the denitrifying bacterial community compositions of both soils. However, straw amendment decreased the abundances of the nirS and nosZ genes by 63.7% and 30.3% in the low nitrogen soil from Taizhou (TZ) but increased the nirK, nirS, and nosZ gene abundances by 116%, 81.0%, and 155.5% for the high nitrogen soil from Yixing (YX). Correspondingly, straw amendment decreased the relative abundance of root exudates in the categories of amino acids and benzenes for rice cultivated in TZ soil but increased the relative abundance of root exudates in the categories of amino acids for rice grown in YX soil. With elevated root exudates, straw amendment enhanced the relative abundances of many soil metabolites in YX soil such as sorbitol, myristic acid, and pentadecanoic acid, with fold changes > 2. These results suggest that straw return may alter the composition of root exudates and soil metabolites thereby affecting rhizosphere denitrifying bacterial communities and function genes.

Soil fertility is one of the key determinants of agricultural productivity. Soil food webs play an important role in driving soil nutrient cycling and plant health. However, it is poorly known how the soil food web composition and complexity affect plant growth and soil fertility. In this study, soil microorganisms and nematodes isolated from two soil types (i.e., calcareous soil and red soil) and two land use types (i.e., corn-soybean cultivation and natural grass-shrubland) were used to sequentially establish four soil micro-food webs (FW1, FW2, FW3, and FW4) with increasing levels of community complexity based on food web complexity. The four micro-food webs were inoculated to sterilized soils which were then planted with soybeans for three months in a pot experiment under ambient environment. The sterilized soil without food web inoculation was employed as control (C) and unsterilized soil with its original food web was also regarded as a treatment (US) in the experiment. The effects of soil micro-food web complexity on soil nutrient and soybean growth were explored. The results showed that soil total nitrogen (TN) and phosphorus (TP), soil microbial biomasses, and plant nitrogen and phosphorus were generally higher in the four food web inoculation treatments than in the control or unsterilized soil. Surprisingly, the original soil food web treatment (i.e., unsterilized soil) had lower soil or soybean nutrient than the no food web treatment (i.e., sterilized soil). In addition, the complexity of inoculated food webs was positively correlated with soil TN, TP, and total potassium (TK). These results suggest that soil micro-food web complexity is an important driver of soil fertility and affects crop growth. Particularly, complex soil micro-food web maintains higher soil fertility and crop growth. This study provides solid evidence of the roles of soil food web in controlling ecosystem services; and the findings could provide a better understanding of the soil food web structure and soil fertility relationships.

● Earthworms significantly reduced soil CH₄ uptake at both temperatures, and warming significantly promoted soil CH₄ uptake.

The function and service of biologically driven ecosystems are undergoing significant changes due to climate warming. Earthworms play a crucial role as soil engineer by modulating the effects of climate change on soil nutrient cycle through alterations to biotic and abiotic soil conditions. However, there is currently a scarcity of information regarding the impacts of earthworms and warming on soil CH₄ uptake and their associated microbial mechanisms. This study conducted a 61-day microcosm experiment to investigate the impact of warming (temperature rise from 14.2 °C to 17.2 °C) and the presence of earthworms (Eisenia fetida and Moniligaster japonicus) on soil CH₄ uptake. We employed gas chromatography and high-throughput sequencing to investigate the fluctuations in soil CH₄ uptake and the microbial communities involved in methane cycling. Compared to low temperature conditions (14.2 °C), we observed that warming significantly increased soil CH₄ uptake in all treatments (non-earthworm: 51.85%; Eisenia fetida: 50.88%; Moniligaster japonicus: 71.78%). Both Eisenia fetida and Moniligaster japonicus significantly reduced soil CH₄ uptake at two temperatures compared to the non-earthworm treatment. Nevertheless, no significant impacts were found on soil CH₄ uptake due to the interactions between earthworms and warming. The methanotroph communities exhibited notable variations among earthworm treatments, whereas the methanogenic communities displayed significant differences among temperature treatments. The interaction between earthworm and warming also resulted in noticeable variations in both methanogenic and methanotrophic communities. The FAPROTAX analysis revealed that earthworms and warming altered relative abundance of methanogens and methanotroph associated with CH₄ cycle functions. Soil properties exhibited a negative impact on CH₄ uptake, with DOC identified as the most crucial variable in predicting soil CH₄ uptake, while the α-diversity of methanotrophs was associated with enhanced CH₄ uptake. This study emphasized the crucial role of soil fauna in adjusting soil greenhouse gas emissions under the context of global warming.

● Cd alone or combined with microplastics (MPs) enhanced wheat biomass.

Microplastics and heavy metal contamination poses major threats to soil function and food security; however, their synergistic effects remain largely unclear. This study investigated the effects of single or combined addition of polyethylene (PE) microplastic (1% w/w) and cadmium (Cd; 1.5 and 5 mg kg^–1) on functional microbial communities in the wheat rhizosphere soil. We observed that the biomass of wheat increased by 142.44% under high doses of Cd addition. The bacterial alpha diversity in wheat bulk soil reduced by 37.34%–37.83% with the combined addition of microplastic and Cd. The addition of microplastic reduced the relative abundance of Proteus involved in nitrogen fixation by 19.93%, while the relative abundance of Proteus and Actinobacteria involved in nitrogen cycling increased with the increase of Cd concentration, increasing by 27.96%–37.37% and 51.14%–55.04%, respectively. FAPROTAX analysis revealed that increasing Cd concentration promoted the abundance of functional bacterial communities involved in nitrification/denitrification and nitrate/nitrite respiration in rhizosphere soil. A FunGuild analysis showed that the synergy of PE-microplastics and Cd increased the abundance of saprophytic fungi, suggesting an enhanced degradation function. Our findings provide new knowledge on the effects of microplastics and heavy metals on soil microorganisms and functional microbial communities in agricultural soil.

● Moderate dilution of natural soil with clay mineral complexes generated oligotrophic soils with a gradient of microbial abundance but similar C availability.

The regulatory gate hypothesis suggests that the mineralization of soil organic matter (SOM) is controlled by carbon accessibility due to microbial redundancy. However, this opinion is contentious because the extensively high available carbon released during the fumigation in these studies strongly stimulated microbial activity, which is unlikely to occur in real soil and would compensate for the effect of reduced microbial abundance. In this study, natural soil was moderately diluted with mineral complexes in varying proportions to obtain soils with a gradient of microbial abundance and low carbon availability. The results revealed that despite minimal changes in the dissolved organic carbon content (DOC), the CO₂ emission rate and activity of SOM hydrolysis significantly decreased with decreasing microbial abundance. Regression analysis and the random forest model highlighted microbial abundance as the primary factor influencing carbon decomposition, which was more fundamental than DOC and microbial diversity. These findings underline the crucial role of microbes in soil carbon turnover and the importance of maintaining microbial abundance to preserve the soil carbon cycling capacity.

● Rhizosphere microbial network in crater had higher complexity than in volcanic cone.

Volcanic eruptions are significant natural disturbances that provide valuable opportunities to study their impacts on soil microorganisms. However, no previous studies have compared the rhizosphere microbial communities of Boehmeria nivea L. in volcanic craters and cones. To address this gap, we conducted a comprehensive investigation using Illumina MiSeq high-throughput sequencing to compare the rhizosphere microbial communities in volcanic craters and cones. Principal Coordinate Analysis revealed significant differences in the rhizosphere microbial communities between the crater and cone. The bacterial communities in the rhizosphere of the crater exhibited higher diversity and evenness compared to the cones. Moreover, the cones displayed more intricate bacterial networks than the crater (nodes 556 vs. 440). Conversely, fungal networks were more complex in the crater than the cone (nodes 943 vs. 967). Additionally, bacterial communities demonstrated greater stability than fungal ones within these volcanic soils (avgK 241.1 vs. 499.7) and (avgCC 1.047 vs. 1.092). Furthermore, the Structural Equation Model demonstrated a direct positive impact of alpha diversity on soil microbial community multifunctionality in the crater (λ = 0.920, P < 0.001). Our findings have presented the opportunity to investigate the characteristics of the rhizosphere microbial communities of Boehmeria nivea L. in the crater and cone.

● The Transformer model precisely predicts soil health status from high-throughput sequencing data.

Inhibiting the occurrence of soil-borne diseases is considered as the most favorable approach for promoting sustainable agricultural development. Constructing soil disease prediction models can serve precision agriculture. However, the analysis results of the meta-framework often contradict each other, causing inconsistency in the important features of machine learning results. Therefore, it is necessary to compare the classification accuracy of various machine learning models and further optimize the features of the models to enhance their classification accuracy. Here, we conducted a comparison of eight common machine learning algorithms (XGBoost, CatBoost, Decision Tree, LGBM, Naïve Byes, Perceptron, Logistic, and Random Forest) at the levels of family, genus, and class. The important features of the model were extracted based on the differences in model accuracy and important features, followed by an interpretable analysis of these important features using feature importance. Subsequently, the data underwent resampling using the SMOTE algorithm, and the results show that the SMOTE-Transformer model performs well, surpassing the training results of the voting and stacking strategies, with an accuracy reaching 90%. We have also deployed the SMOTE-Transformer model on sequencing data, which has an accuracy of over 80%. The construction of SMOTE-Transformer model provides a new idea for soil microbial data analysis by greatly improving the accuracy and robustness of soil microbial data processing tools.

● Bacterial and fungal necromass in soil showed opposite trends with rice growth.

Microbial residues play an important role in soil organic carbon (SOC) sequestration. Paddy fields are important agricultural ecosystems involved in the carbon cycle; however, microbial residues change with rice growth in soil from double-season rice, and the influence of these residues on SOC sequestration is uncertain. Here, we investigated the microbial residues (amino sugars (AS) and glomalin-related soil protein (GRSP)) content and their contribution to SOC during the tillering stage (TS), heading stage (HS), and ripening stage (RS) in both early- and late-season rice in a double-cropping rice-growing area wherein the straw is returned after the early-season rice is harvested. Microbial biomass significantly increased from the early- to the late-season. In addition, the content of bacterial residues decreased (7.94%, P=0.008), while the fungal residues increased (8.15%, P<0.001) in the late-season compared with the early-season, suggesting that bacterial residues were recycled more rapidly than fungal residues. Amino sugar content and its contribution to SOC decreased from the TS to the RS in the late-season soil, probably because of the nutrient requirements of the rapidly growing rice. The contribution of GRSP to SOC increased by 10.5%, whereas that of ASs decreased by 4.5% from the early- to the late-season. Living soil microbes rather than soil physicochemical properties were the main factors influencing microbial residue accumulation. The results of this study provide a theoretical basis from a microbial perspective which will facilitate future efforts to enhance SOC sequestration during paddy field management.

● Bridge constructions decreased soil bacterial alpha and beta diversity.

Soils in mangrove ecosystems are home to diverse and unique microbes, which support many crucial ecosystem services. Despite their vulnerability, the impact of bridge construction on the soil microbiome in mangroves is poorly understood. This study assessed the bacterial community profiles and microbial biomass in mangrove soils under different bridge construction techniques: Sheet Pile Cofferdam (SP) and Steel Casing Pipe (SC), compared to the non-disturbed (ND) counterpart. Bridge construction significantly decreased the alpha diversity and caused biotic homogenization of soil bacterial communities, indicating a loss of microbial biodiversity due to human disturbance. Bridge construction also reduced the microbial biomass carbon and nitrogen. The assembly of soil bacterial communities was dominated by stochastic processes, and bridge construction increased the relative importance of stochasticity. However, the impacts on ecological networks varied with the construction technique, with SC soils showing higher network complexity and stability compared to the ND habitats. Changes in soil bacterial communities were primarily attributed to the shifts in soil pH and nutrient levels. This study identified the effects of sea-crossing bridge construction on the soil microbiome in mangrove ecosystems, aiding in careful planning and environmental impact assessments to minimize the negative effects of urbanization on mangrove ecosystems.