● 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.

● 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.

● 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.

● 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.

● 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.

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.

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.

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.

Protists are essential components of the rhizosphere microbiome, which is crucial for plant growth, but little is known about the relationship between plant growth and rhizosphere protists under salinity stress. Here we investigated wheat (Triticum aestivum L.) rhizosphere protistan communities under naturally occurring salinity (NOS) and irrigation-reduced salinity (IRS), and linked a plant salinity stress index (PSSI) to different protistan groups in a nontidal coastal saline soil. We found that the PSSI was significantly correlated with rhizosphere cercozoan communities (including bacterivores, eukaryvores, and omnivores) and that these communities were important predictors of the PSSI. Structural equation modeling suggested that root exudation-induced change in bacterial community composition affected the communities of bacterivorous and omnivorous Cercozoa, which were significantly associated with the PSSI across wheat cultivars. Network analysis indicated more complex connections between rhizosphere bacteria and their protistan predators under IRS than under NOS, implying that alleviation of salinity stress promotes the predation of specific cercozoans on bacteria in rhizospheres. Moreover, the Cercomonas directa inoculation was conducive to alleviation of salinity stress. Taken together, these results suggest that the physiological response of wheat plants to salinity stress is closely linked to rhizosphere Cercozoa through trophic regulation within the rhizosphere microbiome.

Nanoplastics and antibiotics are among the most abundant chemical pollutants of soils, but their interplay with global warming remains poorly understood. The springtail Folsomia candida (Class Collembola) is a standard model for ecotoxicological assays with potential as a bioindicator ofxenobiotics. Little is known, however, about their gut microbiome and how itmight respond to warming and these pollutants. We exposed populations of F. candida to nanoplastics and antibiotic under two temperatures. The antibiotic treatment consisted of colistin addition, and the nanoplastic treatment consisted of polystyrene particles (50 mg kg^‒1 and 0.1 g kg^‒1 of dry soil, respectively). Both treatments were incubated at 20 and 22 °C for two months, and the bacterial gut microbiomes of springtails were then sequenced. Exposure to nanoplastics at 20 °C decreased the abundance of the dominant bacterial phyla and families, and decreased the evenness of the gut microbiome. At 22 °C, however, the abundances and evenness of the dominant families increased. Surprisingly, Gram-negative bacteria targeted by colistin were not globally affected. And at genus-level, the endosymbiont Wolbachia controlled the compositional shifts under nanoplastic addition, potentially driving the gut microbiome. Our results also indicated that warming was a major driver modulating the impacts of the antibiotic and nanoplastics. We illustrate how the gut microbiomes of springtails are sensitive communities responsive to xenobiotics and provide evidence of the need to combine multiple factors of global change operating simultaneously if we are to understand the responses of communities of soil arthropods and their microbiomes.

Microalgae play a key role as primary colonizers of soil, enhancing plant growth and improving soil health. Seed priming is a widely used method to improve seedling performance, counteract soil-related stresses, and boost plant productivity. Here we investigated the impact of priming dwarf pea seeds with live cells or disrupted cell mass of two microalgae, Desmodesmus sp. MAS1 and Heterochlorella sp. MAS3, on plant growth response and rhizosphere health. Plant growth metrics, rhizosphere health parameters, and nutrient status indicators were investigated 21 days after sowing in two different soils (designated as A and B) with varying pH. Results revealed that priming significantly improved the biochemistry of rhizosphere in soil B (pH 8), with over 30% increases in leaf count and fresh weight compared to soil A (pH 6). While flowering rates remained low, priming with strain MAS1 significantly enhanced chlorophyll (20%), indole-3-acetic acid (61%), and dehydrogenase activity (50%). Furthermore, strain MAS1 boosted nutrient availability in the rhizosphere, with a 30%–60% increase in carbon and nitrogen levels, promoting exopolysaccharide release. Our findings thus demonstrate the potential of seed priming with microalgae in modulating rhizosphere health, thereby enhancing plant growth and productivity.