Soil Amoebae Affect Iron and Chromium Reduction through Preferential Predation between Two Metal-Reducing Bacteria

Organophosphorus mineralizing-Streptomyces species underpins uranate immobilization and phosphorus availability in uranium tailings

Phosphate-solubilizing bacteria (PSB) are important but often overlooked regulators of uranium (U) cycling in soil. However, the impact of PSB on uranate fixation coupled with the decomposition of recalcitrant phosphorus (P) in mining land remains poorly understood. Here, we combined gene amplicon sequencing, metagenome and metatranscriptome sequencing analysis and strain isolation to explore the effects of PSB on the stabilization of uranate and P availability in U mining areas. We found that the content of available phosphorus (AP), carbonate-U and Fe-Mn-U oxides in tailings was significantly (P < 0.05) higher than their adjacent soils. Also, organic phosphate mineralizing (PhoD) bacteria (e.g., Streptomyces) and inorganic phosphate solubilizing (gcd) bacteria (e.g., Rhodococcus) were enriched in tailings and soils, but only organic phosphate mineralizing-bacteria substantially contributed to the AP. Notably, most genes involved in organophosphorus mineralization and uranate resistance were widely present in tailings rather than soil. Comparative genomics analyses supported that organophosphorus mineralizing-Streptomyces species could increase soil AP content and immobilize U(VI) through organophosphorus mineralization (e.g., PhoD, ugpBAEC) and U resistance related genes (e.g., petA). We further demonstrated that the isolated Streptomyces sp. PSBY1 could enhance the U(VI) immobilization mediated by the NADH-dependent ubiquinol-cytochrome c reductase (petA) through decomposing organophosphorous compounds. This study advances our understanding of the roles of PSB in regulating the fixation of uranate and P availability in U tailings.

In-situ enrichment of ARGs and their carriers in soil by hydroxamate siderophore: A promising biocontrol approach for source reduction

Pathogenic microorganisms with antibiotic resistance genes (ARGs) pose a serious threat to public health and soil ecology. Although new drugs and available antibacterial materials can kill ARG carriers but accidentally kill beneficial microorganisms. Therefore, the rapid enrichment and separation of ARGs and their carriers from soil is becoming an important strategy for controlling the diffusion of ARGs. Hydroxamate siderophore (HDS) has gained widespread attentions for its involvement in trace element transfer among microorganisms in the soil environment, we thus explored an in-situ trapping-enrichment method for ARGs and their carriers via a small molecular HDS secreted by Pseudomonas fluorescens HMP01. In this study, we demonstrate that HDS significantly in-situ traps and enriches certain ARGs, including chloramphenicol, MLS, rifamycin, and tetracycline resistance genes in the soil environment. The enrichment efficiencies were 1473-fold, 38-fold, 17-fold, and 5-fold, respectively, higher than those in the control group. Specifically, the primary enriched ARGs were rpoB, mphL, catB2, and tetA(60), and Bacillus, Rhizobium, Rossellomorea, and Agrobacterium were hosts for these ARGs. This enrichment was caused by the upregulation of chemotaxis genes (e.g., cheW, cheC, and cheD) and rapid biofilm formation within the enriched bacterial population. Notably, representative ARGs such as cat, macB, and rpoB were significantly reduced by 36%, 85.7%, and 72%, respectively, in the paddy soil after HDS enrichment. Our research sheds light on the potential application of siderophore as a rapping agent for the eco-friendly reduction of ARGs and their carriers in soil environments.

Characteristics of iron (hydr)oxides and Cr(VI) retention mechanisms in soils from tropical and subtropical areas of China

Though both iron (hydr)oxides and soil organic matter (SOM) significantly influence heavy metal behaviors in soils, studies on the characteristics of natural minerals and the synergic effects of the two on Cr(VI) transformation are limited. This study investigated Cr(VI) retention mechanisms in four soils from tropical and subtropical regions of China based on a comprehensive characterization of Fe (hydr)oxides. These soils exhibited varying quantities of hematite, ferrihydrite and goethite, with distinct Al substitution levels and varied exposed crystallographic facets. Adsorption experiments revealed a positive correlation between Fe (hydr)oxide content and Cr(VI) fixation amount on colloid, which was influenced by the mineral types, Al substitution levels and facet exposures. Further, Cr(VI) was sequestered on soil by adsorption and reduction. In soils enriched with crystalline Fe (hydr)oxides, Cr(VI) reduction was primarily governed by SOM, while in soils enriched with poorly crystalline Fe (hydr)oxides, mineral-associated Fe(II) also contributed to Cr(VI) reduction. Aging experiments demonstrated that SOM and mineral-associated Fe(II) expedited Cr (VI) passivation and diminished the Cr leaching. These results improve our understanding of natural Fe (hydr)oxide structures and their impact on Cr(VI) behavior in soils, and shed light on complex soil-contaminant interactions and remediation of Cr(VI) polluted soils.

Soil physical structure drives N-glycan mediated trophic interactions in soil amoebae: Mechanisms and environmental implications

Soil protozoa are an essential part of the terrestrial ecosystem, playing a vital role in the global element cycling and energy flow. However, one research gap is what are the key factors driving their diversity and environmental fates. In this study, we hypothesized that soil texture could affect soil protozoa's predation and their interactions with environmental pollutants, and we tested it by using a soil amoeba Dictyostelium discoideum as a model system. We found that soil texture affected amoeba's growth and development. In addition, environmental factors cannot explain the variation of amoeba's fitness in different soil textures. Soil sandy particles and water content rather than particle size contribute to amoeba's fitness. Furthermore, different soil textures induced distinct transcriptional responses to amoebae, especially N-glycan-related and multiple signaling pathways and the expression of key genes (e.g., Ras superfamily, cxgE, trap1). The expression of N-glycan-related pathways, which is positively correlated with amoeba predation, was inhibited in sand soil, decreasing amoeba's fitness. Finally, the results showed that soil texture also affects amoeba's interaction with environmental pollutants. In conclusion, this study shows that soil physical structures affect amoeba's interactions with bacteria and environmental pollutants. SYNOPSIS: Soil texture affects soil protozoa's growth and development and their interactions with environmental pollutants.

Biochar-based microporous nanosheets-mediated nanoconfinement for high-efficiency reduction of Cr(VI)

Biochar-based materials have been widely used to remove Cr(VI). However, current strategies mainly focus on slow adsorption through electrostatic and functional group properties, ignoring the confinement catalytic fast kinetics caused by inherent porous properties. Herein, we designed a confinement strategy to achieve high-efficiency Cr(VI) reduction by encapsulating the catalytic reaction of Cr(VI) and oxalic acid (OA) in the micropore of PCRN-3-10-2-800. The results showed that the removal rate constant of the PCRN-3-10-2-800/OA system was 14.3 and 146.8 times higher than that of the BC-800/OA system (low porosity) and PCRN-3-10-2-800 alone (adsorption), which was highest removal rate constant in the current reported materials under the same system. The structure-activity relationship indicated that the catalytic activity of Cr(VI) depended on the micropore characteristics of the catalyst. Density functional theory calculations confirmed that nanoscale space could enhance Cr(VI) adsorption and reduce the energy barrier of the rate-determining step. The electron paramagnetic resonance spectrum demonstrated the rapid conversion of Cr(VI) to Cr(III). Furthermore, the PCRN-3-10-2-800/OA system showed good applicability and high efficiency for Cr(VI) removal (nearly 100% in 5 min) in industrial electroplating wastewater treatment. This work first proposes a nanoconfinement-induced heavy metal reduction strategy and guides biochar's universality design in wastewater treatment.

Linking groundwater microbiome and functional ecological clusters to geogenic high hexavalent chromium from deep aquifers in a loess plateau

Geogenic high hexavalent chromium [Cr(Ⅵ)] in groundwater is a global environmental problem. However, the groundwater microbiome and its linkage to geogenic high Cr(Ⅵ) from deep aquifers still need to be elucidated. Here, we evaluated geogenic Cr(Ⅵ), groundwater microbiome with featured functional ecological clusters and their interactive responses in groundwater from a deep aquifer in a loess plateau of Northern Shaanxi, China. We found that the compositions and structures of microbial communities in groundwater from the deep aquifer were significantly different between low Cr(Ⅵ) (LCG, < 50 μg/L) and high Cr(Ⅵ) groundwater (HCG, > 50 μg/L), with higher microbial diversity and richness in HCG (p < 0.05). Functional "specialists" related to Cr biotransformation, including Cr(Ⅵ) reducing bacteria (CRB) Rhodococcus, Nocardioides, Novosphingobium, and Acidovorax and Mn-oxidizing bacteria (MnOB) Sphingobium, and Ralstonia were positively correlated to total Cr and Cr(VI) concentrations in groundwater. Moreover, these CRB and MnOB were dominant in high Cr(VI) groundwater and associated by strong interspecific relation in an ecological cluster (p < 0.05), suggesting their indicator roles for high Cr(Ⅵ) and the contribution of MnOB mediated Cr(III) oxidation to Cr(VI) enrichment. RDA and path analysis further revealed that the geogenic Cr(Ⅵ) directly promoted the key Cr-related functional cluster with the groundwater depth, dissolved oxygen, and total dissolved solids as the cofactors indirectly influencing Cr(Ⅵ) and the functional clusters (p < 0.05). Collectively, our results highlight the significant roles of microbial ecological clusters especially functional "specialists" MnOB and CRB in groundwater Cr(Ⅵ) from deep aquifers in the loess plateau and provide a basis for sustainable management of high Cr(Ⅵ) groundwater.

Effects of Fe oxides and their redox cycling on Cd activity in paddy soils: A review

Cadmium (Cd) contamination of soils is a global problem, particularly in paddy soils. Fe oxides, as a key fraction of paddy soils, can significantly affect the environmental behavior of Cd, which is controlled by complicated environmental factors. Therefore, it is necessary to systematically collect and generalize relevant knowledge, which can provide more insight into the migration mechanism of Cd and a theoretical basis for future remediation of Cd contaminated paddy soils. This paper summarized that (1) Fe oxides influence Cd activity through adsorption, complexation, and coprecipitation during transformation; (2) compared with the flooded period, the activity of Cd during the drainage period is stronger in paddy soils, and the affinity of different Fe components for Cd was distinct; (3) Fe plaque reduced Cd activity but was associated with plant Fe²⁺ nutritional status; (4) the physicochemical properties of paddy soils have the greatest impact on the interaction between Fe oxides and Cd, especially with pH and water fluctuations.

Protozoa as Hotspots for Potential Pathogens in the Drinking Water of a Subtropical Megacity: Diversity, Treatment, and Health Risk

Drinking water systems host a wide range of microorganisms essential for biosafety. However, one major group of waterborne pathogens, protozoa, is relatively neglected compared to bacteria and other microorganisms. Until now, little is known about the growth and fate of protozoa and their associated bacteria in drinking water systems. In this study, we aim to investigate how drinking water treatment affects the growth and fate of protozoa and their associated bacteria in a subtropical megacity. The results showed that viable protozoa were prevalent in the city's tap water, and amoebae were the major component of tap water protozoa. In addition, protozoan-associated bacteria contained many potential pathogens and were primarily enriched in amoeba hosts. Furthermore, this study showed that current drinking water disinfection methods have little effect on protozoa and their associated bacteria. Besides, ultrafiltration membranes unexpectedly served as an ideal growth surface for amoebae in drinking water systems, and they could significantly promote the growth of amoeba-associated bacteria. In conclusion, this study shows that viable protozoa and their associated bacteria are prevalent in tap water, which may present an emerging health risk in drinking water biosafety.

Phagotrophic Protists Modulate Copper Resistance of the Bacterial Community in Soil

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.

Environmental stress promotes the persistence of facultative bacterial symbionts in amoebae

Amoebae are one major group of protists that are widely found in natural and engineered environments. They are a significant threat to human health not only because many of them are pathogenic but also due to their unique role as an environmental shelter for pathogens. However, one unsolved issue in the amoeba-bacteria relationship is why so many bacteria live within amoeba hosts while they can also live independently in the environments. By using a facultative amoeba- Paraburkholderia bacteria system, this study shows that facultative bacteria have higher survival rates within amoebae under various environmental stressors. In addition, bacteria survive longer within the amoeba spore than in free living. This study demonstrates that environmental stress can promote the persistence of facultative bacterial symbionts in amoebae. Furthermore, environmental stress may potentially select and produce more amoeba-resisting bacteria, which may increase the biosafety risk related to amoebae and their intracellular bacteria.

Dam construction alters planktonic microbial predator‒prey communities in the urban reaches of the Yangtze River

While dam construction supports social and economic development, changes in hydraulic conditions can also affect natural aquatic ecosystems, especially microbial ecosystems. The compositional and functional traits of multi-trophic microbiota can be altered by dam construction, which may result in changes in aquatic predator-prey interactions. To understand this process, we performed a large-scale sampling campaign in the urban reaches of the dam-impacted Yangtze River (1 995 km) and obtained 211 metagenomic datasets and water quality data. We first compared the compositional traits of planktonic microbial communities upstream, downstream, and in a dam reservoir. Results showed that Bacteroidetes (R-strategy) bacteria were more likely to survive upstream, whilst the reservoir and downstream regions were more conducive to the survival of K-strategy bacteria such as Actinobacteria. Eukaryotic predators tended to be enriched upstream, whilst phototrophs tended to be enriched in the reservoir and downstream regions. Based on bipartite networks, we inferred that the potential microbial predator-prey interactions gradually and significantly decreased from upstream to the downstream and dam regions, affecting 56% of keystone microbial species. Remarkably, functional analysis showed that the abundance of the photosynthetic gene psbO was higher in the reservoir and downstream regions, whilst the abundance of the KEGG carbohydrate metabolic pathway was higher upstream. These results indicate that dam construction in the Yangtze River induced planktonic microbial ecosystem transformation from detritus-based food webs to autotroph-based food webs.