Root exudates enhanced rhizobacteria complexity and microbial carbon metabolism of toxic plants

Enhancing the efficiency of P-SMFCs in degrading phenanthrene by modifying the anode with carbon nanomaterials

In plant-sediment microbial fuel cells (P-SMFCs), the anode serves as the primary site for biochemical reactions. In this study, different carbon nanomaterials (graphenes (GNs), carbon nanotubes (CNT), hydroxylated-carbon nanotubes (CNT-OH), and carboxylated-carbon nanotubes (CNT-COOH)) were used to modify the anode of the P-SMFCs to explore the enhancement of phenanthrene (Phe) degradation. The devices were operated for 131 days, CNT-COOH-modified P-SMFCs (P-CNT-COOH) exhibited a shorter start-up period and higher voltage during the stable operation stage. The voltage of P-CNT-COOH during the stationary phase was approximately 250 mV higher than that of the control device. The voltage and Phe removal of P-CNT-COOH were higher than those of CNT-COOH (without plants in the SMFC), which achieved 67.5% Phe removal, which was 1.25 times higher than the P-CNT, whereas CNT (without plants in the SMFC) showed higher performance than P-CNT. The anode modified with P-CNT-COOH became enriched with small-molecule volatile fatty acids (VFAs) (e.g., acetic acid) and degrading bacteria (e.g., Thiobacillus and Desulfobulbus) attributed to the higher hydrophilicity. The removal of Phe was positively correlated with dehydrogenase activity (DHAA).

Effects of planting patterns on physicochemical properties, metabolites and microbial community structure of rhizosphere soil in perennial cultivated grassland

Establishing perennial cultivated grasslands on the Qinghai-Tibet Plateau helps address the seasonal imbalance of forage resources and supports the restoration of degraded grasslands. The most common planting patterns-monocropping and mixed cropping-are well-studied in terms of vegetation structure, productivity, and soil nutrients. Despite their significance, the influence of prolonged planting practices on underground soil microbial communities and metabolites has often been neglected. In this study, two characteristic plants, Festuca sinensis 'Qinghai' and Poa pratensis 'Qinghai', from the area around Qinghai Lake were selected as the experimental subjects by employing 16 S and ITS sequencing methods in conjunction with non-targeted metabolomics analysis. The effects of planting patterns (monocropping and mixed cropping) on rhizosphere soil characteristics, metabolites and microbial community structure were examined. The results showed that compared with monocropping, mixed cropping significantly increased the contents of soil nutrients and key metabolites. In addition, it had a greater impact on fungal diversity than bacterial diversity, particularly in terms of β-diversity. While microbial α-diversity and dominant phyla remained stable, soil fungi were more responsive to changes in soil properties and metabolites. These results show that the new niche differentiation between different species in mixed grassland stimulates the secretion of trehalose and valine, which further affects the fungal community structure and enhances the soil nutrients and ecological functions of degraded grasslands. These findings will guide the restoration of degraded grasslands around Qinghai Lake and the selection of planting strategies to improve local sustainable grassland productivity.

Changes in the potato rhizosphere microbiota richness and diversity occur in a growth stage-dependent manner

Plant root and soil-associated microbiomes are influenced by niches, including bulk and rhizosphere soil. In this work, we collected bulk and rhizosphere soil samples at four potato developmental stages (leaf growth, flowering, tuber elongation and harvest) to identify whether rhizosphere microbiota are structured in a growth stage-dependent manner. The bacterial and fungal microbiota showed significant temporal differences in the rhizosphere and bulk soil. Rhizobacteria were most diverse at the tuber elongation stage, and dominant ASVs identified as Sphingomonas, Rhodanobacter, Sphingobium, Hyphomicrobium, and Solirubrobacter spp. In contrast, rhizosphere fungal diversity peaked at flowering stage, with Lecanicillium spp. being prominent. Furthermore, the abundance of saprophytic fungal genera, including Colletotrichum and Fusarium, and Alternaria, sharply increased at harvest stage, likely contributing to plant residue decomposition. Indicator taxa analysis highlighted the dominance of these genera at harvest. Network analysis revealed increased microbial complexity during the later growth stage, with 721 edges compared to 521 edges in the early growth stage. This increase included positive correlations between bacteria and negative correlations between bacteria and fungi. These changes suggest that microbial interactions become more interconnected and complex as potato plants mature. Our findings highlight the potential role of saprophytic fungi in shaping microbial dynamics during the later growth stage in rhizosphere soil.

Allelopathy and potential allelochemicals of Ligularia sagitta as an invasive plant

Allelopathy is the main chemical means in the invasion process of exotic plants and one of the key factors in grassland degradation. In this experiment, we investigated the effects of ethyl acetate phase extract (EAE), n-butanol phase extract (BE) and aqueous phase extract (AE) from the aboveground (stems and leaves) and roots of Ligularia sagitta on seed germination and seedling growth of four Gramineae forages (Poa pratensis L. Festuca ovina L. Elymus nutans Griseb. Agropyron cristatum (L.) Gaertn.) in their sympatric domains and one Legosuminae forage (Medicago sativa L.). The chemical components in each phase extract of L. sagitta were determined with UHPLC-MS/MS non-targeted metabolomics, and the differential compounds were screened using Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA). Within a set concentration range, EAE significantly inhibited seed germination and seedling growth of four Gramineae forages. BE and AE acted mainly in the seedling growth stage and did not significantly inhibit forage seed germination. P. pratensis was most sensitive to L. sagitta extracts; at 2.0 mg/mL of EAE from roots, germination energy and germination rate of P. pratensis seeds were 0. L. sagitta extracts inhibited the growth of M. sativa seedlings and did not inhibit its seed germination. A total of 904 compounds were identified with UHPLC-MS/MS, among which 31, 64, 81 and 66 metabolites displayed different accumulation patterns in the four comparison groups (R.EAE vs. R.BE, R.EAE vs. R.AE, SL.EAE vs. SL.BE, SL.EAE vs. SL.AE), respectively. In particular, 9 compounds were found to be common up-regulated differential metabolites in the four comparison groups and were enriched in EAE. Additionally, N,N-dimethylaniline, Caffeic acid, 4-Hydroxybenzoic acid, 4-Hydroxybenzaldehyde and cis-9-Octadecenoic acid as potential allelochemicals in L. sagitta. The results of this study support efforts at finding alternative control plants for the restoration of poisonous grass-type degraded grasslands.

Arbuscular mycorrhizal symbiosis enhances the accumulation of plant-derived carbon in soil organic carbon by regulating the biosynthesis of plant biopolymers and soil metabolism

Plant-derived carbon (C) is a critical constituent of particulate organic carbon (POC) and plays an essential role in soil organic carbon (SOC) sequestration. Yet, how arbuscular mycorrhizal fungi (AMF) control the contribution of plant-derived C to SOC storage through two processes (biosynthesis of plant biopolymers and soil metabolism) remains poorly understood. Here, we utilized transcriptome analysis to examine the effects of AMF on P. communis roots. Under the AM symbiosis, root morphological growth and tolerance to stress were strengthened, and the biosynthetic pathways of key plant biopolymers (long-chain fatty acids, cutin, suberin, and lignin) contributing to the plant-derived C were enhanced. In the subsequent metabolic processes, AMF increased soil metabolites contributing to plant-derived C (such as syringic acid) and altered soil metabolic pathways, including carbohydrate metabolism. Additionally, C-acquiring soil extracellular enzyme activities were enhanced by AMF, which could affect the stabilization of plant-derived C in soil. The contents of POC (21.71 g kg-1 soil), MAOC (10.75 g kg-1 soil), and TOC (32.47 g kg-1 soil) in soil were significantly increased by AMF. The concentrations of plant-derived C and microbial-derived C were quantified based on biomarker analysis. AMF enhanced the content of plant-derived C in both POC and MAOC fractions. What's more, plant-derived C presented the highest level in the POC fraction under the AMF treatment. This research broadens our understanding of the mechanism through which plant-derived C contributes to the accumulation of POC and SOC induced by AM symbiosis, and evidences the benefits of AMF application in SOC sequestration.

Diversity of hydrocarbon-degrading bacteria in mangroves rhizosphere as an indicator of oil-pollution bioremediation in mangrove forests

Mangrove ecosystems, characterized by high levels of productivity, are susceptible to anthropogenic activities, notably oil pollution arising from diverse origins including spills, transportation, and industrial effluents. Owing to their role in climate regulation and economic significance, there is a growing interest in developing mangrove conservation strategies. In the Arabian Gulf, mangroves stand as the sole naturally occurring green vegetation due to the region's hot and arid climate. However, they have faced persistent oil pollution for decades. This review focuses on global mangrove distribution, with a specific emphasis on Qatar's mangroves. It highlights the ongoing challenges faced by mangroves, particularly in relation to the oil industry, and the impact of oil pollution on these vital ecosystems. It outlines major oil spill incidents worldwide and the diverse hydrocarbon-degrading bacterial communities within polluted areas, elucidating their potential for bioremediation. The use of symbiotic interactions between mangrove plants and bacteria offers a more sustainable, cost-effective and environmentally friendly alternative. However, the success of these bioremediation strategies depends on a deep understanding of the dynamics of bacterial communities, environmental factors and specific nature of the pollutants.

Using rice straw-augmented ecological floating beds to enhance nitrogen removal in carbon-limited wastewater

Agricultural biomass used as solid carbon substrates in ecological floating beds (EFBs) has been proven to be applicable in nitrogen removal for carbon-limited wastewater treatment. However, the subtle interactions among plants, rhizosphere microorganisms, and supplementary carbon sources have not been thoroughly studied. This study combined rice straw mats with different aquatic macrophytes in EFBs to investigate denitrification efficiency in carbon-limited eutrophic waters. Results showed that rice straw significantly enhanced the nitrogen removal efficiency of EFBs, while enriching nitrogen-fixing and denitrifying bacteria (such as Rhizobium, Rubrivivax, and Rhodobacter, etc.). Additionally, during the denitrification process in EFBs, rice straw can release humic acid-like fraction as electron donors to support the metabolic activities of microorganisms, while aquatic macrophytes provide a more diverse range of dissolved organic matters, facilitating a sustainable denitrification process. These findings help to understand the synergistic effect of denitrification processes within wetland ecosystems using agricultural biomass.

Deciphering Microbial Adaptation in the Rhizosphere: Insights into Niche Preference, Functional Profiles, and Cross-Kingdom Co-occurrences

Rhizosphere microbial communities are to be as critical factors for plant growth and vitality, and their adaptive differentiation strategies have received increasing amounts of attention but are poorly understood. In this study, we obtained bacterial and fungal amplicon sequences from the rhizosphere and bulk soils of various ecosystems to investigate the potential mechanisms of microbial adaptation to the rhizosphere environment. Our focus encompasses three aspects: niche preference, functional profiles, and cross-kingdom co-occurrence patterns. Our findings revealed a correlation between niche similarity and nucleotide distance, suggesting that niche adaptation explains nucleotide variation among some closely related amplicon sequence variants (ASVs). Furthermore, biological macromolecule metabolism and communication among abundant bacteria increase in the rhizosphere conditions, suggesting that bacterial function is trait-mediated in terms of fitness in new habitats. Additionally, our analysis of cross-kingdom networks revealed that fungi act as intermediaries that facilitate connections between bacteria, indicating that microbes can modify their cooperative relationships to adapt. Overall, the evidence for rhizosphere microbial community adaptation, via differences in gene and functional and co-occurrence patterns, elucidates the adaptive benefits of genetic and functional flexibility of the rhizosphere microbiota through niche shifts.

Actas Pink-2B dye removal in biochar nanocomposites augmented vertical flow constructed wetland (VF-CWs)

Industries generate hazardous dye wastewater, posing significant threats to public health and the environment. Removing dyes before discharge is crucial. The ongoing study primarily focused on synthesizing, applying, and understanding the mechanism of green nano-biochar composites. These composites, including zinc oxide/biochar, copper oxide/biochar, magnesium oxide/biochar, and manganese oxide/biochar, are designed to effectively remove Actas Pink-2B (Direct Red-31) in conjunction with constructed wetlands. Constructed wetland maintained pH 6.0-7.9. At the 10th week, the copper oxide/biochar treatment demonstrated the highest removal efficiency of total suspended solids (72%), dissolved oxygen (7.2 mg/L), and total dissolved solids (79.90%), followed by other biochar composites. The maximum removal efficiency for chemical oxygen demand (COD) and color was observed at a retention time of 60 days. The electrical conductivity also followed the same order, with a decrease observed up to the 8th week before becoming constant. A comprehensive statistical analysis was conducted, encompassing various techniques including variance analysis, regression analysis, correlation analysis, and principal component analysis. The rate of color and COD removal followed a second-order and first-order kinetics, respectively. A significant negative relationship was observed between dissolved oxygen and COD. The study indicates that employing biochar composites in constructed wetlands improves textile dye removal efficiency.

The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria

Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.

Root colonization by beneficial rhizobacteria

Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.

Gamma-Aminobutyric Acid Enhances Cadmium Phytoextraction by Coreopsis grandiflora by Remodeling the Rhizospheric Environment

Gamma-aminobutyric acid (GABA) significantly affects plant responses to heavy metals in hydroponics or culture media, but its corresponding effects in plant-soil systems remain unknown. In this study, different GABA dosages (0-8 g kg^-1) were added to the rhizosphere of Coreopsis grandiflora grown in Cd-contaminated soils. Cd accumulation in the shoots of C. grandiflora was enhanced by 38.9-159.5% by GABA in a dose-dependent approach because of accelerated Cd absorption and transport. The increase in exchangeable Cd transformed from Fe-Mn oxide and carbonate-bound Cd, which may be mainly driven by decreased soil pH rather than GABA itself, could be a determining factor responsible for this phenomenon. The N, P, and K availability was affected by multiple factors under GABA treatment, which may regulate Cd accommodation and accumulation in C. grandiflora. The rhizospheric environment dynamics remodeled the bacterial community composition, resulting in a decline in overall bacterial diversity and richness. However, several important plant growth-promoting rhizobacteria, especially Pseudomonas and Sphingomonas, were recruited under GABA treatment to assist Cd phytoextraction in C. grandiflora. This study reveals that GABA as a soil amendment remodels the rhizospheric environment (e.g., soil pH and rhizobacteria) to enhance Cd phytoextraction in plant-soil systems.

Direct and indirect effects of dominant plants on ecosystem multifunctionality

Biodiversity is essential for the provision of multiple ecosystem functions simultaneously (ecosystem multifunctionality EMF). Yet, it remains unclear whether and how dominant plant species impact EMF. Here, we aimed at disentangling the direct from indirect above- and belowground pathways by which dominant plant species influence EMF. We evaluated the effects of two dominant plant species (Dasiphora fruticosa, and the toxic perennial plant Ligularia virgaurea) with expected positive and negative impacts on the abiotic environment (soil water content and pH), surrounding biological communities (plant and nematode richness, biomass, and abundance in the vicinity), and on the EMF of alpine meadows, respectively. We found that the two dominant plants enhanced EMF, with a positive effect of L. virgaurea on EMF greater than that of D. fruticosa. We also observed that dominant plants impacted on EMF through changes in soil water content and pH (indirect abiotic effects), but not through changes in biodiversity of surrounding plants and nematodes (indirect biotic pathway). Our study suggests that dominant plants may play an important role in promoting EMF, thus expanding the pervasive mass-ratio hypothesis originally framed for individual functions, and could mitigate the negative impacts of vegetation changes on EMF in the alpine meadows.

Research progress and hotspot analysis of rhizosphere microorganisms based on bibliometrics from 2012 to 2021

Rhizosphere microorganisms are important organisms for plant growth promotion and bio-control. To understand the research hot topics and frontier trends of rhizosphere microorganisms comprehensively and systematically, we collected 6,056 publications on rhizosphere microorganisms from Web of Science and performed a bibliometric analysis by CiteSpace 6.1.3 and R 5.3.1. The results showed that the total number of references issued in this field has been on the rise in the past decades. China, India, and Pakistan are the top three countries in terms of the number of articles issued, while Germany, the United States, and Spain were the countries with the highest number of co-published papers with other countries. The core research content in this field were the bio-control, bacterial community, ACC deaminase, phytoremediation, induced systematic resistance, and plant growth promotion. Seeding growth, Bacillus velezensis, plant-growth, and biological-control were currently and may be the highlights in the field of rhizosphere microorganisms research for a long time in the future. The above study results quantitatively, objectively, and scientifically described the research status and research focus of rhizosphere microorganisms from 2012 to 2021 from the perspective of referred papers, with a view to promoting in-depth research in this field and providing reference information for scholars in related fields to refine research trends and scientific issues.

Leymus chinensis resists degraded soil stress by modulating root exudate components to attract beneficial microorganisms

Phytoremediation is an effective means to improve degraded soil nutrients and soil structure. Here, we investigated the remediation effects of Leymus chinensis on the physicochemical properties and structure of degraded soil after 3 years of cultivation and explored the bacterial and fungal drivers in root exudates by metabolomics and high-throughput sequencing. The results showed that root exudates increased soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP) and soil aggregates, and organic acids in root exudates reduced pH and activated insoluble nutrients into forms that are available to plants, such as available nitrogen (NH₄ ⁺-N), nitrate nitrogen (NO₃ ^--N), and available phosphorus (AP). The cultivation of L. chinensis restored the diversity and richness of soil microorganisms and recruited potential beneficial bacteria and fungi to resist degraded soil stress, and L. chinensis also regulated the abundances of organic acids, amino acids and fatty acids in root exudates to remediate degraded soils. Spearman correlation analysis indicated that glutaric acid, 3-hydroxybutyric acid and 4-methylcatechol in root exudates attracted Haliangium, Nitrospira and Mortierella to the rhizosphere and dispersed the relative abundance of the harmful microorganisms Fusicolla and Fusarium. Our results demonstrate that L. chinensis enhances soil fertility, improves soil structure, promotes microbial diversity and abundance, and recruits potentially beneficial microorganisms by modulating root exudate components.