Nitrogen transfer and cross-feeding between Azotobacter chroococcum and Paracoccus aminovorans promotes pyrene degradation

Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals

Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling

Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.

Important soil microbiota's effects on plants and soils: a comprehensive 30-year systematic literature review

Clarifying the relationship between soil microorganisms and the plant-soil system is crucial for encouraging the sustainable development of ecosystems, as soil microorganisms serve a variety of functional roles in the plant-soil system. In this work, the influence mechanisms of significant soil microbial groups on the plant-soil system and their applications in environmental remediation over the previous 30 years were reviewed using a systematic literature review (SLR) methodology. The findings demonstrated that: (1) There has been a general upward trend in the number of publications on significant microorganisms, including bacteria, fungi, and archaea. (2) Bacteria and fungi influence soil development and plant growth through organic matter decomposition, nitrogen, phosphorus, and potassium element dissolution, symbiotic relationships, plant growth hormone production, pathogen inhibition, and plant resistance induction. Archaea aid in the growth of plants by breaking down low-molecular-weight organic matter, participating in element cycles, producing plant growth hormones, and suppressing infections. (3) Microorganism principles are utilized in soil remediation, biofertilizer production, denitrification, and phosphorus removal, effectively reducing environmental pollution, preventing soil pathogen invasion, protecting vegetation health, and promoting plant growth. The three important microbial groups collectively regulate the plant-soil ecosystem and help maintain its relative stability. This work systematically summarizes the principles of important microbial groups influence plant-soil systems, providing a theoretical reference for how to control soil microbes in order to restore damaged ecosystems and enhance ecosystem resilience in the future.

Multi-omics analysis reveals the collaboration and metabolisms of the anammox consortia driven by soluble/non-soluble Fe(III) as the sole iron element

Iron is recognized as a physiological requirement for anammox bacteria (AnAOB), with Fe(II) considered to be the most effective form. However, Fe(III), instead of Fe(II) is the common iron form in natural and artificial ecosystems. In this study, the nitrogen removal performance and metabolic mechanisms in anammox consortia with soluble and non-soluble Fe(III) as the sole iron element were investigated. After the 150-day operation, the soluble (FeCl3) and insoluble (Fe2O3) Fe(III)-fed anammox systems reached nitrogen removal rates of 71.84 ± 0.80% and 50.20 ± 0.98%, respectively. AnAOB could survive with soluble (FeCl3) or insoluble (Fe2O3) Fe(III) as the sole iron element, reaching relative abundances of 18.49% and 13.16%, respectively. The results show that the formation of anammox core consortia can enable AnAOB's survival to adverse external conditions of Fe(II) deficiency. Metagenomic and metatranscriptomic analysis reveal that Ca. Kuenenia can only uptake Fe(II) into the cell for metabolisms either independently through the extracellular electron transfer or with the cross-feeding of symbiotic microbes. This study provides insight into the utilization and metabolic mechanisms of Fe(III) in Ca. Kuenenia-dominated consortia, and deepens the understanding of anammox core consortia in the nitrogen, carbon, and iron cycling, further promoting the practical applications of anammox processes.

Aerobic Denitrification Promoting by Actinomycetes Coculture: Investigating Performance, Carbon Source Metabolic Characteristic, and Raw Water Restoration

The coculture theory that promotes denitrification relies on effectively utilizing the resources of low-efficiency denitrification microbes. Here, the strains Streptomyces sp. PYX97 and Streptomyces sp. TSJ96 were isolated and showed lower denitrification capacity when cultured individually. However, the coculture of strains PYX97 and TSJ96 enhanced nitrogen removal (removed 96.40% of total nitrogen) and organic carbon reduction (removed 92.13% of dissolved organic carbon) under aerobic conditions. Nitrogen balance analysis indicated that coculturing enhanced the efficiency of nitrate converted into gaseous nitrogen reaching 70.42%. Meanwhile, the coculturing promoted the cell metabolism capacity and carbon source metabolic activity. The coculture strains PYX97 and TSJ96 thrived in conditions of C/N = 10, alkalescence, and 150 rpm shaking speed. The coculturing reduced total nitrogen and CODMn in the raw water treatment by 83.32 and 84.21%, respectively. During this treatment, the cell metabolic activity and cell density increased in the coculture strains PYX97 and TSJ96 reactor. Moreover, the coculture strains could utilize aromatic protein and soluble microbial products during aerobic denitrification processes in raw water treatment. This study suggests that coculturing inefficient actinomycete strains could be a promising approach for treating polluted water bodies.