Metagenomics, metatranscriptomics, and proteomics reveal the metabolic mechanism of biofilm sequencing batch reactor with higher phosphate enrichment capacity under low phosphorus load

Influence of operation sequences on phosphorus enrichment by polyphosphate accumulating organisms biofilm: Performance, phosphorus transfer and phosphate metabolism in biofilm

This study investigated the impact of different operational sequences on phosphorus removal and enrichment in biofilm phosphorus enrichment system. The research com-pared two distinct operational modes, analyzing phosphorus uptake and release characteristics in cells and extracellular polymeric substances (EPS) over a single cycle, while also examining microbial community composition and associated functional genes. After long-term acclimation, the Ae/An system achieved higher phosphorus concentration (120 mg/L) than the An/Ae system (65 mg/L). However, the An/Ae system showed stronger phosphorus uptake and release capabilities due to higher phosphorus load during the aerobic phase. In both systems, Mg-P and Ca-P dominated in cells and EPS. Compared to the Ae/An system, the An/Ae system stored phosphorus mainly in EPS, with higher orthophosphate content. However, EPS-associated phosphorus is more easily released, explaining the An/Ae system's higher aerobic phosphorus load but lower overall storage capacity. Microbial analysis revealed higher abundance of phosphorus accumulating organisms (PAOs) in the An/Ae system (25.99 % vs. 19.69 %), while glycogen accumulating organisms (GAOs) showed the opposite trend. Candidatus Competibacter was abundant in both systems and correlated with phosphorus metabolism genes. The An/Ae system expressed the pst system more, whereas the Ae/An favored the pit system, suggesting that transfer system variations affect enrichment solution concentration. Lower expression of polyphosphate kinase (ppk1) in the An/Ae system may explain its unsatisfied phosphorus enrichment performance. Mantel analysis confirmed connections among environmental factors, kinetic parameters, phosphorus metabolism genes, and phosphorus morphology in EPS, demonstrating their combined influence on enrichment solution concentration.

Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health

Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.

Glycogen-accumulating organisms promote phosphate recovery from wastewater by pilot-scale biofilm sequencing batch reactor: Performance and mechanism

A high phosphate (P) recovery concentration was achieved in pilot-scale biofilm sequencing batch reactor (BSBR) with a low carbon source (C) cost. Especially, a high-abundance glycogen-accumulating organisms (GAOs) (13.93-31.72%) was detected that was accompanied by a high P recovery concentration of BSBR. High-abundance GAOs obtain additional C through various C compensation pathways (split tricarboxylic acid cycle (TCA cycle), glyoxylate shunt and gluconeogenesis), thus reducing the need to compete with polyphosphate-accumulating organisms (PAOs) for C and weakening the adverse effects on P recovery by PAO cells. Under the action of N-acyl homoserine lactones (AHLs)-mediated quorum sensing (QS), GAOs promoted the secretion of a large amount of extracellular polymeric substances (EPS), which helped to realize the P recovery of EPS-dominated biofilms (68.02%-96.89%). This study provides a low-carbon technology for the recovery of high concentration P from municipal wastewater, and improves the ecological theory of P recovery in collaboration with GAOs and PAOs.

Cultivation of phosphate-accumulating biofilm: Study of the effects of acyl-homoserine lactones (AHLs) and cyclic dimeric guanosine monophosphate (c-di-GMP) on the formation of biofilm and the enhancement of phosphate metabolism capacity

This study investigated the mechanisms of microbial growth and metabolism during biofilm cultivation in the biofilm sequencing batch reactor (BSBR) process for phosphate (P) enrichment. The results showed that the sludge discharge was key to biofilm growth, as it terminated the competition for carbon (C) source between the nascent biofilm and the activated sludge. For the tested reactor, after the sludge discharge on 18 d, P metabolism and C source utilization improved significantly, and the biofilm grew rapidly. The P concentration of the recovery liquid reached up to 157.08 mg/L, which was sufficient for further P recovery via mineralization. Meta-omics methods were used to analyze metabolic pathways and functional genes in microbial growth during biofilm cultivation. It appeared that the sludge discharge activated the key genes of P metabolism and inhibited the key genes of C metabolism, which strengthened the polyphosphate-accumulating metabolism (PAM) as a result. The sludge discharge not only changed the types of polyphosphate-accumulating organisms (PAOs) but also promoted the growth of dominant PAOs. Before the sludge discharge, the necessary metabolic abilities that were spread among different microorganisms gradually concentrated into a small number of PAOs, and after the sludge discharge, they further concentrated into Candidatus_Contendobacter (P3) and Candidatus_Accumulibacter (P17). The messenger molecule C-di-GMP, produced mostly by P3 and P17, facilitated P enrichment by regulating cellular P and C metabolism. The glycogen-accumulating organism (GAO) Candidatus_Competibacter secreted N-Acyl homoserine lactones (AHLs), which stimulated the secretion of protein in extracellular polymeric substances (EPS), thus promoting the adhesion of microorganisms to biofilm and improving P metabolism via EPS-based P adsorption. Under the combined action of the dominant GAOs and PAOs, AHLs and C-di-GMP mediated QS to promote biofilm development and P enrichment. The research provides theoretical support for the cultivation of biofilm and its wider application.

PD-1/PD-L1 axis induced host immunosuppression via PI3K/Akt/mTOR signalling pathway in piglets infected by Glaesserella Parasuis

Glaesserella parasuis, an important respiratory bacterial pathogen, causes Glässer's disease in piglets, with potential immunosuppression. We established a piglet infection model and explored the immunosuppression mechanism to improve our understanding of the host immune response to G. parasuis. Twenty piglets were randomly divided into two groups (n = 10). The infection group was intraperitoneally challenged with 2 × 108 CFU of G. parasuis in 2 mL TSB. The control group was intraperitoneally injected with equivalent TSB. After 72 h, the piglets were sacrificed, and spleen tissue was collected. PD-1/PD-L1 expression was determined. The splenocytes were isolated to detect CD3+ T, CD3+CD4+ T, CD3+CD8+ T and CD3-CD21+cell differentiation. Via data-independent acquisition (DIA), we compared the proteomics of healthy and infected spleen tissues. Glaesserella parasuis modified CD3+ T, CD3+CD4+ T, CD3+CD8+ T and CD3-CD21+ cell differentiation and PD-1/PD-L1 expression in the spleen. The infection group had 596 proteins with significant differences in expression, of which 301 were significantly upregulated and 295 downregulated. Differentially expressed proteins (DEPs) were mainly related to immune responses. This is the first study on PD-1/PD-L1 expression in the spleen associated with immunosuppression in a piglet model to explore the protein changes related to immune responses via DIA.

A novel process based on powder carriers demonstrates robustness in nitrogen and phosphorus removal from real municipal wastewater

The development of efficient and low-consumption wastewater upgrading process is currently at the forefront of the wastewater treatment field. In this study, a novel wastewater treatment process based on powder carriers was proposed. Three systems, namely the activated sludge (AS) system, powder carrier (PC) system, and moving bed biofilm reactor (MBBR) system, were established and operated for over 140 days to treat real municipal wastewater. The characteristics and differences between the three systems were comprehensively investigated. The results suggested that the PC system exhibited notable advantages in nitrogen and phosphorus removal, especially under high influent load and low aeration conditions. The PC system, characterized by a higher nitrification rate compared to the MBBR system and a higher denitrification rate compared to the AS system, contributed to the stable nitrogen removal performance. The particle size of the zoogloea increased under the linkage of the powder carriers, and the mean size of micro-granules reached 170.88 μm. Large number of hydrophobic functional groups on sludge surface, coupled with increased protein content in EPS, further promoted sludge aggregation. Micro-granules formation improved settling performance and enhanced the abundance and activity of functional microbes. A significant enrichment in denitrifying bacteria and denitrifying phosphorus accumulating bacteria was observed in PC system. Up-regulation of the napA, narG, and nosZ genes was responsible for efficient nitrogen removal of the PC system. Moreover, a higher abundance in polyphosphate phosphotransferase (2.11 %) was found in PC system compared with AS and MBBR systems. The increase in the enzymes associated with poly-β-hydroxybutyrate (PHB) synthesis metabolism in PC system provided the energy for denitrification and phosphorus removal processes.

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.