Toll/interleukin-1 receptor domains in bacterial and plant immunity.

The Toll/interleukin-1 receptor (TIR) domain is found in animal, plant, and bacterial immune systems. It was first described as a protein-protein interaction module mediating signalling downstream of the Toll-like receptor and interleukin-1 receptor families in animals. However, studies of the pro-neurodegenerative protein sterile alpha and TIR motif containing 1, plant immune receptors, and many bacterial TIR domain-containing proteins revealed that TIR domains have enzymatic activities and can produce diverse nucleotide products using nicotinamide adenine dinucleotide (NAD+) or nucleic acids as substrates. Recent work has led to key advances in understanding how TIR domain enzymes work in bacterial and plant immune systems as well as the function of their signalling molecules.

Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products.

Toll/interleukin-1 receptor (TIR) domain proteins function in cell death and immunity. In plants and bacteria, TIR domains are often enzymes that produce isomers of cyclic adenosine 5'-diphosphate-ribose (cADPR) as putative immune signaling molecules. The identity and functional conservation of cADPR isomer signals is unclear. A previous report found that a plant TIR could cross-activate the prokaryotic Thoeris TIR-immune system, suggesting the conservation of plant and prokaryotic TIR-immune signals. Here, we generate autoactive Thoeris TIRs and test the converse hypothesis: Do prokaryotic Thoeris TIRs also cross-activate plant TIR immunity? Using in planta and in vitro assays, we find that Thoeris and plant TIRs generate overlapping sets of cADPR isomers and further clarify how plant and Thoeris TIRs activate the Thoeris system via producing 3'cADPR. This study demonstrates that the TIR signaling requirements for plant and prokaryotic immune systems are distinct and that TIRs across kingdoms generate a diversity of small-molecule products.

Cyclic ADP ribose isomers: Production, chemical structures, and immune signaling.

Cyclic adenosine diphosphate (ADP)-ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide (oxidized form) (NAD+) hydrolysis. We show that v-cADPR (2'cADPR) and v2-cADPR (3'cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of 2'cADPR-producing TIR domains reveal conformational changes that lead to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan that is essential for cyclization. We show that 3'cADPR is an activator of ThsA effector proteins from the bacterial antiphage defense system termed Thoeris and a suppressor of plant immunity when produced by the effector HopAM1. Collectively, our results reveal the molecular basis of cADPR isomer production and establish 3'cADPR in bacteria as an antiviral and plant immunity-suppressing signaling molecule.

Structural Evolution of TIR-Domain Signalosomes.

TIR (Toll/interleukin-1 receptor/resistance protein) domains are cytoplasmic domains widely found in animals and plants, where they are essential components of the innate immune system. A key feature of TIR-domain function in signaling is weak and transient self-association and association with other TIR domains. An additional new role of TIR domains as catalytic enzymes has been established with the recent discovery of NAD+-nucleosidase activity by several TIR domains, mostly involved in cell-death pathways. Although self-association of TIR domains is necessary in both cases, the functional specificity of TIR domains is related in part to the nature of the TIR : TIR interactions in the respective signalosomes. Here, we review the well-studied TIR domain-containing proteins involved in eukaryotic immunity, focusing on the structures, interactions and their corresponding functional roles. Structurally, the signalosomes fall into two separate groups, the scaffold and enzyme TIR-domain assemblies, both of which feature open-ended complexes with two strands of TIR domains, but differ in the orientation of the two strands. We compare and contrast how TIR domains assemble and signal through distinct scaffolding and enzymatic roles, ultimately leading to distinct cellular innate-immunity and cell-death outcomes.

Combined effects of seasonality and stagnation on tap water quality: Changes in chemical parameters, metabolic activity and co-existence in bacterial community.

In drinking water distribution pipeline systems, the tap water quality is regulated by several biotic and abiotic factors, which can threaten the health of consumers. Stagnation is inevitable in the water distribution pipeline however, the combined effects of seasonal changes and stagnation on tap water quality are not well understood. Here, we investigated the seasonal variations in the chemical and biological quality of water after overnight stagnation for a period of one year. The results showed that the tap water quality deteriorated after overnight stagnation, with up to a 2.7-fold increase in the total iron concentrations. The total bacterial cell concentrations increased by 59-231% after overnight stagnation. The total cell and cell-bound adenosine triphosphate (ATP) of the stagnant water samples peaked in summer. In addition, Biolog analysis showed that the metabolic activities of microbes were higher in spring. The bacterial community based on Illumina Miseq DNA sequence analysis found that Proteobacteria dominated the drinking water bacterial community. The bacterial community structure varied significantly among different seasons, where the diversity and richness of the community were much higher in spring. Structural equation modeling (SEM) was constructed to determine the correlations between bacterial metabolic functions and the community structure. The redundancy analysis (RDA) indicated that the residual chlorine played a critical role in the construction of the bacterial community. Altogether, the overall findings from the present work provide novel insights into how the quality of tap water quality impacted by the seasonal changes and overnight stagnation.

Aerobic denitrifying bacterial communities drive nitrate removal: Performance, metabolic activity, dynamics and interactions of core species.

Three novel mix-cultured aerobic denitrifying bacteria (Mix-CADB) consortia named D14, X21, and CL exhibited excellent total organic carbon (TOC) removal and aerobic denitrification capacities. The TOC and nitrate removal efficiencies were higher than 93.00% and 98.00%. The results of Biolog demonstrated that three communities displayed high carbon metabolic activity. nirS gene sequencing and ecological network model revealed that Pseudomonas stutzeri, Paracoccus sp., and Paracoccus denitrificans dominated in the D14, X21, and CL communities. The dynamics and co-existence of core species in communities drove the nutrient removal. Response surface methodology showed the predicted total nitrogen removal efficiency reached 99.43% for D14 community. The three Mix-CADB consortia have great potential for nitrogen-polluted aquatic water treatment because of their strong adaptability and removal performance. These results will provide new understanding of co-existence, interaction and dynamics of Mix-CADB consortia for nitrogen removal in nitrogen-polluted aquatic ecosystems.

Nitrate reduction by Paracoccus thiophilus strain LSL 251 under aerobic condition: Performance and intracellular central carbon flux pathways.

The intracellular carbon metabolic flux pathways of denitrifying bacteria under aerobic conditions remain unclear. Here, a newly strain LSL251 was identified as Paracoccus thiophilus. Strain LSL251 removed 94.79% and 98.78% of total organic carbon and nitrate. 74.66% of nitrogen in culture system was lost as gaseous nitrogen. Moreover, 13C stable isotopic labeling and metabolic flux analyses revealed that the primary intracellular carbon metabolic pathways were the Entner-Doudoroff pathway and the tricarboxylic acid (TCA) cycle. Electrons are primarily donated as direct electron donor-NADH through the TCA cycle. Furthermore, response surface methodology modeled that the highest total nitrogen removal efficiency was 98.43%, where the optimal parameters were C/N ratio of 8.00, 32.98 °C, 50.18 rpm, and initial pH of 7.73. All together, these results have shed new lights on intracellular central carbon metabolic distribution and flux pathways of aerobic denitrifying bacteria.

Nitrate removal characteristics and 13C metabolic pathways of aerobic denitrifying bacterium Paracoccus denitrificans Z195.

Strain Z195 was isolated and identified as Paracoccus denitrificans. Z195 exhibited efficient aerobic denitrification and carbon removal abilities, and removed 93.74% of total nitrogen (TN) and 97.81% of total organic carbon.71.88% of nitrogen was lost as gaseous products.13C-metabolic flux analysis revealed that 95% and 132% of the carbon fluxes entered the Entner-Doudoroff (ED) pathway and tricarboxylic acid (TCA) cycle, respectively. Electrons produced by carbon metabolism markedly promoted the processes of nitrogen metabolism process and aerobic respiration. A response surface methodology model demonstrated that the optimal conditions for the maximum TN removal were a C/N ratio of 7.47, shaking speed of 108 rpm, temperature of 31 °C and initial pH of 8.02. Additionally, the average TN and chemical oxygen demand removal efficiencies of raw wastewater were 89% and 91%, respectively. The results give new insight for understanding metabolic flux analysis of aerobic denitrifying bacteria.

Immobilization of Ni3Co Nanoparticles into N-Doped Carbon Nanotube/Nanofiber Integrated Hierarchically Branched Architectures toward Efficient Overall Water Splitting.

Exploring cost-effective and high-performance bifunctional electrocatalysts for both hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) is of paramount importance for the advancement of H2 production technology, yet remains a huge challenge. Herein, a simple electrospinning-pyrolysis strategy is developed to directly immobilize uniform Ni3Co nanoparticles into a hierarchical branched architecture constructed by in situ formed N-doped carbon-nanotube-grafted carbon nanofibers. The elaborate construction of such hybrid hierarchical architecture can effectively modulate the electronic structure of the active sites, enlarge the exposure of active sites, and facilitate the electron transfer and mass diffusion, favoring both the HER and OER. As a result, the optimized catalyst requires relatively low overpotentials of 114 and 243 mV for HER and OER, respectively, to deliver a current density of 10 mA cm-2 in 0.1 m KOH electrolyte. When employed as a bifunctional catalyst for overall water splitting, the resultant catalyst shows a low cell voltage of 1.57 V to achieve a current density of 10 mA cm-2, along with an impressive stability without noticeable attenuation even after 27 h. This work presents a successful demonstration in optimizing the electrocatalytic performance of Ni-based bifunctional electrocatalysts by simultaneously considering modulation of electronic structure, hybridization with carbon substrate, and nanostructuring through a facile synthetic strategy, which provides a new avenue to the design of a rich variety of robust transition-metal-based electrocatalysts for large-scale water electrolysis.

Geographical Patterns of nirS Gene Abundance and nirS-Type Denitrifying Bacterial Community Associated with Activated Sludge from Different Wastewater Treatment Plants.

Denitrifying bacteria is a driver of nitrogen removal process in wastewater treatment ecosystem. However, the geographical characteristics of denitrifying bacterial communities associated with activated sludge from diverse wastewater treatment plants (WWTPs) are still unclear. Here, quantitative PCR and next-generation sequencing of the nirS gene were applied to characterize the abundance and denitrifying bacterial communities from 18 geographically distributed WWTPs. The results showed that the nirS abundance ranged from 4.6 × 102 to 2.4 × 103 copies per ng DNA, while nirS-type denitrifying bacterial populations were diverse and distinct from activated sludge communities. Among WWTPs, total nitrogen removal efficiencies varied from 25.8 to 84%, which was positively correlated with diversity indices, whereas abundance-based coverage estimator index decreased with an increase in latitude. The dominant phyla across all samples were proteobacteria, accounting for 46.23% (ranging from 17.98 to 87.07%) of the sequences. Eight of the 22 genera detected were dominant: Thauera sp., Alicycliphilus sp., and Pseudomonas sp., etc. Based on network analysis, the coexistence and interaction between dominant genera may be vital for regulating the nitrogen and carbon removal behaviors. Multivariate statistical analysis revealed that both geographic location and wastewater factors concurrently govern the distribution patterns of nirS-type denitrifying bacterial community harbored in WWTPs. Taking together, these results from the present study provide novel insights into the nirS gene abundance and nirS-type denitrifying bacterial community composition in geographically distributed WWTPs. Moreover, the knowledge gained will improve the operation and management of WWTPs for nitrogen removal.

Dynamics of Bacterial and Fungal Communities during the Outbreak and Decline of an Algal Bloom in a Drinking Water Reservoir.

The microbial communities associated with algal blooms play a pivotal role in organic carbon, nitrogen and phosphorus cycling in freshwater ecosystems. However, there have been few studies focused on unveiling the dynamics of bacterial and fungal communities during the outbreak and decline of algal blooms in drinking water reservoirs. To address this issue, the compositions of bacterial and fungal communities were assessed in the Zhoucun drinking water reservoir using 16S rRNA and internal transcribed spacer (ITS) gene Illumina MiSeq sequencing techniques. The results showed the algal bloom was dominated by Synechococcus, Microcystis, and Prochlorothrix. The bloom was characterized by a steady decrease of total phosphorus (TP) from the outbreak to the decline period (p < 0.05) while Fe concentration increased sharply during the decline period (p < 0.05). The highest algal biomass and cell concentrations observed during the bloom were 51.7 mg/L and 1.9×108 cell/L, respectively. The cell concentration was positively correlated with CODMn (r = 0.89, p = 0.02). Illumina Miseq sequencing showed that algal bloom altered the water bacterial and fungal community structure. During the bloom, the dominant bacterial genus were Acinetobacter sp., Limnobacter sp., Synechococcus sp., and Roseomonas sp. The relative size of the fungal community also changed with algal bloom and its composition mainly contained Ascomycota, Basidiomycota and Chytridiomycota. Heat map profiling indicated that algal bloom had a more consistent effect upon fungal communities at genus level. Redundancy analysis (RDA) also demonstrated that the structure of water bacterial communities was significantly correlated to conductivity and ammonia nitrogen. Meanwhile, water temperature, Fe and ammonia nitrogen drive the dynamics of water fungal communities. The results from this work suggested that water bacterial and fungal communities changed significantly during the outbreak and decline of algal bloom in Zhoucun drinking water reservoir. Our study highlights the potential role of microbial diversity as a driving force for the algal bloom and biogeochemical cycling of reservoir ecology.

Geographical patterns of denitrifying bacterial communities associated with different urban lakes.

The geographical variation of denitrifying bacterial communities and water quality parameters in urban lakes distributed across nine provinces in China were determined. The Illumina sequencing data of the denitrifying encoding gene nirS was examined in the samples collected from nine localities (pairwise geographical distance: 200-2600 km). The results showed that fundamental differences in water quality were observed among different urban lakes. The highest nitrate (2.02 mg L-1) and total nitrogen (3.82 mg L-1) concentrations were observed in Pingzhuang (P < 0.01). The algal cell concentration ranged from 1.29 × 108 to 3.0 × 109 cell per L. The sequencing data generated a total of 421058 high quality nirS gene reads that resulted in 6369 OTUs (97% cutoff), with Proteobacteria and Firmicutes being the dominant taxa. A co-occurrence network analysis indicated that the top five genera identified as keystone taxa were Dechlorospirillum sp., Alicycliphilus sp., Dechloromonas sp., Pseudogulbenkiania sp., and Paracoccus sp. A redundancy analysis (RDA) further revealed that distinct denitrifying bacterial communities inhabited the different urban lakes, and influenced by urban lake water ammonia nitrogen, manganese and algal cell concentrations. A variance partitioning analysis (VPA) also showed that geographic location was more important than water quality factors in structuring the denitrifying bacterial communities. Together, these results provide new insight into understanding of denitrifying bacterial communities associated with geographically distributed urban lakes on a larger scale, and these results also expand our exploration of aquatic microbial ecology in freshwater bodies.