Flocculation-Related Gene Identification by Whole-Genome Sequencing of Thauera aminoaromatica MZ1T Floc-Defective Mutants

Enhancing Waste Sludge Solubilization through Radio Frequency Treatment Perforating Bacterial Cells

Sludge solubilization is known as a rate-limiting step of anaerobic digestion. Although radio frequency (RF) has been applied for sludge pretreatment due to its similar thermal effect as microwave, the potential non-thermal effects of RF treatment remain controversial. In this study, we demonstrate that RF pretreatment enhances the solubilization and lysis of sludge by 8.02%∼19.69% through both thermal and non-thermal mechanisms with less energy input. Scanning electron microscope images provide direct evidence that RF-induced microcurrents penetrated bacterial cells, leading to the release of intracellular substances through formed pores. Additionally, the non-thermal effect of RF treatment which could weaken the cell protection and accelerate the lysis rate involves the disruption of binding forces between extracellular polymeric substances and microbial cells. On average, the utilization of RF at a frequency of 27.12 MHz demonstrates its efficacy as a sludge pretreatment technique, as evidenced by a 13.39% reduction in energy consumption and a 16.9% improvement in treatment performance compared to CH. The findings of this study elucidate the possible mechanism of RF treatment of sludge and could establish a theoretical basis for the practical application of RF treatment in sludge management.

Activated sludge microbial community assembly: the role of influent microbial community immigration

Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater. However, the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analyzed by harvesting wastewater biomass solids from three different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 14% of the sequencing reads in the AS. By modeling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principles for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs.IMPORTANCEIn biological wastewater treatment processes, the microbial community composition is essential in the performance and stability of the system. This study developed a reproducible protocol to investigate the impact of influent immigration (or perpetual coalescence of the sewer and activated sludge communities) with appropriate reproducibility and controls, allowing intrinsic definitions of core and immigrant populations to be established. The method developed herein will allow sequential manipulative experiments to be performed to test specific hypothesis and optimize wastewater treatment processes to meet new treatment goals.

Physicochemical and Rheological Properties of Succinoglycan Overproduced by Sinorhizobium meliloti 1021 Mutant

Commercial bacterial exopolysaccharide (EPS) applications have been gaining interest; therefore, strains that provide higher yields are required for industrial-scale processes. Succinoglycan (SG) is a type of bacterial anionic exopolysaccharide produced by Rhizobium, Agrobacterium, and other soil bacterial species. SG has been widely used as a pharmaceutical, cosmetic, and food additive based on its properties as a thickener, texture enhancer, emulsifier, stabilizer, and gelling agent. An SG-overproducing mutant strain (SMC1) was developed from Sinorhizobium meliloti 1021 through N-methyl-N'-nitro-N-nitrosoguanidine (NTG) mutation, and the physicochemical and rheological properties of SMC1-SG were analyzed. SMC1 produced (22.3 g/L) 3.65-fold more SG than did the wild type. Succinoglycan (SMC1-SG) overproduced by SMC1 was structurally characterized by FT-IR and 1H NMR spectroscopy. The molecular weights of SG and SMC1-SG were 4.20 × 105 and 4.80 × 105 Da, respectively, as determined by GPC. Based on DSC and TGA, SMC1-SG exhibited a higher endothermic peak (90.9 °C) than that of SG (77.2 °C). Storage modulus (G') and loss modulus (G″) measurements during heating and cooling showed that SMC1-SG had improved thermal behavior compared to that of SG, with intersections at 74.9 °C and 72.0 °C, respectively. The SMC1-SG's viscosity reduction pattern was maintained even at high temperatures (65 °C). Gelation by metal cations was observed in Fe3+ and Cr3+ solutions for both SG and SMC1-SG. Antibacterial activities of SG and SMC1-SG against Escherichia coli and Staphylococcus aureus were also observed. Therefore, like SG, SMC1-SG may be a potential biomaterial for pharmaceutical, cosmetic, and food industries.

A novel biomineralization-inspired flocculation approach for harvesting high quality microalgal biomass: Dual action of cationic polyelectrolytes and nanosilica

This study posed a novel biomimetic flocculation approach, aiming to efficiently harvest high-quality biomass of Scenedesmus quadricauda cultured with anaerobic digestate. Here, that poly(diallyldimethylammonium chloride) (PDADMAC) could serve as mimetic silicified proteins to spontaneously incorporate nanosilica onto microalgal cells, imparting diatom-like characteristics to S. quadricauda. Compared to the exponential growth phase (day 3), the highest harvesting efficiency (93.49%) was obtained at a lower dosage of PDADMAC (5 mg/g) in the stationary phase (day 6), which was attributed to changes in properties and composition of microalgal LB-EPS. On day 6, the hydrophobic functional groups in LB-EPS provided more binding sites during the flocculation process and formed a network structure of microalgal cells-flocculants-nanosilica. The resulting larger and more stable biomimetic silica shell promoted microalgal flocculation and sedimentation. Compared to conventional harvesting methods (centrifugation, polyacrylamide, alkaline flocculation), this method had the minimal negative impact on harvested biomass, with 9.95% of cell membranes damaged.

Linking Genome-Centric Metagenomics to Kinetic Analysis Reveals the Regulation Mechanism of Hydroxylamine in Nitrite Accumulation of Biological Denitrification

Given hydroxylamine accumulation in various nitrification systems and its potential mechanism in regulating the subsequent denitrification process were unraveled in this study. Hydroxylamine (>0.5 mgN/L) immediately induced nitrite accumulation of activated sludge by inhibiting the activities of nitrite reductases and their electron transport modules (Complex III and cytochrome c). Moreover, long-term exposure to 0.5-2.5 mgN/L hydroxylamine accelerated the functional transformation from denitrification to denitratation under low C/N conditions. However, genome-centric metagenomics indicated that a genotypic complete rather than truncated denitrifier Thauera aminoaromatica TJ127 was enriched and mainly responsible for acetate storage and nitrate reduction of the denitratation community. Interestingly, its enrichment resulted in nitrite production and reduction sequentially but reduced nitrate only to nitrite under carbon-limited conditions (C/N ≤ 3.0). Thus, it showed higher tolerance to hydroxylamine than the concurrent phenotype denitrifiers in activated sludge. Moreover, due to its higher anoxic storage capability in the feast phase, this enrichment became highly specialized by decreasing the feast/famine ratio, and thus a satisfactory denitratation performance was still maintained without hydroxylamine. These results suggested that the transient release of hydroxylamine from nitrification may interfere with subsequent denitrification metabolism, but its continuous accumulation is beneficial for achieving denitratation, which could steadily provide nitrite for mainstream anammox.

Rapid start-up of photo-granule process in a photo-sequencing batch reactor under low aeration conditions: Effect of inoculum AGS size

The photo-granule process is an effective and economically feasible alternative for wastewater treatment, but little information is available regarding how to speed up the photo-granulation process. In this study, the effect of inoculum aerobic granular sludge (AGS) size on the start-up of the photo-granule process was investigated under low aeration conditions (superficial gas velocity of 0.5 cm/s). For this purpose, the inoculum AGS was sorted into various size-categories (0.4-0.8 mm, 0.8-1.4 mm, 1.4-2.2 mm, and > 2.2 mm) to serve as individual inoculum sludge. The excellent settling properties (SVI₅ of 39.3 mL/g), strong mechanical strength, efficient nutrient removal (COD: 94.2-97.1%; TN: 80.1-84.8%; TP: 60.4-91.5%), and high biodiesel yields (12.11 mg/g MLSS) were rapidly achieved in the system inoculated with 0.8-1.4 mm AGS. The granulation process was facilitated by filamentous algae as the nucleus, extracellular polymeric substances as the backbone, and the enrichment of functional bacteria (such as Thauera and Sphingorhabdus). Furthermore, the inherent influencing mechanisms of inoculum AGS size on the photo-granulation were revealed from cellular hydrophobicity, surface thermodynamics, and sludge aggregation behavior. This study provides a novel start-up approach of the photo-granule process by inoculating with the optimal AGS size, which is convenient, practically feasible and significantly reduced the aeration consumption.

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

In bacteria functionally related genes comprising metabolic pathways and protein complexes are frequently encoded in operons and are widely conserved across phylogenetically diverse species. The evolution of these operon-encoded processes is affected by diverse mechanisms such as gene duplication, loss, rearrangement, and horizontal transfer. These mechanisms can result in functional diversification, increasing the potential evolution of novel biological pathways, and enabling pre-existing pathways to adapt to the requirements of particular environments. Despite the fundamental importance that these mechanisms play in bacterial environmental adaptation, a systematic approach for studying the evolution of operon organization is lacking. Herein, we present a novel method to study the evolution of operons based on phylogenetic clustering of operon-encoded protein families and genomic-proximity network visualizations of operon architectures. We applied this approach to study the evolution of the synthase dependent exopolysaccharide (EPS) biosynthetic systems: cellulose, acetylated cellulose, poly-β-1,6-N-acetyl-D-glucosamine (PNAG), Pel, and alginate. These polymers have important roles in biofilm formation, antibiotic tolerance, and as virulence factors in opportunistic pathogens. Our approach revealed the complex evolutionary landscape of EPS machineries, and enabled operons to be classified into evolutionarily distinct lineages. Cellulose operons show phyla-specific operon lineages resulting from gene loss, rearrangement, and the acquisition of accessory loci, and the occurrence of whole-operon duplications arising through horizonal gene transfer. Our evolution-based classification also distinguishes between PNAG production from Gram-negative and Gram-positive bacteria on the basis of structural and functional evolution of the acetylation modification domains shared by PgaB and IcaB loci, respectively. We also predict several pel-like operon lineages in Gram-positive bacteria and demonstrate in our companion paper (Whitfield et al PLoS Pathogens, in press) that Bacillus cereus produces a Pel-dependent biofilm that is regulated by cyclic-3',5'-dimeric guanosine monophosphate (c-di-GMP).

The Shared and Specific Genes and a Comparative Genomics Analysis within Three Hanseniaspora Strains

Kloeckera apiculata plays an important role in the inhibition of citrus postharvest blue and green mould diseases. This study was based on the previous genome sequencing of K. apiculata strain 34-9. After homologous comparison, scaffold 27 was defined as the mitochondrial (mt) sequence of K. apiculata 34-9. The comparison showed a high level of sequence identity between scaffold 27 and the known mtDNA of Hanseniaspora uvarum. The genome sequence of H. vineae T02/19AF showed several short and discontinuous fragments homologous to the mtDNA of H. uvarum. The shared and specific genes of K. apiculata, H. uvarum, and H. vineae were analysed by family using the TreeFam methodology. GO analysis was used to classify the shared and specific genes. Most of the gene families were classified into the functional categories of cellular component and metabolic processes. The whole-genome phylogram and genome synteny analysis showed that K. apiculata was more closely related to H. uvarum than to H. vineae. The genomic comparisons clearly displayed the locations of the homologous regions in each genome. This analysis could contribute to discovering the genomic similarities and differences within the genus Hanseniaspora. In addition, some regions were not collinearity-matched in the genome of K. apiculata compared with that of H. uvarum or H. vineae, and these sequences might have resulted from evolutionary variations.

Stability of aerobic granular sludge under condition of low influent C/N ratio: Correlation of sludge property and functional microorganism

Aerobic granular sludge process treating domestic wastewater with low C/N ratio is necessary to be studied for rapid urbanization in China and other countries. In this study, two parallel reactors with different influent C/N ratio (15 in R1, 5 in R2) were established. Compared to the disintegrated granule in R1 with high influent C/N ratio, granules with large size (650 μm) and compact structure (integrity coefficient <0.1) were stable in R2 along with influent C/N ratio decreased to 5. High-through sequencing illustrated the functional microbes like Thauera and Paracoccus enriched under low influent C/N ratio, and principal component analysis further showed these microbes were positive correlation with tryptophan and protein-like substances in extracellular polymeric substances (EPS) and granular strength. It was indicated that under low influent C/N ratio, several resistant microbes like Thauera (19.5%) enriched and then secreted tryptophan and protein-like substances, and stable granules with multi-functional microbes could be formed finally.

Meta-proteomic analysis of protein expression distinctive to electricity-generating biofilm communities in air-cathode microbial fuel cells

BACKGROUND

Bioelectrochemical systems (BESs) harness electrons from microbial respiration to generate power or chemical products from a variety of organic feedstocks, including lignocellulosic biomass, fermentation byproducts, and wastewater sludge. In some BESs, such as microbial fuel cells (MFCs), bacteria living in a biofilm use the anode as an electron acceptor for electrons harvested from organic materials such as lignocellulosic biomass or waste byproducts, generating energy that may be used by humans. Many BES applications use bacterial biofilm communities, but no studies have investigated protein expression by the anode biofilm community as a whole.

RESULTS

To discover functional protein expression during current generation that may be useful for MFC optimization, a label-free meta-proteomics approach was used to compare protein expression in acetate-fed anode biofilms before and after the onset of robust electricity generation. Meta-proteomic comparisons were integrated with 16S rRNA gene-based community analysis at four developmental stages. The community composition shifted from dominance by aerobic Gammaproteobacteria (90.9 ± 3.3%) during initial biofilm formation to dominance by Deltaproteobacteria, particularly Geobacter (68.7 ± 3.6%) in mature, electricity-generating anodes. Community diversity in the intermediate stage, just after robust current generation began, was double that at the early stage and nearly double that of mature anode communities. Maximum current densities at the intermediate stage, however, were relatively similar (~ 83%) to those achieved by mature-stage biofilms. Meta-proteomic analysis, correlated with population changes, revealed significant enrichment of categories specific to membrane and transport functions among proteins from electricity-producing biofilms. Proteins detected only in electricity-producing biofilms were associated with gluconeogenesis, the glyoxylate cycle, and fatty acid β-oxidation, as well as with denitrification and competitive inhibition.

CONCLUSIONS

The results demonstrate that it is possible for an MFC microbial community to generate robust current densities while exhibiting high taxonomic diversity. Moreover, these data provide evidence to suggest that startup growth of air-cathode MFCs under conditions that promote the establishment of aerobic-anaerobic syntrophy may decrease startup times. This study represents the first investigation into protein expression of a complex BES anode biofilm community as a whole. The findings contribute to understanding of the molecular mechanisms at work during BES startup and suggest options for improvement of BES generation of bioelectricity from renewable biomass.

Amino acids in cell wall of Gram-positive bacterium Micrococcus sp. hsn08 with flocculation activity on Chlorella vulgaris biomass

The aim of this work was to investigate the flocculation mechanism by Gram-positive bacterium, Micrococcus sp. hsn08 as a means for harvesting Chlorella vulgaris biomass. Bacterial cells of Micrococcus sp. hsn08 were added into algal culture to harvest algal cells through direct contacting with algae to form flocs. Viability dependence test confirmed that flocculation activity does not depend on live bacteria, but on part of the peptidoglycan. The further investigation has determined that amino acids in cell wall play an important role to flocculate algal cells. Positively charged calcium can combine bacterial and algal cells together, and form a bridge between them, thereby forming the flocs, suggesting that ions bridging is the main flocculation mechanism. These results suggest that bacterial cells of Micrococcus sp. hsn08 can be applied to harvest microalgae biomass with the help of amino acids in cell wall.

RpoN (σ54) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain

Some bacteria are capable of forming flocs, in which bacterial cells become self-flocculated by secreted extracellular polysaccharides and other biopolymers. The floc-forming bacteria play a central role in activated sludge, which has been widely utilized for the treatment of municipal sewage and industrial wastewater. Here, we use a floc-forming bacterium, Aquincolatertiaricarbonis RN12, as a model to explore the biosynthesis of extracellular polysaccharides and the regulation of floc formation. A large gene cluster for exopolysaccharide biosynthesis and a gene encoding the alternative sigma factor RpoN1, one of the four paralogues, have been identified in floc formation-deficient mutants generated by transposon mutagenesis, and the gene functions have been further confirmed by genetic complementation analyses. Interestingly, the biosynthesis of exopolysaccharides remained in the rpoN1-disrupted flocculation-defective mutants, but most of the exopolysaccharides were secreted and released rather than bound to the cells. Furthermore, the expression of exopolysaccharide biosynthesis genes seemed not to be regulated by RpoN1. Taken together, our results indicate that RpoN1 may play a role in regulating the expression of a certain gene(s) involved in the self-flocculation of bacterial cells but not in the biosynthesis and secretion of exopolysaccharides required for floc formation.IMPORTANCE Floc formation confers bacterial resistance to predation of protozoa and plays a central role in the widely used activated sludge process. In this study, we not only identified a large gene cluster for biosynthesis of extracellular polysaccharides but also identified four rpoN paralogues, one of which (rpoN1) is required for floc formation in A. tertiaricarbonis RN12. In addition, this RpoN sigma factor regulates the transcription of genes involved in biofilm formation and swarming motility, as previously shown in other bacteria. However, this RpoN paralogue is not required for the biosynthesis of exopolysaccharides, which are released and dissolved into culture broth by the rpoN1 mutant rather than remaining tightly bound to cells, as observed during the flocculation of the wild-type strain. These results indicate that floc formation is a regulated complex process, and other yet-to-be identified RpoN1-dependent factors are involved in self-flocculation of bacterial cells via exopolysaccharides and/or other biopolymers.