Proteogenomic Refinement of the Neomegalonema perideroedesT Genome Annotation

Deciphering the role of micro/nano-hydroxyapatite in aerobic granular sludge system: Effects on treatment performance and enhancement mechanism

Hydroxyapatite (HAP), a mineral nucleus identified within aerobic granular sludge (AGS), plays a vital role in enhancing the AGS systems. However, the microscopic mechanism underlying their roles remains largely unexplored. Herein, a systematic investigation was carried out to elucidate the impact and enhanced mechanisms associated with HAP of different sizes, i.e. micro-HAP (mHAP) and nano-HAP (nHAP), on the aerobic granulation, nutrient removal and microbial diversity of AGS. Results showed that the presence of nHAP and mHAP significantly shortened the granulation process to 15 and 20 days, respectively. This might be ascribed to the fact that the large specific surface area of nHAP aggregates was conducive to microbial adhesion, biomass accumulation and sludge granulation. Compared with mHAP, the granules with nHAP showed better settlement performance, mechanical strength and larger diameter. The X-ray diffraction (XRD) and Raman spectrometer analysis confirmed the presence of HAP within the granules, which was found to stimulate the secretion of extracellular polymeric substance, improve the compactness of granule structure and suppress the growth of filamentous bacteria, thereby contributing to a stable AGS system. The presence of HAP, especially nHAP, effectively enriched the functional microorganisms, such as nitrifying and denitrifying bacteria (e.g. Candidatus_Competibacter) and phosphorus accumulating organisms (e.g. Flavobacterium), leading to the improved nutrient removal efficiencies (COD > 96%, TN > 76%, and TP > 74%). Further analysis revealed the up-regulation of functional enzymes (e.g. nitrite oxidoreductase and polyphosphate kinase) involved in nutrient metabolism, underlying the inherent mechanisms for the excellent nutrient removal. This study deepens the understanding of granulation mechanisms from the perspective of mineral cores, and proposes an economically feasible strategy for rapid initiation and stabilization of AGS reactors.

Genome-centric metagenomics provides new insights into metabolic pathways of polyhydroxyalkanoates biosynthesis and functional microorganisms subsisting on municipal organic wastes

The microbial community of a sequencing batch reactor operated under feast and famine conditions for production of polyhydroxyalkanoates (PHAs) was characterized through high-throughput sequencing and metagenomic analysis. The fermented food waste and chemically-enhanced primary sludge was fed in this bioreactor. After acclimation, the PHA yield achieved as high as 0.60-0.69 g CODPHA/g CODS. The complete changes of microbial community structure were found during shifts of feedstock. A synthesis of SCL/MCL-PHAs pathway was established for PHA-producing bioreactor in this mixed-culture system. The structure-performance relationship of PHA-producing microbial community and feedstock composition was investigated. The results showed that microbial community tends to be decentralized and prefer team work for PHA synthesis to consume the multiple substrates and digest inevitable non-VFA contents in fermented liquor. This study also discovered unreported potential PHA producers (e.g., genera Tabrizicola, Nannocystis, Ga0077539, Ga0077559, JOSHI-001, SNC69-320 and UBA2334) subsisting on municipal organic wastes and expands the current knowledge about mixed-culture system that the PHA synthesis pathway is widely existed in activated sludge.

Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC2 155 by proteogenomic analysis

Accurate identification of novel peptides remains challenging because of the lack of evaluation criteria in large-scale proteogenomic studies. Mirror proteases of trypsin and lysargiNase can generate complementary b/y ion series, providing the opportunity to efficiently assess authentic novel peptides in experiments other than filter potential targets by different false discovery rates (FDRs) ranking. In this study, a pair of in-house developed acetylated mirror proteases, Ac-Trypsin and Ac-LysargiNase, were used in Mycolicibacterium smegmatis MC² 155 for proteogenomic analysis. The mirror proteases accurately identified 368 novel peptides, exhibiting 75–80% b and y ion coverages against 65–68% y or b ion coverages of Ac-Trypsin (38.9% b and 68.3% y) or Ac-LysargiNase (65.5% b and 39.6% y) as annotated peptides from M. smegmatis MC² 155. The complementary b and y ion series largely increased the reliability of overlapped sequences derived from novel peptides. Among these novel peptides, 311 peptides were annotated in other public M. smegmatis strains, and 57 novel peptides with more continuous b and y pairs were obtained for further analysis after spectral quality assessment. This enabled mirror proteases to successfully correct six annotated proteins' N-termini and detect 17 new coding open reading frames (ORFs). We believe that mirror proteases will be an effective strategy for novel peptide detection in both prokaryotic and eukaryotic proteogenomics.

Revealing the influencing mechanisms of polystyrene microplastics (MPs) on the performance and stability of the algal-bacterial granular sludge

Algal-bacterial granular sludge (ABGS) is an energy-saving and environment-friendly wastewater treatment technology; however, the effects of microplastics (MPs) on the performance and stability of the ABGS system remain unknown. Herein, the influencing mechanisms of polystyrene MPs (50 μm) on the ABGS were systematically investigated. The ABGS exhibited a high removal efficiency of MPs (over 96%) at 1 mg/L and 20 mg/L. Although the biomass content, sludge settling and particle size were not obviously affected by MPs, the COD and total phosphorus (TP) removal efficiencies were inhibited by 2.6%-4.1% and 2.9%-5.8%, respectively. Meanwhile, the structural stability of ABGS was damaged by MPs, owing to the excessive oxidative stress, low content of protein-like substance (especially tryptophan and tyrosine), and the large portion of loose protein secondary structure. Microbial community analysis revealed that the relative abundance of some functional bacteria (Candidatus_Competibacter and Rhodobacter) and algal species (Tetradesmus) were decreased under the MPs stress.

Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct annotated encoding genes

Mycobacterium tuberculosis (MTB) is a severe causing agent of tuberculosis (TB). Although H37Rv, the type strain of M. tuberculosis was sequenced in 1998, annotation errors of encoding genes have been frequently reported in hundreds of papers. This phenomenon is particularly severe at the 5' end of the genes. Here, we applied a TMPP [(N-Succinimidyloxycarbonylmethyl) tris (2,4,6-trimethoxyphenyl) phosphonium bromide] labeling combined with StageTip separating strategy on M. tuberculosis H37Rv to characterize the N-terminal start sites of its annotated encoding genes. Totally, 1047 proteins were identified with 2058 TMPP labeled N-terminal peptides from all the 2625 mass spectrometer (MS) sequenced proteins. Comparative genomics analysis allowed the re-annotation of 43 proteins' N-termini in H37Rv and 762 proteins in Mycobacteriaceae. All revised N-termini start sites were distributed in 5'-UTR of annotated genes due to over-annotation of previous N-terminal initiation codon, especially the ATG. In addition, we identified and verified a novel gene Rv1078A in +3 frame different from the annotated gene Rv1078 in +2 frame. Altogether, our findings contribute to the better understanding of N-terminal of H37Rv and other species from Mycobacteriaceae that can assist future studies on biological study.