1
|
Shi W, Tang Y, Liu Y, Fan J, Huang S, Guo Y, Zhang B, Lens PNL. Deciphering the role of micro/nano-hydroxyapatite in aerobic granular sludge system: Effects on treatment performance and enhancement mechanism. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 366:121850. [PMID: 39018842 DOI: 10.1016/j.jenvman.2024.121850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/26/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
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.
Collapse
Affiliation(s)
- Wenxin Shi
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China
| | - Yi Tang
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China
| | - Yi Liu
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China
| | - Jiawei Fan
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China
| | - Shuchang Huang
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China
| | - Yuan Guo
- State Key Laboratory of Eco-hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, China
| | - Bing Zhang
- College of Environment and Ecology, Chongqing University, Chongqing, 400044, China.
| | - Piet N L Lens
- UNESCO-IHE, Institute for Water Education, Westvest 7, 2601, DA, Delft, the Netherlands
| |
Collapse
|
2
|
Li RH, Huang J, Liu CX, Yu K, Guo F, Li Y, Chen ZH, Wang X, Zhao RX, Zhang JY, Liang JJ, Li Y, Lin L, Sun L, Li XY, Li B. Genome-centric metagenomics provides new insights into metabolic pathways of polyhydroxyalkanoates biosynthesis and functional microorganisms subsisting on municipal organic wastes. WATER RESEARCH 2023; 244:120512. [PMID: 37633209 DOI: 10.1016/j.watres.2023.120512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/23/2023] [Accepted: 08/18/2023] [Indexed: 08/28/2023]
Abstract
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.
Collapse
Affiliation(s)
- Ruo-Hong Li
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China; School of Environmental Science and Engineering, Sun Yat-sen University, China
| | - Jin Huang
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, China
| | - Cheng-Xi Liu
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, China
| | - Feng Guo
- School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Xiamen University, Xiamen, China
| | - You Li
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China
| | - Zuo-Hong Chen
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, China
| | - Xuan Wang
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China
| | - Ren-Xin Zhao
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China
| | - Jia-Yu Zhang
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China
| | - Jia-Jin Liang
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China
| | - Yun Li
- Environmental Engineering Research Centre, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China
| | - Lin Lin
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China
| | - Lianpeng Sun
- School of Environmental Science and Engineering, Sun Yat-sen University, China
| | - Xiao-Yan Li
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China; Shenzhen Environmental Science and New Energy Laboratory, Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, China; Environmental Engineering Research Centre, Department of Civil Engineering, The University of Hong Kong, Hong Kong, China.
| | - Bing Li
- Shenzhen Engineering Research Laboratory for Sludge and Food Waste Treatment and Resource Recovery, Tsinghua Shenzhen International Graduate School, Tsinghua University, China.
| |
Collapse
|
3
|
Jiang S, Shi J, Li Y, Zhang Z, Chang L, Wang G, Wu W, Yu L, Dai E, Zhang L, Lyu Z, Xu P, Zhang Y. Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC2 155 by proteogenomic analysis. Front Microbiol 2022; 13:1015140. [PMID: 36312923 PMCID: PMC9597629 DOI: 10.3389/fmicb.2022.1015140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/12/2022] [Indexed: 11/22/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Songhao Jiang
- Key Laboratory of Microbial Diversity Research and Application of Hebei, School of Life Sciences, Hebei University, Baoding, China
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Jiahui Shi
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Yanchang Li
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Zhenpeng Zhang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Lei Chang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Guibin Wang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Wenhui Wu
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
- Guangzhou University of Chinese Medicine, Second Clinical Medicine College, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Liyan Yu
- Research Unit of Proteomics and Research and Development of New Drug, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Erhei Dai
- The Fifth Hospital of Shijiazhuang, School of Public Health, Shijiazhuang, China
| | - Lixia Zhang
- Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Haihe Hospital, Tianjin University, Tianjin, China
| | - Zhitang Lyu
- Key Laboratory of Microbial Diversity Research and Application of Hebei, School of Life Sciences, Hebei University, Baoding, China
- Zhitang Lyu
| | - Ping Xu
- Key Laboratory of Microbial Diversity Research and Application of Hebei, School of Life Sciences, Hebei University, Baoding, China
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
- Guangzhou University of Chinese Medicine, Second Clinical Medicine College, Guangzhou Higher Education Mega Center, Guangzhou, China
- Research Unit of Proteomics and Research and Development of New Drug, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Ping Xu
| | - Yao Zhang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
- Yao Zhang
| |
Collapse
|
4
|
Huang S, Zhang B, Liu Y, Feng X, Shi W. Revealing the influencing mechanisms of polystyrene microplastics (MPs) on the performance and stability of the algal-bacterial granular sludge. BIORESOURCE TECHNOLOGY 2022; 354:127202. [PMID: 35460843 DOI: 10.1016/j.biortech.2022.127202] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
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.
Collapse
Affiliation(s)
- Shuchang Huang
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Bing Zhang
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China.
| | - Yi Liu
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Xueli Feng
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| | - Wenxin Shi
- College of Environment and Ecology, Chongqing University, Chongqing 400044, China
| |
Collapse
|
5
|
Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct annotated encoding genes. Genomics 2021; 114:292-304. [PMID: 34915127 DOI: 10.1016/j.ygeno.2021.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/28/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022]
Abstract
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.
Collapse
|