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Zheng Y, Zhu X, Jiang M, Cao F, You Q, Chen X. Development and Applications of D-Amino Acid Derivatives-based Metabolic Labeling of Bacterial Peptidoglycan. Angew Chem Int Ed Engl 2024; 63:e202319400. [PMID: 38284300 DOI: 10.1002/anie.202319400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 01/30/2024]
Abstract
Peptidoglycan, an essential component within the cell walls of virtually all bacteria, is composed of glycan strands linked by stem peptides that contain D-amino acids. The peptidoglycan biosynthesis machinery exhibits high tolerance to various D-amino acid derivatives. D-amino acid derivatives with different functionalities can thus be specifically incorporated into and label the peptidoglycan of bacteria, but not the host mammalian cells. This metabolic labeling strategy is highly selective, highly biocompatible, and broadly applicable, which has been utilized in various fields. This review introduces the metabolic labeling strategies of peptidoglycan by using D-amino acid derivatives, including one-step and two-step strategies. In addition, we emphasize the various applications of D-amino acid derivative-based metabolic labeling, including bacterial peptidoglycan visualization (existence, biosynthesis, and dynamics, etc.), bacterial visualization (including bacterial imaging and visualization of growth and division, metabolic activity, antibiotic susceptibility, etc.), pathogenic bacteria-targeted diagnostics and treatment (positron emission tomography (PET) imaging, photodynamic therapy, photothermal therapy, gas therapy, immunotherapy, etc.), and live bacteria-based therapy. Finally, a summary of this metabolic labeling and an outlook is provided.
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Affiliation(s)
- Yongfang Zheng
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Xinyu Zhu
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Mingyi Jiang
- Fujian-Taiwan Science and Technology Cooperation Base of Biomedical Materials and Tissue Engineering, Engineering Research Center of Industrial Biocatalysis, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Provincial Key Laboratory of Polymer Materials, College of Chemistry and Materials Science, Fujian Normal University, 32 Shangsan Road, Fuzhou, 350007, P.R. China
| | - Fangfang Cao
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Qing You
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119074, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
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Hu X, Wang H, Ji B, Wang B, Guo W, Chen R, Jiang C, Chen Y, Zhou D, Zhang Q. Metagenomic insights into the mechanism for the rapid enrichment and high stability of Candidatus Brocadia facilitated by Fe(Ⅲ). WATER RESEARCH 2024; 252:121224. [PMID: 38309072 DOI: 10.1016/j.watres.2024.121224] [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: 09/12/2023] [Revised: 12/09/2023] [Accepted: 01/28/2024] [Indexed: 02/05/2024]
Abstract
The rapid enrichment of anammox bacteria and its fragile resistance to adverse environment are the critical problems facing of anammox processes. As an abundant component in anammox bacteria, iron has been proved to promote the activity and growth of anammox bacteria in the mature anammox systems, but the functional and metabolic profiles in Fe(III) enhanced emerging anammox systems have not been evaluated. Results indicated that the relative abundance of functional genes involved in oxidative phosphorylation, nitrogen metabolism, cofactors synthesis, and extracellular polymers synthesis pathways was significantly promoted in the system added with 5 mg/L Fe(III) (R5). These enhanced pathways were crucial to energy generation, nitrogen removal, cell activity and proliferation, and microbial self-defense, thereby accelerating the enrichment of anammox bacteria Ca. Brocadia and facilitating their resistance to adverse environments. Microbial community analysis showed that the proportion of Ca. Brocadia in R5 also increased to 64.42 %. Hence, R5 could adapt rapidly to the increased nitrogen loading rate and increase the nitrogen removal rate by 108 % compared to the system without Fe(III) addition. However, the addition of 10 and 20 mg/L Fe(III) showed inhibitory effects on the growth and activity of anammox bacteria, which exhibited the lower relative abundance of Ca. Brocadia and unstable or even collapsed nitrogen removal performance. This study not only clarified the concentration range of Fe(III) that promoted and inhibited the enrichment of anammox bacteria, but also deepened our understanding of the functional and metabolic mechanisms underlying enhanced enrichment of anammox bacteria by Fe(III), providing a potential strategy to hasten the start-up of anammox from conventional activated sludge.
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Affiliation(s)
- Xiaoling Hu
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Hongyu Wang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China.
| | - Bin Ji
- Department of Water and Wastewater Engineering, School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Bin Wang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Wenbin Guo
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Rongfan Chen
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Can Jiang
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Yanfang Chen
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Dao Zhou
- School of Civil Engineering, Wuhan University, Wuhan 430072, China
| | - Qian Zhang
- School of Civil Engineering & Architecture, Wuhan University of Technology, Wuhan 430070, China
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Wurzbacher CE, Haufschild T, Hammer J, van Teeseling MCF, Kallscheuer N, Jogler C. Planctoellipticum variicoloris gen. nov., sp. nov., a novel member of the family Planctomycetaceae isolated from wastewater of the aeration lagoon of a sugar processing plant in Northern Germany. Sci Rep 2024; 14:5741. [PMID: 38459238 PMCID: PMC10923784 DOI: 10.1038/s41598-024-56373-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/05/2024] [Indexed: 03/10/2024] Open
Abstract
In the present study, we characterise a strain isolated from the wastewater aeration lagoon of a sugar processing plant in Schleswig (Northern Germany) by Heinz Schlesner. As a pioneer in planctomycetal research, he isolated numerous strains belonging to the phylum Planctomycetota from aquatic habitats around the world. Phylogenetic analyses show that strain SH412T belongs to the family Planctomycetaceae and shares with 91.6% the highest 16S rRNA gene sequence similarity with Planctopirus limnophila DSM 3776T. Its genome has a length of 7.3 Mb and a G + C content of 63.6%. Optimal growth of strain SH412T occurs at pH 7.0-7.5 and 28 °C with its pigmentation depending on sunlight exposure. Strain SH412T reproduces by polar asymmetric division ("budding") and forms ovoid cells. The cell size determination was performed using a semi-automatic pipeline, which we first evaluated with the model species P. limnophila and then applied to strain SH412T. Furthermore, the data acquired during time-lapse analyses suggests a lifestyle switch from flagellated daughter cells to non-flagellated mother cells in the subsequent cycle. Based on our data, we suggest that strain SH412T represents a novel species within a novel genus, for which we propose the name Planctoellipticum variicoloris gen. nov., sp. nov., with strain SH412T (= CECT 30430T = STH00996T, the STH number refers to the Jena Microbial Resource Collection JMRC) as the type strain of the new species.
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Affiliation(s)
- Carmen E Wurzbacher
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Tom Haufschild
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Jonathan Hammer
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Muriel C F van Teeseling
- Junior Research Group "Prokaryotic Cell Biology", Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Nicolai Kallscheuer
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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Hancock TL, Dahedl EK, Kratz MA, Urakawa H. Bacterial community shifts induced by high concentration hydrogen peroxide treatment of Microcystis bloom in a mesocosm study. HARMFUL ALGAE 2024; 133:102587. [PMID: 38485437 DOI: 10.1016/j.hal.2024.102587] [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: 09/11/2023] [Revised: 12/18/2023] [Accepted: 01/30/2024] [Indexed: 03/19/2024]
Abstract
Hydrogen peroxide has gained popularity as an environmentally friendly treatment for cyanobacterial harmful algal blooms (cHABs) that takes advantage of oxidative stress sensitivity in cyanobacteria at controlled concentrations. Higher concentrations of hydrogen peroxide treatments may seem appealing for more severe cHABs but there is currently little understanding of the environmental impacts of this approach. Of specific concern is the associated microbial community, which may play key roles in the succession/recovery process post-treatment. To better understand impacts of a high concentration treatment on non-target microbial communities, we applied a hydrogen peroxide spray equating to a total volume concentration of 14 mM (473 mg/L, 0.04%) to 250 L mesocosms containing Microcystis bloom biomass, monitoring treatment and control mesocosms for 4 days. Cyanobacteria dominated control mesocosms throughout the experiment while treatment mesocosms experienced a 99% reduction, as determined by bacterial amplicon sequencing, and a 92% reduction in bacterial cell density within 1 day post-treatment. Only the bacterial community exhibited signs of regrowth, with a fold change of 9.2 bacterial cell density from day 1 to day 2. Recovery consisted of succession by Planctomycetota (47%) and Gammaproteobacteria (17%), which were likely resilient due to passive cell component compartmentalization and rapid upregulation of dnaK and groEL oxidative stress genes, respectively. The altered microbiome retained beneficial functionality of microcystin degradation through a currently recognized but unidentified pathway in Gammaproteobacteria, resulting in a 70% reduction coinciding with bacterial regrowth. There was also an 81% reduction of both total nitrogen and phosphorus, as compared to 91 and 93% in the control, respectively, due to high expressions of genes related to nitrogen (argH, carB, glts, glnA) and phosphorus (pntAB, phoB, pstSCB) cycling. Overall, we found a portion of the bacterial community was resilient to the high-concentration hydrogen peroxide treatment, resulting in Planctomycetota and Gammaproteobacteria dominance. This high-concentration treatment may be suitable to rapidly end cHABs which have already negatively impacted the aquatic environment rather than allow them to persist.
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Affiliation(s)
- Taylor L Hancock
- School of Geosciences, University of South Florida, Tampa, FL 33620, United States; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, United States
| | - Elizabeth K Dahedl
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, United States
| | - Michael A Kratz
- Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, United States
| | - Hidetoshi Urakawa
- School of Geosciences, University of South Florida, Tampa, FL 33620, United States; Department of Ecology and Environmental Studies, Florida Gulf Coast University, Fort Myers, FL, United States.
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Qiao X, Ding L, Fang F, Fu C, Wei R, Chen Y, Zheng S, Wang X, Yan Y, Yang K, Xu N, Tao H, Yu K, Zhang L. An integrated meta-omics approach reveals the different response mechanisms of two anammox bacteria towards fluoroquinolone antibiotics. ENVIRONMENT INTERNATIONAL 2024; 185:108505. [PMID: 38394916 DOI: 10.1016/j.envint.2024.108505] [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: 12/15/2023] [Revised: 02/03/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
The emerging fluoroquinolone antibiotics (FQs) are highly influential in nitrogen removal from livestock wastewater. However, beyond the capability of nitrogen removal, little is known about the molecular mechanisms (e.g., shift of core metabolism and energy allocation) of different anaerobic ammonium-oxidizing bacteria (AnAOB) under continuous FQ stress. This study investigated the effects of ciprofloxacin, ofloxacin and their mixture at concentrations detected in livestock wastewater on two key anammox species in membrane bioreactors. It was found 20 μg/L FQs promoted nitrogen removal efficiency and community stability, and42-51 % of FQs were removed simultaneously. Integrated meta-omics analysis revealed varied gene expression patterns between the two dominant AnAOB, Candidatus Brocadia sapporoensis (B AnAOB) and Candidatus Kuenenia stuttgartiensis (K AnAOB). The nitrogen metabolic processes were bolstered in B AnAOB, while those involved in anammox pathway of K AnAOB were inhibited. This difference was tentatively attributed to the up-regulation of reactive oxygen species scavenger genes (ccp and dxf) and FQ resistance gene (qnrB72) in B AnAOB. Importantly, most enhanced core biosynthesis/metabolism of AnAOB and close cross-feeding with accompanying bacteria were also likely to contribute to their higher levels of biomass yield and metabolism activity under FQ stress. This finding suggests that B AnAOB has the advantage of higher nitrogen metabolism capacity over K AnAOB in livestock wastewater containing FQs, which is helpful for efficient and stable nitrogen removal by the functional anammox species.
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Affiliation(s)
- Xuejiao Qiao
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Lingyun Ding
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen 518118, China
| | - Fang Fang
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Chenkun Fu
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ruqian Wei
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yizhen Chen
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Sihan Zheng
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xisong Wang
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yan Yan
- State Key Laboratory of Isotope Geochemistry, CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510000, China
| | - Kai Yang
- China MCC5 Group Corporation Limited, Chengdu 610023, China
| | - Nan Xu
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Huchun Tao
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ke Yu
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Lijuan Zhang
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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6
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Rivas-Marin E, Moyano-Palazuelo D, Henriques V, Merino E, Devos DP. Essential gene complement of Planctopirus limnophila from the bacterial phylum Planctomycetes. Nat Commun 2023; 14:7224. [PMID: 37940686 PMCID: PMC10632474 DOI: 10.1038/s41467-023-43096-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023] Open
Abstract
Planctopirus limnophila belongs to the bacterial phylum Planctomycetes, a relatively understudied lineage with remarkable cell biology features. Here, we report a genome-wide analysis of essential gene content in P. limnophila. We show that certain genes involved in peptidoglycan synthesis or cell division, which are essential in most other studied bacteria, are not essential for growth under laboratory conditions in this species. We identify essential genes likely involved in lipopolysaccharide biosynthesis, consistent with the view of Planctomycetes as diderm bacteria, and highlight other essential genes of unknown functions. Furthermore, we explore potential stages of evolution of the essential gene repertoire in Planctomycetes and the related phyla Verrucomicrobia and Chlamydiae. Our results provide insights into the divergent molecular and cellular biology of Planctomycetes.
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Affiliation(s)
- Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain.
| | - David Moyano-Palazuelo
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain
| | - Valentina Henriques
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain
| | - Enrique Merino
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain.
- Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, University of Lille, Lille, France.
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Liu J, Xu H, Wang Z, Liu J, Gong X. Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae). Microorganisms 2023; 11:2364. [PMID: 37764208 PMCID: PMC10537169 DOI: 10.3390/microorganisms11092364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to the composition of the endophytic microorganisms in cycad coralloid roots. However, the roles of host and environment in shaping the composition of endophytic bacteria during the recruitment process remain unclear. Here, we determined the diversity, composition, and function prediction of endophytic bacteria from the coralloid roots of a widely cultivated cycad, Cycas revoluta Thunb. Using next-generation sequencing techniques, we comprehensively investigated the diversity and community structure of the bacteria in coralloid roots and bulk soils sampled from 11 sites in China, aiming to explore the variations in core endophytic bacteria and to predict their potential functions. We found a higher microbe diversity in bulk soils than in coralloid roots. Meanwhile, there was no significant difference in the diversity and composition of endophytic bacteria across different localities, and the same result was found after removing cyanobacteria. Desmonostoc was the most dominant in coralloid roots, followed by Nostoc, yet these two cyanobacteria were not shared by all samples. Rhodococcus, Edaphobacter, Niastella, Nordella, SH-PL14, and Virgisporangium were defined as the core microorganisms in coralloid roots. A function prediction analysis revealed that endophytic bacteria majorly participated in the plant uptake of phosphorus and metal ions and in disease resistance. These results indicate that the community composition of the bacteria in coralloid roots is affected by both the host and environment, in which the host is more decisive. Despite the very small proportion of core microbes, their interactions are significant and likely contribute to functions related to host survival. Our study contributes to an understanding of microbial diversity and composition in cycads, and it expands the knowledge on the association between hosts and symbiotic microbes.
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Affiliation(s)
- Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Xu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Zhaochun Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
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Sun Y, Xu Y, Zhang J, Bello A, Li X, Liu W, Egbeagu UU, Zhao L, Han Y, Cheng L, Zhang W, Meng Q, Bi R, Zhao M, Liu X, Sun L, Gai Z, Shi S, Jong C, Xu X. Investigation of underlying links between nitrogen transformation and microorganisms' network modularity in the novel static aerobic composting of dairy manure by "stepwise verification interaction analysis". THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163674. [PMID: 37100152 DOI: 10.1016/j.scitotenv.2023.163674] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/21/2023] [Accepted: 04/18/2023] [Indexed: 06/03/2023]
Abstract
Conventional composting is a viable method treating agricultural solid waste, and microorganisms and nitrogen transformation are the two major components of this proces. Unfortunately, conventional composting is time-consuming and laborious, and limited efforts have been made to mitigate these problems. Herein, a novel static aerobic composting technology (NSACT) was developed and employed for the composting of cow manure and rice straw mixtures. During the composting process, physicochemical parameters were analyzed to evaluate the quality of compost products, and microbial abundance dynamics were determined using high-throughput sequencing technique. The results showed that NSACT achieved compost maturity within 17 days as the thermophilic stage (≥55 °C) lasted for 11 days. GI, pH, and C/N were 98.71 %, 8.38, and 19.67 in the top layer, 92.32 %, 8.24, and 22.38 in the middle layer, 102.08 %, 8.33, and 19.95 in the bottom layer. These observations indicate compost products maturated and met the requirements of current legislation. Compared with fungi, bacterial communities dominated NSACT composting system. Based on the stepwise verification interaction analysis (SVIA), the novel combination utilization of multiple statistical analyses (Spearman, RDA/CCA, Network modularity, and Path analyses), bacterial genera Norank Anaerolineaceae (-0.9279*), norank Gemmatimonadetes (1.1959*), norank Acidobacteria (0.6137**) and unclassified Proteobacteria (-0.7998*), and fungi genera Myriococcum thermophilum (-0.0445), unclassified Sordariales (-0.0828*), unclassified Lasiosphaeriaceae (-0.4174**), and Coprinopsis calospora (-0.3453*) were the identified key microbial taxa affecting NH4+-N, NO3--N, TKN and C/N transformation in the NSACT composting matrix respectively. This work revealed that NSACT successfully managed cow manure-rice straw wastes and significantly shorten the composting period. Interestingly, most microorganisms observed in this composting matrix acted in a synergistic manner, promoting nitrogen transformation.
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Affiliation(s)
- Yu Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yonghui Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Jining Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ayodeji Bello
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China; College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Xiang Li
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Wanying Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ugochi Uzoamaka Egbeagu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Liyan Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Yue Han
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Lijun Cheng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Wenhao Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Qingxin Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Ruixin Bi
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Mingming Zhao
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Xinda Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Lei Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Zhaoxue Gai
- School of Public Administration and Law, Northeast Agricultural University, Harbin 150030, China
| | - Shuai Shi
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China
| | - Chol Jong
- College of Agriculture, Kimjewon Haeju University of Agriculture, Haeju City, Hwanghae South Province 999093, Republic of Korea
| | - Xiuhong Xu
- College of Resources and Environment, Northeast Agricultural University, Harbin 150030, China.
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Li L, Bian D, Wang Q, Xue C, Zhang Q, Zhang SM. Performance of anammox enchanced by pulsed electric fields under added organic carbon sources using integrated network and metagenomics analyses. BIORESOURCE TECHNOLOGY 2023; 380:129116. [PMID: 37137447 DOI: 10.1016/j.biortech.2023.129116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023]
Abstract
This paper aims to investigate the function of a pulsed electric field (PEF) in the anaerobic ammonia oxidation (anammox) process after adding certain chemical oxygen demand (COD) through integrated network and metagenomics analyses. The findings showed that the presence of COD was detrimental to anammox, but PEF could significantly reduce the adverse effect. The total nitrogen removal in the reactor for applying PEF was 16.99% higher on average than the reactor for only dosing COD. Additionally, PEF upgraded the abundance of anammox bacteria subordinate to the phylum Planctomycetes by 9.64%. The analysis of molecular ecological networks promulgated that PEF resulted in an increase in network scale and topology complexity, thereby boosting the potential collaboration of the communities. Metagenomics analyses demonstrated that PEF dramatically promoted anammox central metabolism in the presence of COD, specifically enhancing pivotal N functional genes (hzs, hdh, amo, hao, nas, nor and nos).
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Affiliation(s)
- Liang Li
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Di Bian
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China.
| | - Qichun Wang
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - ChengYao Xue
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Qiuying Zhang
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
| | - Shi Meng Zhang
- College of Resources & Civil Engineering, Northeastern University, Shenyang 110819, PR China
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10
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Radziemska M, Gusiatin MZ, Cydzik-Kwiatkowska A, Blazejczyk A, Holatko J, Brtnicky M. Does biochar in combination with compost effectively promote phytostabilization of heavy metals in soil under different temperature regimes? THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163634. [PMID: 37088391 DOI: 10.1016/j.scitotenv.2023.163634] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
The article presents the effect of a combined amendment, i.e., biochar+compost (BC), on the process of Cd, Cu, Ni, Pb and Zn immobilization in soil cultivated with L. perenne under freezing and thawing conditions (FTC). In particular, the speciation analysis of the examined elements in phytostabilized soils based on their response using the sequential extraction, and the variability of the soil microbiome using 16S rRNA gene amplicon sequencing were systematically assessed. Metal stability in soils was evaluated by the reduced distribution index (Ir). Plants were grown in pots for 52 days under greenhouse conditions. After termination, phytostabilization was continued in a temperature chamber for 64 days to provide FTC. As a result, it was noted that biomass yield of L. perenne was promoted by BC (39 % higher than in the control pots) and reduced by FTC (45 % lower than in the BC-enriched soil not exposed to FTC). An efficacious level of phytostabilization, i.e., higher content of heavy metals in plant roots, was found in the BC-enriched soil, regardless of the changes in soil temperature conditions. BC improved soil pH before applying FTC more than after applying FTC. BC had the greatest impact on increasing Cu stability by redistributing it from the F1 and F2 fractions to the F3 and F4 fractions. For most metals, phytostabilization under FTC resulted in an increase in the proportion of the F1 fraction and a decrease in its stability. Only for Pb and Zn, FTC had greater impact on their stability than BC addition. In all soil samples, the core genera with about 2-3 % abundances were Sphingomonas sp. and Mycobacterium sp. FTC favored the growth of Bacteroidetes and Proteobacteria in soil. Microbial taxa that coped well with FTC but only in the absence of BC were Rhodococcus, Alkanindiges sp., Flavobacterium sp., Williamsia sp. Thermomonas sp.
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Affiliation(s)
- Maja Radziemska
- Institute of Environmental Engineering, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Mariusz Z Gusiatin
- Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Słoneczna St. 45G, 10-719 Olsztyn, Poland
| | - Agnieszka Cydzik-Kwiatkowska
- Institute of Environmental Engineering, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Aurelia Blazejczyk
- Institute of Civil Engineering, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Jiri Holatko
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 61300 Brno, Czech Republic; Agrovyzkum Rapotin, Ltd., Vyzkumniku 267, 788 13 Rapotin, Czech Republic
| | - Martin Brtnicky
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, 61300 Brno, Czech Republic
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11
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Shan A, Huang L, Chen D, Lin Q, Liu R, Wang M, Kang KJ, Pan M, Wang G, He Z, Yang X. Trade-offs between fertilizer-N availability and Cd pollution potential under crop straw incorporation by 15 N stable isotopes in rice. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:51075-51088. [PMID: 36807262 DOI: 10.1007/s11356-022-25085-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/27/2022] [Indexed: 04/16/2023]
Abstract
Application of crop residues and chemical nitrogen (N) fertilizer is a conventional practice for achieving high yield in a rice system. However, the fallacious combination of N fertilizers with crop straw not only significantly reduces the N use efficiencies (NUEs) but also leads to serious environmental problems. The present study employed five treatments including no N fertilization and no straw incorporation (ck), N fertilization incorporation only (S0), N fertilization with 40% straw (S40), N fertilization with 60% straw (S60), and N fertilization with 100% straw (S100) to improve N use efficiency as well as reduced Cd distribution in rice. The crop yields were largely enhanced by fertilization ranging from 13 to 52% over the straw addition treatments. Compared with ck, N fertilizer input significantly decreased soil pH, while DOC contents were raised in response to straw amendment, reaching the highest in S60 and S100 treatments, respectively. Moreover, straw addition substantially impacted the Cd accumulation and altered the bacterial community structure. The soil NH4+-N concentration under S0 performed the maximum in yellow soil, while the minimum in black soil compared to straw-incorporated pots. In addition, the soil NO3--N concentration in straw-incorporated plots tended to be higher than that in straw-removed plots in both soils, indicating that crop straw triggering the N mineralization was associated with native soil N condition. Furthermore, the NUE increased with 15 N uptake in the plant, and the residual 15 N in soil was increased by 26.8% with straw addition across four straw application rates. Overall, our study highlights the trade-offs between straw incorporation with N fertilizer in eliminating potential Cd toxicity, increasing fertilizer-N use efficiencies and help to provide a feasible agricultural management.
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Affiliation(s)
- Anqi Shan
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Lukuan Huang
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Dan Chen
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Qiang Lin
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Rongjie Liu
- Technical Extension Station of Soil Fertilizer and Rural Energy, Ninghai, Ningbo, People's Republic of China
| | - Mei Wang
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Kyong Ju Kang
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Minghui Pan
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Gang Wang
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Zhenli He
- Indian River Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Fort Pierce, FL, 34945, USA
| | - Xiaoe Yang
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China.
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12
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Kang P, Liang Z, Zhang Q, Zheng P, Yu G, Cui L, Liang Y. The optimum particle size of anaerobic ammonia oxidation granular sludge under different substrate concentrations. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 328:116992. [PMID: 36502703 DOI: 10.1016/j.jenvman.2022.116992] [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: 11/02/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The nitrogen removal performance of anaerobic ammonia oxidation granular sludge (AnGS) varies widely among particle sizes. In this paper, the nitrogen removal performance, extracellular polymeric substances (EPS) secretion level and microbial community of AnGS with different particle sizes were investigated to select the optimal particle size for different substrate concentrations. The results showed that the optimal particle size migrated from 0.6-1.6 mm to 1.6-2.5 mm and then to 2.5-3.2 mm as the substrate concentration increased. When the influent concentration of NH4+-N was 110 mg/L, granular sludge with particle size of 1.6-2.5 mm showed excellent nitrogen removal performance with the highest EPS secretion, while the highest EPS secretion gradually migrated to smaller particles as the substrate concentration decreased. The nitrogen removal performance of AnGS with different particle sizes depends on different proportions of anaerobic ammonium-oxidizing (anammox) bacteria (Candidates_Jettenia, Candidates_Kuenenia, Candidatus_Brocadia), heterotrophic nitrification aerobic denitrifying bacteria (Acinetobacter) and denitrifying bacteria (Denitratisoma). The optimum particle size range for AnGS has been clarified for different influent nitrogen concentrations, which can provide some new understanding for the application of anammox reactors.
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Affiliation(s)
- Peilun Kang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Zile Liang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Qian Zhang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Peihan Zheng
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Guangwei Yu
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Lihua Cui
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Yuhai Liang
- Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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13
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van Kasteren S, Rozen DE. Using click chemistry to study microbial ecology and evolution. ISME COMMUNICATIONS 2023; 3:9. [PMID: 36721064 PMCID: PMC9889756 DOI: 10.1038/s43705-022-00205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 02/01/2023]
Abstract
Technological advances have largely driven the revolution in our understanding of the structure and function of microbial communities. Culturing, long the primary tool to probe microbial life, was supplanted by sequencing and other -omics approaches, which allowed detailed quantitative insights into species composition, metabolic potential, transcriptional activity, secretory responses and more. Although the ability to characterize "who's there" has never been easier or cheaper, it remains technically challenging and expensive to understand what the diverse species and strains that comprise microbial communities are doing in situ, and how these behaviors change through time. Our aim in this brief review is to introduce a developing toolkit based on click chemistry that can accelerate and reduce the expense of functional analyses of the ecology and evolution of microbial communities. After first outlining the history of technological development in this field, we will discuss key applications to date using diverse labels, including BONCAT, and then end with a selective (biased) view of areas where click-chemistry and BONCAT-based approaches stand to have a significant impact on our understanding of microbial communities.
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Affiliation(s)
- Sander van Kasteren
- Leiden Institute of Chemistry and The Institute of Chemical Immunology, Leiden University, Einsteinweg 55, Leiden, 2300 RA, The Netherlands.
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2300 RA, The Netherlands.
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14
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Zhu Y, Liu Y, Chang H, Yang H, Zhang W, Zhang Y, Sun H. Deciphering the microbial community structures and functions of wastewater treatment at high-altitude area. Front Bioeng Biotechnol 2023; 11:1107633. [PMID: 36923457 PMCID: PMC10009103 DOI: 10.3389/fbioe.2023.1107633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/30/2023] [Indexed: 03/02/2023] Open
Abstract
Introduction: The proper operation of wastewater treatment plants is a key factor in maintaining a stable river and lake environment. Low purification efficiency in winter is a common problem in high-altitude wastewater treatment plants (WWTPs), and analysis of the microbial community involved in the sewage treatment process at high-altitude can provide valuable references for improving this problem. Methods: In this study, the bacterial communities of high- and low-altitude WWTPs were investigated using Illumina high-throughput sequencing (HTS). The interaction between microbial community and environmental variables were explored by co-occurrence correlation network. Results: At genus level, Thauera (5.2%), unclassified_Rhodocyclaceae (3.0%), Dokdonella (2.5%), and Ferribacterium (2.5%) were the dominant genera in high-altitude group. The abundance of nitrogen and phosphorus removal bacteria were higher in high-altitude group (10.2% and 1.3%, respectively) than in low-altitude group (5.4% and 0.6%, respectively). Redundancy analysis (RDA) and co-occurrence network analysis showed that altitude, ultraviolet index (UVI), pH, dissolved oxygen (DO) and total nitrogen (TN) were the dominated environmental factors (p < 0.05) affecting microbial community assembly, and these five variables explained 21.4%, 20.3%, 16.9%, 11.5%, and 8.2% of the bacterial assembly of AS communities. Discussion: The community diversity of high-altitude group was lower than that of low-altitude group, and WWTPs of high-altitude aeras had a unique microbial community structure. Low temperature and strong UVI are pivotal factors contributing to the reduced diversity of activated sludge microbial communities at high-altitudes.
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Affiliation(s)
- Yuliang Zhu
- School of Environmental and Material Engineering, Yantai University, Yantai, China.,School of Civil Engineering, Yantai University, Yantai, Shandong, China
| | - Yucan Liu
- School of Civil Engineering, Yantai University, Yantai, Shandong, China
| | - Huanhuan Chang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, China
| | - Hao Yang
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou, China
| | - Wei Zhang
- School of Environmental and Material Engineering, Yantai University, Yantai, China
| | - Yanxiang Zhang
- School of Environmental and Material Engineering, Yantai University, Yantai, China
| | - Hongwei Sun
- School of Environmental and Material Engineering, Yantai University, Yantai, China
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15
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Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria. Nat Microbiol 2022; 7:2114-2127. [PMID: 36411352 DOI: 10.1038/s41564-022-01257-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022]
Abstract
The division and cell wall (dcw) gene cluster in Bacteria comprises 17 genes encoding key steps in peptidoglycan synthesis and cytokinesis. To understand the origin and evolution of this cluster, we analysed its presence in over 1,000 bacterial genomes. We show that the dcw gene cluster is strikingly conserved in both gene content and gene order across all Bacteria and has undergone only a few rearrangements in some phyla, potentially linked to cell envelope specificities, but not directly to cell shape. A large concatenation of the 12 most conserved dcw cluster genes produced a robust tree of Bacteria that is largely consistent with recent phylogenies based on frequently used markers. Moreover, evolutionary divergence analyses show that the dcw gene cluster offers advantages in defining high-rank taxonomic boundaries and indicate at least two main phyla in the Candidate Phyla Radiation (CPR) matching a sharp dichotomy in dcw gene cluster arrangement. Our results place the origin of the dcw gene cluster in the Last Bacterial Common Ancestor and show that it has evolved vertically for billions of years, similar to major cellular machineries such as the ribosome. The strong phylogenetic signal, combined with conserved genomic synteny at large evolutionary distances, makes the dcw gene cluster a robust alternative set of markers to resolve the ever-growing tree of Bacteria.
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16
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Qi H, Huang D, Wang F, Ye M, Jiang X. Spatial dynamics of prokaryotic microbial communities in sediments of the Yellow Sea: Assembly process, co-occurrence relationships, and environmental implications. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 319:115645. [PMID: 35797911 DOI: 10.1016/j.jenvman.2022.115645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Marine sediment microorganisms play an important role in the biogeochemical cycle of elements and the transformation of exogenous pollutants; therefore, it is important to study the microbial assembly process and inter taxa associations. In this study, we investigated the profiles and assembly processes of microbial communities of sediments collected from 19 points in the Yellow Sea. As revealed by 16S rRNA sequencing, Proteobacteria (43.11%-65.54%) was the dominant phylum in marine sediment. Further, the physicochemical properties of sediments were significantly influenced by depth (P < 0.05), and the effects of homogeneous selection became greater with increasing depth. The microbial species located in marine sediment at 35°N had a significantly higher co-occurrence relationship (82.76%) than those at 34°N (57.99%) and 36°N (54.07%). Additionally, the microbial community structure of the sediments changed significantly at the genus level with strong fluctuations in the physicochemical properties. By contrast, the carbon, nitrogen, and sulfur associated functional gene diversity and abundance showed no clear variation among different locations, indicating the probable functional redundancy and a potential functional gene pool of the microbes in marine sediments. This study could provide new insights into the composition of microorganisms in sediments in the Yellow Sea, the driving force of microbial diversity, the assembly process, the modes of species' co-occurrence, and their ecological functions.
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Affiliation(s)
- Huiyuan Qi
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dan Huang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Fenghe Wang
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China.
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
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17
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Miyamoto H, Asano F, Ishizawa K, Suda W, Miyamoto H, Tsuji N, Matsuura M, Tsuboi A, Ishii C, Nakaguma T, Shindo C, Kato T, Kurotani A, Shima H, Moriya S, Hattori M, Kodama H, Ohno H, Kikuchi J. A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 836:155520. [PMID: 35508250 DOI: 10.1016/j.scitotenv.2022.155520] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/21/2022] [Accepted: 04/21/2022] [Indexed: 05/02/2023]
Abstract
Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive microbial structures are expected to reveal a novel rule underlying wood biomass processing. Here, structural inferences for inhabitant bacteria involved in carbon and nitrogen metabolism for beetle larvae, an insect model, were performed to explore the potential rules. Bacterial analysis of larval feces showed enrichment of the phyla Chroloflexi, Gemmatimonadetes, and Planctomycetes, and the genera Bradyrhizobium, Chonella, Corallococcus, Gemmata, Hyphomicrobium, Lutibacterium, Paenibacillus, and Rhodoplanes, as bacteria potential involved in plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The fecal abundances of these bacteria were not necessarily positively correlated with their abundances in the habitat, indicating that they were selectively enriched in the feces of the larvae. Correlation and association analyses predicted that common fecal bacteria might affect carbon and nitrogen metabolism. Based on these hypotheses, structural equation modeling (SEM) statistically estimated that inhabitant bacterial groups involved in carbon and nitrogen metabolism were composed of the phylum Gemmatimonadetes and Planctomycetes, and the genera Bradyrhizobium, Corallococcus, Gemmata, and Paenibacillus, which were among the fecal-enriched bacteria. Nevertheless, the selected common bacteria, i.e., the phyla Acidobacteria, Armatimonadetes, and Bacteroidetes and the genera Candidatus Solibacter, Devosia, Fimbriimonas, Gemmatimonas Opitutus, Sphingobium, and Methanobacterium, were necessary to obtain good fit indices in the SEM. In addition, the composition of the bacterial groups differed depending upon metabolic targets, carbon and nitrogen, and their stable isotopes, δ13C and δ15N, respectively. Thus, the statistically derived causal structural models highlighted that the larval fecal-enriched bacteria and common symbiotic bacteria might selectively play a role in wood biomass carbon and nitrogen metabolism. This information could confer a new perspective that helps us use wood biomass more efficiently and might stimulate innovation in environmental industries in the future.
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Affiliation(s)
- Hirokuni Miyamoto
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan; Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba 260-0034, Japan.
| | - Futo Asano
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan
| | | | - Wataru Suda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | | | - Naoko Tsuji
- Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
| | - Makiko Matsuura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
| | - Arisa Tsuboi
- Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan; Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba 260-0034, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Chitose Ishii
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan
| | - Teruno Nakaguma
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; Sermas Co., Ltd., Ichikawa, Chiba 272-0033, Japan; Japan Eco-science (Nikkan Kagaku) Co., Ltd., Chiba, Chiba 260-0034, Japan
| | - Chie Shindo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Tamotsu Kato
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Hideaki Shima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Shigeharu Moriya
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Masahira Hattori
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan; School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Hiroaki Kodama
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8501, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.
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18
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Naufal M, Wu JH, Shao YH. Glutamate Enhances Osmoadaptation of Anammox Bacteria under High Salinity: Genomic Analysis and Experimental Evidence. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11310-11322. [PMID: 35913201 DOI: 10.1021/acs.est.2c01104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
An osmoprotectant that alleviates the bacterial osmotic stress can improve the bioreactor treatment of saline wastewater. However, proposed candidates are expensive, and osmoprotectants of anammox bacteria and their ecophysiological roles are not fully understood. In this study, a comparative analysis of 34 high-quality public metagenome-assembled genomes from anammox bacteria revealed two distinct groups of osmoadaptation. Candidatus Scalindua and Kuenenia share a close phylogenomic relation and osmoadaptation gene profile and have pathways for glutamate transport and metabolisms for enhanced osmoadaptation. The batch assay results demonstrated that the reduced Ca. Kuenenia activity in saline conditions was substantially alleviated with the addition and subsequent synergistic effects of potassium and glutamate. The operational test of two reactors demonstrated that the reduced anammox performance under brine conditions rapidly recovered by 35.7-43.1% as a result of glutamate treatment. The Ca. Kuenenia 16S rRNA and hydrazine gene expressions were upregulated significantly (p < 0.05), and the abundance increased by approximately 19.9%, with a decrease in dominant heterotrophs. These data demonstrated the effectiveness of glutamate in alleviating the osmotic stress of Ca. Kuenenia. This study provides genomic insight into group-specific osmoadaptation of anammox bacteria and can facilitate the precision management of anammox reactors under high salinity.
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Affiliation(s)
- Muhammad Naufal
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, East District, Tainan City 70101, Taiwan
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, East District, Tainan City 70101, Taiwan
| | - Yung-Hsien Shao
- Department of Environmental Engineering, National Cheng Kung University, No. 1, University Road, East District, Tainan City 70101, Taiwan
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19
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Kouba V, Bachmannová C, Podzimek T, Lipovová P, van Loosdrecht MCM. Physiology of anammox adaptation to low temperatures and promising biomarkers: A review. BIORESOURCE TECHNOLOGY 2022; 349:126847. [PMID: 35167904 DOI: 10.1016/j.biortech.2022.126847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
The adaptation of bacteria involved in the anaerobic ammonium oxidation (anammox) to low temperatures in the mainstream of WWTP will unlock substantial treatment savings. However, their adaptation mechanisms have begun to be revealed only very recently. This study reviewed the state-of-the-art knowledge on these mechanisms from -omics studies, crucially including metaproteomics and metabolomics. Anammox bacteria adapt to low temperatures by synthesizing both chaperones of RNA and proteins and chemical chaperones. Furthermore, they preserve energy for the core metabolism by reducing biosynthesis in general. Thus, in this study, a number of biomarkers are proposed to help practitioners assess the extent of anammox bacteria adaptation and predict the decomposition of biofilms/granules or slower growth. The promising biomarkers also include unique ladderane lipids. Further proteomic and metabolomic studies are necessary for a more detailed understanding of anammox low-temperature adaptation, thus easing the transition to more cost-effective and sustainable wastewater treatment.
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Affiliation(s)
- V Kouba
- University of Chemistry and Technology Prague, Department of Water Technology and Environmental Engineering, Technická 5, 166 28 Prague, Czechia.
| | - Ch Bachmannová
- University of Chemistry and Technology Prague, Department of Water Technology and Environmental Engineering, Technická 5, 166 28 Prague, Czechia
| | - T Podzimek
- University of Chemistry and Technology Prague, Department of Biochemistry and Microbiology, Technická 5, 166 28 Prague, Czechia
| | - P Lipovová
- University of Chemistry and Technology Prague, Department of Biochemistry and Microbiology, Technická 5, 166 28 Prague, Czechia
| | - M C M van Loosdrecht
- The Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, Netherlands
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20
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Wang S, Li J, Wang C, Ma J, Li Z, Zheng Z, Zhang J. Reaction of the anammox granules to various antibiotics and operating the anammox coupled denitrifying reactor for oxytetracycline wastetwater treatment. BIORESOURCE TECHNOLOGY 2022; 348:126756. [PMID: 35077812 DOI: 10.1016/j.biortech.2022.126756] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The anaerobic ammonium oxidation (anammox) basedtechnology has been considered as an economic and efficient way to remove nitrogen. However, the anammox bacteria could be strongly inhibited by antibiotics. In present research, inhibiting properties of oxytetracycline, penicillin and polymyxin sulfate upon the anammox activity were investigated through batch experiment. The results implied that anammox activity was significantly inhibited by oxytetracycline and polymyxin sulfate. The non-competitive inhibiting model showed that the inhibiting constants (Ki) of oxytetracycline and polymyxin sulfate were 188.5 and 17.7 mg/L, respectively. Meanwhile, the anammox process was not suppressed while the concentration of penicillin reached 3000 mg/L. In long-run experiment, the influent oxytetracycline concentration of the anammox coupled denitrifying reactor was operated at 20 mg/L. It was observed that the anammox performance completely deteriorated, while the NO2--N removing efficiency reached 15.8%. The obtained findings could provide important instruction for the treatment of antibiotic contaminated wastewater.
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Affiliation(s)
- Shuailing Wang
- National Engineering Laboratory for Wastewater Treatment Technology, Beijing University of Technology, Beijing 100124, China
| | - Jun Li
- National Engineering Laboratory for Wastewater Treatment Technology, Beijing University of Technology, Beijing 100124, China
| | - ChangWen Wang
- School of Urban and Architectural Engineering, Zaozhuang University, Zaozhuang, Shandong 277100, China
| | - Jing Ma
- Beijing Municipal Engineering Professional Design Institute Co., Ltd., Beijing 100037, China
| | - Zhe Li
- National Engineering Laboratory for Wastewater Treatment Technology, Beijing University of Technology, Beijing 100124, China
| | - Zhaoming Zheng
- National Engineering Laboratory for Wastewater Treatment Technology, Beijing University of Technology, Beijing 100124, China.
| | - Jing Zhang
- National Engineering Laboratory for Wastewater Treatment Technology, Beijing University of Technology, Beijing 100124, China
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21
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Wang H, Fan Y, Zhou M, Wang W, Li X, Wang Y. Function of Fe(III)-minerals in the enhancement of anammox performance exploiting integrated network and metagenomics analyses. WATER RESEARCH 2022; 210:117998. [PMID: 34968878 DOI: 10.1016/j.watres.2021.117998] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Iron is a recognized physiological requirement for microorganisms but, for anaerobic ammonium oxidation (anammox) bacteria, its role extends well beyond that of a nutritional necessity. In this study, the function of two typical Fe(III)-minerals (ferrihydrite and magnetite) in anammox processes was evaluated in the absence/presence of Fe(II) by integrated network and metagenomics analyses. Results showed that Fe-(III) minerals addition increased the activity of cellular processes and pathways associated with granule formation, enabling the peak values of particle size to increase by 144% and 115%, respectively. Notably, ferrihydrite (5 mM) enhanced nitrogen removal by 4.8% and 4.1%, respectively, in the short-term and long-term absence of Fe(II). Ferrihydrite also promoted the retention of anammox bacteria affiliated with phylum Planctomycetes in the reactor, contributing to an 11% higher abundance with ferrihydrite amendment when compared with the control (without iron additions) in the short-term absence of Fe(II). Network-based analyses revealed that ferrihydrite facilitated the microbial community to form densely clustered and complex topologies to improve resistance to environmental disturbance (i.e., Fe(II) deficiency), and effectively increased the underlying cooperation and facilitation in the community. Metagenomic analysis revealed that there was limited promotion of anammox central metabolism by the extra addition of Fe(III)-minerals in the presence of Fe(II), highlighting the poor utilization of Fe(III)-minerals by anammox bacteria under Fe(II) sufficiency. This study deepens our understanding of the function of Fe(III)-minerals in anammox systems at the community and functional level, and provides a fundamental basis for developing Fe-based anammox enhancement technologies.
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Affiliation(s)
- Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P R China
| | - Yufei Fan
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P R China
| | - Mingda Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P R China
| | - Weigang Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P R China
| | - Xiang Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, P R China.
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22
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Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
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Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
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23
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Pabst M, Grouzdev DS, Lawson CE, Kleikamp HBC, de Ram C, Louwen R, Lin YM, Lücker S, van Loosdrecht MCM, Laureni M. A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium. THE ISME JOURNAL 2022; 16:346-357. [PMID: 34341504 PMCID: PMC8776859 DOI: 10.1038/s41396-021-01073-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
The enormous chemical diversity and strain variability of prokaryotic protein glycosylation makes their large-scale exploration exceptionally challenging. Therefore, despite the universal relevance of protein glycosylation across all domains of life, the understanding of their biological significance and the evolutionary forces shaping oligosaccharide structures remains highly limited. Here, we report on a newly established mass binning glycoproteomics approach that establishes the chemical identity of the carbohydrate components and performs untargeted exploration of prokaryotic oligosaccharides from large-scale proteomics data directly. We demonstrate our approach by exploring an enrichment culture of the globally relevant anaerobic ammonium-oxidizing bacterium Ca. Kuenenia stuttgartiensis. By doing so we resolve a remarkable array of oligosaccharides, which are produced by two seemingly unrelated biosynthetic routes, and which modify the same surface-layer protein simultaneously. More intriguingly, the investigated strain also accomplished modulation of highly specialized sugars, supposedly in response to its energy metabolism-the anaerobic oxidation of ammonium-which depends on the acquisition of substrates of opposite charges. Ultimately, we provide a systematic approach for the compositional exploration of prokaryotic protein glycosylation, and reveal a remarkable example for the evolution of complex oligosaccharides in bacteria.
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Affiliation(s)
- Martin Pabst
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | | | - Christopher E. Lawson
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA
| | - Hugo B. C. Kleikamp
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Carol de Ram
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Rogier Louwen
- grid.5645.2000000040459992XDepartment of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Yue Mei Lin
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mark C. M. van Loosdrecht
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Michele Laureni
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
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24
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Kallscheuer N, Jogler C, Peeters SH, Boedeker C, Jogler M, Heuer A, Jetten MSM, Rohde M, Wiegand S. Mucisphaera calidilacus gen. nov., sp. nov., a novel planctomycete of the class Phycisphaerae isolated in the shallow sea hydrothermal system of the Lipari Islands. Antonie van Leeuwenhoek 2022; 115:407-420. [PMID: 35050438 PMCID: PMC8882080 DOI: 10.1007/s10482-021-01707-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 12/29/2021] [Indexed: 02/07/2023]
Abstract
For extending the current collection of axenic cultures of planctomycetes, we describe in this study the isolation and characterisation of strain Pan265T obtained from a red biofilm in the hydrothermal vent system close to the Lipari Islands in the Tyrrhenian Sea, north of Sicily, Italy. The strain forms light pink colonies on solid medium and grows as a viscous colloid in liquid culture, likely as the result of formation of a dense extracellular matrix observed during electron microscopy. Cells of the novel isolate are spherical, motile and divide by binary fission. Strain Pan265T is mesophilic (temperature optimum 30-33 °C), neutrophilic (pH optimum 7.0-8.0), aerobic and heterotrophic. The strain has a genome size of 3.49 Mb and a DNA G + C content of 63.9%. Phylogenetically, the strain belongs to the family Phycisphaeraceae, order Phycisphaerales, class Phycisphaerae. Our polyphasic analysis supports the delineation of strain Pan265T from the known genera in this family. Therefore, we conclude to assign strain Pan265T to a novel species within a novel genus, for which we propose the name Mucisphaera calidilacus gen. nov., sp. nov. The novel species is the type species of the novel genus and is represented by strain Pan265T (= DSM 100697T = CECT 30425T) as type strain.
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Affiliation(s)
- Nicolai Kallscheuer
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
| | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | | | - Mareike Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sandra Wiegand
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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25
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Zhang X, Ding S, Lv H, Cui G, Yang M, Wang Y, Guan T, Li XD. Microbial controls on heavy metals and nutrients simultaneous release in a seasonally stratified reservoir. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:1937-1948. [PMID: 34363164 DOI: 10.1007/s11356-021-15776-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
The eutrophication of reservoirs can change the physicochemical parameters of water, thus affecting the migration and transformation of heavy metals. At present, there is insufficient research on the coupling mechanisms between nutrients and heavy metals, especially between heavy metals in suspended particles. In this paper, spatial and temporal distribution characteristics of nutrients dissolved heavy metals, and heavy metals in suspended particles were analyzed in a seasonally stratified reservoir. Combined with the nitrogen and phosphorus biogeochemical process, the coupling mechanisms between heavy metals and nutrients were discussed. The results showed that the Aha Reservoir had temperature and dissolved oxygen stratification in April and July. The reduction and dissolution of Fe and Mn oxide/hydroxide and the resuspension of sediments might result in a simultaneous increase in the concentrations of nutrients, dissolved heavy metals and heavy metals in suspended particles in hypolimnion in July and October. In the presence of dissimilatory iron-reducing bacteria (DRIB), the dissolution of iron-bound phosphorus in sediments and suspended particulate matter (SPM) might lead to the simultaneous release of iron and phosphorus into the water. The dissolution of metal sulfides in the sediments and SPM under the action of dissimilatory nitrate reduction to ammonium (DNRA) bacteria might lead to the simultaneous release of ammonia nitrogen and heavy metals into the water. Due to the coupling between nitrogen and phosphorus and heavy metals, seasonal stratified reservoir may face the risk of periodic simultaneous pollution of eutrophication and heavy metals in summer and autumn. This research provides theoretical support for the treatment of heavy metal and eutrophication combined pollution in karst areas.
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Affiliation(s)
- Xuecheng Zhang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Shiyuan Ding
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
- State Key Laboratory of Environmental Geochemistry, Guiyang, 550081, China.
| | - Hong Lv
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Gaoyang Cui
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
- The College of Environment and Planning, Henan University, Kaifeng, 475004, China
| | - Mengdi Yang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Yiyao Wang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Tianhao Guan
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Xiao-Dong Li
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin, 300072, China.
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26
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Gambelli L, Mesman R, Versantvoort W, Diebolder CA, Engel A, Evers W, Jetten MSM, Pabst M, Daum B, van Niftrik L. The Polygonal Cell Shape and Surface Protein Layer of Anaerobic Methane-Oxidizing Methylomirabilis lanthanidiphila Bacteria. Front Microbiol 2021; 12:766527. [PMID: 34925275 PMCID: PMC8671808 DOI: 10.3389/fmicb.2021.766527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022] Open
Abstract
Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from M. lanthanidiphila cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of M. lanthanidiphila cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of M. lanthanidiphila a distinctive and intriguing case to study.
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Affiliation(s)
- Lavinia Gambelli
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands.,Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - Rob Mesman
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Christoph A Diebolder
- Netherlands Centre for Electron Nanoscopy (NeCEN), Leiden University, Leiden, Netherlands
| | - Andreas Engel
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands
| | - Wiel Evers
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Department of Chemical Engineering, Delft University of Technology, Delft, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Laura van Niftrik
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
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27
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Seeger C, Dyrhage K, Mahajan M, Odelgard A, Lind SB, Andersson SGE. The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns. Front Microbiol 2021; 12:643045. [PMID: 34745019 PMCID: PMC8567305 DOI: 10.3389/fmicb.2021.643045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/25/2021] [Indexed: 11/13/2022] Open
Abstract
The Planctomycetes bacteria have unique cell architectures with heavily invaginated membranes as confirmed by three-dimensional models reconstructed from FIB-SEM images of Tuwongella immobilis and Gemmata obscuriglobus. The subcellular proteome of T. immobilis was examined by differential solubilization followed by LC-MS/MS analysis, which identified 1569 proteins in total. The Tris-soluble fraction contained mostly cytoplasmic proteins, while inner and outer membrane proteins were found in the Triton X-100 and SDS-soluble fractions, respectively. For comparisons, the subcellular proteome of Escherichia coli was also examined using the same methodology. A notable difference in the overall fractionation pattern of the two species was a fivefold higher number of predicted cytoplasmic proteins in the SDS-soluble fraction in T. immobilis. One category of such proteins is represented by innovations in the Planctomycetes lineage, including unique sets of serine/threonine kinases and extracytoplasmic sigma factors with WD40 repeat domains for which no homologs are present in E. coli. Other such proteins are members of recently expanded protein families in which the newly evolved paralog with a new domain structure is recovered from the SDS-soluble fraction, while other paralogs may have similar domain structures and fractionation patterns as the single homolog in E. coli. The expanded protein families in T. immobilis include enzymes involved in replication-repair processes as well as in rRNA and tRNA modification and degradation. These results show that paralogization and domain shuffling have yielded new proteins with distinct fractionation characteristics. Understanding the molecular intricacies of these adaptive changes might aid in the development of a model for the evolution of cellular complexity.
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Affiliation(s)
- Christian Seeger
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Karl Dyrhage
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Mayank Mahajan
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Anna Odelgard
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Siv G E Andersson
- Science for Life Laboratory, Molecular Evolution, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
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28
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Kruppa OC, Gerlach D, Fan R, Czermak P. Development of a chemically defined medium for Planctopirus limnophila to increase biomass production. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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29
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Cao S, Yan W, Yu L, Zhang L, Lay W, Zhou Y. Challenges of THP-AD centrate treatment using partial nitritation-anammox (PN/A) - inhibition, biomass washout, low alkalinity, recalcitrant and more. WATER RESEARCH 2021; 203:117555. [PMID: 34416648 DOI: 10.1016/j.watres.2021.117555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
The centrate produced from a thermal hydrolysis pretreatment coupled anaerobic digestion (THP-AD) system is generally characterized by high concentrations of ammonium and recalcitrant organics. In this study, a cost-effective partial nitritation-anammox (PN/A) process was developed to evaluate the potential challenges in THP-AD centrate treatment. The results show ammonium oxidizing bacteria (AOB) and anammox bacteria were seriously inhibited by THP-AD centrate, while long-term acclimation together with aeration optimization can mitigate such inhibition. A nitrogen removal rate (NRR) of 0.55 kg N/m3/d was obtained and maintained with 60% THP-AD centrate as feed. However, 100% THP-AD centrate caused sludge wash-out from PN reactor due to excessive polymer and high solids in influent. The alkalinity deficit also reduced the AOB activity. Moreover, anammox activity and overall NRR also declined (to 0.37 kg N/m3/d). The organics transformation mainly occurred in PN reactor with very low removal efficiency due to their recalcitrant characteristics. The humic acid-like, fulvic acid-like substances and building blocks were revealed as the major organic compounds in THP-AD centrate (51.5-53.8% TOC), which likely contributed to the recalcitrant. Nitrosomonas and Candidatus Brocadia were the major AOB and anammox bacteria in the PN and anammox reactors respectively. With the increased THP-AD centrate proportion in the feed, the abundance of both population declined. Interestingly, Denitratisoma, being the major denitrifying bacteria in anammox reactor, had relatively stable abundance (7.0-7.9%) when THP-AD centrate was improved from 3 and 100%, suggesting the inhibition on anammox bacteria was not due to the overgrowth of denitrifying microorganism despite the high organics loading rate. Overall, this study provides a guide to develop the energy-saving PN/A process for THP-AD centrate treatment by pointing out potential challenges and mitigating strategies.
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Affiliation(s)
- Shenbin Cao
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore; College of Architecture and Civil engineering, Beijing University of Technology, Beijing 100124, China
| | - Wangwang Yan
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Lei Yu
- Water Reclamation (Plants) Department, Public Utilities Board, 40 Scotts Road, #15-01, Singapore 228231, Singapore
| | - Liang Zhang
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Winson Lay
- Water Reclamation (Plants) Department, Public Utilities Board, 40 Scotts Road, #15-01, Singapore 228231, Singapore
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore.
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Phylo-taxogenomics of the genus Tautonia with descriptions of Tautonia marina sp. nov., Tautonia rosea sp. nov., and emended description of the genus. Syst Appl Microbiol 2021; 44:126229. [PMID: 34273679 DOI: 10.1016/j.syapm.2021.126229] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 12/21/2022]
Abstract
Four strains of Planctomycetes, (JC636, JC649, JC650T, JC657T) which are all salt and alkali tolerant, pink coloured, with spherical to oval shaped, Gram-stain-negative, non-motile cells were isolated from different regions of Chilika lagoon, India. All strains have obligate requirement for N-acetylglucosamine (NAG) and share highest 16S rRNA gene sequence identity with members of the genus Tautonia (<95%) of the family Isosphaeraceae. The 16S rRNA gene sequence identity between strains was >99.5%. Respiratory quinone for all the strains was MK6. Major fatty acids of all the strains were C18:1ω9c, C16:0 and C18:0. Major polar lipid of the strain JC650T was phosphatidylethanolamine, while, phosphatidylcholine and phosphatidylglycerol for strain JC657T. Spermidine was the only common polyamine for all the four strains. Strains JC657T, JC636 and JC649 shared highest phenotypic similarity along with 100% 16S rRNA gene sequence identity. Strains JC657T, JC636 and JC649 differed from strain JC650T phenotypically, chemotaxonomically and genotypically, thus belong to a different species. The genomic size of strain JC650T and JC657T are 7.06 Mb and 6.96 Mb with DNA G + C content of 63.9 and 62.7 mol%, respectively. Based on phylogenetic, genomic (ANI, AAI, POCP, dDDH), chemotaxonomic, physiological and biochemical characteristics, we conclude that strains JC650T and JC657T (together with strains JC636, JC649) belong to the genus Tautonia and constitute two novel species for which we propose the names Tautonia marina sp. nov., and Tautonia rosea sp. nov., respectively. These two novel species are represented by the type strains JC650T (=KCTC 72177T = NBRC 113885T) and JC657T (=KCTC 72597T = NBRC 113883T) respectively.
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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Seasonal Succession of Bacterial Communities in Three Eutrophic Freshwater Lakes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18136950. [PMID: 34209591 PMCID: PMC8295879 DOI: 10.3390/ijerph18136950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/17/2021] [Accepted: 06/26/2021] [Indexed: 12/24/2022]
Abstract
Urban freshwater lakes play an indispensable role in maintaining the urban environment and are suffering great threats of eutrophication. Until now, little has been known about the seasonal bacterial communities of the surface water of adjacent freshwater urban lakes. This study reported the bacterial communities of three adjacent freshwater lakes (i.e., Tangxun Lake, Yezhi Lake and Nan Lake) during the alternation of seasons. Nan Lake had the best water quality among the three lakes as reflected by the bacterial eutrophic index (BEI), bacterial indicator (Luteolibacter) and functional prediction analysis. It was found that Alphaproteobacteria had the lowest abundance in summer and the highest abundance in winter. Bacteroidetes had the lowest abundance in winter, while Planctomycetes had the highest abundance in summer. N/P ratio appeared to have some relationships with eutrophication. Tangxun Lake and Nan Lake with higher average N/P ratios (e.g., N/P = 20) tended to have a higher BEI in summer at a water temperature of 27 °C, while Yezhi Lake with a relatively lower average N/P ratio (e.g., N/P = 14) tended to have a higher BEI in spring and autumn at a water temperature of 9-20 °C. BEI and water temperature were identified as the key parameters in determining the bacterial communities of lake water. Phosphorus seemed to have slightly more impact on the bacterial communities than nitrogen. It is expected that this study will help to gain more knowledge on urban lake eutrophication.
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Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer. Microorganisms 2021; 9:microorganisms9061326. [PMID: 34207399 PMCID: PMC8233860 DOI: 10.3390/microorganisms9061326] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 12/12/2022] Open
Abstract
Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO3−/NH4+ ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.
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Chen Y, Li S, Liu N, He H, Cao X, Lv C, Zhang K, Dai J. Effects of different types of microbial inoculants on available nitrogen and phosphorus, soil microbial community, and wheat growth in high-P soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:23036-23047. [PMID: 33438124 DOI: 10.1007/s11356-020-12203-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/22/2020] [Indexed: 05/03/2023]
Abstract
Irrational application of chemical fertilizers causes soil nutrient imbalance, reduced microbial diversity, soil diseases, and other soil quality problems and is one of the main sources of non-point pollution. The application of microbial inoculant (MI) can improve the soil environment and crop growth to reduce problems caused by irrational application of chemical fertilizers. Field experiments were carried out in high-phosphorus soils to study the effects of the addition of various MIs combined with chemical fertilizers on soil properties, wheat growth, and soil microbial composition and structure. The MIs consisted of one fungal agent: Trichoderma compound agent (TC) and five bacterial agents, namely soil remediation agent (SR), anti-repeat microbial agent (AM), microbial agent (MA), plant growth-promoting rhizobacteria (PG), and biological fertilizer agent (BF). The wheat yield increased by 15.2-33.4% with the addition of MIs, and PG with Bacillus subtilis as the core microorganism had the most obvious effect on increasing the production (p < 0.05). For the entire growth period of wheat, all MIs applied significantly increased the available nitrogen (AN) (p < 0.05) but did not significantly affect the available phosphorus (AP). BF has the best effect on increasing AN in the soil. The 16S rRNA sequencing results indicated that the dominant phyla of soil bacteria were Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. The addition of MIs increased the relative abundance of Acidobacteria, Actinobacteria, Chloroflexi and decreased Proteobacteria and Bacteroidetes. The diversity of soil bacterial community (Chao1) was significantly higher in the soil added with TC than that added with BF (p < 0.05). All bacterial agents significantly enriched various genera (p < 0.05), while the fungal agent (TC) did not enrich the genera significantly. pH and AN, but not TP, were closely related to the dominant bacteria phylum in high-P soil. The application of MIs improved AN in soil, increased the wheat yield, and changed the relative abundance of the soil dominant phylum, and these changes were closely related to the type of MIs. The results provide a scientific basis for rational use of different types of MIs in high-P soil.
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Affiliation(s)
- Yihui Chen
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Shuangshuang Li
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Na Liu
- College of Resource and Environment, Shanxi Agricultural University, Taigu, 030801, China
| | - Huan He
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Xiaoyu Cao
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Cheng Lv
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Ke Zhang
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China
| | - Jiulan Dai
- Environment Research Institute, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, China.
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35
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Iturbe-Espinoza P, Brandt BW, Braster M, Bonte M, Brown DM, van Spanning RJM. Effects of DNA preservation solution and DNA extraction methods on microbial community profiling of soil. Folia Microbiol (Praha) 2021; 66:597-606. [PMID: 33834428 PMCID: PMC8298342 DOI: 10.1007/s12223-021-00866-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 11/28/2022]
Abstract
Microbial community profiling using high-throughput sequencing relies in part on the preservation of the DNA and the effectiveness of the DNA extraction method. This study aimed at understanding to what extent these parameters affect the profiling. We obtained samples treated with and without a preservation solution. Also, we compared DNA extraction kits from Qiagen and Zymo-Research. The types of samples were defined strains, both as single species and mixtures, as well as undefined indigenous microbial communities from soil. We show that the use of a preservation solution resulted in substantial changes in the 16S rRNA gene profiles either due to an overrepresentation of Gram-positive bacteria or to an underrepresentation of Gram-negative bacteria. In addition, 16S rRNA gene profiles were substantially different depending on the type of kit that was used for extraction. The kit from Zymo extracted DNA from different types of bacteria in roughly equal amounts. In contrast, the kit from Qiagen preferentially extracted DNA from Gram-negative bacteria while DNA from Gram-positive bacteria was extracted less effectively. These differences in kit performance strongly influenced the interpretation of our microbial ecology studies.
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Affiliation(s)
- Paul Iturbe-Espinoza
- Systems Biology Lab, Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martin Braster
- Systems Biology Lab, Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Matthijs Bonte
- Shell Global Solutions International BV, The Hague, The Netherlands
| | | | - Rob J M van Spanning
- Systems Biology Lab, Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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Ignacio BJ, Bakkum T, Bonger KM, Martin NI, van Kasteren SI. Metabolic labeling probes for interrogation of the host-pathogen interaction. Org Biomol Chem 2021; 19:2856-2870. [PMID: 33725048 DOI: 10.1039/d0ob02517h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial infections are still one of the leading causes of death worldwide; despite the near-ubiquitous availability of antibiotics. With antibiotic resistance on the rise, there is an urgent need for novel classes of antibiotic drugs. One particularly troublesome class of bacteria are those that have evolved highly efficacious mechanisms for surviving inside the host. These contribute to their virulence by immune evasion, and make them harder to treat with antibiotics due to their residence inside intracellular membrane-limited compartments. This has sparked the development of new chemical reporter molecules and bioorthogonal probes that can be metabolically incorporated into bacteria to provide insights into their activity status. In this review, we provide an overview of several classes of metabolic labeling probes capable of targeting either the peptidoglycan cell wall, the mycomembrane of mycobacteria and corynebacteria, or specific bacterial proteins. In addition, we highlight several important insights that have been made using these metabolic labeling probes.
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Affiliation(s)
- Bob J Ignacio
- Institute for Molecules and Materials, Radbout Universiteit, Nijmegen, Gelderland, Netherlands
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37
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Gilmore MC, Ritzl-Rinkenberger B, Cava F. An updated toolkit for exploring bacterial cell wall structure and dynamics. Fac Rev 2021; 10:14. [PMID: 33659932 PMCID: PMC7894271 DOI: 10.12703/r/10-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The bacterial cell wall is made primarily from peptidoglycan, a complex biomolecule which forms a bag-like exoskeleton that envelops the cell. As it is unique to bacteria and typically essential for their growth and survival, it represents one of the most successful targets for antibiotics. Although peptidoglycan has been studied intensively for over 50 years, the past decade has seen major steps in our understanding of this molecule because of the advent of new analytical and imaging methods. Here, we outline the most recent developments in tools that have helped to elucidate peptidoglycan structure and dynamics.
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Affiliation(s)
- Michael C Gilmore
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Barbara Ritzl-Rinkenberger
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
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38
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Zhang ZZ, Zhang Y, Cheng YF, Jin RC. Linear anionic surfactant (SDBS) destabilized anammox process through sludge disaggregation and metabolic inhibition. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123641. [PMID: 33264860 DOI: 10.1016/j.jhazmat.2020.123641] [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: 05/16/2020] [Revised: 07/29/2020] [Accepted: 08/04/2020] [Indexed: 06/12/2023]
Abstract
The increase of emerging contaminants, such as surfactants, is one of the major challenges to biological wastewater treatment. However, the potential impact of linear alkylbenzene sulphonates (LAS), a major class of anionic surfactants, on anammox process is unclear. The long-term effects of sodium dodecyl benzene sulfonate (SDBS, as a model LAS) on reactor performance, microbial community and sludge properties were investigated in this study. The presence of 5 mg L-1 SDBS promoted the release of extracellular microbial products from anammox granules and the wash-out of anammox population via effluent. Despite sludge disaggregation, the reactor performance was robust to the exposure of 5 mg L-1 SDBS due to functional redundancy. With the further increase of SDBS to 10 mg L-1, the metabolic activity of anammox biomass and the transcription and post-translation of hydrazine dehydrogenase were significantly decreased. The potential mechanism might be associated with the damage on cell membrane that induced the leakage of intracellular matrix. These results highlight the need to consider the potential risk of LAS to operation of anammox process in biological wastewater treatment plant.
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Affiliation(s)
- Zheng-Zhe Zhang
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yu Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Ya-Fei Cheng
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ren-Cun Jin
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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39
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de Souza FH, Roecker PB, Silveira DD, Sens ML, Campos LC. Influence of slow sand filter cleaning process type on filter media biomass: backwashing versus scraping. WATER RESEARCH 2021; 189:116581. [PMID: 33186813 DOI: 10.1016/j.watres.2020.116581] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
Biomass was assessed as a new approach for evaluating backwashed slow sand filters (BSF). Slow sand filtration (SSF) is a simple technology for water treatment, where biological mechanisms play a key role in filtration efficiency. Backwashed slow sand filters were previously recommended for small-scale filters (~1 m² of filtration area) as an alternative to conventional filters that are usually cleaned by scraping (ScSF). Biomass was never evaluated in BSF, which is a gap in the knowledge of this technology, considering the importance of its biological mechanisms. Therefore, for the first time, two filters operating under the same conditions were used to compare the influence of backwashing on biomass; one filter was cleaned by backwashing and the other by scraping. Biomass along the filter media depth (40 cm) was assessed by different techniques and compared in terms of cellular biomass (by chloroform fumigation), volatile solids, bacterial community (by 16S rRNA gene sequencing), and observations by scanning electron and fluorescence microscopy. Filters were also monitored and compared regarding filtered water quality and headloss; their differences were related to the different cleaning processes. Overall, filtered water quality was acceptable for slow sand filter standards (turbidity < 1 NTU and total coliform removal > 1 log). However, headloss developed faster on scraped filters, and biomass was different between the two filters. Backwashing did not significantly disturb biomass while scraping changed its surface sand layers. Cell biomass was more abundant and spread across the filtration depth, related to lower headloss, turbidity, and cyanobacterial breakthrough. These results agreed with the water quality and microscopy observations. The bacterial community was also less stratified in the backwashed filter media. These results expand the knowledge of backwashing use in slow sand filters, demonstrating that this process preserves more biomass than scraping. In addition, biomass preservation can lead to bacterial selectivity and faster filter ripening. Considering the importance of biomass preservation on slow sand filtration and its biological filtration mechanisms, the results presented in this paper are promising. The novel insight that BSF can preserve biomass after backwashing may contribute to increasing its application in small communities.
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Affiliation(s)
- F H de Souza
- Departamento de Engenharia Sanitária e Ambiental (ENS), Centro Tecnológico (CTC), Universidade Federal de Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, Brazil, 88040-900; Department of Civil, Geomatic and Environmental Engineering (CEGE), University College London (UCL), Chadwick Building, Room GM11, Gower St, London WC1E 6BT, United Kingdom
| | - P B Roecker
- Departamento de Engenharia Sanitária e Ambiental (ENS), Centro Tecnológico (CTC), Universidade Federal de Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, Brazil, 88040-900
| | - D D Silveira
- Departamento de Engenharia Sanitária e Ambiental (ENS), Centro Tecnológico (CTC), Universidade Federal de Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, Brazil, 88040-900
| | - M L Sens
- Departamento de Engenharia Sanitária e Ambiental (ENS), Centro Tecnológico (CTC), Universidade Federal de Santa Catarina (UFSC), Campus Reitor João David Ferreira Lima, Florianópolis, Santa Catarina, Brazil, 88040-900
| | - L C Campos
- Department of Civil, Geomatic and Environmental Engineering (CEGE), University College London (UCL), Chadwick Building, Room GM11, Gower St, London WC1E 6BT, United Kingdom.
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40
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van Teeseling MCF, Jogler C. Cultivation of elusive microbes unearthed exciting biology. Nat Commun 2021; 12:75. [PMID: 33398002 PMCID: PMC7782747 DOI: 10.1038/s41467-020-20393-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
Many newly-discovered microbial phyla have been studied solely by cultivation-independent techniques such as metagenomics. Much of their biology thus remains elusive, because the organisms have not yet been isolated and grown in the lab. Katayama et al. lift the curtain on some intriguing biology by cultivating and studying bacteria from the elusive OP9 phylum (Atribacterota).
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Affiliation(s)
| | - Christian Jogler
- Institute of Microbiology, Department of Microbial Interactions, Friedrich Schiller University Jena, Jena, Germany.
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41
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Kallistova AY, Nikolaev YA, Mardanov AV, Berestovskaya YY, Grachev VA, Kostrikina NA, Pelevina AV, Ravin NV, Pimenov NV. Investigation of Formation and Development of Anammox Biofilms by Light, Epifluorescence, and Electron Microscopy. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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42
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Ozumchelouei EJ, Hamidian AH, Zhang Y, Yang M. A critical review on the effects of antibiotics on anammox process in wastewater. REV CHEM ENG 2020. [DOI: 10.1515/revce-2020-0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Anaerobic ammonium oxidation (anammox) has recently become of significant interest due to its capability for cost-effective nitrogen elimination from wastewater. However, anaerobic ammonia-oxidizing bacteria (AnAOB) are sensitive to environmental changes and toxic substances. In particular, the presence of antibiotics in wastewater, which is considered unfavorable to the anammox process, has become a growing concern. Therefore, it is necessary to evaluate the effects of these inhibitors to acquire information on the applicability of the anammox process. Hence, this review summarizes our knowledge of the effects of commonly detected antibiotics in water matrices, including fluoroquinolone, macrolide, β-lactam, chloramphenicol, tetracycline, sulfonamide, glycopeptide, and aminoglycoside, on the anammox process. According to the literature, the presence of antibiotics in wastewater could partially or completely inhibit anammox reactions, in which antibiotics targeting protein synthesis or DNA replication (excluding aminoglycoside) were the most effective against the AnAOB strains.
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Affiliation(s)
- Elnaz Jafari Ozumchelouei
- School of Chemical Engineering , University College of Engineering, University of Tehran , Tehran , Iran
| | - Amir Hossein Hamidian
- Department of Environmental Science and Engineering, Faculty of Natural Resources , University of Tehran , Karaj , Iran
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
| | - Min Yang
- Department of Environmental Science and Engineering, Faculty of Natural Resources , University of Tehran , Karaj , Iran
- State Key Laboratory of Environmental Aquatic Chemistry , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, P.R. China
- University of Chinese Academy of Sciences , Beijing 100049, P.R. China
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43
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Waqqas M, Salbreiter M, Kallscheuer N, Jogler M, Wiegand S, Heuer A, Rast P, Peeters SH, Boedeker C, Jetten MSM, Rohde M, Jogler C. Rosistilla oblonga gen. nov., sp. nov. and Rosistilla carotiformis sp. nov., isolated from biotic or abiotic surfaces in Northern Germany, Mallorca, Spain and California, USA. Antonie Van Leeuwenhoek 2020; 113:1939-1952. [PMID: 32623658 PMCID: PMC7716947 DOI: 10.1007/s10482-020-01441-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/17/2020] [Indexed: 02/07/2023]
Abstract
Planctomycetes are ubiquitous bacteria with fascinating cell biological features. Strains available as axenic cultures in most cases have been isolated from aquatic environments and serve as a basis to study planctomycetal cell biology and interactions in further detail. As a contribution to the current collection of axenic cultures, here we characterise three closely related strains, Poly24T, CA51T and Mal33, which were isolated from the Baltic Sea, the Pacific Ocean and the Mediterranean Sea, respectively. The strains display cell biological features typical for related Planctomycetes, such as division by polar budding, presence of crateriform structures and formation of rosettes. Optimal growth was observed at temperatures of 30-33 °C and at pH 7.5, which led to maximal growth rates of 0.065-0.079 h-1, corresponding to generation times of 9-11 h. The genomes of the novel isolates have a size of 7.3-7.5 Mb and a G + C content of 57.7-58.2%. Phylogenetic analyses place the strains in the family Pirellulaceae and suggest that Roseimaritima ulvae and Roseimaritima sediminicola are the current closest relatives. Analysis of five different phylogenetic markers, however, supports the delineation of the strains from members of the genus Roseimaritima and other characterised genera in the family. Supported by morphological and physiological differences, we conclude that the strains belong to the novel genus Rosistilla gen. nov. and constitute two novel species, for which we propose the names Rosistilla carotiformis sp. nov. and Rosistilla oblonga sp. nov. (the type species). The two novel species are represented by the type strains Poly24T (= DSM 102938T = VKM B-3434T = LMG 31347T = CECT 9848T) and CA51T (= DSM 104080T = LMG 29702T), respectively.
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Affiliation(s)
- Muhammad Waqqas
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
| | - Markus Salbreiter
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
| | | | - Mareike Jogler
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | | | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany.
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
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44
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Peeters SH, Wiegand S, Kallscheuer N, Jogler M, Heuer A, Jetten MSM, Boedeker C, Rohde M, Jogler C. Description of Polystyrenella longa gen. nov., sp. nov., isolated from polystyrene particles incubated in the Baltic Sea. Antonie Van Leeuwenhoek 2020; 113:1851-1862. [PMID: 32239304 PMCID: PMC7716846 DOI: 10.1007/s10482-020-01406-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/15/2020] [Indexed: 11/28/2022]
Abstract
Planctomycetes occur in almost all aquatic ecosystems on earth. They have a remarkable cell biology, and members of the orders Planctomycetales and Pirellulales feature cell division by polar budding, perform a lifestyle switch from sessile to motile cells and have an enlarged periplasmic space. Here, we characterise a novel planctomycetal strain, Pla110T, isolated from the surface of polystyrene particles incubated in the Baltic Sea. After phylogenetic analysis, the strain could be placed in the family Planctomycetaceae. Strain Pla110T performs cell division by budding, has crateriform structures and grows in aggregates or rosettes. The strain is a chemoheterotroph, grows under mesophilic and neutrophilic conditions, and exhibited a doubling time of 21 h. Based on our phylogenetic and morphological characterisation, strain Pla110T (DSM 103387T = LMG 29693T) is concluded to represent a novel species belonging to a novel genus, for which we propose the name Polystyrenella longa gen. nov., sp. nov.
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Affiliation(s)
- Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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45
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Wiegand S, Jogler M, Boedeker C, Heuer A, Peeters SH, Kallscheuer N, Jetten MSM, Kaster AK, Rohde M, Jogler C. Updates to the recently introduced family Lacipirellulaceae in the phylum Planctomycetes: isolation of strains belonging to the novel genera Aeoliella, Botrimarina, Pirellulimonas and Pseudobythopirellula and the novel species Bythopirellula polymerisocia and Posidoniimonas corsicana. Antonie Van Leeuwenhoek 2020; 113:1979-1997. [PMID: 33151460 PMCID: PMC7717034 DOI: 10.1007/s10482-020-01486-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
Eight novel strains of the phylum Planctomycetes were isolated from different aquatic habitats. Among these habitats were the hydrothermal vent system close to Panarea Island, a public beach at Mallorca Island, the shore of Costa Brava (Spain), and three sites with brackish water in the Baltic Sea. The genome sizes of the novel strains range from 4.33 to 6.29 Mb with DNA G+C contents between 52.8 and 66.7%. All strains are mesophilic (Topt 24-30 °C) and display generation times between 17 and 94 h. All eight isolates constitute novel species of either already described or novel genera within the family Lacipirellulaceae. Two of the novel species, Posidoniimonas polymericola (type strain Pla123aT = DSM 103020T = LMG 29466T) and Bythopirellula polymerisocia (type strain Pla144T = DSM 104841T = VKM B-3442T), belong to established genera, while the other strains represent the novel genera Aeoliella gen. nov., Botrimarina gen. nov., Pirellulimonas gen. nov. and Pseudobythopirellula gen. nov. Based on our polyphasic analysis, we propose the species Aeoliella mucimassa sp. nov. (type strain Pan181T = DSM 29370T = LMG 31346T = CECT 9840T = VKM B-3426T), Botrimarina colliarenosi sp. nov. (type strain Pla108T = DSM 103355T = LMG 29803T), Botrimarina hoheduenensis sp. nov. (type strain Pla111T = DSM 103485T = STH00945T, Jena Microbial Resource Collection JMRC), Botrimarina mediterranea sp. nov. (type strain Spa11T = DSM 100745T = LMG 31350T = CECT 9852T = VKM B-3431T), Pirellulimonas nuda sp. nov. (type strain Pla175T = DSM 109594T = CECT 9871T = VKM B-3448T) and Pseudobythopirellula maris sp. nov. (type strain Mal64T = DSM 100832T = LMG 29020T).
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Affiliation(s)
- Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Friedrich Schiller University, Jena, Germany.
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46
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Peeters SH, Wiegand S, Kallscheuer N, Jogler M, Heuer A, Jetten MSM, Boedeker C, Rohde M, Jogler C. Lignipirellula cremea gen. nov., sp. nov., a planctomycete isolated from wood particles in a brackish river estuary. Antonie Van Leeuwenhoek 2020; 113:1863-1875. [PMID: 32239303 PMCID: PMC7717058 DOI: 10.1007/s10482-020-01407-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/15/2020] [Indexed: 02/07/2023]
Abstract
A novel planctomycetal strain, designated Pla85_3_4T, was isolated from the surface of wood incubated at the discharge of a wastewater treatment plant in the Warnow river near Rostock, Germany. Cells of the novel strain have a cell envelope architecture resembling that of Gram-negative bacteria, are round to pear-shaped (length: 2.2 ± 0.4 µm, width: 1.2 ± 0.3 µm), form aggregates and divide by polar budding. Colonies have a cream colour. Strain Pla85_3_4T grows at ranges of 10-30 °C (optimum 26 °C) and at pH 6.5-10.0 (optimum 7.5), and has a doubling time of 26 h. Phylogenetically, strain Pla85_3_4T (DSM 103796T = LMG 29741T) is concluded to represent a novel species of a novel genus within the family Pirellulaceae, for which we propose the name Lignipirellula cremea gen. nov., sp. nov.
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Affiliation(s)
- Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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47
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Wiegand S, Jogler M, Boedeker C, Heuer A, Rast P, Peeters SH, Jetten MSM, Kaster AK, Rohde M, Kallscheuer N, Jogler C. Additions to the genus Gimesia: description of Gimesia alba sp. nov., Gimesia algae sp. nov., Gimesia aquarii sp. nov., Gimesia aquatilis sp. nov., Gimesia fumaroli sp. nov. and Gimesia panareensis sp. nov., isolated from aquatic habitats of the Northern Hemisphere. Antonie Van Leeuwenhoek 2020; 113:1999-2018. [PMID: 33231764 PMCID: PMC7716864 DOI: 10.1007/s10482-020-01489-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/19/2020] [Indexed: 11/29/2022]
Abstract
Thirteen novel planctomycetal strains were isolated from five different aquatic sampling locations. These comprise the hydrothermal vent system close to Panarea Island (Italy), a biofilm on the surface of kelp at Monterey Bay (CA, USA), sediment and algae on Mallorca Island (Spain) and Helgoland Island (Germany), as well as a seawater aquarium in Braunschweig, Germany. All strains were shown to belong to the genus Gimesia. Their genomes cover a size range from 7.22 to 8.29 Mb and have a G+C content between 45.1 and 53.7%. All strains are mesophilic (Topt 26-33 °C) with generation times between 12 and 32 h. Analysis of fatty acids yielded palmitic acid (16:0) and a fatty acid with the equivalent chain length of 15.817 as major compounds. While five of the novel strains belong to the already described species Gimesia maris and Gimesia chilikensis, the other strains belong to novel species, for which we propose the names Gimesia alba (type strain Pan241wT = DSM 100744T = LMG 31345T = CECT 9841T = VKM B-3430T), Gimesia algae (type strain Pan161T = CECT 30192T = STH00943T = LMG 29130T), Gimesia aquarii (type strain V144T = DSM 101710T = VKM B-3433T), Gimesia fumaroli (type strain Enr17T = DSM 100710T = VKM B-3429T) and Gimesia panareensis (type strain Enr10T = DSM 100416T = LMG 29082T). STH numbers refer to the Jena Microbial Resource Collection (JMRC).
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Affiliation(s)
- Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | | | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | | | - Christian Jogler
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany.
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
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48
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Jogler C, Wiegand S, Boedeker C, Heuer A, Peeters SH, Jogler M, Jetten MSM, Rohde M, Kallscheuer N. Tautonia plasticadhaerens sp. nov., a novel species in the family Isosphaeraceae isolated from an alga in a hydrothermal area of the Eolian Archipelago. Antonie Van Leeuwenhoek 2020; 113:1889-1900. [PMID: 32399714 PMCID: PMC7716859 DOI: 10.1007/s10482-020-01424-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
A novel planctomycetal strain, designated ElPT, was isolated from an alga in the shallow hydrothermal vent system close to Panarea Island in the Tyrrhenian Sea. Cells of strain ElPT are spherical, form pink colonies and display typical planctomycetal characteristics including division by budding and presence of crateriform structures. Strain ElPT has a mesophilic (optimum at 30 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. It reaches a generation time of 29 h (µmax = 0.024 h-1). The strain has a genome size of 9.40 Mb with a G + C content of 71.1% and harbours five plasmids, the highest number observed in the phylum Planctomycetes thus far. Phylogenetically, the strain represents a novel species of the recently described genus Tautonia in the family Isosphaeraceae. A characteristic feature of the strain is its tendency to attach strongly to a range of plastic surfaces. We thus propose the name Tautonia plasticadhaerens sp. nov. for the novel species, represented by the type strain ElPT (DSM 101012T = LMG 29141T).
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Affiliation(s)
- Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
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49
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Rivas-Marin E, Wiegand S, Kallscheuer N, Jogler M, Peeters SH, Heuer A, Jetten MSM, Boedeker C, Rohde M, Devos DP, Jogler C. Maioricimonas rarisocia gen. nov., sp. nov., a novel planctomycete isolated from marine sediments close to Mallorca Island. Antonie Van Leeuwenhoek 2020; 113:1901-1913. [PMID: 32583192 PMCID: PMC7716917 DOI: 10.1007/s10482-020-01436-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Planctomycetes are ubiquitous bacteria with environmental and biotechnological relevance. Axenic cultures of planctomycetal strains are the basis to analyse their unusual biology and largely uncharacterised metabolism in more detail. Here, we describe strain Mal4T isolated from marine sediments close to Palma de Mallorca, Spain. Strain Mal4T displays common planctomycetal features, such as division by polar budding and the presence of fimbriae and crateriform structures on the cell surface. Cell growth was observed at ranges of 10-39 °C (optimum at 31 °C) and pH 6.5-9.0 (optimum at 7.5). The novel strain shows as pear-shaped cells of 2.0 ± 0.2 × 1.4 ± 0.1 µm and is one of the rare examples of orange colony-forming Planctomycetes. Its genome has a size of 7.7 Mb with a G+C content of 63.4%. Phylogenetically, we conclude that strain Mal4T (= DSM 100296T = LMG 29133T) is the type strain representing the type species of a novel genus, for which we propose the name Maioricimonas rarisocia gen. nov., sp. nov.
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Affiliation(s)
- Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Seville, Spain
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Mareike Jogler
- Department of Microbial Interactions, Friedrich-Schiller University, Jena, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Seville, Spain
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Friedrich-Schiller University, Jena, Germany.
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50
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Rivas-Marin E, Wiegand S, Kallscheuer N, Jogler M, Peeters SH, Heuer A, Jetten MSM, Boedeker C, Rohde M, Devos DP, Jogler C. Thalassoglobus polymorphus sp. nov., a novel Planctomycete isolated close to a public beach of Mallorca Island. Antonie Van Leeuwenhoek 2020; 113:1915-1926. [PMID: 32583191 PMCID: PMC7716918 DOI: 10.1007/s10482-020-01437-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/11/2020] [Indexed: 02/07/2023]
Abstract
Access to axenic cultures is crucial to extend the knowledge of the biology, lifestyle or metabolic capabilities of bacteria from different phyla. The phylum Planctomycetes is an excellent example since its members display an unusual cell biology and complex lifestyles. As a contribution to the current collection of axenic planctomycete cultures, here we describe strain Mal48T isolated from phytoplankton material sampled at the coast of S'Arenal close to Palma de Mallorca (Spain). The isolated strain shows optimal growth at pH 7.0-7.5 and 30 °C and exhibits typical features of Planctomycetes. Cells of the strain are spherical to pear-shaped, divide by polar budding with daughter cells showing the same shape as the mother cell, tend to aggregate, display a stalk and produce matrix or fimbriae. Strain Mal48T showed 95.8% 16S rRNA gene sequence similarity with the recently described Thalassoglobus neptunius KOR42T. The genome sequence of the novel isolate has a size of 6,357,355 bp with a G+C content of 50.3%. A total of 4874 protein-coding genes, 41 tRNA genes and 2 copies of the 16S rRNA gene are encoded in the genome. Based on phylogenetic, morphological and physiological analyses, we conclude that strain Mal48T (= DSM 100737T = LMG 29019T) should be classified as the type strain of a new species in the genus Thalassoglobus, for which the name Thalassoglobus polymorphus sp. nov. is proposed.
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Affiliation(s)
- Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Seville, Spain
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Mareike Jogler
- Department of Microbial Interactions, Friedrich-Schiller University, Jena, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Seville, Spain
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Friedrich-Schiller University, Jena, Germany.
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