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Gopalakrishnan V, Saxena P, Thakur P, Lipatov A, Sani RK. Impact of Graphene Layers on Genetic Expression and Regulation within Sulfate-Reducing Biofilms. Microorganisms 2024; 12:1759. [PMID: 39338434 PMCID: PMC11433944 DOI: 10.3390/microorganisms12091759] [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: 07/15/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/30/2024] Open
Abstract
Bacterial adhesion and biofilm maturation is significantly influenced by surface properties, encompassing both bare surfaces and single or multi-layered coatings. Hence, there is an utmost interest in exploring the intricacies of gene regulation in sulfate-reducing bacteria (SRB) on copper and graphene-coated copper surfaces. In this study, Oleidesulfovibrio alaskensis G20 was used as the model SRB to elucidate the pathways that govern pivotal roles during biofilm formation on the graphene layers. Employing a potent reporter green fluorescent protein (GFP) tagged to O. alaskensis G20, the spatial structure of O. alaskensis G20 biofilm on copper foil (CuF), single-layer graphene-coated copper (Cu-GrI), and double-layer graphene-coated copper (Cu-GrII) surfaces was investigated. Biofilm formation on CuF, Cu-GrI, and Cu-GrII surfaces was quantified using CLSM z-stack images within COMSTAT v2 software. The results revealed that CuF, Cu-GrI, and Cu-GrII did not affect the formation of the GFP-tagged O. alaskensis G20 biofilm architecture. qPCR expression showed insignificant fold changes for outer membrane components regulating the quorum-sensing system, and global regulatory proteins between the uncoated and coated surfaces. Notably, a significant expression was observed within the sulfate reduction pathway confined to dissimilatory sulfite reductases on the Cu-GrII surface compared to the CuF and Cu-GrI surfaces.
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Affiliation(s)
- Vinoj Gopalakrishnan
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Payal Thakur
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Alexey Lipatov
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
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2
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Mohamed DFMS, Tarafdar A, Lee SY, Oh HB, Kwon JH. Assessment of biodegradation and toxicity of alternative plasticizer di(2-ethylhexyl) terephthalate: Impacts on microbial biofilms, metabolism, and reactive oxygen species-mediated stress response. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 355:124217. [PMID: 38797346 DOI: 10.1016/j.envpol.2024.124217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/04/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Although di(2-ethylhexyl) terephthalate (DOTP) is being widely adopted as a non-phthalate plasticizer, existing research primarily focuses on human and rat toxicity. This leaves a significant gap in our understanding of their impact on microbial communities. This study assessed the biodegradation and toxicity of DOTP on microbes, focusing on its impact on biofilms and microbial metabolism using Rhodococcus ruber as a representative bacterial strain. DOTP is commonly found in mass fractions between 0.6 and 20% v/v in various soft plastic products. This study used polyvinyl chloride films (PVC) with varying DOTP concentrations (range 1-10% v/v) as a surface for analysis of biofilm growth. Cell viability and bacterial stress responses were tested using LIVE/DEAD™ BacLight™ Bacterial Viability Kit and by the detection of reactive oxygen species using CellROX™ Green Reagent, respectively. An increase in the volume of dead cells (in the plastisphere biofilm) was observed with increasing DOTP concentrations in experiments using PVC films, indicating the potential negative impact of DOTP on microbial communities. Even at a relatively low concentration of DOTP (1%), signs of stress in the microbes were noticed, while concentrations above 5% compromised their ability to survive. This research provides a new understanding of the environmental impacts of alternative plasticizers, prompting the need for additional research into their wider effects on both the environment and human health.
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Affiliation(s)
- Dana Fahad M S Mohamed
- Division of Environmental Science and Ecological Engineering, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Abhrajyoti Tarafdar
- Division of Environmental Science and Ecological Engineering, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea; School of Food Science and Environmental Health, Technological University Dublin, City Campus, Grangegorman, Dublin, D07ADY7, Ireland
| | - So Yeon Lee
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul, 04107, Republic of Korea
| | - Jung-Hwan Kwon
- Division of Environmental Science and Ecological Engineering, Korea University, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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Gado WS, Al-Gamal AG, Badawy MSEM, Labena A, Zakaria K, Kabel KI. Detectable quorum signaling molecule via PANI-metal oxides nanocomposites sensors. Sci Rep 2024; 14:10041. [PMID: 38693218 PMCID: PMC11063039 DOI: 10.1038/s41598-024-60093-8] [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: 08/02/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024] Open
Abstract
The detection of N-hexanoyl-l-homoserine lactone (C6-HSL), a crucial signal in Gram-negative bacterial communication, is essential for addressing microbiologically influenced corrosion (MIC) induced by sulfate-reducing bacteria (SRB) in oil and gas industries. Metal oxides (MOx) intercalated into conducting polymers (CPs) offer a promising sensing approach due to their effective detection of biological molecules such as C6-HSL. In this study, we synthesized and characterized two MOx/polyaniline-dodecyl benzene sulfonic acid (PANI-DBSA) nanocomposites, namely ZnO/PANI-DBSA and Fe2O3/PANI-DBSA. These nanocomposites were applied with 1% by-weight carbon paste over a carbon working electrode (WE) for qualitative and quantitative detection of C6-HSL through electrochemical analysis. The electrochemical impedance spectroscopy (EIS) confirmed the composites' capability to monitor C6-HSL produced by SRB-biofilm, with detection limits of 624 ppm for ZnO/PANI-DBSA and 441 ppm for Fe2O3/PANI-DBSA. Furthermore, calorimetric measurements validated the presence of SRB-biofilm, supporting the EIS analysis. The utilization of these MOx/CP nanocomposites offers a practical approach for detecting C6-HSL and monitoring SRB-biofilm formation, aiding in MIC management in oil and gas wells. The ZnO/PANI-DBSA-based sensor exhibited higher sensitivity towards C6-HSL compared to Fe2O3/PANI-DBSA, indicating its potential for enhanced detection capabilities in this context. Stability tests revealed ZnO/PANI-DBSA's superior stability over Fe2O3/PANI-DBSA, with both sensors retaining approximately 85-90% of their initial current after 1 month, demonstrating remarkable reproducibility and durability.
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Affiliation(s)
- Walaa S Gado
- Egyptian Petroleum Research Institute (EPRI), 11727, Nasr City, Cairo, Egypt.
| | | | - Mona Shaban E M Badawy
- Department of Microbiology and Immunology, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - A Labena
- Egyptian Petroleum Research Institute (EPRI), 11727, Nasr City, Cairo, Egypt
| | - Khaled Zakaria
- Egyptian Petroleum Research Institute (EPRI), 11727, Nasr City, Cairo, Egypt
| | - Khalid I Kabel
- Egyptian Petroleum Research Institute (EPRI), 11727, Nasr City, Cairo, Egypt
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4
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Chen X, Li J, Liao R, Shi X, Xing Y, Xu X, Xiao H, Xiao D. Bibliometric analysis and visualization of quorum sensing research over the last two decade. Front Microbiol 2024; 15:1366760. [PMID: 38646636 PMCID: PMC11026600 DOI: 10.3389/fmicb.2024.1366760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Background Quorum sensing (QS) research stands as a pivotal and multifaceted domain within microbiology, holding profound implications across various scientific disciplines. This bibliometric analysis seeks to offer an extensive overview of QS research, covering the period from 2004 to 2023. It aims to elucidate the hotspots, trends, and the evolving dynamics within this research domain. Methods We conducted an exhaustive review of the literature, employing meticulous data curation from the Science Citation Index Extension (SCI-E) within the Web of Science (WOS) database. Subsequently, our survey delves into evolving publication trends, the constellation of influential authors and institutions, key journals shaping the discourse, global collaborative networks, and thematic hotspots that define the QS research field. Results The findings demonstrate a consistent and growing interest in QS research throughout the years, encompassing a substantial dataset of 4,849 analyzed articles. Journals such as Frontiers in Microbiology have emerged as significant contributor to the QS literature, highlighting the increasing recognition of QS's importance across various research fields. Influential research in the realm of QS often centers on microbial communication, biofilm formation, and the development of QS inhibitors. Notably, leading countries engaged in QS research include the United States, China, and India. Moreover, the analysis identifies research focal points spanning diverse domains, including pharmacological properties, genetics and metabolic pathways, as well as physiological and signal transduction mechanisms, reaffirming the multidisciplinary character of QS research. Conclusion This bibliometric exploration provides a panoramic overview of the current state of QS research. The data portrays a consistent trend of expansion and advancement within this domain, signaling numerous prospects for forthcoming research and development. Scholars and stakeholders engaged in the QS field can harness these findings to navigate the evolving terrain with precision and speed, thereby enhancing our comprehension and utilization of QS in various scientific and clinical domains.
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Affiliation(s)
- Xinghan Chen
- Research Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical College of North Sichuan Medical College, Nanchong, Sichuan, China
- Department of Burns and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiaqi Li
- Department of Dermatology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ruohan Liao
- Research Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical College of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xiujun Shi
- Research Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical College of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Yan Xing
- Research Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical College of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xuewen Xu
- Department of Burns and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Haitao Xiao
- Department of Burns and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dongqin Xiao
- Research Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical College of North Sichuan Medical College, Nanchong, Sichuan, China
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5
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Maza-Márquez P, Lee MD, Bebout BM. Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat. Sci Rep 2024; 14:2561. [PMID: 38297006 PMCID: PMC10831059 DOI: 10.1038/s41598-024-52626-y] [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: 11/12/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.
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Affiliation(s)
- P Maza-Márquez
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA.
- University of Granada, Granada, Spain.
| | - M D Lee
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
- Blue Marble Space Institute of Science, Seattle, WA, USA
| | - B M Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
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6
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Narla AV, Hwa T, Murugan A. Dynamic coexistence driven by physiological transitions in microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575059. [PMID: 38260536 PMCID: PMC10802591 DOI: 10.1101/2024.01.10.575059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they are forced out of the exponential state into stressed or non-growing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states. Our model bypasses specific interactions (e.g., nutrient starvation, stress, aggregation) that lead to different combinations of physiological states, referred to collectively as "community states", and modeled by specifying the growth preference of each species along a global ecological coordinate, taken here to be the total community biomass density. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: increased tolerance of community diversity to fast growth rates of species dominating different community states, enhanced community stability through staggered dominance of different species in different community states, and increased requirement on growth dominance for the inclusion of late-growing species. These features, derived explicitly for simplified models, are proposed here to be principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on idealized inter-species interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.
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Affiliation(s)
| | - Terence Hwa
- Department of Physics, University of California, San Diego
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7
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Rodriguez MN, Campetella DM, Carmona NB, Ponce JJ, Parada MN. Microbial mats and their palaeoenvironmental analysis in offshore - shelf facies of the Los Molles Formation (Toarcian - Lower Callovian) in the Chacay Melehue area, Neuquén Basin, Argentina. GEOBIOLOGY 2024; 22:e12580. [PMID: 37990865 DOI: 10.1111/gbi.12580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 08/11/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
This contribution presents the first study focused on the analysis of microbial mats in the Los Molles Formation (Toarcian - Early Callovian), Neuquén Basin, Argentina. This unit mainly represents offshore-to-shelf environments affected by storms and density currents. The Los Molles Formation is one of the oldest source rocks in the Neuquén Basin and constitutes an unconventional shale gas reservoir of great economic importance. The aim of this work was to identify the microbial activity from the description and interpretation of microbially induced sedimentary structures (MISS), to determine the paleoenvironmental and paleoecological conditions under which they formed, and to establish a possible relationship between these structures and the trace fossil Trichichnus. Samples from the levels with MISS were analyzed and described from macroscopic and binocular observations, petrographic microscope thin sections, and SEM samples with EDS analyses. The results showed several levels of microbial mats presenting diverse MISS, including biolaminations and Kinneyia-like wrinkles structures that were described at the macroscopic level. In thin sections, biolaminations, filament-like microstructures with different degrees of development, oriented grains and pyrite were observed. SEM images and EDS analyses showed different types of filaments, coccoids and EPS with high concentrations of carbon. These results revealed that the studied levels fulfill the established biogenicity criteria, guaranteeing that they have a bacterial origin. The abundance of the trace fossil Trichichnus sp. throughout the section and the proximity to some Kinneyia-like wrinkle structures levels suggests that the same organisms may have generated them. Furthermore, they revealed that the Los Molles Formation, at the time of its deposition, experienced paleoecological and paleoenvironmental conditions appropriate for the establishment and development of microbial mats. The extensive levels of microbial mats in the study area suggest that they may have been a source of organic matter for the generation of hydrocarbons from the Los Molles Formation.
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Affiliation(s)
- Maximiliano Nicolás Rodriguez
- Universidad Nacional de Río Negro, Instituto de Investigación en Paleobiología y Geología, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigación en Paleobiología y Geología, Río Negro, Argentina
| | - Débora Mical Campetella
- Universidad Nacional de Río Negro, Instituto de Investigación en Paleobiología y Geología, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigación en Paleobiología y Geología, Río Negro, Argentina
| | - Noelia Beatriz Carmona
- Universidad Nacional de Río Negro, Instituto de Investigación en Paleobiología y Geología, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigación en Paleobiología y Geología, Río Negro, Argentina
| | - Juan José Ponce
- Universidad Nacional de Río Negro (UNRN), Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Negro, Argentina
- Servicio Geológico Minero Argentino (SEGEMAR), Centro General Roca, Río Negro, Argentina
| | - Martín Nazareno Parada
- Universidad Nacional de Río Negro, Instituto de Investigación en Paleobiología y Geología, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigación en Paleobiología y Geología, Río Negro, Argentina
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Zhou T, Wang J, Todd JD, Zhang XH, Zhang Y. Quorum Sensing Regulates the Production of Methanethiol in Vibrio harveyi. Microorganisms 2023; 12:35. [PMID: 38257862 PMCID: PMC10819757 DOI: 10.3390/microorganisms12010035] [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: 11/20/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Methanethiol (MeSH) and dimethyl sulfide (DMS) are important volatile organic sulfur compounds involved in atmospheric chemistry and climate regulation. However, little is known about the metabolism of these compounds in the ubiquitous marine vibrios. Here, we investigated MeSH/DMS production and whether these processes were regulated by quorum-sensing (QS) systems in Vibrio harveyi BB120. V. harveyi BB120 exhibited strong MeSH production from methionine (Met) (465 nmol mg total protein-1) and weak DMS production from dimethylsulfoniopropionate (DMSP) cleavage. The homologs of MegL responsible for MeSH production from L-Met widely existed in vibrio genomes. Using BB120 and its nine QS mutants, we found that the MeSH production was regulated by HAI-1, AI-2 and CAI-1 QS pathways, as well as the luxO gene located in the center of this QS cascade. The regulation role of HAI-1 and AI-2 QS systems in MeSH production was further confirmed by applying quorum-quenching enzyme MomL and exogenous autoinducer AI-2. By contrast, the DMS production from DMSP cleavage showed no significant difference between BB120 and its QS mutants. Such QS-regulated MeSH production may help to remove excess Met that can be harmful for vibrio growth. These results emphasize the importance of QS systems and the MeSH production process in vibrios.
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Affiliation(s)
- Tiantian Zhou
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (T.Z.); (J.W.); (X.-H.Z.)
| | - Jinyan Wang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (T.Z.); (J.W.); (X.-H.Z.)
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (T.Z.); (J.W.); (X.-H.Z.)
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao 266071, China
| | - Yunhui Zhang
- Institute of Evolution & Marine Biodiversity, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
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9
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Wang C, Kuzyakov Y. Energy use efficiency of soil microorganisms: Driven by carbon recycling and reduction. GLOBAL CHANGE BIOLOGY 2023; 29:6170-6187. [PMID: 37646316 DOI: 10.1111/gcb.16925] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/02/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023]
Abstract
Carbon use efficiency (CUE) is being intensively applied to quantify carbon (C) cycling processes from microbial cell to global scales. Energy use efficiency (EUE) is at least as important as the CUE because (i) microorganisms use organic C mainly as an energy source and not as elemental C per se, and (ii) microbial growth and maintenance are limited by energy, but not by C as a structural element. We conceptualize and review the importance of EUE by soil microorganisms and focus on (i) the energy content in organic compounds depending on the nominal oxidation state of carbon (NOSC), (ii) approaches to assess EUE, (iii) similarities and differences between CUE and EUE, and (iv) discuss mechanisms responsible for lower EUE compared to CUE. The energy content per C atom (enthalpy of combustion, the total energy stored in a compound) in organic compounds is very closely (R2 = 0.98) positively related to NOSC and increases by 108 kJ mol-1 C per one NOSC unit. For the first time we assessed the NOSC of microbial biomass in soil (-0.52) and calculated the corresponding energy content of -510 kJ mol-1 C. We linked CUE and EUE considering the NOSC of microbial biomass and element compositions of substrates utilized by microorganisms. The mean microbial EUE (0.32-0.35) is 18% lower than CUE (0.41) using glucose as a substrate. This definitely indicates that microbial growth is limited by energy relative to C. Based on the comparison of a broad range of processes of C and energy utilization for cell growth and maintenance, as well as database of experimental CUE from various compounds, we clearly explained five mechanisms and main factors why EUE is lower than CUE. The two main mechanisms behind lower EUE versus CUE are: (i) microbial recycling: C can be microbially recycled, whereas energy is always utilized only once, and (ii) chemical reduction of organic and inorganic compounds: Energy is used for reduction, which is ongoing without C utilization.
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Affiliation(s)
- Chaoqun Wang
- Biogeochemistry of Agroecosystems, University of Goettingen, Goettingen, Germany
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, Canada
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Goettingen, Germany
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10
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Moreno-Gámez S, Hochberg ME, van Doorn GS. Quorum sensing as a mechanism to harness the wisdom of the crowds. Nat Commun 2023; 14:3415. [PMID: 37296108 PMCID: PMC10256802 DOI: 10.1038/s41467-023-37950-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/05/2023] [Indexed: 06/12/2023] Open
Abstract
Bacteria release and sense small molecules called autoinducers in a process known as quorum sensing. The prevailing interpretation of quorum sensing is that by sensing autoinducer concentrations, bacteria estimate population density to regulate the expression of functions that are only beneficial when carried out by a sufficiently large number of cells. However, a major challenge to this interpretation is that the concentration of autoinducers strongly depends on the environment, often rendering autoinducer-based estimates of cell density unreliable. Here we propose an alternative interpretation of quorum sensing, where bacteria, by releasing and sensing autoinducers, harness social interactions to sense the environment as a collective. Using a computational model we show that this functionality can explain the evolution of quorum sensing and arises from individuals improving their estimation accuracy by pooling many imperfect estimates - analogous to the 'wisdom of the crowds' in decision theory. Importantly, our model reconciles the observed dependence of quorum sensing on both population density and the environment and explains why several quorum sensing systems regulate the production of private goods.
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Affiliation(s)
- Stefany Moreno-Gámez
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Michael E Hochberg
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, 34095, Montpellier, France
- Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - G S van Doorn
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
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11
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Diversity of Bacteria with Quorum Sensing and Quenching Activities from Hydrothermal Vents in the Okinawa Trough. Microorganisms 2023; 11:microorganisms11030748. [PMID: 36985321 PMCID: PMC10052519 DOI: 10.3390/microorganisms11030748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
Quorum sensing (QS) is a chemical communication system by which bacteria coordinate gene expression and social behaviors. Quorum quenching (QQ) refers to processes of inhibiting the QS pathway. Deep-sea hydrothermal vents are extreme marine environments, where abundant and diverse microbial communities live. However, the nature of chemical communication in bacteria inhabiting the hydrothermal vent is poorly understood. In this study, the QS and QQ activities with N-acyl homoserine lactones (AHLs) as the autoinducer were detected in bacteria isolated from hydrothermal vents in the Okinawa Trough. A total of 18 and 108 isolates possessed AHL-producing and AHL-degrading abilities, respectively. Bacteria mainly affiliated with Rhodobacterales, Hyphomicrobiales, Enterobacterales and Sphingomonadales showed QS activities; QQ was mainly associated with Bacillales, Rhodospirillales and Sphingomonadales. The results showed that the bacterial QS and QQ processes are prevalent in hydrothermal environments in the Okinawa Trough. Furthermore, QS significantly affected the activities of extracellular enzymes represented by β-glucosidase, aminopeptidase and phosphatase in the four isolates with higher QS activities. Our results increase the current knowledge of the diversity of QS and QQ bacteria in extreme marine environments and shed light on the interspecific relationships to better investigate their dynamics and ecological roles in biogeochemical cycling.
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12
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Patel R, Soni M, Soyantar B, Shivangi S, Sutariya S, Saraf M, Goswami D. A clash of quorum sensing vs quorum sensing inhibitors: an overview and risk of resistance. Arch Microbiol 2023; 205:107. [PMID: 36881156 DOI: 10.1007/s00203-023-03442-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
Indiscriminate use of antibiotics to treat microbial pathogens has caused emergence of multiple drug resistant strains. Most infectious diseases are caused by microbes that are capable of intercommunication using signaling molecules, which is known as quorum sensing (QS). Such pathogens express their pathogenicity through various QS-regulated virulence factors. Interference of QS could lead to decisive results in controlling such pathogenicity. Hence, QS inhibition has become an attractive new approach for the development of novel drugs. Many quorum sensing inhibitors (QSIs) of diverse origins have been reported. It is imperative that more such anti-QS compounds be found and studied, as they have significant effect on microbial pathogenicity. This review attempts to give a brief account of QS mechanism, its inhibition and describes some compounds with anti-QS potential. Also discussed is the possibility of emergence of quorum sensing resistance.
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Affiliation(s)
- Rohit Patel
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Mansi Soni
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Bilv Soyantar
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Suruchi Shivangi
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Swati Sutariya
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Meenu Saraf
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India
| | - Dweipayan Goswami
- Department of Microbiology and Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, Gujarat, 380009, India.
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13
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Identification of AHL Synthase in Desulfovibrio vulgaris Hildenborough Using an In-Silico Methodology. Catalysts 2023. [DOI: 10.3390/catal13020364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are anaerobic bacteria that form biofilm and induce corrosion on various material surfaces. The quorum sensing (QS) system that employs acyl homoserine lactone (AHL)-type QS molecules primarily govern biofilm formation. Studies on SRB have reported the presence of AHL, but no AHL synthase have been annotated in SRB so far. In this computational study, we used a combination of data mining, multiple sequence alignment (MSA), homology modeling and docking to decode a putative AHL synthase in the model SRB, Desulfovibrio vulgaris Hildenborough (DvH). Through data mining, we shortlisted 111 AHL synthase genes. Conserved domain analysis of 111 AHL synthase genes generated a consensus sequence. Subsequent MSA of the consensus sequence with DvH genome indicated that DVU_2486 (previously uncharacterized protein from acetyltransferase family) is the gene encoding for AHL synthase. Homology modeling revealed the existence of seven α-helices and six β sheets in the DvH AHL synthase. The amalgamated study of hydrophobicity, binding energy, and tunnels and cavities revealed that Leu99, Trp104, Arg139, Trp97, and Tyr36 are the crucial amino acids that govern the catalytic center of this putative synthase. Identifying AHL synthase in DvH would provide more comprehensive knowledge on QS mechanism and help design strategies to control biofilm formation.
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14
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The Role of Quorum Sensing Molecules in Bacterial-Plant Interactions. Metabolites 2023; 13:metabo13010114. [PMID: 36677039 PMCID: PMC9863971 DOI: 10.3390/metabo13010114] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/03/2023] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Quorum sensing (QS) is a system of communication of bacterial cells by means of chemical signals called autoinducers, which modulate the behavior of entire populations of Gram-negative and Gram-positive bacteria. Three classes of signaling molecules have been recognized, Al-1, Al-2, Al-3, whose functions are slightly different. However, the phenomenon of quorum sensing is not only concerned with the interactions between bacteria, but the whole spectrum of interspecies interactions. A growing number of research results confirm the important role of QS molecules in the growth stimulation and defense responses in plants. Although many of the details concerning the signaling metabolites of the rhizosphere microflora and plant host are still unknown, Al-1 compounds should be considered as important components of bacterial-plant interactions, leading to the stimulation of plant growth and the biological control of phytopathogens. The use of class 1 autoinducers in plants to induce beneficial activity may be a practical solution to improve plant productivity under field conditions. In addition, researchers are also interested in tools that offer the possibility of regulating the activity of autoinducers by means of degrading enzymes or specific inhibitors (QSI). Current knowledge of QS and QSI provides an excellent foundation for the application of research to biopreparations in agriculture, containing a consortia of AHL-producing bacteria and QS inhibitors and limiting the growth of phytopathogenic organisms.
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15
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AHL-mediated quorum sensing to regulate bacterial substance and energy metabolism: A review. Microbiol Res 2022; 262:127102. [DOI: 10.1016/j.micres.2022.127102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/08/2022] [Accepted: 06/22/2022] [Indexed: 01/09/2023]
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16
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Hubas C, Monti D, Mortillaro JM, Augagneur S, Carbon A, Duran R, Karama S, Meziane T, Pardon P, Risser T, Tapie N, Thiney N, Budzinski H, Lauga B. Chlordecone-contaminated epilithic biofilms show increased adsorption capacities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 825:153942. [PMID: 35189234 DOI: 10.1016/j.scitotenv.2022.153942] [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: 12/05/2021] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 06/14/2023]
Abstract
The rivers of Guadeloupe and Martinique (French West Indies) show high levels of chlordecone (CLD) contamination. This persistent molecule has a dramatic impact on both aquatic ecosystems and human health. In these rivers, epilithic biofilms are the main endogenous primary producers and represent a central food source for fish and crustaceans. Recently, their viscoelastic properties have been shown to be effective in bio-assessing pollution in tropical environments. As these properties are closely related to the biochemical composition of the biofilms, biochemical (fatty acids, pigments, extracellular polymeric substances (EPS) monosaccharides) and molecular markers (T-RFLP fingerprints of bacteria, archaea and eukaryotes) were investigated. Strong links between CLD pollution and both biofilm biochemistry and microbial community composition were found. In particular, high levels of CLD were linked with modified exo-polysaccharides corresponding to carbohydrates with enhanced adsorption and adhesion properties. The observed change probably resulted from a preferential interaction between CLD and sugars and/or a differential microbial secretion of EPS in response to the pollutant. These changes were expected to impact viscoelastic properties of epilithic biofilms highlighting the effect of CLD pollution on biofilm EPS matrix. They also suggested that microorganisms implement a CLD scavenging strategy, providing new insights on the role of EPS in the adaptation of microorganisms to CLD-polluted environments.
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Affiliation(s)
- Cédric Hubas
- Muséum National d'Histoire Naturelle, Laboratoire Biologie des Organismes et Ecosystème Aquatiques (UMR 8067 BOREA), Sorbonne Université, CNRS, IRD, Université de Caen Normandie, Université des Antilles, Station Marine de Concarneau, Quai de la croix, 29900 Concarneau, France.
| | - Dominique Monti
- Université des Antilles, Laboratoire Biologie des Organismes et Ecosystème Aquatiques (UMR 8067 BOREA), Muséum National d'Histoire Naturelle, Sorbonne Université, CNRS, IRD, Université de Caen Normandie, Campus de Fouillole, 97110 Pointe-à-Pitre, France; Université des Antilles, Institut de Systématique, Evolution, Biodiversité (UMR 7205 ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, 97110 Pointe-à-Pitre, France
| | - Jean-Michel Mortillaro
- Muséum National d'Histoire Naturelle, Laboratoire Biologie des Organismes et Ecosystème Aquatiques (UMR 8067 BOREA), Sorbonne Université, CNRS, IRD, Université de Caen Normandie, Université des Antilles, 61 rue Buffon, 75005 Paris, France; ISEM, Univ Montpellier, CNRS, IRD, CIRAD, Montpellier, France
| | - Sylvie Augagneur
- Université de Bordeaux, Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC - UMR 5805 CNRS), Equipe LPTC, 33405 Talence, France; CNRS, Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC - UMR 5805 CNRS), Equipe LPTC, 33405 Talence, France
| | - Anne Carbon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Solange Karama
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Tarik Meziane
- Muséum National d'Histoire Naturelle, Laboratoire Biologie des Organismes et Ecosystème Aquatiques (UMR 8067 BOREA), Sorbonne Université, CNRS, IRD, Université de Caen Normandie, Université des Antilles, 61 rue Buffon, 75005 Paris, France
| | - Patrick Pardon
- Université de Bordeaux, Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC - UMR 5805 CNRS), Equipe LPTC, 33405 Talence, France; CNRS, Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC - UMR 5805 CNRS), Equipe LPTC, 33405 Talence, France
| | - Théo Risser
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Nathalie Tapie
- Université de Bordeaux, Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC - UMR 5805 CNRS), Equipe LPTC, 33405 Talence, France; CNRS, Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC - UMR 5805 CNRS), Equipe LPTC, 33405 Talence, France
| | - Najet Thiney
- Muséum National d'Histoire Naturelle, Laboratoire Biologie des Organismes et Ecosystème Aquatiques (UMR 8067 BOREA), Sorbonne Université, CNRS, IRD, Université de Caen Normandie, Université des Antilles, 61 rue Buffon, 75005 Paris, France
| | - Hélène Budzinski
- Université de Bordeaux, Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC - UMR 5805 CNRS), Equipe LPTC, 33405 Talence, France; CNRS, Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC - UMR 5805 CNRS), Equipe LPTC, 33405 Talence, France
| | - Béatrice Lauga
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
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17
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Kolodkin-Gal I, Cohen-Cymberknoh M, Zamir G, Tsesis I, Rosen E. Targeting Persistent Biofilm Infections: Reconsidering the Topography of the Infection Site during Model Selection. Microorganisms 2022; 10:microorganisms10061164. [PMID: 35744683 PMCID: PMC9231179 DOI: 10.3390/microorganisms10061164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/17/2022] Open
Abstract
The physiology of an organism in the environment reflects its interactions with the diverse physical, chemical, and biological properties of the surface. These principles come into consideration during model selection to study biofilm–host interactions. Biofilms are communities formed by beneficial and pathogenic bacteria, where cells are held together by a structured extracellular matrix. When biofilms are associated with a host, chemical gradients and their origins become highly relevant. Conventional biofilm laboratory models such as multiwall biofilm models and agar plate models poorly mimic these gradients. In contrast, ex vivo models possess the partial capacity to mimic the conditions of tissue-associated biofilm and a biofilm associated with a mineralized surface enriched in inorganic components, such as the human dentin. This review will highlight the progress achieved using these settings for two models of persistent infections: the infection of the lung tissue by Pseudomonas aeruginosa and the infection of the root canal by Enterococcus faecalis. For both models, we conclude that the limitations of the conventional in vitro systems necessitate a complimentary experimentation with clinically relevant ex vivo models during therapeutics development.
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Affiliation(s)
- Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Correspondence: (I.K.-G.); (I.T.); (E.R.)
| | - Malena Cohen-Cymberknoh
- Pediatric Pulmonary Unit and Cystic Fibrosis Center, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112001, Israel;
| | - Gideon Zamir
- Department of Experimental Surgery, Hadassah Hebrew University Medical School, Jerusalem 9112001, Israel;
| | - Igor Tsesis
- Department of Endodontics, Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Correspondence: (I.K.-G.); (I.T.); (E.R.)
| | - Eyal Rosen
- Department of Endodontics, Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- Correspondence: (I.K.-G.); (I.T.); (E.R.)
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18
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Jo J, Price-Whelan A, Dietrich LEP. Gradients and consequences of heterogeneity in biofilms. Nat Rev Microbiol 2022; 20:593-607. [PMID: 35149841 DOI: 10.1038/s41579-022-00692-2] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 12/15/2022]
Abstract
Historically, appreciation for the roles of resource gradients in biology has fluctuated inversely to the popularity of genetic mechanisms. Nevertheless, in microbiology specifically, widespread recognition of the multicellular lifestyle has recently brought new emphasis to the importance of resource gradients. Most microorganisms grow in assemblages such as biofilms or spatially constrained communities with gradients that influence, and are influenced by, metabolism. In this Review, we discuss examples of gradient formation and physiological differentiation in microbial assemblages growing in diverse settings. We highlight consequences of physiological heterogeneity in microbial assemblages, including division of labour and increased resistance to stress. Our impressions of microbial behaviour in various ecosystems are not complete without complementary maps of the chemical and physical geographies that influence cellular activities. A holistic view, incorporating these geographies and the genetically encoded functions that operate within them, will be essential for understanding microbial assemblages in their many roles and potential applications.
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Affiliation(s)
- Jeanyoung Jo
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, USA.
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19
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Wang X, Yu D, Chen G, Liu C, Xu A, Tang Z. Effects of interactions between quorum sensing and quorum quenching on microbial aggregation characteristics in wastewater treatment: A review. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:2883-2902. [PMID: 34719836 DOI: 10.1002/wer.1657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/14/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Due to the increasingly urgent demand for effective wastewater denitrification and dephosphorization systems, there is a need to improve the performance of existing biological treatment technologies. As a bacteria-level communication mechanism, quorum sensing (QS) synchronizes gene expression in a density-dependent manner and regulates bacterial physiological behavior. On this basis, the QS-based bacterial communication mechanism and environmental factors affecting QS are discussed. This paper reviews the influence of QS on sludge granulation, biofilm formation, emerging contaminants (ECs) removal, and horizontal gene transfer in sewage treatment system. Furthermore, the QS inhibition strategies are compared. Based on the coexistence and balance of QQ and QS in the long-term operation system, QQ, as an effective tool to regulate the growth density of microorganisms, provides a promising exogenous regulation strategy for residual sludge reduction and biofilm pollution control. This paper reviews the potential of improving wastewater treatment efficiency based on QS theory and points out the feasibility and prospect of exogenous regulation strategy. PRACTITIONER POINTS: The mechanism of bacterial communication based on QS and the environmental factors affecting QS were discussed. The application of QS and QQ in improving the sludge performance of biological treatment systems was described. The significance of QS and QQ coexistence in sewage treatment process was described.
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Affiliation(s)
- Xueping Wang
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
| | - Deshuang Yu
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
| | - Guanghui Chen
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Beijing University of Technology, Beijing, China
| | - Chengju Liu
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
| | - Ao Xu
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
| | - Zhihao Tang
- School of Environmental Science and Engineering, Qingdao University, Qingdao, China
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20
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Tripathi AK, Thakur P, Saxena P, Rauniyar S, Gopalakrishnan V, Singh RN, Gadhamshetty V, Gnimpieba EZ, Jasthi BK, Sani RK. Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion. Front Microbiol 2021; 12:754140. [PMID: 34777309 PMCID: PMC8586430 DOI: 10.3389/fmicb.2021.754140] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/24/2021] [Indexed: 01/02/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) have a unique ability to respire under anaerobic conditions using sulfate as a terminal electron acceptor, reducing it to hydrogen sulfide. SRB thrives in many natural environments (freshwater sediments and salty marshes), deep subsurface environments (oil wells and hydrothermal vents), and processing facilities in an industrial setting. Owing to their ability to alter the physicochemical properties of underlying metals, SRB can induce fouling, corrosion, and pipeline clogging challenges. Indigenous SRB causes oil souring and associated product loss and, subsequently, the abandonment of impacted oil wells. The sessile cells in biofilms are 1,000 times more resistant to biocides and induce 100-fold greater corrosion than their planktonic counterparts. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation and corrosion. Here, we examine the critical genes involved in biofilm formation and microbiologically influenced corrosion and categorize them into various functional categories. The current effort also discusses chemical and biological methods for controlling the SRB biofilms. Finally, we highlight the importance of surface engineering approaches for controlling biofilm formation on underlying metal surfaces.
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Affiliation(s)
- Abhilash Kumar Tripathi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Payal Thakur
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Vinoj Gopalakrishnan
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Venkataramana Gadhamshetty
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Department of Civil and Environmental Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Etienne Z Gnimpieba
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Biomedical Engineering Program, University of South Dakota, Sioux Falls, SD, United States
| | - Bharat K Jasthi
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Department of Materials and Metallurgical Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Composite and Nanocomposite Advanced Manufacturing Centre-Biomaterials, Rapid City, SD, United States
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21
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Carreira C, Lønborg C, Kühl M, Lillebø AI, Sandaa RA, Villanueva L, Cruz S. Fungi and viruses as important players in microbial mats. FEMS Microbiol Ecol 2021; 96:5910486. [PMID: 32966583 DOI: 10.1093/femsec/fiaa187] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/18/2020] [Indexed: 11/14/2022] Open
Abstract
Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.
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Affiliation(s)
- Cátia Carreira
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Christian Lønborg
- Section for Applied Marine Ecology and Modelling, Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark
| | - Ana I Lillebø
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Utrecht University, Texel, The Netherlands
| | - Sónia Cruz
- ECOMARE, CESAM-Centre for Environmental and Marine Studies, Departament of Biology, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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22
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Wang J, Liu Q, Dong D, Hu H, Wu B, Ren H. AHLs-mediated quorum sensing threshold and its response towards initial adhesion of wastewater biofilms. WATER RESEARCH 2021; 194:116925. [PMID: 33609904 DOI: 10.1016/j.watres.2021.116925] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/29/2021] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Quorum sensing (QS) plays a crucial role during initial biofilm formation, however the QS threshold and the response of biofilm formation towards N-acyl-homoserine lactones (AHLs) remains largely unknown due to the limitation of nondestructive online methods for monitoring bacterial adherence and the complexity of QS system, which limits the application of QS signal reagents in biofilm reactors. In this study, bacterial QS threshold and its response of biofilm formation to AHLs in purely cultured Sphingomonas rubra biofilm as well as in three different wastewater biofilms #1-3 were investigated via real time cell analysis (RTCA). The main perspective was to study the biomass adherence in response to 12 different forms of AHLs at different concentrations. Results showed that bacterial adhesion was significantly improved by exogenous AHLs with the maximum increase of 2.26-, 2.36-, 2.52-, and 2.80- times biomass production in the four respective biofilms. Although the preferred form of AHL differed for various biofilms, the long-chain AHLs (12-14 carbons) resulted in an overall improvement of bacterial adhesion due to their stronger hydrophobicity and hydrolysis resistance. In addition, bacterial QS threshold of AHLs was observed to have a wide range of concentration from 10 ng/L to 10 μg/L. Meanwhile, QS response time to AHLs also showed a significant difference in different biofilms. Biofilm #2 inoculated with bulking sludge had lower QS threshold of 10 ng/L and faster response to most AHLs that is less than 6 h. Thus, considering the improvement of biofilm adhesion by AHLs, 10 ng/L of C12-HSL, 10 ng/L of C12-HSL, and 10 ng/L of C6-HSL were preferentially selected for wastewater biofilms #1-3 respectively. Unexpectedly, adding high-concentration of AHLs detected in sludges did not significantly improved the bacterial adhesion. Infact the addition of these AHLs at low concentrations or even undetected concentrations substantially improved bacterial adhesion, which could be explained by bacterial communities composition. According to the Pearson correlation analysis, 62% of the top 50 most abundant genera in bacterial communities were significantly negatively related to the response time of multiple AHLs, representing their fast QS response. The QS bacteria, Dechloromonas and Nitrospira have fast QS response for C4-HSL and C8-HSL while, Comamonadaceae has fast QS response for 3OC8-HSL, 3OC10-HSL, 3OC12-HSL, and 3OC14-HSL. In contrast, the rest 38% of the top most abundant genera, such as Ferruginibacter, Hyphomicrobium, and Terrimonas quickly responded to only one AHL, showing significant negative relationship with the response time of C6-HSL. Overall, this study provides an effective and convenient means to select appropriate AHL reagents to promote bacterial adhesion in biofilm systems. Moreover, it also suggests that exogenous AHLs may be useful in improving the settling property of bulking sludge.
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Affiliation(s)
- Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, P.R. China
| | - Qiuju Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, P.R. China
| | - Deyuan Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, P.R. China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, P.R. China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, P.R. China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, P.R. China.
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Ishkov IP, Kaspar JR, Hagen SJ. Spatial Correlations and Distribution of Competence Gene Expression in Biofilms of Streptococcus mutans. Front Microbiol 2021; 11:627992. [PMID: 33510740 PMCID: PMC7835332 DOI: 10.3389/fmicb.2020.627992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 12/17/2020] [Indexed: 11/13/2022] Open
Abstract
Streptococcus mutans is an important pathogen in the human oral biofilm. It expresses virulent behaviors that are linked to its genetic competence regulon, which is controlled by comX. Expression of comX is modulated by two diffusible signaling peptides, denoted CSP and XIP, and by other environmental cues such as pH and oxidative stress. The sensitivity of S. mutans competence to environmental inputs that may vary on microscopic length scales raises the question of whether the biofilm environment creates microniches where competence and related phenotypes are concentrated, leading to spatial clustering of S. mutans virulence behaviors. We have used two-photon microscopy to characterize the spatial distribution of comX expression among individual S. mutans cells in biofilms. By analyzing correlations in comX activity, we test for spatial clustering that may suggest localized competence microenvironments. Our data indicate that both competence-signaling peptides diffuse efficiently through the biofilm. XIP elicits a population-wide response. CSP triggers a Poisson-like, spatially random comX response from a subpopulation of cells that is homogeneously dispersed. Our data indicate that competence microenvironments if they exist are small enough that the phenotypes of individual cells are not clustered or correlated to any greater extent than occurs in planktonic cultures.
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Affiliation(s)
- Ivan P Ishkov
- Department of Physics, University of Florida, Gainesville, FL, United States
| | - Justin R Kaspar
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, United States
| | - Stephen J Hagen
- Department of Physics, University of Florida, Gainesville, FL, United States
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Liu J, Sun X, Ma Y, Zhang J, Xu C, Zhou S. Quorum Quenching Mediated Bacteria Interruption as a Probable Strategy for Drinking Water Treatment against Bacterial Pollution. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17249539. [PMID: 33419234 PMCID: PMC7765942 DOI: 10.3390/ijerph17249539] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/02/2020] [Accepted: 12/06/2020] [Indexed: 02/04/2023]
Abstract
Pseudomonas aeruginosa in water lines may cause bacteria pollution indrinking fountains that could affect the quality of potable water, thus posing a risk to public health. A clean and efficient strategy is required for drinking water treatment for food safety. In this study, an AiiA-homologous lactonase was cloned from a deep-sea probiotics Bacillus velezensis (DH82 strain), and was heterologously expressed so that the capacity of the enzyme on the N-acyl-L-homoserine lactone (AHL)-degrading, effect of bacterial proliferation, biofilm formation and toxic factors release, and membrane pollution from P. aeruginosa could each be investigated to analyze the effect of the enzyme on water treatment. The enzyme effectively degraded the signal molecules of P. aeruginosa (C6-HSL and C12-HSL), inhibited early proliferation and biofilm formation, significantly reduced toxic products (pyocyanin and rhamnolipid), and inhibited bacterial fouling on the filter membrane, which prevented the secondary contamination of P. aeruginosa in drinking water. The findings demonstrated that the quorum quenching enzyme from probiotics could prevent bacteria pollution and improve potable water quality, and that the enzyme treatment could be used as a probable strategy for drinking water treatment.
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Affiliation(s)
- Jia Liu
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (Y.M.); (J.Z.)
| | - Xiaohui Sun
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (Y.M.); (J.Z.)
- Correspondence: (X.S.); (S.Z.); Tel./Fax: +86-59-2616-2300 (X.S.); +86-59-2616-2288 (S.Z.)
| | - Yuting Ma
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (Y.M.); (J.Z.)
| | - Junyi Zhang
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (Y.M.); (J.Z.)
| | - Changan Xu
- Engineering Research Center of Marine Biological Resources Comprehensive Utilization, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China;
| | - Shufeng Zhou
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China; (J.L.); (Y.M.); (J.Z.)
- Correspondence: (X.S.); (S.Z.); Tel./Fax: +86-59-2616-2300 (X.S.); +86-59-2616-2288 (S.Z.)
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25
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Structural and enzymatic analysis of a dimeric cholylglycine hydrolase like acylase active on N-acyl homoserine lactones. Biochimie 2020; 177:108-116. [PMID: 32835734 DOI: 10.1016/j.biochi.2020.07.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 01/17/2023]
Abstract
The prevalence of substrate cross-reactivity between AHL acylases and β-lactam acylases provides a glimpse of probable links between quorum sensing and antibiotic resistance in bacteria. Both these enzyme classes belong to the N-terminal nucleophile (Ntn)-hydrolase superfamily. Penicillin V acylases alongside bile salt hydrolases constitute the cholylglycine hydrolase (CGH) group of the Ntn-hydrolase superfamily. Here we report the ability of two acylases, Slac1 and Slac2, from the marine bacterium Shewanella loihica-PV4 to hydrolyze AHLs. Three-dimensional structure of Slac1reveals the conservation of the Ntn hydrolase fold and CGH active site, making it a unique CGH exclusively active on AHLs. Slac1homologs phylogenetically cluster separate from reported CGHs and AHL acylases, thereby representing a functionally distinct sub-class of CGH that might have evolved as an adaptation to the marine environment. We hypothesize that Slac1 could provide the structural framework for understanding this subclass, and further our understanding of the evolutionary link between AHL acylases and β-lactam acylases.
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26
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Communication within East Antarctic Soil Bacteria. Appl Environ Microbiol 2019; 86:AEM.01968-19. [PMID: 31628145 DOI: 10.1128/aem.01968-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/09/2019] [Indexed: 01/01/2023] Open
Abstract
Antarctica, being the coldest, driest, and windiest continent on Earth, represents the most extreme environment in which a living organism can survive. Under constant exposure to harsh environmental threats, terrestrial Antarctica remains home to a great diversity of microorganisms, indicating that the soil bacteria must have adapted a range of survival strategies that require cell-to-cell communication. Survival strategies include secondary metabolite production, biofilm formation, bioluminescence, symbiosis, conjugation, sporulation, and motility, all of which are often regulated by quorum sensing (QS), a type of bacterial communication. Until now, such mechanisms have not been explored in terrestrial Antarctica. In this study, LuxI/LuxR-based quorum sensing (QS) activity was delineated in soil bacterial isolates recovered from Adams Flat, in the Vestfold Hills region of East Antarctica. Interestingly, we identified the production of potential homoserine lactones (HSLs) with chain lengths ranging from medium to long in 19 bacterial species using three biosensors, namely, Agrobacterium tumefaciens NTL4, Chromobacterium violaceum CV026, and Escherichia coli MT102, in conjunction with thin-layer chromatography (TLC). The majority of detectable HSLs were from Gram-positive species not previously known to produce HSLs. This discovery further expands our understanding of the microbial community capable of this type of communication, as well as provides insights into physiological adaptations of microorganisms that allow them to survive in the harsh Antarctic environment.IMPORTANCE Quorum sensing, a type of bacterial communication, is widely known to regulate many processes, including those that confer a survival advantage. However, little is known about communication by bacteria residing within Antarctic soils. Employing a combination of bacterial biosensors, analytical techniques, and genome mining, we found a variety of Antarctic soil bacteria speaking a common language, via LuxI/LuxR-based quorum sensing, thus potentially supporting survival in a mixed microbial community. This study reports potential quorum sensing activity in Antarctic soils and has provided a platform for studying physiological adaptations of microorganisms that allow them to survive in the harsh Antarctic environment.
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28
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Dobretsov S, Coutinho R, Rittschof D, Salta M, Ragazzola F, Hellio C. The oceans are changing: impact of ocean warming and acidification on biofouling communities. BIOFOULING 2019; 35:585-595. [PMID: 31282218 DOI: 10.1080/08927014.2019.1624727] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/19/2019] [Accepted: 05/20/2019] [Indexed: 06/09/2023]
Abstract
Climate change (CC) is driving modification of the chemical and physical properties of estuaries and oceans with profound consequences for species and ecosystems. Numerous studies investigate CC effects from species to ecosystem levels, but little is known of the impacts on biofilm communities and on bioactive molecules such as cues, adhesives and enzymes. CC is induced by anthropogenic activity increasing greenhouse emissions leading to rises in air and water temperatures, ocean acidification, sea level rise and changes in ocean gyres and rainfall patterns. These environmental changes are resulting in alterations within marine communities and changes in species ranges and composition. This review provides insights and synthesis of knowledge about the effect of elevated temperature and ocean acidification on microfouling communities and bioactive molecules. The existing studies suggest that CC will impact production of bioactive compounds as well as the growth and composition of biofouling communities. Undoubtedly, with CC fouling management will became an even greater challenge.
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Affiliation(s)
- Sergey Dobretsov
- Marine Science and Fisheries Department, College of Agricultural and Marine Sciences, Sultan Qaboos University , Sultanate of Oman
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University , Sultanate of Oman
| | - Ricardo Coutinho
- Instituto de Estudos do Mar Almirante Paulo Moreira , Praia dos Anjos, Arraial do Cabo , RJ , Brazil
| | - Daniel Rittschof
- Nicholas School, Duke University Marine Laboratory , Beaufort USA
| | - Maria Salta
- School of Biological Sciences, University of Portsmouth , Portsmouth , UK
| | - Federica Ragazzola
- School of Biological Sciences, University of Portsmouth , Portsmouth , UK
| | - Claire Hellio
- Laboratoire des Sciences de l'Envionnement Marin (LEMAR), Université de Brest, CNRS, IRD, Ifremer , Plouzané , France
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29
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Charlesworth JC, Watters C, Wong HL, Visscher PT, Burns BP. Isolation of novel quorum-sensing active bacteria from microbial mats in Shark Bay Australia. FEMS Microbiol Ecol 2019; 95:5382036. [PMID: 30877766 DOI: 10.1093/femsec/fiz035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/15/2019] [Indexed: 11/13/2022] Open
Abstract
Quorum sensing is a potent system of genetic control allowing phenotypes to be coordinated across localized communities. In this study, quorum sensing systems in Shark Bay microbial mats were delineated using a targeted approach analyzing whole mat extractions as well as the creation of an isolate library. A library of 165 isolates from different mat types were screened using the AHL biosensor E. coli MT102. Based on sequence identity 30 unique isolates belonging to Proteobacteria, Actinobacteria and Firmicutes were found to activate the AHL biosensor, suggesting AHLs or analogous compounds were potentially present. Several of the isolates have not been shown previously to produce signal molecules, particularly the members of the Actinobacteria and Firmicutes phyla including Virgibacillus, Halobacillius, Microbacterium and Brevibacterium. These active isolates were further screened using thin-layer chromatography (TLC) providing putative identities of AHL molecules present within the mat communities. Nine isolates were capable of producing several spots of varying sizes after TLC separation, suggesting the presence of multiple signalling molecules. This study is the first to delineate AHL-based signalling in the microbial mats of Shark Bay, and suggests quorum sensing may play a role in the ecosphysiological coordination of complex phenotypes across microbial mat communities.
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Affiliation(s)
- James C Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia
| | - Cara Watters
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia
| | - Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia.,Department of Marine Sciences, University of Connecticut, Storrs, 06269, CT, USA
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.,Australian Centre for Astrobiology, University of New South Wales, Sydney, 2052, Australia
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Gao J, Duan Y, Liu Y, Zhuang X, Liu Y, Bai Z, Ma W, Zhuang G. Long- and short-chain AHLs affect AOA and AOB microbial community composition and ammonia oxidation rate in activated sludge. J Environ Sci (China) 2019; 78:53-62. [PMID: 30665656 DOI: 10.1016/j.jes.2018.06.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 05/03/2023]
Abstract
Quorum sensing (QS) regulation of the composition of ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) communities and functions in wastewater treatment was investigated. Specifically, we explored the role of N-acyl-l-homoserine lactones (AHLs) in microbial community dynamics in activated sludge. On average, the specific ammonia-oxidising-rate increased from 1.6 to 2.8 mg NH4+-N/g MLSS/hr after treatment with long-chain AHLs for 16 days, and the addition of AHLs to sludge resulted in an increased number of AOA/AOB amoA genes. Significant differences were observed in the AOA communities of control and AHL-treated cultures, but not the AOB community. Furthermore, the dominant functional AOA strains of the Crenarchaeota altered their ecological niche in response to AHL addition. These results provide evidence that AHLs play an important role in mediating AOA/AOB microbial community parameters and demonstrate the potential for application of QS to the regulation of nitrogen compound metabolism in wastewater treatment.
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Affiliation(s)
- Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Duan
- Beijing Enterprises Water Group Limited, Beijing 100124, China
| | - Ying Liu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xuliang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Liu
- Beijing Climate Change Response Research and Education Center, Department of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Zhihui Bai
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenlin Ma
- Beijing Climate Change Response Research and Education Center, Department of Environment and Energy Engineering, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Sivakumar K, Scarascia G, Zaouri N, Wang T, Kaksonen AH, Hong PY. Salinity-Mediated Increment in Sulfate Reduction, Biofilm Formation, and Quorum Sensing: A Potential Connection Between Quorum Sensing and Sulfate Reduction? Front Microbiol 2019; 10:188. [PMID: 30787924 PMCID: PMC6373464 DOI: 10.3389/fmicb.2019.00188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/23/2019] [Indexed: 11/30/2022] Open
Abstract
Biocorrosion in marine environment is often associated with biofilms of sulfate reducing bacteria (SRB). However, not much information is available on the mechanism underlying exacerbated rates of SRB-mediated biocorrosion under saline conditions. Using Desulfovibrio (D.) vulgaris and Desulfobacterium (Db.) corrodens as model SRBs, the enhancement effects of salinity on sulfate reduction, N-acyl homoserine lactone (AHL) production and biofilm formation by SRBs were demonstrated. Under saline conditions, D. vulgaris and Db. corrodens exhibited significantly higher specific sulfate reduction and specific AHL production rates as well as elevated rates of biofilm formation compared to freshwater medium. Salinity-induced enhancement traits were also confirmed at transcript level through reverse transcription quantitative polymerase chain reaction (RT-qPCR) approach, which showed salinity-influenced increase in the expression of genes associated with carbon metabolism, sulfate reduction, biofilm formation and histidine kinase signal transduction. In addition, by deploying quorum sensing (QS) inhibitors, a potential connection between sulfate reduction and AHL production under saline conditions was demonstrated, which is most significant during early stages of sulfate metabolism. The findings collectively revealed the interconnection between QS, sulfate reduction and biofilm formation among SRBs, and implied the potential of deploying quorum quenching approaches to control SRB-based biocorrosion in saline conditions.
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Affiliation(s)
- Krishnakumar Sivakumar
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Giantommaso Scarascia
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Noor Zaouri
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tiannyu Wang
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Anna H Kaksonen
- Land and Water, Commonwealth Scientific and Industrial Research Organization, Floreat, WA, Australia
| | - Pei-Ying Hong
- Water Desalination and Reuse Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Stal LJ, Bolhuis H, Cretoiu MS. Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities. Environ Microbiol 2018; 21:1529-1551. [PMID: 30507057 DOI: 10.1111/1462-2920.14494] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 01/02/2023]
Abstract
Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.
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Affiliation(s)
- Lucas J Stal
- IBED Department of Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, The Netherlands.,Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Netherlands Institute for Sea Research, Den Burg, Texel, The Netherlands
| | - Mariana S Cretoiu
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
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33
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Kalia VC, Patel SKS, Kang YC, Lee JK. Quorum sensing inhibitors as antipathogens: biotechnological applications. Biotechnol Adv 2018; 37:68-90. [PMID: 30471318 DOI: 10.1016/j.biotechadv.2018.11.006] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/19/2018] [Accepted: 11/18/2018] [Indexed: 12/20/2022]
Abstract
The mechanisms through which microbes communicate using signal molecules has inspired a great deal of research. Microbes use this exchange of information, known as quorum sensing (QS), to initiate and perpetuate infectious diseases in eukaryotic organisms, evading the eukaryotic defense system by multiplying and expressing their pathogenicity through QS regulation. The major issue to arise from such networks is increased bacterial resistance to antibiotics, resulting from QS-dependent mediation of the formation of biofilm, the induction of efflux pumps, and the production of antibiotics. QS inhibitors (QSIs) of diverse origins have been shown to act as potential antipathogens. In this review, we focus on the use of QSIs to counter diseases in humans as well as plants and animals of economic importance. We also discuss the challenges encountered in the potential applications of QSIs.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | - Sanjay K S Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Yun Chan Kang
- Department of Materials Science and Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 02841, Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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Huang X, Zhu J, Cai Z, Lao Y, Jin H, Yu K, Zhang B, Zhou J. Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach. Microbiol Res 2018; 217:1-13. [PMID: 30384903 DOI: 10.1016/j.micres.2018.08.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/26/2018] [Accepted: 08/29/2018] [Indexed: 01/09/2023]
Abstract
The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.
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Affiliation(s)
- Xinqing Huang
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Jianming Zhu
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Zhonghua Cai
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Yongmin Lao
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Hui Jin
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China
| | - Ke Yu
- The Division of Environment and Energy, Graduate School at Shenzhen, Peking University, Guangdong Province, Shenzhen, China
| | - Boya Zhang
- The Division of Environment and Energy, Graduate School at Shenzhen, Peking University, Guangdong Province, Shenzhen, China
| | - Jin Zhou
- Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, The Graduate School at Shenzhen, Tsinghua University, Guangdong Province, Shenzhen, China.
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Wong HL, White RA, Visscher PT, Charlesworth JC, Vázquez-Campos X, Burns BP. Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes. ISME JOURNAL 2018; 12:2619-2639. [PMID: 29980796 DOI: 10.1038/s41396-018-0208-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/27/2018] [Accepted: 06/01/2018] [Indexed: 11/09/2022]
Abstract
The functional metagenomic potential of Shark Bay microbial mats was examined for the first time at a millimeter scale, employing shotgun sequencing of communities via the Illumina NextSeq 500 platform in conjunction with defined chemical analyses. A detailed functional metagenomic profile has elucidated key pathways and facilitated inference of critical microbial interactions. In addition, 87 medium-to-high-quality metagenome-assembled genomes (MAG) were assembled, including potentially novel bins under the deep-branching archaeal Asgard group (Thorarchaetoa and Lokiarchaeota). A range of pathways involved in carbon, nitrogen, sulfur, and phosphorus cycles were identified in mat metagenomes, with the Wood-Ljungdahl pathway over-represented and inferred as a major carbon fixation mode. The top five sets of genes were affiliated to sulfate assimilation (cysNC cysNCD, sat), methanogenesis (hdrABC), Wood-Ljungdahl pathways (cooS, coxSML), phosphate transport (pstB), and copper efflux (copA). Polyhydroxyalkanoate (PHA) synthase genes were over-represented at the surface, with PHA serving as a potential storage of fixed carbon. Sulfur metabolism genes were highly represented, in particular complete sets of genes responsible for both assimilatory and dissimilatory sulfate reduction. Pathways of environmental adaptation (UV, hypersalinity, oxidative stress, and heavy metal resistance) were also delineated, as well as putative viral defensive mechanisms (core genes of the CRISPR, BREX, and DISARM systems). This study provides new metagenome-based models of how biogeochemical cycles and adaptive responses may be partitioned in the microbial mats of Shark Bay.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Richard Allen White
- Institute of Biological Chemistry, Washington State University, Pullman, USA
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia.,Department of Marine Sciences, University of Connecticut, Storrs, CT, USA
| | - James C Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia. .,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia.
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36
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Pace A, Bourillot R, Bouton A, Vennin E, Braissant O, Dupraz C, Duteil T, Bundeleva I, Patrier P, Galaup S, Yokoyama Y, Franceschi M, Virgone A, Visscher PT. Formation of stromatolite lamina at the interface of oxygenic-anoxygenic photosynthesis. GEOBIOLOGY 2018; 16:378-398. [PMID: 29573198 DOI: 10.1111/gbi.12281] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
In modern stromatolites, mineralization results from a complex interplay between microbial metabolisms, the organic matrix, and environmental parameters. Here, we combined biogeochemical, mineralogical, and microscopic analyses with measurements of metabolic activity to characterize the mineralization processes and products in an emergent (<18 months) hypersaline microbial mat. While the nucleation of Mg silicates is ubiquitous in the mat, the initial formation of a Ca-Mg carbonate lamina depends on (i) the creation of a high-pH interface combined with a major change in properties of the exopolymeric substances at the interface of the oxygenic and anoxygenic photoautotrophic layers and (ii) the synergy between two major players of sulfur cycle, purple sulfur bacteria, and sulfate-reducing bacteria. The repetition of this process over time combined with upward growth of the mat is a possible pathway leading to the formation of a stromatolite.
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Affiliation(s)
- A Pace
- EA 4592, Géoressources & Environnement, Ensegid, Bordeaux INP, Pessac, France
- Université Bordeaux Montaigne, Pessac, France
| | - R Bourillot
- EA 4592, Géoressources & Environnement, Ensegid, Bordeaux INP, Pessac, France
| | - A Bouton
- Laboratoire Biogéosciences, UMR 6282 UBFC/CNRS, Université Bourgogne Franche-Comté, Dijon, France
- Total, CSTJF, Pau, France
| | - E Vennin
- Laboratoire Biogéosciences, UMR 6282 UBFC/CNRS, Université Bourgogne Franche-Comté, Dijon, France
| | - O Braissant
- Center for Biomechanics and Biocalorimetry, University of Basel, Basel, Switzerland
| | - C Dupraz
- Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | - T Duteil
- EA 4592, Géoressources & Environnement, Ensegid, Bordeaux INP, Pessac, France
| | - I Bundeleva
- Laboratoire Biogéosciences, UMR 6282 UBFC/CNRS, Université Bourgogne Franche-Comté, Dijon, France
| | - P Patrier
- UMR 7285 CNRS IC2MP, Université de Poitiers, Poitiers, France
| | - S Galaup
- EA 4592, Géoressources & Environnement, Ensegid, Bordeaux INP, Pessac, France
| | - Y Yokoyama
- Department of Earth and Planetary Sciences, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - M Franceschi
- EA 4592, Géoressources & Environnement, Ensegid, Bordeaux INP, Pessac, France
| | | | - P T Visscher
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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Living Dendrolitic Microbial Mats in Hamelin Pool, Shark Bay, Western Australia. GEOSCIENCES 2018. [DOI: 10.3390/geosciences8060212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Hörnlein C, Confurius-Guns V, Stal LJ, Bolhuis H. Daily rhythmicity in coastal microbial mats. NPJ Biofilms Microbiomes 2018; 4:11. [PMID: 29796291 PMCID: PMC5953948 DOI: 10.1038/s41522-018-0054-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/26/2018] [Accepted: 04/17/2018] [Indexed: 12/31/2022] Open
Abstract
Cyanobacteria are major primary producers in coastal microbial mats and provide biochemical energy, organic carbon, and bound nitrogen to the mat community through oxygenic photosynthesis and dinitrogen fixation. In order to anticipate the specific requirements to optimize their metabolism and growth during a day-and-night cycle, Cyanobacteria possess a unique molecular timing mechanism known as the circadian clock that is well-studied under laboratory conditions but little is known about its function in a natural complex community. Here, we investigated daily rhythmicity of gene expression in a coastal microbial mat community sampled at 6 time points during a 24-h period. In order to identify diel expressed genes, meta-transcriptome data was fitted to periodic functions. Out of 24,035 conserved gene transcript clusters, approximately 7% revealed a significant rhythmic expression pattern. These rhythmic genes were assigned to phototrophic micro-eukaryotes, Cyanobacteria but also to Proteobacteria and Bacteroidetes. Analysis of MG-RAST annotated genes and mRNA recruitment analysis of two cyanobacterial and three proteobacterial microbial mat members confirmed that homologs of the cyanobacterial circadian clock genes were also found in other bacterial members of the microbial mat community. These results suggest that various microbial mat members other than Cyanobacteria have their own molecular clock, which can be entrained by a cocktail of Zeitgebers such as light, temperature or metabolites from neighboring species. Hence, microbial mats can be compared to a complex organism consisting of multiple sub-systems that have to be entrained in a cooperative way such that the corpus functions optimally.
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Affiliation(s)
- Christine Hörnlein
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
| | - Veronique Confurius-Guns
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
| | - Lucas J Stal
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands.,2Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Henk Bolhuis
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, and Utrecht University, Den Hoorn, The Netherlands
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Wilén BM, Liébana R, Persson F, Modin O, Hermansson M. The mechanisms of granulation of activated sludge in wastewater treatment, its optimization, and impact on effluent quality. Appl Microbiol Biotechnol 2018; 102:5005-5020. [PMID: 29705957 PMCID: PMC5960003 DOI: 10.1007/s00253-018-8990-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 12/14/2022]
Abstract
Granular activated sludge has gained increasing interest due to its potential in treating wastewater in a compact and efficient way. It is well-established that activated sludge can form granules under certain environmental conditions such as batch-wise operation with feast-famine feeding, high hydrodynamic shear forces, and short settling time which select for dense microbial aggregates. Aerobic granules with stable structure and functionality have been obtained with a range of different wastewaters seeded with different sources of sludge at different operational conditions, but the microbial communities developed differed substantially. In spite of this, granule instability occurs. In this review, the available literature on the mechanisms involved in granulation and how it affects the effluent quality is assessed with special attention given to the microbial interactions involved. To be able to optimize the process further, more knowledge is needed regarding the influence of microbial communities and their metabolism on granule stability and functionality. Studies performed at conditions similar to full-scale such as fluctuation in organic loading rate, hydrodynamic conditions, temperature, incoming particles, and feed water microorganisms need further investigations.
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Affiliation(s)
- Britt-Marie Wilén
- Division of Water Environment Technology, Department of Architecture and Civil and Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
| | - Raquel Liébana
- Division of Water Environment Technology, Department of Architecture and Civil and Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil and Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Oskar Modin
- Division of Water Environment Technology, Department of Architecture and Civil and Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Malte Hermansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30, Gothenburg, Sweden
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Muras A, López-Pérez M, Mayer C, Parga A, Amaro-Blanco J, Otero A. High Prevalence of Quorum-Sensing and Quorum-Quenching Activity among Cultivable Bacteria and Metagenomic Sequences in the Mediterranean Sea. Genes (Basel) 2018; 9:E100. [PMID: 29462892 PMCID: PMC5852596 DOI: 10.3390/genes9020100] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/08/2018] [Accepted: 02/12/2018] [Indexed: 11/22/2022] Open
Abstract
There is increasing evidence being accumulated regarding the importance of N-acyl homoserine lactones (AHL)-mediated quorum-sensing (QS) and quorum-quenching (QQ) processes in the marine environment, but in most cases, data has been obtained from specific microhabitats, and subsequently little is known regarding these activities in free-living marine bacteria. The QS and QQ activities among 605 bacterial isolates obtained at 90 and 2000 m depths in the Mediterranean Sea were analyzed. Additionally, putative QS and QQ sequences were searched in metagenomic data obtained at different depths (15-2000 m) at the same sampling site. The number of AHL producers was higher in the 90 m sample (37.66%) than in the 2000 m sample (4.01%). However, the presence of QQ enzymatic activity was 1.63-fold higher in the 2000 m sample. The analysis of putative QQ enzymes in the metagenomes supports the relevance of QQ processes in the deepest samples, found in cultivable bacteria. Despite the unavoidable biases in the cultivation methods and biosensor assays and the possible promiscuous activity of the QQ enzymes retrieved in the metagenomic analysis, the results indicate that AHL-related QS and QQ processes could be common activity in the marine environment.
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Affiliation(s)
- Andrea Muras
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan de Alicante 03202, Spain.
| | - Celia Mayer
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Ana Parga
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Jaime Amaro-Blanco
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Ana Otero
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
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Liébana R, Modin O, Persson F, Wilén BM. Integration of aerobic granular sludge and membrane bioreactors for wastewater treatment. Crit Rev Biotechnol 2018; 38:801-816. [PMID: 29400086 DOI: 10.1080/07388551.2017.1414140] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Environmental deterioration together with the need for water reuse and the increasingly restrictive legislation of water quality standards have led to a demand for compact, efficient and less energy consuming technologies for wastewater treatment. Aerobic granular sludge and membrane bioreactors (MBRs) are two technologies with several advantages, such as small footprint, high-microbial density and activity, ability to operate at high organic- and nitrogen-loading rates, and tolerance to toxicity. However, they also have some disadvantages. The aerobic granular sludge process generally requires post-treatment in order to fulfill effluent standards and MBRs suffer from fouling of the membranes. Integrating the two technologies could be a way of combining the advantages and addressing the main problems associated with both processes. The use of membranes to separate the aerobic granules from the treated water would ensure high-quality effluents suitable for reuse. Moreover, the use of granular sludge in MBRs has been shown to reduce fouling. Several recent studies have shown that the aerobic granular membrane bioreactor (AGMBR) is a promising hybrid process with many attractive features. However, major challenges that have to be addressed include how to achieve granulation and maintain granular stability during continuous operation of reactors. This paper aims to review the current state of research on AGMBR technology while drawing attention to relevant findings and highlight current limitations.
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Affiliation(s)
- Raquel Liébana
- a Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , Gothenburg , Sweden
| | - Oskar Modin
- a Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , Gothenburg , Sweden
| | - Frank Persson
- a Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , Gothenburg , Sweden
| | - Britt-Marie Wilén
- a Division of Water Environment Technology, Department of Architecture and Civil Engineering , Chalmers University of Technology , Gothenburg , Sweden
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Sheng H, Wang F, Gu C, Stedtfeld R, Bian Y, Liu G, Wu W, Jiang X. Sorption characteristics of N-acyl homserine lactones as signal molecules in natural soils based on the analysis of kinetics and isotherms. RSC Adv 2018; 8:9364-9374. [PMID: 35541870 PMCID: PMC9078661 DOI: 10.1039/c7ra10421a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/19/2018] [Indexed: 11/21/2022] Open
Abstract
Quorum sensing, the communication between microorganisms, is mediated by specific diffusible signal molecules. Adsorption is an important process that influences the transport, transformation and bioavailability of N-acyl homoserine lactone (AHL) in complex natural environments such as soil. To examine the adsorption characteristics of N-hexanoyl, N-octanoyl, N-decanoyl and N-dodecanoyl homoserine lactones in soil, equilibrium and kinetic experiments were conducted in two types of soils (oxisol and alfisol) and monitored using Fourier-transform infrared spectroscopy (FTIR). A pseudo-second-order equation accurately described the sorption kinetics of AHLs in the two soils (R2 ≥ 0.97, NSD ≤ 21.25%). The AHL sorption reached equilibrium within 24 h and 12 h for oxisol and alfisol, respectively. The sorption kinetics of AHLs adsorbed on the soils were fitted to the Boyd model, suggesting that film diffusion was the rate-limiting process. Partition played a more vital role than surface adsorption in the AHL adsorption process. The adsorption isotherms of AHLs could be described by the Langmuir and Freundlich equation (R2 ≥ 0.98), indicating that the sorption process involved monolayer sorption and heterogeneous energetic distribution of active sites on the surfaces of the soils. The thermodynamic parameter, Gibbs free energy (ΔG), and a dimensionless parameter showed that the sorption of AHLs was mainly dominated by physical adsorption. Additionally, according to the FTIR data, the electrostatic forces and hydrogen bonding possibly influenced the adsorption of AHLs on the above mentioned two soils. The sorption characteristics of AHLs in soils correlated well with the molecular structure, solubility speciation and log P (n-octanol/water partition coefficient) of AHLs. Sorption characteristics of N-acyl homoserine lactones (signal molecules) in natural soils.![]()
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Affiliation(s)
- Hongjie Sheng
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Chenggang Gu
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Robert Stedtfeld
- Department of Civil and Environmental Engineering
- Michigan State University
- East Lansing
- USA
| | - Yongrong Bian
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Guangxia Liu
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Wei Wu
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation
- Institute of Soil Science
- Chinese Academy of Sciences
- Nanjing 210008
- China
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Guan C, Parrot D, Wiese J, Sönnichsen FD, Saha M, Tasdemir D, Weinberger F. Identification of rosmarinic acid and sulfated flavonoids as inhibitors of microfouling on the surface of eelgrass Zostera marina. BIOFOULING 2017; 33:867-880. [PMID: 29032711 DOI: 10.1080/08927014.2017.1383399] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
A bioassay-guided approach was used to identify defense compounds that are present on the surface of Zostera marina and which inhibit settlement of microfoulers at natural concentrations. Moderately polar eelgrass surface extracts inhibited the settlement of seven marine bacteria and one yeast that originated from non-living substrata. In contrast, five other bacterial strains that had been directly isolated from eelgrass surfaces were all insensitive, which suggested a selective effect of surface metabolites on the microbial communities present on eelgrass. Bioassay-guided isolation of active compounds from the extracts in combination with UPLC-MS and 1H-NMR spectroscopy resulted in the identification of rosmarinic acid, luteolin-7-sulfate and diosmetin-7-sulfate or its isomer chrysoeriol-7-sulfate. All three compounds are nontoxic repellents, as they did not inhibit bacterial growth, but prevented bacterial settlement in a dose-dependent manner. Between 15.6 and 106.8 μg ml-1 of rosmarinic acid were present on the eelgrass surface, enough for half maximal settlement inhibition of bacteria.
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Affiliation(s)
- Chi Guan
- a Research Unit Benthic Ecology , GEOMAR Helmholtz Centre for Ocean Research Kiel , Kiel , Germany
| | - Delphine Parrot
- b Research Unit Marine Natural Products Chemistry , GEOMAR Helmholtz Centre for Ocean Research Kiel, GEOMAR Centre for Marine Biotechnology , Kiel , Germany
| | - Jutta Wiese
- c Research Unit Marine Microbiology , GEOMAR Helmholtz Centre for Ocean Research Kiel , Kiel , Germany
| | - Frank D Sönnichsen
- d Otto-Diels-Institute für Organische Chemie , Christian-Albrechts-Universität zu Kiel , Kiel , Germany
| | - Mahasweta Saha
- a Research Unit Benthic Ecology , GEOMAR Helmholtz Centre for Ocean Research Kiel , Kiel , Germany
- e School of Biological Science , Trace Gas Biology , Colchester , UK
| | - Deniz Tasdemir
- b Research Unit Marine Natural Products Chemistry , GEOMAR Helmholtz Centre for Ocean Research Kiel, GEOMAR Centre for Marine Biotechnology , Kiel , Germany
- f Faculty of Mathematics and Natural Sciences , Christian-Albrechts-Universitätzu Kiel , Kiel , Germany
| | - Florian Weinberger
- a Research Unit Benthic Ecology , GEOMAR Helmholtz Centre for Ocean Research Kiel , Kiel , Germany
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44
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Decho AW, Gutierrez T. Microbial Extracellular Polymeric Substances (EPSs) in Ocean Systems. Front Microbiol 2017; 8:922. [PMID: 28603518 PMCID: PMC5445292 DOI: 10.3389/fmicb.2017.00922] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/08/2017] [Indexed: 12/13/2022] Open
Abstract
Microbial cells (i.e., bacteria, archaea, microeukaryotes) in oceans secrete a diverse array of large molecules, collectively called extracellular polymeric substances (EPSs) or simply exopolymers. These secretions facilitate attachment to surfaces that lead to the formation of structured 'biofilm' communities. In open-water environments, they also lead to formation of organic colloids, and larger aggregations of cells, called 'marine snow.' Secretion of EPS is now recognized as a fundamental microbial adaptation, occurring under many environmental conditions, and one that influences many ocean processes. This relatively recent realization has revolutionized our understanding of microbial impacts on ocean systems. EPS occur in a range of molecular sizes, conformations and physical/chemical properties, and polysaccharides, proteins, lipids, and even nucleic acids are actively secreted components. Interestingly, however, the physical ultrastructure of how individual EPS interact with each other is poorly understood. Together, the EPS matrix molecules form a three-dimensional architecture from which cells may localize extracellular activities and conduct cooperative/antagonistic interactions that cannot be accomplished efficiently by free-living cells. EPS alter optical signatures of sediments and seawater, and are involved in biogeomineral precipitation and the construction of microbial macrostructures, and horizontal-transfers of genetic information. In the water-column, they contribute to the formation of marine snow, transparent exopolymer particles (TEPs), sea-surface microlayer biofilm, and marine oil snow. Excessive production of EPS occurs during later-stages of phytoplankton blooms as an excess metabolic by product and releases a carbon pool that transitions among dissolved-, colloidal-, and gel-states. Some EPS are highly labile carbon forms, while other forms appear quite refractory to degradation. Emerging studies suggest that EPS contribute to efficient trophic-transfer of environmental contaminants, and may provide a protective refugia for pathogenic cells within marine systems; one that enhances their survival/persistence. Finally, these secretions are prominent in 'extreme' environments ranging from sea-ice communities to hypersaline systems to the high-temperatures/pressures of hydrothermal-vent systems. This overview summarizes some of the roles of exopolymer in oceans.
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Affiliation(s)
- Alan W. Decho
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, ColumbiaSC, United States
| | - Tony Gutierrez
- School of Engineering and Physical Sciences, Heriot-Watt UniversityEdinburgh, United Kingdom
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45
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Louyakis AS, Mobberley JM, Vitek BE, Visscher PT, Hagan PD, Reid RP, Kozdon R, Orland IJ, Valley JW, Planavsky NJ, Casaburi G, Foster JS. A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses. ASTROBIOLOGY 2017; 17:413-430. [PMID: 28520472 PMCID: PMC5767104 DOI: 10.1089/ast.2016.1563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities. Analyses revealed three distinctive zones within the thrombolite-forming mats that exhibited stratified populations of bacteria and archaea. Predictive metagenomics also revealed vertical profiles of metabolic capabilities, such as photosynthesis and carboxylic and fatty acid synthesis within the mats that had not been previously observed. The carbonate precipitates within the thrombolite-forming mats exhibited isotopic geochemical signatures suggesting that the precipitation within the Bahamian thrombolites is photosynthetically induced. Together, this study provides the first look at the spatial organization of the microbial populations within Bahamian thrombolites and enables the distribution of microbes to be correlated with their activities within modern thrombolite systems. Key Words: Thrombolites-Microbial diversity-Metagenome-Stable isotopes-Microbialites. Astrobiology 17, 413-430.
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Affiliation(s)
- Artemis S. Louyakis
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Jennifer M. Mobberley
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Brooke E. Vitek
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut
| | - Paul D. Hagan
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - R. Pamela Reid
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Reinhard Kozdon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - Ian J. Orland
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - John W. Valley
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - Noah J. Planavsky
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut
| | - Giorgio Casaburi
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Jamie S. Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
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46
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Wong HL, Visscher PT, White RA, Smith DL, Patterson MM, Burns BP. Dynamics of archaea at fine spatial scales in Shark Bay mat microbiomes. Sci Rep 2017; 7:46160. [PMID: 28397816 PMCID: PMC5387419 DOI: 10.1038/srep46160] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/09/2017] [Indexed: 01/07/2023] Open
Abstract
The role of archaea in microbial mats is poorly understood. Delineating the spatial distribution of archaea with mat depth will enable resolution of putative niches in these systems. In the present study, high throughput amplicon sequencing was undertaken in conjunction with analysis of key biogeochemical properties of two mats (smooth and pustular) from Shark Bay, Australia. One-way analysis of similarity tests indicated the archaeal community structures of smooth and pustular mats were significantly different (global R = 1, p = 0.1%). Smooth mats possessed higher archaeal diversity, dominated by Parvarchaeota. The methanogenic community in smooth mats was dominated by hydrogenotrophic Methanomicrobiales, as well as methylotrophic Methanosarcinales, Methanococcales, Methanobacteriales and Methanomassiliicoccaceae. Pustular mats were enriched with Halobacteria and Parvarchaeota. Key metabolisms (bacterial and archaeal) were measured, and the rates of oxygen production/consumption and sulfate reduction were up to four times higher in smooth than in pustular mats. Methane production peaked in the oxic layers and was up to seven-fold higher in smooth than pustular mats. The finding of an abundance of anaerobic methanogens enriched at the surface where oxygen levels were highest, coupled with peak methane production in the oxic zone, suggests putative surface anoxic niches in these microbial mats.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Pieter T Visscher
- Department of Marine Sciences, University of Connecticut, USA.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
| | - Richard Allen White
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Daniela-Lee Smith
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
| | | | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Australia
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47
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Tan CH, Lee KWK, Burmølle M, Kjelleberg S, Rice SA. All together now: experimental multispecies biofilm model systems. Environ Microbiol 2017; 19:42-53. [DOI: 10.1111/1462-2920.13594] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Chuan Hao Tan
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
| | - Kai Wei Kelvin Lee
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
| | - Mette Burmølle
- Section of Microbiology, Department of BiologyUniversity of CopenhagenCopenhagen Denmark
| | - Staffan Kjelleberg
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
- The School of Biological SciencesNanyang Technological University Singapore
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
- The School of Biological SciencesNanyang Technological University Singapore
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48
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Quorum Sensing and the Use of Quorum Quenchers as Natural Biocides to Inhibit Sulfate-Reducing Bacteria. Antibiotics (Basel) 2016; 5:antibiotics5040039. [PMID: 27983678 PMCID: PMC5187520 DOI: 10.3390/antibiotics5040039] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/23/2016] [Accepted: 12/06/2016] [Indexed: 11/17/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) are one of the main protagonist groups of biocorrosion in the seawater environment. Given their principal role in biocorrosion, it remains a crucial task to develop strategies to reduce the abundance of SRBs. Conventional approaches include the use of biocides and antibiotics, which can impose health, safety, and environmental concerns. This review examines an alternative approach to this problem. This is achieved by reviewing the role of quorum sensing (QS) in SRB populations and its impact on the biofilm formation process. Genome databases of SRBs are mined to look for putative QS systems and homologous protein sequences representative of autoinducer receptors or synthases. Subsequently, this review puts forward the potential use of quorum quenchers as natural biocides against SRBs and outlines the potential strategies for the implementation of this approach.
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49
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Bodelón G, Montes-García V, López-Puente V, Hill EH, Hamon C, Sanz-Ortiz MN, Rodal-Cedeira S, Costas C, Celiksoy S, Pérez-Juste I, Scarabelli L, La Porta A, Pérez-Juste J, Pastoriza-Santos I, Liz-Marzán LM. Detection and imaging of quorum sensing in Pseudomonas aeruginosa biofilm communities by surface-enhanced resonance Raman scattering. NATURE MATERIALS 2016; 15:1203-1211. [PMID: 27500808 PMCID: PMC5082732 DOI: 10.1038/nmat4720] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/04/2016] [Indexed: 05/15/2023]
Abstract
Most bacteria in nature exist as biofilms, which support intercellular signalling processes such as quorum sensing (QS), a cell-to-cell communication mechanism that allows bacteria to monitor and respond to cell density and changes in the environment. As QS and biofilms are involved in the ability of bacteria to cause disease, there is a need for the development of methods for the non-invasive analysis of QS in natural bacterial populations. Here, by using surface-enhanced resonance Raman scattering spectroscopy, we report rationally designed nanostructured plasmonic substrates for the in situ, label-free detection of a QS signalling metabolite in growing Pseudomonas aeruginosa biofilms and microcolonies. The in situ, non-invasive plasmonic imaging of QS in biofilms provides a powerful analytical approach for studying intercellular communication on the basis of secreted molecules as signals.
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Affiliation(s)
- Gustavo Bodelón
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
| | | | | | - Eric H Hill
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | - Cyrille Hamon
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | - Marta N Sanz-Ortiz
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | | | - Celina Costas
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
| | - Sirin Celiksoy
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
| | | | - Leonardo Scarabelli
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | - Andrea La Porta
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
| | - Jorge Pérez-Juste
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
| | | | - Luis M Liz-Marzán
- Departamento de Química Física, Universidade de Vigo, 36310 Vigo, Spain
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), 20009 Donostia - San Sebastián, Spain
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50
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Zhang C, Zhu S, Wu H, Jatt AN, Pan Y, Zeng M. Quorum Sensing Involved in the Spoilage Process of the Skin and Flesh of Vacuum-Packaged Farmed Turbot (Scophthalmus maximus) Stored at 4 °C. J Food Sci 2016; 81:M2776-M2784. [DOI: 10.1111/1750-3841.13510] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 08/12/2016] [Accepted: 08/30/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Caili Zhang
- College of Food Science and Engineering; Ocean Univ. of China; Qingdao 266003 China
| | - Suqin Zhu
- College of Food Science and Engineering; Ocean Univ. of China; Qingdao 266003 China
| | - Haohao Wu
- College of Food Science and Engineering; Ocean Univ. of China; Qingdao 266003 China
| | | | - Yurong Pan
- College of Food Science and Engineering; Ocean Univ. of China; Qingdao 266003 China
| | - Mingyong Zeng
- College of Food Science and Engineering; Ocean Univ. of China; Qingdao 266003 China
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