1
|
Morriss CE, Cheung CK, Nunn E, Parmeggiani F, Powell NA, Kimber RL, Haigh SJ, Lloyd JR. Biosynthesis Parameters Control the Physicochemical and Catalytic Properties of Microbially Supported Pd Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2311016. [PMID: 38461530 DOI: 10.1002/smll.202311016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/12/2024] [Indexed: 03/12/2024]
Abstract
The biosynthesis of Pd nanoparticles supported on microorganisms (bio-Pd) is achieved via the enzymatic reduction of Pd(II) to Pd(0) under ambient conditions using inexpensive buffers and electron donors, like organic acids or hydrogen. Sustainable bio-Pd catalysts are effective for C-C coupling and hydrogenation reactions, but their industrial application is limited by challenges in controlling nanoparticle properties. Here, using the metal-reducing bacterium Geobacter sulfurreducens, it is demonstrated that synthesizing bio-Pd under different Pd loadings and utilizing different electron donors (acetate, formate, hydrogen, no e- donor) influences key properties such as nanoparticle size, Pd(II):Pd(0) ratio, and cellular location. Controlling nanoparticle size and location controls the activity of bio-Pd for the reduction of 4-nitrophenol, whereas high Pd loading on cells synthesizes bio-Pd with high activity, comparable to commercial Pd/C, for Suzuki-Miyaura coupling reactions. Additionally, the study demonstrates the novel synthesis of microbially-supported ≈2 nm PdO nanoparticles due to the hydrolysis of biosorbed Pd(II) in bicarbonate buffer. Bio-PdO nanoparticles show superior activity in 4-nitrophenol reduction compared to commercial Pd/C catalysts. Overall, controlling biosynthesis parameters, such as electron donor, metal loading, and solution chemistry, enables tailoring of bio-Pd physicochemical and catalytic properties.
Collapse
Affiliation(s)
- Christopher Egan Morriss
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
- Department of Materials, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Casey K Cheung
- Department of Materials, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Elliot Nunn
- Department of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Fabio Parmeggiani
- Dipartimento di Chimica, Materiali ed Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci, Milan, 20133, Italy
| | | | - Richard L Kimber
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Sarah J Haigh
- Department of Materials, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Jonathan R Lloyd
- Department of Earth and Environmental Sciences, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| |
Collapse
|
2
|
Nikeleit V, Maisch M, Byrne JM, Harwood C, Kappler A, Bryce C. Phototrophic Fe(II) oxidation by Rhodopseudomonas palustris TIE-1 in organic and Fe(II)-rich conditions. Environ Microbiol 2024; 26:e16608. [PMID: 38504412 DOI: 10.1111/1462-2920.16608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/28/2024] [Indexed: 03/21/2024]
Abstract
Rhodopseudomonas palustris TIE-1 grows photoautotrophically with Fe(II) as an electron donor and photoheterotrophically with a variety of organic substrates. However, it is unclear whether R. palustris TIE-1 conducts Fe(II) oxidation in conditions where organic substrates and Fe(II) are available simultaneously. In addition, the effect of organic co-substrates on Fe(II) oxidation rates or the identity of Fe(III) minerals formed is unknown. We incubated R. palustris TIE-1 with 2 mM Fe(II), amended with 0.6 mM organic co-substrate, and in the presence/absence of CO2 . We found that in the absence of CO2 , only the organic co-substrates acetate, lactate and pyruvate, but not Fe(II), were consumed. When CO2 was present, Fe(II) and all organic substrates were consumed. Acetate, butyrate and pyruvate were consumed before Fe(II) oxidation commenced, whereas lactate and glucose were consumed at the same time as Fe(II) oxidation proceeded. Lactate, pyruvate and glucose increased the Fe(II) oxidation rate significantly (by up to threefold in the case of lactate). 57 Fe Mössbauer spectroscopy revealed that short-range ordered Fe(III) oxyhydroxides were formed under all conditions. This study demonstrates phototrophic Fe(II) oxidation proceeds even in the presence of organic compounds, and that the simultaneous oxidation of organic substrates can stimulate Fe(II) oxidation.
Collapse
Affiliation(s)
- Verena Nikeleit
- Department of Geoscience, University of Tübingen, Tübingen, Germany
| | - Markus Maisch
- Department of Geoscience, University of Tübingen, Tübingen, Germany
| | - James M Byrne
- School of Earth Sciences, University of Bristol, Bristol, UK
| | - Caroline Harwood
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Andreas Kappler
- Department of Geoscience, University of Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infections, Tübingen, Germany
| | - Casey Bryce
- School of Earth Sciences, University of Bristol, Bristol, UK
| |
Collapse
|
3
|
Moon S, Martin LMA, Kim S, Zhang Q, Zhang R, Xu W, Luo T. Direct observation and identification of nanoplastics in ocean water. SCIENCE ADVANCES 2024; 10:eadh1675. [PMID: 38277449 PMCID: PMC10816700 DOI: 10.1126/sciadv.adh1675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 12/26/2023] [Indexed: 01/28/2024]
Abstract
Millions of tons of plastics enter the oceans yearly, and they can be fragmented by ultraviolet and mechanical means into nanoplastics. Here, we report the direct observation of nanoplastics in global ocean water leveraging a unique shrinking surface bubble deposition (SSBD) technique. SSBD involves optically heating plasmonic nanoparticles to form a surface bubble and leveraging the Marangoni flow to concentrate suspended nanoplastics onto the surface, allowing direct visualization using electron microscopy. With the plasmonic nanoparticles co-deposited in SSBD, the surface-enhanced Raman spectroscopy effect is enabled for direct chemical identification of trace amounts of nanoplastics. In the water samples from two oceans, we observed nanoplastics made of nylon, polystyrene, and polyethylene terephthalate-all common in daily consumables. The plastic particles have diverse morphologies, such as nanofibers, nanoflakes, and ball-stick nanostructures. These nanoplastics may profoundly affect marine organisms, and our results can provide critical information for appropriately designing their toxicity studies.
Collapse
Affiliation(s)
- Seunghyun Moon
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Leisha M. A. Martin
- Department of Life Sciences, Texas A&M University, Corpus Christi, TX 78412, USA
- MNT SmartSolutions, 204 Bryn Mawr, Albuquerque, NM 87106, USA
| | - Seongmin Kim
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Qiushi Zhang
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Renzheng Zhang
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Wei Xu
- Department of Life Sciences, Texas A&M University, Corpus Christi, TX 78412, USA
| | - Tengfei Luo
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Center for Sustainable Energy of Notre Dame (ND Energy), University of Notre Dame, Notre Dame, IN 46556, USA
| |
Collapse
|
4
|
Singleton SL, Davis EW, Arnold HK, Daniels AMY, Brander SM, Parsons RJ, Sharpton TJ, Giovannoni SJ. Identification of rare microbial colonizers of plastic materials incubated in a coral reef environment. Front Microbiol 2023; 14:1259014. [PMID: 37869676 PMCID: PMC10585116 DOI: 10.3389/fmicb.2023.1259014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/15/2023] [Indexed: 10/24/2023] Open
Abstract
Plastic waste accumulation in marine environments has complex, unintended impacts on ecology that cross levels of community organization. To measure succession in polyolefin-colonizing marine bacterial communities, an in situ time-series experiment was conducted in the oligotrophic coastal waters of the Bermuda Platform. Our goals were to identify polyolefin colonizing taxa and isolate bacterial cultures for future studies of the biochemistry of microbe-plastic interactions. HDPE, LDPE, PP, and glass coupons were incubated in surface seawater for 11 weeks and sampled at two-week intervals. 16S rDNA sequencing and ATR-FTIR/HIM were used to assess biofilm community structure and chemical changes in polymer surfaces. The dominant colonizing taxa were previously reported cosmopolitan colonizers of surfaces in marine environments, which were highly similar among the different plastic types. However, significant differences in rare community composition were observed between plastic types, potentially indicating specific interactions based on surface chemistry. Unexpectedly, a major transition in community composition occurred in all material treatments between days 42 and 56 (p < 0.01). Before the transition, Alteromonadaceae, Marinomonadaceae, Saccharospirillaceae, Vibrionaceae, Thalassospiraceae, and Flavobacteriaceae were the dominant colonizers. Following the transition, the relative abundance of these taxa declined, while Hyphomonadaceae, Rhodobacteraceae and Saprospiraceae increased. Over the course of the incubation, 8,641 colonizing taxa were observed, of which 25 were significantly enriched on specific polyolefins. Seven enriched taxa from families known to include hydrocarbon degraders (Hyphomonadaceae, Parvularculaceae and Rhodobacteraceae) and one n-alkane degrader (Ketobacter sp.). The ASVs that exhibited associations with specific polyolefins are targets of ongoing investigations aimed at retrieving plastic-degrading microbes in culture.
Collapse
Affiliation(s)
| | - Edward W. Davis
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K. Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - Susanne M. Brander
- Department of Fisheries, Wildlife, and Conservation Sciences, Coastal Oregon Marine Experiment Station, Oregon State University, Newport, OR, United States
| | | | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | |
Collapse
|
5
|
Mather CC, Lampinen HM, Tucker M, Leopold M, Dogramaci S, Raven M, Gilkes RJ. Microbial influence on dolomite and authigenic clay mineralisation in dolocrete profiles of NW Australia. GEOBIOLOGY 2023; 21:644-670. [PMID: 36973880 DOI: 10.1111/gbi.12555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/02/2023] [Accepted: 03/12/2023] [Indexed: 06/18/2023]
Abstract
Dolomite (CaMg(CO3 )2 ) precipitation is kinetically inhibited at surface temperatures and pressures. Experimental studies have demonstrated that microbial extracellular polymeric substances (EPS) as well as certain clay minerals may catalyse dolomite precipitation. However, the combined association of EPS with clay minerals and dolomite and their occurrence in the natural environment are not well documented. We investigated the mineral and textural associations within groundwater dolocrete profiles from arid northwest Australia. Microbial EPS is a site of nucleation for both dolomite and authigenic clay minerals in this Late Miocene to Pliocene dolocrete. Dolomite crystals are commonly encased in EPS alveolar structures, which have been mineralised by various clay minerals, including montmorillonite, trioctahedral smectite and palygorskite-sepiolite. Observations of microbial microstructures and their association with minerals resemble textures documented in various lacustrine and marine microbialites, indicating that similar mineralisation processes may have occurred to form these dolocretes. EPS may attract and bind cations that concentrate to form the initial particles for mineral nucleation. The dolomite developed as nanocrystals, likely via a disordered precursor, which coalesced to form larger micritic crystal aggregates and rhombic crystals. Spheroidal dolomite textures, commonly with hollow cores, are also present and may reflect the mineralisation of a biofilm surrounding coccoid bacterial cells. Dolomite formation within an Mg-clay matrix is also observed, more commonly within a shallow pedogenic horizon. The ability of the negatively charged surfaces of clay and EPS to bind and dewater Mg2+ , as well as the slow diffusion of ions through a viscous clay or EPS matrix, may promote the incorporation of Mg2+ into the mineral and overcome the kinetic effects to allow disordered dolomite nucleation and its later growth. The results of this study show that the precipitation of clay and carbonate minerals in alkaline environments may be closely associated and can develop from the same initial amorphous Ca-Mg-Si-rich matrix within EPS. The abundance of EPS preserved within the profiles is evidence of past microbial activity. Local fluctuations in chemistry, such as small increases in alkalinity, associated with the degradation of EPS or microbial activity, were likely important for both clay and dolomite formation. Groundwater environments may be important and hitherto understudied settings for microbially influenced mineralisation and for low-temperature dolomite precipitation.
Collapse
Affiliation(s)
- Caroline C Mather
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
- School of Social Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Heta M Lampinen
- Commonwealth Scientific and Industrial Research Organisation, Mineral Resources, 26 Dick Perry Avenue, Kensington, Western Australia, 6151, Australia
| | - Maurice Tucker
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
| | - Matthias Leopold
- UWA-School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - Shawan Dogramaci
- School of Earth Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
- National Centre for Groundwater Research and Training & College of Science and Engineering, Flinders University, Adelaide, South Australia, 5042, Australia
| | - Mark Raven
- Commonwealth Scientific and Industrial Research Organisation, Mineralogical Services, Waite Campus, Urrbrae, South Australia, 5064, Australia
| | - Robert J Gilkes
- UWA-School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| |
Collapse
|
6
|
Binda G, Carnati S, Spanu D, Bellasi A, Hurley R, Bettinetti R, Monticelli D, Pozzi A, Nizzetto L. Selection of the optimal extraction protocol to investigate the interaction between trace elements and environmental plastic. JOURNAL OF HAZARDOUS MATERIALS 2023; 452:131330. [PMID: 37004438 DOI: 10.1016/j.jhazmat.2023.131330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/09/2023] [Accepted: 03/29/2023] [Indexed: 06/19/2023]
Abstract
The interaction between environmental plastic and trace elements is an issue of concern. Understanding their interaction mechanisms is key to evaluate the potential threats for the environment. To this regard, consolidating confidence in extraction protocols can help in understanding the amount of different species present on plastic surface, as well as the potential mobility of trace elements present inside the plastic matrix (e.g., additives). Here we tested the efficacy of different reagents to mimic the elemental phases bonded to meso- and microplastic in the environment, in relation to the grade of ageing and the polymer composition. Results showed that a relatively high portion of trace elements is bonded in a weak phase and that other phases abundant in other matrices (e.g., oxides and bonded to organic matter) are only present to a limited degree in the plastic samples. The comparison of different sample types highlighted the important role of plastic ageing in governing interactions with trace elements, while the polymer composition has a limited influence on this process. Finally, the future steps toward a tailored extraction scheme for environmental plastic are proposed.
Collapse
Affiliation(s)
- Gilberto Binda
- Norwegian Institute for Water Research (NIVA), Økernveien 94, 0579 Oslo, Norway.
| | - Stefano Carnati
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Davide Spanu
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Arianna Bellasi
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Rachel Hurley
- Norwegian Institute for Water Research (NIVA), Økernveien 94, 0579 Oslo, Norway
| | - Roberta Bettinetti
- Department of Human and Innovation for the Territory, University of Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Damiano Monticelli
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Andrea Pozzi
- Department of Science and High Technology, University of Insubria, Via Valleggio 11, 22100 Como, Italy
| | - Luca Nizzetto
- Norwegian Institute for Water Research (NIVA), Økernveien 94, 0579 Oslo, Norway; RECETOX, Masarik University, Kamenice 753/5, 625 00 Brno, Czech Republic
| |
Collapse
|
7
|
Bedendi G, De Moura Torquato LD, Webb S, Cadoux C, Kulkarni A, Sahin S, Maroni P, Milton RD, Grattieri M. Enzymatic and Microbial Electrochemistry: Approaches and Methods. ACS MEASUREMENT SCIENCE AU 2022; 2:517-541. [PMID: 36573075 PMCID: PMC9783092 DOI: 10.1021/acsmeasuresciau.2c00042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 06/17/2023]
Abstract
The coupling of enzymes and/or intact bacteria with electrodes has been vastly investigated due to the wide range of existing applications. These span from biomedical and biosensing to energy production purposes and bioelectrosynthesis, whether for theoretical research or pure applied industrial processes. Both enzymes and bacteria offer a potential biotechnological alternative to noble/rare metal-dependent catalytic processes. However, when developing these biohybrid electrochemical systems, it is of the utmost importance to investigate how the approaches utilized to couple biocatalysts and electrodes influence the resulting bioelectrocatalytic response. Accordingly, this tutorial review starts by recalling some basic principles and applications of bioelectrochemistry, presenting the electrode and/or biocatalyst modifications that facilitate the interaction between the biotic and abiotic components of bioelectrochemical systems. Focus is then directed toward the methods used to evaluate the effectiveness of enzyme/bacteria-electrode interaction and the insights that they provide. The basic concepts of electrochemical methods widely employed in enzymatic and microbial electrochemistry, such as amperometry and voltammetry, are initially presented to later focus on various complementary methods such as spectroelectrochemistry, fluorescence spectroscopy and microscopy, and surface analytical/characterization techniques such as quartz crystal microbalance and atomic force microscopy. The tutorial review is thus aimed at students and graduate students approaching the field of enzymatic and microbial electrochemistry, while also providing a critical and up-to-date reference for senior researchers working in the field.
Collapse
Affiliation(s)
- Giada Bedendi
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | | | - Sophie Webb
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Cécile Cadoux
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Amogh Kulkarni
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Selmihan Sahin
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Plinio Maroni
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Ross D. Milton
- Department
of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
- National
Centre of Competence in Research (NCCR) Catalysis, University of Geneva, Quai Ernest-Ansermet 30, 1211 Geneva 4, Switzerland
| | - Matteo Grattieri
- Dipartimento
di Chimica, Università degli Studi
di Bari “Aldo Moro”, via E. Orabona 4, Bari 70125, Italy
- IPCF-CNR
Istituto per i Processi Chimico Fisici, Consiglio Nazionale delle Ricerche, via E. Orabona 4, Bari 70125, Italy
| |
Collapse
|
8
|
Huang Z, Niu Q, Nie W, Li X, Yang C. Effects of heavy metals and antibiotics on performances and mechanisms of anaerobic digestion. BIORESOURCE TECHNOLOGY 2022; 361:127683. [PMID: 35882314 DOI: 10.1016/j.biortech.2022.127683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Anaerobic digestion (AD) is an efficacious technology to recover energy from organic wastes/wastewater, while the efficiency of AD could be limited by metals and antibiotics in substrates. It is of great significance to deeply understand the interaction mechanisms of metals and antibiotics with anaerobic microorganisms, as well as the combined effects of metals and antibiotics, which will help us break the inherent dysfunction of AD system and promote the efficient operation of AD. Therefore, this paper reviews the effects of metals, antibiotics and their combinations on AD performance, as well as the combined effects and interactional mechanisms of metals and antibiotics with anaerobic microorganisms. In addition, control strategies and future research needs are proposed. This review provides valuable information for the enhancement strategies and engineering applications of AD for organic wastes/wastewater containing metals and antibiotics.
Collapse
Affiliation(s)
- Zhiwei Huang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Qiuya Niu
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Wenkai Nie
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Xiang Li
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China
| | - Chunping Yang
- College of Environmental Science and Engineering, Hunan University and Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha, Hunan 410082, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, Key Laboratory of Petrochemical Pollution Control of Guangdong Higher Education Institutes, School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong 525000, China; Hunan Provincial Environmental Protection Engineering Center for Organic Pollution Control of Urban Water and Wastewater, Changsha, Hunan 410001, China.
| |
Collapse
|
9
|
Abiotic aging assisted bio-oxidation and degradation of LLDPE/LDPE packaging polyethylene film by stimulated enrichment culture. Polym Degrad Stab 2022. [DOI: 10.1016/j.polymdegradstab.2022.110156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
10
|
Mena-Bueno S, Poveda-Urkixo I, Irazoki O, Palacios L, Cava F, Zabalza-Baranguá A, Grilló MJ. Brucella melitensis Wzm/Wzt System: Changes in the Bacterial Envelope Lead to Improved Rev1Δwzm Vaccine Properties. Front Microbiol 2022; 13:908495. [PMID: 35875565 PMCID: PMC9306315 DOI: 10.3389/fmicb.2022.908495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
The lipopolysaccharide (LPS) O-polysaccharide (O-PS) is the main virulence factor in Brucella. After synthesis in the cytoplasmic membrane, O-PS is exported to the periplasm by the Wzm/Wzt system, where it is assembled into a LPS. This translocation also engages a bactoprenol carrier required for further biosynthesis pathways, such as cell wall biogenesis. Targeting O-PS export by blockage holds great potential for vaccine development, but little is known about the biological implications of each Wzm/Wzt moiety. To improve this knowledge and to elucidate its potential application as a vaccine, we constructed and studied wzm/wzt single- and double-deletion mutants, using the attenuated strain Brucella melitensis Rev1 as the parental strain. This allowed us to describe the composition of Brucella peptidoglycan for the first time. We observed that these mutants lack external O-PS yet trigger changes in genetic transcription and in phenotypic properties associated with the outer membrane and cell wall. The three mutants are highly attenuated; unexpectedly, Rev1Δwzm also excels as an immunogenic and effective vaccine against B. melitensis and Brucella ovis in mice, revealing that low persistence is not at odds with efficacy. Rev1Δwzm is attenuated in BeWo trophoblasts, does not infect mouse placentas, and is safe in pregnant ewes. Overall, these attributes and the minimal serological interference induced in sheep make Rev1Δwzm a highly promising vaccine candidate.
Collapse
Affiliation(s)
- Sara Mena-Bueno
- Animal Health Department, Instituto de Agrobiotecnología (IdAB, CSIC-Gobierno de Navarra), Pamplona, Spain
- Agronomy, Biotecnology and Food Department, Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Irati Poveda-Urkixo
- Animal Health Department, Instituto de Agrobiotecnología (IdAB, CSIC-Gobierno de Navarra), Pamplona, Spain
| | - Oihane Irazoki
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Leyre Palacios
- Animal Health Department, Instituto de Agrobiotecnología (IdAB, CSIC-Gobierno de Navarra), Pamplona, Spain
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Ana Zabalza-Baranguá
- Animal Health Department, Instituto de Agrobiotecnología (IdAB, CSIC-Gobierno de Navarra), Pamplona, Spain
| | - María Jesús Grilló
- Animal Health Department, Instituto de Agrobiotecnología (IdAB, CSIC-Gobierno de Navarra), Pamplona, Spain
- *Correspondence: María Jesús Grilló,
| |
Collapse
|
11
|
Anglés A, He Q, Sánchez García L, Carrizo D, Rodriguez N, Huang T, Shen Y, Amils R, Fernández-Remolar DC. Biospeleothems Formed by Fungal Activity During the Early Holocene in the “Salar de Uyuni”. Front Microbiol 2022; 13:913452. [PMID: 35814676 PMCID: PMC9260512 DOI: 10.3389/fmicb.2022.913452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/28/2022] [Indexed: 11/28/2022] Open
Abstract
The Chiquini and Galaxias caves contain speleothems that are templated by long fungal structures. They have been associated with the carbonate lacustrine deposits in the margins of the Coipasa and Uyuni Salar basins. During a wetter episode, such carbonates formed at the end of the last glaciation raising the lake level to more than 100 m in the Tauca events (15–12 ky). Such an event flooded the caves that eventually became a cryptic habitat in the lake. The caves show bizarre speleothems framed by large (>1 m) fungal buildings covering the older algal mineralized structures. Although the origin of the caves is not fully understood, the occurrence of two carbonatic units with very distinctive fabric suggests that they formed in two separated humid events. In this regard, the mineralized algal structures, showing the same features as the lacustrine carbonates, likely formed during the Tauca flooding events in the terminal Pleistocene that inundated older caves. The different caves were exposed to the atmosphere after a drop in the lake level that promoted alluvial erosion by <12–10 ky (Ticaña episode) under arid conditions. A last humid episode rising the lake surface 10 m above the Salar level, which was not enough to inundate the caves a second time, drove the formation of the biospeleothems by fungi biomineralization. The abundance and size of the preserved fungal structures suggest that they were sustained by a stable hydrological activity plus a constant organic supply. While nutrients could have been primarily sourced from the vegetal communities that occupied the exhumated lake margins, they might have also been released from the lacustrine carbonatic unit. The combination of hydrology and biological activities were likely determinants for a fast rock dissolution and mineralization ending in the construction of the fungal biospeleothems.
Collapse
Affiliation(s)
- Angélica Anglés
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
- Blue Marble Space Institute of Science, Seattle, WA, United States
- *Correspondence: Angélica Anglés
| | - Qitao He
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
| | - Laura Sánchez García
- Centro de Astrobiología Instituto Nacional de Tecnica Aeroespacial - Consejo Superior de Investigaciones Científicas (INTA-CSIC), Madrid, Spain
| | - Daniel Carrizo
- Centro de Astrobiología Instituto Nacional de Tecnica Aeroespacial - Consejo Superior de Investigaciones Científicas (INTA-CSIC), Madrid, Spain
| | - Nuria Rodriguez
- Centro de Astrobiología Instituto Nacional de Tecnica Aeroespacial - Consejo Superior de Investigaciones Científicas (INTA-CSIC), Madrid, Spain
| | - Ting Huang
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
| | - Yan Shen
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
| | - Ricardo Amils
- Centro de Astrobiología Instituto Nacional de Tecnica Aeroespacial - Consejo Superior de Investigaciones Científicas (INTA-CSIC), Madrid, Spain
| | - David C. Fernández-Remolar
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
- Carl Sagan Center, The SETI Institute, Mountain View, CA, United States
| |
Collapse
|
12
|
|
13
|
Zhu R, He L, Li Q, Huang T, Gao M, Jiang Q, Liu J, Cai A, Shi D, Gu L, He Q. Mechanism study of improving anaerobic co-digestion performance of waste activated sludge and food waste by Fe 3O 4. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 300:113745. [PMID: 34547575 DOI: 10.1016/j.jenvman.2021.113745] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
A large amount of waste activated sludge (WAS) and food waste (FW) are produced every year in China. Anaerobic co-digestion is considered to be an effective way to solve this problem. This study applied FW/WAS mixture as co-substrate to create different digestive environment, aiming to understand the mechanism of Fe3O4 particles in promoting AD performance. The results showed that the addition of Fe3O4 presented various performances when facing different digestive acidification stress brought by different mixing ratios of WAS and FW. Methanogenic pathways and microbial communities varied with substrates' properties. For group A (WAS mono-digestion), the acetoclastic methanogens dominated, 20 mg/g VS (according to the iron element) Fe3O4 could promote methane production, while 200 mg/g VS Fe3O4 would inhibit microbial activity. The promoted methane production by Fe3O4 was attributable to the promotion of sludge hydrolysis. For group B (WAS: FW = 1:0.5, based on VS addition, similarly hereinafter), Fe3O4 triggered direct interspecific electron transfer (DIET) between bacteria and methanogens. For group C (WAS: FW = 1:1), the hydrogenotrophic methanogens dominated, bacteria excreted more non-conductive polysaccharides in EPS to resist unfavorable environment, thereby it prevented their contact with Fe3O4 particles. So, it was difficult for Fe3O4 to trigger DIET and promote the digestive performance of batch experiments in such condition.
Collapse
Affiliation(s)
- Ruilin Zhu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Linyan He
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Qianyi Li
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - TingXuan Huang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Meng Gao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Qin Jiang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Junyan Liu
- Chongqing Three Gorges Water Drainage (Wulong) Co., Ltd, 130 Jianshe West Road, Wulong County, Chongqing, 408500, PR China
| | - Anrong Cai
- Chongqing Yuxi Water Co., Ltd, No. 36, Fenghuang Avenue, Yongchuan District, Chongqing, 402160, PR China
| | - Dezhi Shi
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| | - Li Gu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China.
| | - Qiang He
- Key Laboratory of the Three Gorges Reservoir Region's Eco-environments, Ministry of Education, College of Environment and Ecology, Chongqing University, 174 Shapingba Road, Chongqing, 400045, PR China
| |
Collapse
|
14
|
Recent Advances in the Production of Exopolysaccharide (EPS) from Lactobacillus spp. and Its Application in the Food Industry: A Review. SUSTAINABILITY 2021. [DOI: 10.3390/su132212429] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exopolysaccharide (EPS) show remarkable properties in various food applications. In this review paper, EPS composition, structural characterization, biosynthesis pathways, and recent advancements in the context of application of EPS-producing Lactobacillus spp. in different food industries are discussed. Various chemical and physical properties of Lactobacillus EPS, such as the structural, rheological, and shelf-life enhancement of different food products, are mentioned. Moreover, EPSs play a characteristic role in starter culture techniques, yogurt production, immunomodulation, and potential prebiotics. It has been seen that the wastes of fermented and non-fermented products are used as biological food for EPS extraction. The main capabilities of probiotics are the use of EPS for technological properties such as texture and flavor enhancement, juiciness, and water holding capacities of specific food products. For these reasons, EPSs are used in functional and fermented food products to enhance the healthy activity of the human digestive system as well as for the benefit of the food industry to lower product damage and increase consumer demand. Additionally, some pseudocereals such as amaranth and quinoa that produce EPS also play an important role in improving the organoleptic properties of food-grade products. In conclusion, more attention should be given to sustainable extraction techniques of LAB EPS to enhance structural and functional use in the developmental process of food products to meet consumer preferences.
Collapse
|
15
|
Shen H, Durkin DP, Aiello A, Diba T, Lafleur J, Zara JM, Shen Y, Shuai D. Photocatalytic graphitic carbon nitride-chitosan composites for pathogenic biofilm control under visible light irradiation. JOURNAL OF HAZARDOUS MATERIALS 2021; 408:124890. [PMID: 33370693 DOI: 10.1016/j.jhazmat.2020.124890] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/05/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
Photocatalysis holds promise for inactivating environmental pathogens. Visible-light-responsive composites of carbon-doped graphitic carbon nitride and chitosan with high reactivity and processability were fabricated, and they can control pathogenic biofilms for environmental, food, biomedical, and building applications. The broad-spectrum biofilm inhibition and eradication of the photocatalytic composites against Staphylococcus epidermidis, Pseudomonas aeruginosa PAO1, and Escherichia coli O157: H7 under visible light irradiation were demonstrated. Extracellular polymeric substances in Escherichia coli O157: H7 biofilms were most resistant to photocatalytic oxidation, which led to reduced performance for biofilm removal. 1O2 produced by the composites was believed to dominate biofilm inactivation. Moreover, the composites exhibited excellent performance for inhibiting biofilm development in urine, highlighting the promise for inactivating environmental biofilms developed from multiple bacterial species. Our study provides fundamental insights into the development of new photocatalytic composites, and elucidates the mechanism of how the photocatalyst reacts with a microbiological system.
Collapse
Affiliation(s)
- Hongchen Shen
- Department of Civil and Environmental Engineering, The George Washington University, Washington, DC, 20052 USA
| | - David P Durkin
- Department of Chemistry, United States Naval Academy, Annapolis, MD, 21402 US
| | - Ashlee Aiello
- Department of Chemistry, United States Naval Academy, Annapolis, MD, 21402 US
| | - Tara Diba
- Department of Biomedical Engineering, The George Washington University, Washington, DC, 20052 USA
| | - John Lafleur
- Department of Emergency Medicine, George Washington University School of Medicine, Washington, DC, 20037 USA
| | - Jason M Zara
- Department of Biomedical Engineering, The George Washington University, Washington, DC, 20052 USA
| | - Yun Shen
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521 USA.
| | - Danmeng Shuai
- Department of Civil and Environmental Engineering, The George Washington University, Washington, DC, 20052 USA.
| |
Collapse
|
16
|
Structure of the Bacterial Cellulose Ribbon and Its Assembly-Guiding Cytoskeleton by Electron Cryotomography. J Bacteriol 2021; 203:JB.00371-20. [PMID: 33199282 PMCID: PMC7811197 DOI: 10.1128/jb.00371-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/26/2020] [Indexed: 12/20/2022] Open
Abstract
This work’s relevance for the microbiology community is twofold. It delivers for the first time high-resolution near-native snapshots of Gluconacetobacter spp. (previously Komagataeibacter spp.) in the process of cellulose ribbon synthesis, in their native biofilm environment. Cellulose is a widespread component of bacterial biofilms, where its properties of exceptional water retention, high tensile strength, and stiffness prevent dehydration and mechanical disruption of the biofilm. Bacteria in the genus Gluconacetobacter secrete crystalline cellulose, with a structure very similar to that found in plant cell walls. How this higher-order structure is produced is poorly understood. We used cryo-electron tomography and focused-ion-beam milling of native bacterial biofilms to image cellulose-synthesizing Gluconacetobacter hansenii and Gluconacetobacter xylinus bacteria in a frozen-hydrated, near-native state. We confirm previous results suggesting that cellulose crystallization occurs serially following its secretion along one side of the cell, leading to a cellulose ribbon that can reach several micrometers in length and combine with ribbons from other cells to form a robust biofilm matrix. We were able to take direct measurements in a near-native state of the cellulose sheets. Our results also reveal a novel cytoskeletal structure, which we have named the cortical belt, adjacent to the inner membrane and underlying the sites where cellulose is seen emerging from the cell. We found that this structure is not present in other cellulose-synthesizing bacterial species, Agrobacterium tumefaciens and Escherichia coli 1094, which do not produce organized cellulose ribbons. We therefore propose that the cortical belt holds the cellulose synthase complexes in a line to form higher-order cellulose structures, such as sheets and ribbons. IMPORTANCE This work’s relevance for the microbiology community is twofold. It delivers for the first time high-resolution near-native snapshots of Gluconacetobacter spp. (previously Komagataeibacter spp.) in the process of cellulose ribbon synthesis, in their native biofilm environment. It puts forward a noncharacterized cytoskeleton element associated with the side of the cell where the cellulose synthesis occurs. This represents a step forward in the understanding of the cell-guided process of crystalline cellulose synthesis, studied specifically in the Gluconacetobacter genus and still not fully understood. Additionally, our successful attempt to use cryo-focused-ion-beam milling through biofilms to image the cells in their native environment will drive the community to use this tool for the morphological characterization of other studied biofilms.
Collapse
|
17
|
Loeffler M, Hilbig J, Velasco L, Weiss J. Usage of in situ exopolysaccharide-forming lactic acid bacteria in food production: Meat products-A new field of application? Compr Rev Food Sci Food Saf 2020; 19:2932-2954. [PMID: 33337046 DOI: 10.1111/1541-4337.12615] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/02/2020] [Accepted: 07/15/2020] [Indexed: 12/01/2022]
Abstract
In the meat industry, hydrocolloids and phosphates are used to improve the quality attributes of meat products. However, latest research results revealed that the usage of exopolysaccharide (EPS)-forming lactic acid bacteria (LAB), which are able to produce EPS in situ during processing could be an interesting alternative. The current review aims to give a better understanding of bacterial EPS production in food matrices with a special focus on meat products. This includes an introduction to microbial EPS production (homopolysaccharides as well as heteropolysaccharides) and an overview of parameters affecting EPS formation and yield depending on LAB used. This is followed by a summary of methods to detect and characterize EPS to facilitate a rational selection of starter cultures and fermentation conditions based on desired structure-function relationships in different food matrices. The mechanism of action of in situ generated EPS is then highlighted with an emphasis on different meat products. In the process, this review also highlights food additives currently used in meat production that could in the future be replaced by in situ EPS-forming LAB.
Collapse
Affiliation(s)
- Myriam Loeffler
- Department of Food Material Science, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 21/25, Stuttgart, Germany
| | - Jonas Hilbig
- Department of Food Material Science, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 21/25, Stuttgart, Germany
| | - Lina Velasco
- Department of Food Material Science, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 21/25, Stuttgart, Germany
| | - Jochen Weiss
- Department of Food Material Science, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstrasse 21/25, Stuttgart, Germany
| |
Collapse
|
18
|
Koch M, Włodarczyk-Biegun MK. Faithful scanning electron microscopic (SEM) visualization of 3D printed alginate-based scaffolds. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.bprint.2020.e00098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
19
|
Heumann A, Assifaoui A, Da Silva Barreira D, Thomas C, Briandet R, Laurent J, Beney L, Lapaquette P, Guzzo J, Rieu A. Intestinal release of biofilm-like microcolonies encased in calcium-pectinate beads increases probiotic properties of Lacticaseibacillus paracasei. NPJ Biofilms Microbiomes 2020; 6:44. [PMID: 33116127 PMCID: PMC7595111 DOI: 10.1038/s41522-020-00159-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/06/2020] [Indexed: 12/15/2022] Open
Abstract
In this study, we show that calcium pectinate beads (CPB) allow the formation of 20 µm spherical microcolonies of the probiotic bacteria Lacticaseibacillus paracasei (formerly designated as Lactobacillus paracasei) ATCC334 with a high cell density, reaching more than 10 log (CFU/g). The bacteria within these microcolonies are well structured and adhere to a three-dimensional network made of calcium-pectinate through the synthesis of extracellular polymeric substances (EPS) and thus display a biofilm-like phenotype, an attractive property for their use as probiotics. During bacterial development in the CPB, a coalescence phenomenon arises between neighboring microcolonies accompanied by their peripheral spatialization within the bead. Moreover, the cells of L. paracasei ATCC334 encased in these pectinate beads exhibit increased resistance to acidic stress (pH 1.5), osmotic stress (4.5 M NaCl), the freeze-drying process and combined stresses, simulating the harsh conditions encountered in the gastrointestinal (GI) tract. In vivo, the oral administration of CPB-formulated L. paracasei ATCC334 in mice demonstrated that biofilm-like microcolonies are successfully released from the CPB matrix in the colonic environment. In addition, these CPB-formulated probiotic bacteria display the ability to reduce the severity of a DSS-induced colitis mouse model, with a decrease in colonic mucosal injuries, less inflammation, and reduced weight loss compared to DSS control mice. To conclude, this work paves the way for a new form of probiotic administration in the form of biofilm-like microcolonies with enhanced functionalities.
Collapse
Affiliation(s)
- Arnaud Heumann
- Université de Bourgogne Franche-Comté (UBFC), AgroSup Dijon, UMR PAM A 02.102, F-21000, Dijon, France
| | - Ali Assifaoui
- Université de Bourgogne Franche-Comté (UBFC), AgroSup Dijon, UMR PAM A 02.102, F-21000, Dijon, France.
| | - David Da Silva Barreira
- Université de Bourgogne Franche-Comté (UBFC), AgroSup Dijon, UMR PAM A 02.102, F-21000, Dijon, France
| | - Charles Thomas
- Université de Bourgogne Franche-Comté (UBFC), LNC UMR 1231, F-21000 Dijon, France; INSERM, LNC UMR 1231, F-21000, Dijon, France
- Université de Bourgogne Franche-Comté (UBFC), LipSTIC LabEx, F-21000, Dijon, France
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Julie Laurent
- Université de Bourgogne Franche-Comté (UBFC), AgroSup Dijon, UMR PAM A 02.102, F-21000, Dijon, France
| | - Laurent Beney
- Université de Bourgogne Franche-Comté (UBFC), AgroSup Dijon, UMR PAM A 02.102, F-21000, Dijon, France
| | - Pierre Lapaquette
- Université de Bourgogne Franche-Comté (UBFC), AgroSup Dijon, UMR PAM A 02.102, F-21000, Dijon, France
| | - Jean Guzzo
- Université de Bourgogne Franche-Comté (UBFC), AgroSup Dijon, UMR PAM A 02.102, F-21000, Dijon, France
| | - Aurélie Rieu
- Université de Bourgogne Franche-Comté (UBFC), AgroSup Dijon, UMR PAM A 02.102, F-21000, Dijon, France.
| |
Collapse
|
20
|
Zambare NM, Naser NY, Gerlach R, Chang CB. Mineralogy of microbially induced calcium carbonate precipitates formed using single cell drop-based microfluidics. Sci Rep 2020; 10:17535. [PMID: 33067478 PMCID: PMC7568533 DOI: 10.1038/s41598-020-73870-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/21/2020] [Indexed: 11/28/2022] Open
Abstract
Microbe-mineral interactions are ubiquitous and can facilitate major biogeochemical reactions that drive dynamic Earth processes such as rock formation. One example is microbially induced calcium carbonate precipitation (MICP) in which microbial activity leads to the formation of calcium carbonate precipitates. A majority of MICP studies have been conducted at the mesoscale but fundamental questions persist regarding the mechanisms of cell encapsulation and mineral polymorphism. Here, we are the first to investigate and characterize precipitates on the microscale formed by MICP starting from single ureolytic E. coli MJK2 cells in 25 µm diameter drops. Mineral precipitation was observed over time and cells surrounded by calcium carbonate precipitates were observed under hydrated conditions. Using Raman microspectroscopy, amorphous calcium carbonate (ACC) was observed first in the drops, followed by vaterite formation. ACC and vaterite remained stable for up to 4 days, possibly due to the presence of organics. The vaterite precipitates exhibited a dense interior structure with a grainy exterior when examined using electron microscopy. Autofluorescence of these precipitates was observed possibly indicating the development of a calcite phase. The developed approach provides an avenue for future investigations surrounding fundamental processes such as precipitate nucleation on bacteria, microbe-mineral interactions, and polymorph transitions.
Collapse
Affiliation(s)
- Neerja M Zambare
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
| | - Nada Y Naser
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Robin Gerlach
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
| |
Collapse
|
21
|
A Hybrid Extracellular Electron Transfer Pathway Enhances the Survival of Vibrio natriegens. Appl Environ Microbiol 2020; 86:AEM.01253-20. [PMID: 32737131 DOI: 10.1128/aem.01253-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
Vibrio natriegens is the fastest-growing microorganism discovered to date, making it a useful model for biotechnology and basic research. While it is recognized for its rapid aerobic metabolism, less is known about anaerobic adaptations in V. natriegens or how the organism survives when oxygen is limited. Here, we describe and characterize extracellular electron transfer (EET) in V. natriegens, a metabolism that requires movement of electrons across protective cellular barriers to reach the extracellular space. V. natriegens performs extracellular electron transfer under fermentative conditions with gluconate, glucosamine, and pyruvate. We characterized a pathway in V. natriegens that requires CymA, PdsA, and MtrCAB for Fe(III) citrate and Fe(III) oxide reduction, which represents a hybrid of strategies previously discovered in Shewanella and Aeromonas Expression of these V. natriegens genes functionally complemented Shewanella oneidensis mutants. Phylogenetic analysis of the inner membrane quinol dehydrogenases CymA and NapC in gammaproteobacteria suggests that CymA from Shewanella diverged from Vibrionaceae CymA and NapC. Analysis of sequenced Vibrionaceae revealed that the genetic potential to perform EET is conserved in some members of the Harveyi and Vulnificus clades but is more variable in other clades. We provide evidence that EET enhances anaerobic survival of V. natriegens, which may be the primary physiological function for EET in Vibrionaceae IMPORTANCE Bacteria from the genus Vibrio occupy a variety of marine and brackish niches with fluctuating nutrient and energy sources. When oxygen is limited, fermentation or alternative respiration pathways must be used to conserve energy. In sedimentary environments, insoluble oxide minerals (primarily iron and manganese) are able to serve as electron acceptors for anaerobic respiration by microorganisms capable of extracellular electron transfer, a metabolism that enables the use of these insoluble substrates. Here, we identify the mechanism for extracellular electron transfer in Vibrio natriegens, which uses a combination of strategies previously identified in Shewanella and Aeromonas We show that extracellular electron transfer enhanced survival of V. natriegens under fermentative conditions, which may be a generalized strategy among Vibrio spp. predicted to have this metabolism.
Collapse
|
22
|
Wei W, Plymale A, Zhu Z, Ma X, Liu F, Yu XY. In Vivo Molecular Insights into Syntrophic Geobacter Aggregates. Anal Chem 2020; 92:10402-10411. [PMID: 32614167 DOI: 10.1021/acs.analchem.0c00653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Direct interspecies electron transfer (DIET) has been considered as a novel and highly efficient strategy in both natural anaerobic environments and artificial microbial fuel cells. A syntrophic model consisting of Geobacter metallireducens and Geobacter sulfurreducens was studied in this work. We conducted in vivo molecular mapping of the outer surface of the syntrophic community as the interface of nutrients and energy exchange. System for Analysis at the Liquid Vacuum Interface combined with time-of-flight secondary ion mass spectrometry was employed to capture the molecular distribution of syntrophic Geobacter communities in the living and hydrated state. Principal component analysis with selected peaks revealed that syntrophic Geobacter aggregates were well differentiated from other control samples, including syntrophic planktonic cells, pure cultured planktonic cells, and single population biofilms. Our in vivo imaging indicated that a unique molecular surface was formed. Specifically, aromatic amino acids, phosphatidylethanolamine components, and large water clusters were identified as key components that favored the DIET of syntrophic Geobacter aggregates. Moreover, the molecular changes in depths of the Geobacter aggregates were captured using dynamic depth profiling. Our findings shed new light on the interface components supporting electron transfer in syntrophic communities based on in vivo molecular imaging.
Collapse
Affiliation(s)
- Wenchao Wei
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, P. R. China.,Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Andrew Plymale
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Zihua Zhu
- Environmental and Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Xiang Ma
- Department of Chemistry, Grand View University, Des Moines, Iowa 50316, United States
| | - Fanghua Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003, P. R. China
| | - Xiao-Ying Yu
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| |
Collapse
|
23
|
Hempel C, Kapishnikov S, Perez-Berna AJ, Werner S, Guttmann P, Pereiro E, Qvortrup K, Andresen TL. The need to freeze-Dehydration during specimen preparation for electron microscopy collapses the endothelial glycocalyx regardless of fixation method. Microcirculation 2020; 27:e12643. [PMID: 32542908 DOI: 10.1111/micc.12643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/25/2020] [Accepted: 06/06/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE The endothelial glycocalyx covers the luminal surface of the endothelium and plays key roles in vascular function. Despite its biological importance, ideal visualization techniques are lacking. The current study aimed to improve the preservation and subsequent imaging quality of the endothelial glycocalyx. METHODS In mice, the endothelial glycocalyx was contrasted with a mixture of lanthanum and dysprosium (LaDy). Standard chemical fixation was compared with high-pressure frozen specimens processed with freeze substitution. Also, isolated brain microvessels and cultured endothelial cells were high-pressure frozen and by transmission soft x-rays, imaged under cryogenic conditions. RESULTS The endothelial glycocalyx was in some tissues significantly more voluminous from chemically fixed specimens compared with high-pressure frozen specimens. LaDy labeling introduced excessive absorption contrast, which impeded glycocalyx measurements in isolated brain microvessels when using transmission soft x-rays. In non-contrasted vessels, the glycocalyx was not resolved. LaDy-contrasted, cultured brain endothelial cells allowed to assess glycocalyx volume in vitro. CONCLUSIONS Both chemical and cryogenic fixation followed by dehydration lead to substantial collapse of the glycocalyx. Cryogenic fixation without freeze substitution could be a way forward although transmission soft x-ray tomography based solely on amplitude contrast seems unsuitable.
Collapse
Affiliation(s)
- Casper Hempel
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.,Centre for Medical Parasitology, Department for Clinical Microbiology, Copenhagen University Hospital, Copenhagen, Denmark.,Department for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Kapishnikov
- Department X-Ray microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany.,Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Stephan Werner
- Department X-Ray microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Peter Guttmann
- Department X-Ray microscopy, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Eva Pereiro
- MISTRAL Beamline-Experiments Division, ALBA Synchrotron Light Source, Barcelona, Spain
| | - Klaus Qvortrup
- Core Facility for Integrated Microscopy (CFIM), University of Copenhagen, Copenhagen, Denmark
| | - Thomas Lars Andresen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
24
|
Bachtarzi N, Speciale I, Kharroub K, De Castro C, Ruiz L, Ruas-Madiedo P. Selection of Exopolysaccharide-Producing Lactobacillus Plantarum ( Lactiplantibacillus Plantarum) Isolated from Algerian Fermented Foods for the Manufacture of Skim-Milk Fermented Products. Microorganisms 2020; 8:E1101. [PMID: 32717902 PMCID: PMC7465087 DOI: 10.3390/microorganisms8081101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 01/02/2023] Open
Abstract
The exopolysaccharide (EPS)-producing Lactobacillus plantarum (renamed as Lactiplantibacillus plantarum) LBIO1, LBIO14 and LBIO28 strains, isolated from fermented dairy products typical from Algeria, were characterized to evaluate the impact of the polymers in milk fermentations. Their genomes revealed the presence of two complete eps clusters of the four described for the reference strain WCFS1. Besides, the three strains presented identical sequences of eps3 and eps4 clusters, but LBIO1 and LBIO28 harbour three genes belonging to eps2 which are absent in the LBIO14 genome. The EPS purified from fermented skim-milks manufactured with the strains showed identical nuclear magnetic resonance (1H-NMR) and size exclusion chromatography coupled with a multiangle laser light scattering detector (SEC-MALLS) profiles for polymers LBIO1 and LBIO28, whereas LBIO14 EPS was different due to the lack of the high-molecular weight (HMW)-EPS and the absence of specific monosaccharide's peaks in the anomeric region of its proton NMR spectrum. The presence of the HMW-EPS correlated with optimal sensorial-physical characteristics of the fermented skim-milks (ropy phenotype). Their microstructures, studied by confocal scanning laser microscopy (CSLM), also showed differences in the organization of the casein-network and the distribution of the bacteria inside this matrix. Therefore, the strain LBIO1 can be proposed for the manufacture of dairy products that require high whey retention capability, whereas LBIO28 could be applied to increase the viscosity.
Collapse
Affiliation(s)
- Nadia Bachtarzi
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (N.B.); (L.R.)
- Laboratoire de Recherche Biotechnologie et Qualité des Aliments (BIOQUAL), Institut de la Nutrition, de l’Alimentation et des Technologies Agro Alimentaires (INATAA), Université Frères Mentouri Constantine 1 (UFMC1), Constantine 25017, Algeria;
| | - Immacolata Speciale
- Department of Sciences, University of Naples Federico II, 80126 Napoli, Italy;
| | - Karima Kharroub
- Laboratoire de Recherche Biotechnologie et Qualité des Aliments (BIOQUAL), Institut de la Nutrition, de l’Alimentation et des Technologies Agro Alimentaires (INATAA), Université Frères Mentouri Constantine 1 (UFMC1), Constantine 25017, Algeria;
| | - Cristina De Castro
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (N.B.); (L.R.)
- Group Functionality and Ecology of Beneficial Microbes, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (N.B.); (L.R.)
- Group Functionality and Ecology of Beneficial Microbes, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Asturias, Spain
| |
Collapse
|
25
|
Thirumurthy MA, Hitchcock A, Cereda A, Liu J, Chavez MS, Doss BL, Ros R, El-Naggar MY, Heap JT, Bibby TS, Jones AK. Type IV Pili-Independent Photocurrent Production by the Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 2020; 11:1344. [PMID: 32714295 PMCID: PMC7344198 DOI: 10.3389/fmicb.2020.01344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/26/2020] [Indexed: 11/13/2022] Open
Abstract
Biophotovoltaic devices utilize photosynthetic organisms such as the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis) to generate current for power or hydrogen production from light. These devices have been improved by both architecture engineering and genetic engineering of the phototrophic organism. However, genetic approaches are limited by lack of understanding of cellular mechanisms of electron transfer from internal metabolism to the cell exterior. Type IV pili have been implicated in extracellular electron transfer (EET) in some species of heterotrophic bacteria. Furthermore, conductive cell surface filaments have been reported for cyanobacteria, including Synechocystis. However, it remains unclear whether these filaments are type IV pili and whether they are involved in EET. Herein, a mediatorless electrochemical setup is used to compare the electrogenic output of wild-type Synechocystis to that of a ΔpilD mutant that cannot produce type IV pili. No differences in photocurrent, i.e., current in response to illumination, are detectable. Furthermore, measurements of individual pili using conductive atomic force microscopy indicate these structures are not conductive. These results suggest that pili are not required for EET by Synechocystis, supporting a role for shuttling of electrons via soluble redox mediators or direct interactions between the cell surface and extracellular substrates.
Collapse
Affiliation(s)
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom
| | - Angelo Cereda
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Jiawei Liu
- Department of Physics, Arizona State University, Tempe, AZ, United States
| | - Marko S. Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States
| | - Bryant L. Doss
- Department of Physics, Arizona State University, Tempe, AZ, United States
| | - Robert Ros
- Department of Physics, Arizona State University, Tempe, AZ, United States
| | - Mohamed Y. El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, United States
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
- Department of Chemistry, University of Southern California, Los Angeles, CA, United States
| | - John T. Heap
- Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Thomas S. Bibby
- Ocean and Earth Science, University of Southampton, Southampton, United Kingdom
| | - Anne K. Jones
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| |
Collapse
|
26
|
Tait AW, Gagen EJ, Wilson SA, Tomkins AG, Southam G. Eukaryotic Colonization of Micrometer-Scale Cracks in Rocks: A "Microfluidics" Experiment Using Naturally Weathered Meteorites from the Nullarbor Plain, Australia. ASTROBIOLOGY 2020; 20:364-374. [PMID: 31873039 DOI: 10.1089/ast.2019.2077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The advent of microfluidics has revolutionized the way we understand how microorganisms propagate through microporous spaces. Here, we apply this understanding to the study of how endolithic environmental microorganisms colonize the interiors of sterile rock. The substrates used for our study are stony meteorites from the Nullarbor Plain, Australia; a semiarid limestone karst that provides an ideal setting for preserving meteorites. Periodic flooding of the Nullarbor provides a mechanism by which microorganisms and exogenous nutrients may infiltrate meteorites. Our laboratory experiments show that environmental microorganisms reach depths greater than 400 μm by propagating through existing brecciation, passing through cracks no wider than the diameter of a resident cell (i.e., ∼5 μm). Our observations are consistent with the propagation of these eukaryotic cells via growth and cell division rather than motility. The morphology of the microorganisms changed as a result of propagation through micrometer-scale cracks, as has been observed previously for bacteria on microfluidic chips. It has been suggested that meteorites could have served as preferred habitats for microorganisms on ancient Mars. Based on our results, the depths reached by terrestrial microorganisms within meteorites would be sufficient to mitigate against the harmful effects of ionizing radiation, such as UV light, in Earth's deserts and potentially on Mars, if similar processes of microbial colonization had once been active there. Thus, meteorites landing in ancient lakes on Mars, that later dried out, could have been some of the last inhabited locations on the surface, serving as refugia before the planet's surface became inhospitable. Finally, our observations suggest that terrestrial microorganisms can colonize very fine cracks within meteorites (and potentially spaceships and rovers) on unexpectedly short timescales, with important implications for both recognition of extraterrestrial life in returned geological samples and planetary protection.
Collapse
Affiliation(s)
- Alastair W Tait
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Australia
- Biological and Environmental Sciences, University of Stirling, Stirling, United Kingdom
| | - Emma J Gagen
- School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, Australia
| | - Siobhan A Wilson
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Australia
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Canada
| | - Andrew G Tomkins
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Australia
| | - Gordon Southam
- School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, Australia
| |
Collapse
|
27
|
Kong G, Song D, Guo J, Sun G, Zhu C, Chen F, Yang Y, Xu M. Lack of Periplasmic Non-heme Protein SorA Increases Shewanella decolorationis Current Generation. Front Microbiol 2020; 11:262. [PMID: 32158435 PMCID: PMC7052111 DOI: 10.3389/fmicb.2020.00262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 02/04/2020] [Indexed: 11/13/2022] Open
Abstract
Bacterial extracellular electron transport (EET) plays an important role in many natural and engineering processes. Some periplasmic non-heme redox proteins usually coexist with c-type cytochromes (CTCs) during the EET process. However, in contrast to CTCs, little is known about the roles of these non-heme redox proteins in EET. In this study, the transcriptome of Shewanella decolorationis S12 showed that the gene encoding a periplasmic sulfite dehydrogenase molybdenum-binding subunit SorA was significantly up-regulated during electrode respiration in microbial fuel cells (MFCs) compared with that during azo-dye reduction. The maximum current density of MFCs catalyzed by a mutant strain lacking SorA (ΔsorA) was 25% higher than that of wild strain S12 (20 vs. 16 μA/cm2). Both biofilm formation and the current generation of the anodic biofilms were increased by the disruption of sorA, which suggests that the existence of SorA in S. decolorationis S12 inhibits electrode respiration. In contrast, disruption of sorA had no effect on respiration by S. decolorationis S12 with oxygen, fumarate, azo dye, or ferric citrate as electron acceptors. This is the first report of the specific effect of a periplasmic non-heme redox protein on EET to electrode and provides novel information for enhancing bacterial current generation.
Collapse
Affiliation(s)
- Guannan Kong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Da Song
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Jun Guo
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Guoping Sun
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Chunjie Zhu
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Fusheng Chen
- College of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yonggang Yang
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou, China
| | - Meiying Xu
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| |
Collapse
|
28
|
Igarashi K, Miyako E, Kato S. Direct Interspecies Electron Transfer Mediated by Graphene Oxide-Based Materials. Front Microbiol 2020; 10:3068. [PMID: 32010112 PMCID: PMC6978667 DOI: 10.3389/fmicb.2019.03068] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/19/2019] [Indexed: 11/30/2022] Open
Abstract
Conductive materials are known to promote direct interspecies electron transfer (DIET) by electrically bridging microbial cells. Previous studies have suggested that supplementation of graphene oxide (GO) based materials, including GO, and reduced GO (rGO), to anaerobic microbial communities, can promote DIET. This promotion mechanism is thought to be involved in electron transfer via rGO or biologically formed rGO. However, concrete evidence that rGO directly promotes DIET is still lacking. Furthermore, the effects of the physicochemical properties of GO-based materials on DIET efficiency have not been elucidated. In the current work, we investigated whether chemically and biologically reduced GO compounds can promote DIET in a defined model coculture system, and also examined the effects of surface properties on DIET-promoting efficiency. Supplementation of GO to a defined DIET coculture composed of an ethanol-oxidizing electron producer Geobacter metallireducens and a methane-producing electron consumer Methanosarcina barkeri promoted methane production from ethanol. X-ray photoelectron spectroscopy revealed that GO was reduced to rGO during cultivation by G. metallireducens activity. The stoichiometry of methane production from ethanol and the isotope labeling experiments clearly showed that biologically reduced GO induced DIET-mediated syntrophic methanogenesis. We also assessed the DIET-promoting efficiency of chemically reduced GO and its derivatives, including hydrophilic amine-functionalized rGO (rGO-NH2) and hydrophobic octadecylamine-functionalized rGO (rGO-ODA). While all tested rGO derivatives induced DIET, the rGO derivatives with higher hydrophilicity showed higher DIET-promoting efficiency. Optical microscope observation revealed that microbial cells, in particular, G. metallireducens, more quickly adhered to more hydrophilic GO-based materials. The superior ability to recruit microbial cells is a critical feature of the higher DIET-promoting efficiency of the hydrophilic materials. This study demonstrates that biologically and chemically reduced GO can promote DIET-mediated syntrophic methanogenesis. Our results also suggested that the surface hydrophilicity (i.e., affinity toward microbial cells) is one of the important determinants of the DIET-promoting efficiencies. These observations will provide useful guidance for the selection of conductive particles for the improvement of methanogenesis in anaerobic digesters.
Collapse
Affiliation(s)
- Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
| | - Eijiro Miyako
- Nanomaterials Research Institute, AIST, Tsukuba, Japan
| | - Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan.,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| |
Collapse
|
29
|
Smułek W, Zdarta A, Pacholak A, Runka T, Kaczorek E. Increased biological removal of 1-chloronaphthalene as a result of exposure: A study of bacterial adaptation strategies. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 185:109707. [PMID: 31561078 DOI: 10.1016/j.ecoenv.2019.109707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 09/12/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Effective biodegradation of hydrophobic pollutants, such as 1-chloronaphthalene, is strictly associated with the adaptation of environmental bacteria to their assimilation. This study explores the relation between the modifications of cell properties of bacteria belonging to Pseudomonas and Serratia genera resulting from a 12-month exposure to 1-chloronaphthalene, and their biodegradation efficiency. In the presented study, both bacterial strains exhibited higher (70%) degradation of this compound after exposure compared to unexposed (55%) systems. This adaptation can be associated with increased ratio of polysaccharides in the outer layers of bacterial cells, which was confirmed using infrared spectroscopy analysis. Additionally, the analysis of Raman spectra indicated conformational changes of extracellular carbohydrates from α- to β-anomeric structure. Moreover, the changes in the cell surface hydrophobicity and cell membrane permeability differed between the strains and the Pseudomonas strain exhibited more significant modifications of these parameters. The results suggest that adaptation strategies of both tested strains are different and involve diverse reconstructions of the cell wall and membranes. The results provide a novel and deep insight into the interactions between environmental bacterial strains and chloroaromatic compounds, which opens new perspectives for applying spectrometric methods in investigation of cell adaptation strategies as a result of long-term contact with toxic pollutants.
Collapse
Affiliation(s)
- Wojciech Smułek
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965, Poznań, Poland.
| | - Agata Zdarta
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Amanda Pacholak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Tomasz Runka
- Institute of Materials Research and Quantum Engineering, Poznan University of Technology, Piotrowo 3, 60-965, Poznań, Poland
| | - Ewa Kaczorek
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| |
Collapse
|
30
|
Engel M, Gemünde A, Holtmann D, Müller‐Renno C, Ziegler C, Tippkötter N, Ulber R. Clostridium Acetobutylicum
’s Connecting World: Cell Appendage Formation in Bioelectrochemical Systems. ChemElectroChem 2019. [DOI: 10.1002/celc.201901656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mareike Engel
- Bioprocess EngineeringUniversity of Kaiserslautern 67663 Kaiserslautern Germany
| | - André Gemünde
- Bioprocess EngineeringUniversity of Kaiserslautern 67663 Kaiserslautern Germany
| | - Dirk Holtmann
- Industrial BiotechnologyDECHEMA Research Institute 60486 Frankfurt am Main Germany
| | | | - Christiane Ziegler
- Department of PhysicsUniversity of Kaiserslautern 67663 Kaiserslautern Germany
| | - Nils Tippkötter
- Bioprocess EngineeringUniversity of Applied Science Aachen 52428 Jülich Germany
| | - Roland Ulber
- Bioprocess EngineeringUniversity of Kaiserslautern 67663 Kaiserslautern Germany
| |
Collapse
|
31
|
Silva S, Matz L, Elmassry MM, San Francisco MJ. Characteristics of monolayer formation in vitro by the chytrid Batrachochytrium dendrobatidis. Biofilm 2019; 1:100009. [PMID: 33447796 PMCID: PMC7798445 DOI: 10.1016/j.bioflm.2019.100009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/26/2019] [Accepted: 10/24/2019] [Indexed: 12/01/2022] Open
Abstract
Batrachochytrium dendrobatidis is a globally distributed generalist pathogen that has driven many amphibian populations to extinction. The life cycle of B. dendrobatidis has two main cell types, motile zoospores, and sessile reproductive sporangia. When grown in a nutrient-rich liquid medium, B. dendrobatidis forms aggregates of sporangia that transition into monolayers on surfaces and at the air-liquid interface. Pathogenic microorganisms use biofilms as mechanisms of group interactions to survive under harsh conditions in the absence of a suitable host. We used fluorescent and electron microscopy, crystal violet, transcriptomic, and gas chromatographic analyses to understand the characteristics of B. dendrobatidis monolayers. The cell-free monolayer fraction showed the presence of extracellular ribose, mannose, xylose, galactose, and glucose. Transcriptome analysis showed that 27%, 26%, and 4% of the genes were differentially expressed between sporangia/zoospores, monolayer/zoospores, and sporangia/monolayer pairs respectively. In pond water studies, zoospores developed into sporangia and formed floating aggregates at the air-water interface and attached film on the bottom of growth flasks. We propose that B. dendrobatidis can form surface-attached monolayers in nutrient-rich environments and aggregates of sporangia in nutrient-poor aquatic systems. These monolayers and aggregates may facilitate dispersal and survival of the fungus in the absence of a host. We provide evidence for using a combination of plant-based chemicals, allicin, gingerol, and curcumin as potential anti-chytrid drugs to mitigate chytridiomycosis.
Collapse
Affiliation(s)
- Shalika Silva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Lisa Matz
- Baylor College of Medicine, Houston, TX, USA
| | - Moamen M Elmassry
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | | |
Collapse
|
32
|
Shen H, López-Guerra EA, Zhu R, Diba T, Zheng Q, Solares SD, Zara JM, Shuai D, Shen Y. Visible-Light-Responsive Photocatalyst of Graphitic Carbon Nitride for Pathogenic Biofilm Control. ACS APPLIED MATERIALS & INTERFACES 2019; 11:373-384. [PMID: 30525377 DOI: 10.1021/acsami.8b18543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Pathogenic biofilms raise significant health and economic concerns, because these bacteria are persistent and can lead to long-term infections in vivo and surface contamination in healthcare and industrial facilities or devices. Compared with conventional antimicrobial strategies, photocatalysis holds promise for biofilm control because of its broad-spectrum effectiveness under ambient conditions, low cost, easy operation, and reduced maintenance. In this study, we investigated the performance and mechanism of Staphylococcus epidermidis biofilm control and eradication on the surface of an innovative photocatalyst, graphitic carbon nitride (g-C3N4), under visible-light irradiation, which overcame the need for ultraviolet light for many current photocatalysts (e.g., titanium dioxide (TiO2)). Optical coherence tomography and confocal laser scanning microscopy (CLSM) suggested that g-C3N4 coupons inhibited biofilm development and eradicated mature biofilms under the irradiation of white light-emitting diodes. Biofilm inactivation was observed occurring from the surface toward the center of the biofilms, suggesting that the diffusion of reactive species into the biofilms played a key role. By taking advantage of scanning electron microscopy, CLSM, and atomic force microscopy for biofilm morphology, composition, and mechanical property characterization, we demonstrated that photocatalysis destroyed the integrated and cohesive structure of biofilms and facilitated biofilm eradication by removing the extracellular polymeric substances. Moreover, reactive oxygen species generated during g-C3N4 photocatalysis were quantified via reactions with radical probes and 1O2 was believed to be responsible for biofilm control and removal. Our work highlights the promise of using g-C3N4 for a broad range of antimicrobial applications, especially for the eradication of persistent biofilms under visible-light irradiation, including photodynamic therapy, environmental remediation, food-industry applications, and self-cleaning surface development.
Collapse
|
33
|
Application of Electron Microscopes in Nanotoxicity Assessment. Methods Mol Biol 2018. [PMID: 30547465 DOI: 10.1007/978-1-4939-8916-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In this chapter, we highlight the applications of electron microscopes (EMs) in nanotoxicity assessment. EMs can provide detailed information about the size and morphology of nanomaterials (NMs), their localization in cells and tissues, the nano-bio interactions, as well as the ultrastructural changes induced by NMs exposure. Here, we share with the readers how we prepare the tissue sample, and the different types of EMs used among the nanotoxicologists. It is possible to deploy conventional EMs along or in combination with other analytical techniques, such as electron energy loss spectroscopy (EELS), energy dispersive X-ray spectroscopy (EDS or EDX), and TEM-assisted scanning transmission X-ray microscopy (STXM), toward further elemental and chemical characterization. Appropriate images are inserted to illustrate throughout this chapter.
Collapse
|
34
|
Downie HF, Standerwick JP, Burgess L, Natrajan LS, Lloyd JR. Imaging redox activity and Fe(II) at the microbe-mineral interface during Fe(III) reduction. Res Microbiol 2018; 169:582-589. [DOI: 10.1016/j.resmic.2018.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/23/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
|
35
|
Hrubanova K, Krzyzanek V, Nebesarova J, Ruzicka F, Pilat Z, Samek O. Monitoring Candida parapsilosis and Staphylococcus epidermidis Biofilms by a Combination of Scanning Electron Microscopy and Raman Spectroscopy. SENSORS 2018; 18:s18124089. [PMID: 30469521 PMCID: PMC6308600 DOI: 10.3390/s18124089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 02/03/2023]
Abstract
The biofilm-forming microbial species Candida parapsilosis and Staphylococcus epidermidis have been recently linked to serious infections associated with implanted medical devices. We studied microbial biofilms by high resolution scanning electron microscopy (SEM), which allowed us to visualize the biofilm structure, including the distribution of cells inside the extracellular matrix and the areas of surface adhesion. We compared classical SEM (chemically fixed samples) with cryogenic SEM, which employs physical sample preparation based on plunging the sample into various liquid cryogens, as well as high-pressure freezing (HPF). For imaging the biofilm interior, we applied the freeze-fracture technique. In this study, we show that the different means of sample preparation have a fundamental influence on the observed biofilm structure. We complemented the SEM observations with Raman spectroscopic analysis, which allowed us to assess the time-dependent chemical composition changes of the biofilm in vivo. We identified the individual spectral peaks of the biomolecules present in the biofilm and we employed principal component analysis (PCA) to follow the temporal development of the chemical composition.
Collapse
Affiliation(s)
- Kamila Hrubanova
- Institute of Scientific Instruments of the Czech Academy of Sciences, CZ-61264 Brno, Czech Republic.
| | - Vladislav Krzyzanek
- Institute of Scientific Instruments of the Czech Academy of Sciences, CZ-61264 Brno, Czech Republic.
| | - Jana Nebesarova
- Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic.
| | - Filip Ruzicka
- Department of Microbiology, Faculty of Medicine, Masaryk University and St. Anne's Faculty Hospital, CZ-65691 Brno, Czech Republic.
| | - Zdenek Pilat
- Institute of Scientific Instruments of the Czech Academy of Sciences, CZ-61264 Brno, Czech Republic.
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, CZ-61264 Brno, Czech Republic.
| |
Collapse
|
36
|
Effect of Bioaugmentation on Biogas Yields and Kinetics in Anaerobic Digestion of Sewage Sludge. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081717. [PMID: 30103443 PMCID: PMC6121296 DOI: 10.3390/ijerph15081717] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/01/2018] [Accepted: 08/08/2018] [Indexed: 01/28/2023]
Abstract
Bioaugmentation with a mixture of microorganisms (Bacteria and Archaea) was applied to improve the anaerobic digestion of sewage sludge. The study was performed in reactors operating at a temperature of 35 °C in semi-flow mode. Three runs with different doses of bioaugmenting mixture were conducted. Bioaugmentation of sewage sludge improved fermentation and allowed satisfactory biogas/methane yields and a biodegradation efficiency of more than 46%, despite the decrease in hydraulic retention time (HRT) from 20 d to 16.7 d. Moreover, in terms of biogas production, the rate constant k increased from 0.071 h−1 to 0.087 h−1 as doses of the bioaugmenting mixture were increased, as compared to values of 0.066 h−1 and 0.069 h−1 obtained with sewage sludge alone. Next-generation sequencing revealed that Cytophaga sp. predominated among Bacteria in digesters and that the hydrogenotrophic methanogen Methanoculleus sp. was the most abundant genus among Archaea.
Collapse
|
37
|
Beblawy S, Bursac T, Paquete C, Louro R, Clarke TA, Gescher J. Extracellular reduction of solid electron acceptors by Shewanella oneidensis. Mol Microbiol 2018; 109:571-583. [PMID: 29995975 DOI: 10.1111/mmi.14067] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
Shewanella oneidensis is the best understood model organism for the study of dissimilatory iron reduction. This review focuses on the current state of our knowledge regarding this extracellular respiratory process and highlights its physiologic, regulatory and biochemical requirements. It seems that we have widely understood how respiratory electrons can reach the cell surface and what the minimal set of electron transport proteins to the cell surface is. Nevertheless, even after decades of work in different research groups around the globe there are still several important questions that were not answered yet. In particular, the physiology of this organism, the possible evolutionary benefit of some responses to anoxic conditions, as well as the exact mechanism of electron transfer onto solid electron acceptors are yet to be addressed. The elucidation of these questions will be a great challenge for future work and important for the application of extracellular respiration in biotechnological processes.
Collapse
Affiliation(s)
- Sebastian Beblawy
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Thea Bursac
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany
| | - Catarina Paquete
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Ricardo Louro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Av. da República-EAN, Oeiras, 2780-157, Portugal
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (CS), Karlsruhe, Germany.,Institute for Biological Interfaces, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| |
Collapse
|
38
|
Cole JK, Morton BR, Cardamone HC, Lake HRR, Dohnalkova AC, Kim YM, Kyle JE, Maezato Y, Dana KL, Metz TO, Romine MF, Nelson WC, Lindemann SR. Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae. Int J Syst Evol Microbiol 2018; 68:2116-2123. [PMID: 29855404 DOI: 10.1099/ijsem.0.002807] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
There was an error in the proposed genus name in the published article, in that the genus 'Salinivirga' was effectively published while this article was in review. Therefore, the genus 'Salinivirga' should be replaced with 'Saliniramus'. For the convenience of future readers, we have included the complete corrected article below, in which all occurrences of the incorrect genus name have been amended: A halophilic bacterial strain, HL-109T, was isolated from the unicyanobacterial consortium UCC-O, which was obtained from the photosynthetic mat of Hot Lake (Washington, USA). A polyphasic approach using phenotypic, genotypic and chemotaxonomic data was used to classify the strain within the order Rhizobiales. The organism stained Gram-negative and was a moderate thermophile with a growth optimum of 45 °C. It was obligately aerobic, heterotrophic and halophilic, growing in both NaCl and MgSO4 brines. The novel isolate had a polymorphic cellular morphology of short rods with occasional branching, and cells were monotrichous. The major fatty acids detected were C18 : 1, C18 : 0, C16 : 0 and C18 : cyc. Phylogenetic analysis of the 16S rRNA gene placed the strain in the order Rhizobiales and it shared 94 % identity with the type strain of its nearest relative, Salinarimonas ramus. Morphological, chemotaxonomic and phylogenetic results did not affiliate the novel organism with any of the families in the Rhizobiales; therefore, HL-109T is representative of a new lineage, for which the name Saliniramus fredricksonii gen. nov., sp. nov. is proposed, with the type strain HL-109T (=JCM 31876T=DSM 102886T). In addition, examination of the phylogenetics of strain HL-109T and its nearest relatives, Salinarimonas ramus and Salinarimonasrosea, demonstrates that these halophiles form a clade distinct from the described families of the Rhizobiales. We further propose the establishment of a new family, Salinarimonadaceae fam. nov., to accommodate the genera Saliniramus and Salinarimonas (the type genus of the family).
Collapse
Affiliation(s)
- Jessica K Cole
- Scientific and Computing Operations, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.,Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Beau R Morton
- Risk and Decision Sciences, Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.,Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hayley C Cardamone
- Present address: Center for Infectious Disease Research, Seattle, WA, USA.,Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hannah R R Lake
- Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Alice C Dohnalkova
- Environmental Dynamics and Simulations, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.,Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Young-Mo Kim
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yukari Maezato
- Present address: U.S. Naval Research Laboratory, Washington, DC, USA.,Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl L Dana
- Present address: Nova Research, Inc., Alexandria, VA, USA.,Chemical, Biological, and Physical Sciences Division, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas O Metz
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Margaret F Romine
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - William C Nelson
- Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephen R Lindemann
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA.,Biological Sciences Division, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.,Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
39
|
Salinivirga fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from a photosynthetic mat, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae. Int J Syst Evol Microbiol 2018; 68:1591-1598. [DOI: 10.1099/ijsem.0.002715] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
40
|
Hrubanova K, Nebesarova J, Ruzicka F, Krzyzanek V. The innovation of cryo-SEM freeze-fracturing methodology demonstrated on high pressure frozen biofilm. Micron 2018; 110:28-35. [PMID: 29715620 DOI: 10.1016/j.micron.2018.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/18/2018] [Accepted: 04/19/2018] [Indexed: 11/30/2022]
Abstract
In this study we present an innovative method for the preparation of fully hydrated samples of microbial biofilms of cultures Staphylococcus epidermidis, Candida parapsilosis and Candida albicans. Cryo-scanning electron microscopy (cryo-SEM) and high-pressure freezing (HPF) rank among cutting edge techniques in the electron microscopy of hydrated samples such as biofilms. However, the combination of these techniques is not always easily applicable. Therefore, we present a method of combining high-pressure freezing using EM PACT2 (Leica Microsystems), which fixes hydrated samples on small sapphire discs, with a high resolution SEM equipped with the widely used cryo-preparation system ALTO 2500 (Gatan). Using a holder developed in house, a freeze-fracturing technique was applied to image and investigate microbial cultures cultivated on the sapphire discs. In our experiments, we focused on the ultrastructure of the extracellular matrix produced during cultivation and the relationships among microbial cells in the biofilm. The main goal of our investigations was the detailed visualization of areas of the biofilm where the microbial cells adhere to the substrate/surface. We show the feasibility of this technique, which is clearly demonstrated in experiments with various freeze-etching times.
Collapse
Affiliation(s)
- Kamila Hrubanova
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jana Nebesarova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Filip Ruzicka
- Department of Microbiology, Faculty of Medicine, Masaryk University and St. Anne's Faculty Hospital, Brno, Czech Republic
| | - Vladislav Krzyzanek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic.
| |
Collapse
|
41
|
Edwards MJ, White GF, Lockwood CW, Lawes MC, Martel A, Harris G, Scott DJ, Richardson DJ, Butt JN, Clarke TA. Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners. J Biol Chem 2018; 293:8103-8112. [PMID: 29636412 PMCID: PMC5971433 DOI: 10.1074/jbc.ra118.001850] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/19/2018] [Indexed: 11/06/2022] Open
Abstract
Many subsurface microorganisms couple their metabolism to the reduction or oxidation of extracellular substrates. For example, anaerobic mineral-respiring bacteria can use external metal oxides as terminal electron acceptors during respiration. Porin-cytochrome complexes facilitate the movement of electrons generated through intracellular catabolic processes across the bacterial outer membrane to these terminal electron acceptors. In the mineral-reducing model bacterium Shewanella oneidensis MR-1, this complex is composed of two decaheme cytochromes (MtrA and MtrC) and an outer-membrane β-barrel (MtrB). However, the structures and mechanisms by which porin-cytochrome complexes transfer electrons are unknown. Here, we used small-angle neutron scattering (SANS) to study the molecular structure of the transmembrane complexes MtrAB and MtrCAB. Ab initio modeling of the scattering data yielded a molecular envelope with dimensions of ∼105 × 60 × 35 Å for MtrAB and ∼170 × 60 × 45 Å for MtrCAB. The shapes of these molecular envelopes suggested that MtrC interacts with the surface of MtrAB, extending ∼70 Å from the membrane surface and allowing the terminal hemes to interact with both MtrAB and an extracellular acceptor. The data also reveal that MtrA fully extends through the length of MtrB, with ∼30 Å being exposed into the periplasm. Proteoliposome models containing membrane-associated MtrCAB and internalized small tetraheme cytochrome (STC) indicate that MtrCAB could reduce Fe(III) citrate with STC as an electron donor, disclosing a direct interaction between MtrCAB and STC. Taken together, both structural and proteoliposome experiments support porin-cytochrome-mediated electron transfer via periplasmic cytochromes such as STC.
Collapse
Affiliation(s)
- Marcus J Edwards
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Gaye F White
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Colin W Lockwood
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Matthew C Lawes
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Anne Martel
- Institut Laue-Langevin, 38042 Grenoble, France
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire OX11 0FA, United Kingdom
| | - David J Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire OX11 0FA, United Kingdom; ISIS Spallation Neutron and Muon Source, Rutherford Appleton Laboratory, Oxfordshire OX11 0QX, United Kingdom; School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - David J Richardson
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Julea N Butt
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Thomas A Clarke
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences and School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom.
| |
Collapse
|
42
|
Ultrastructure of Shewanella oneidensis MR-1 nanowires revealed by electron cryotomography. Proc Natl Acad Sci U S A 2018; 115:E3246-E3255. [PMID: 29555764 DOI: 10.1073/pnas.1718810115] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial nanowires have garnered recent interest as a proposed extracellular electron transfer (EET) pathway that links the bacterial electron transport chain to solid-phase electron acceptors away from the cell. Recent studies showed that Shewanella oneidensis MR-1 produces outer membrane (OM) and periplasmic extensions that contain EET components and hinted at their possible role as bacterial nanowires. However, their fine structure and distribution of cytochrome electron carriers under native conditions remained unclear, making it difficult to evaluate the potential electron transport (ET) mechanism along OM extensions. Here, we report high-resolution images of S. oneidensis OM extensions, using electron cryotomography (ECT). We developed a robust method for fluorescence light microscopy imaging of OM extension growth on electron microscopy grids and used correlative light and electron microscopy to identify and image the same structures by ECT. Our results reveal that S. oneidensis OM extensions are dynamic chains of interconnected outer membrane vesicles (OMVs) with variable dimensions, curvature, and extent of tubulation. Junction densities that potentially stabilize OMV chains are seen between neighboring vesicles in cryotomograms. By comparing wild type and a cytochrome gene deletion mutant, our ECT results provide the likely positions and packing of periplasmic and outer membrane proteins consistent with cytochromes. Based on the observed cytochrome packing density, we propose a plausible ET path along the OM extensions involving a combination of direct hopping and cytochrome diffusion. A mean-field calculation, informed by the observed ECT cytochrome density, supports this proposal by revealing ET rates on par with a fully packed cytochrome network.
Collapse
|
43
|
|
44
|
Hynninen A, Külaviir M, Kirsimäe K. Air-drying is sufficient pre-treatment for in situ visualization of microbes on minerals with scanning electron microscopy. J Microbiol Methods 2018; 146:77-82. [PMID: 29428739 DOI: 10.1016/j.mimet.2018.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/26/2018] [Accepted: 02/07/2018] [Indexed: 11/29/2022]
Abstract
Scanning electron microscopy (SEM) is a powerful tool for observing microbe-mineral interactions in situ. Despite its wide usage in geomicrobiology there is no consensus on how the samples should be handled before visualizing in SEM. We compared response of artificial laboratory-grown bacterial community and natural in situ microbes on terrestrial basalt to different sample pre-treatment methods with the aim to preserve microbe-mineral interaction interface. Air-drying was the only method that maintained the location of loosely attached bacteria on a mineral surface, whereas chemical fixation and drying dislocated the cells. On the contrary, chemical fixation preserved the cellular morphology while air-drying caused the collapse of most of the laboratory-grown cells. Natural microbial communities on dry terrestrial basalt were composed of desiccation resistant microbes which remained attached to the surface and partially maintained their morphology regardless of the sample pre-treatment method. None of the tested methods allowed visualization of microbe-mineral interface in a biofilm. We suggest air-drying as a main sample pre-treatment method for visualizing microbes on mineral surfaces when loss of morphology is secondary to potentially dislocated cells and to potential chemical changes in the sample caused by the chemical fixation reagents.
Collapse
Affiliation(s)
- Anu Hynninen
- Department of Geology, University of Tartu, Tartu, Estonia; Department of Geography and Geology, University of Turku, Turku, Finland.
| | | | - Kalle Kirsimäe
- Department of Geology, University of Tartu, Tartu, Estonia
| |
Collapse
|
45
|
Hernandez-Cerdan P, Mansel BW, Leis A, Lundin L, Williams MA. Structural Analysis of Polysaccharide Networks by Transmission Electron Microscopy: Comparison with Small-Angle X-ray Scattering. Biomacromolecules 2018; 19:989-995. [DOI: 10.1021/acs.biomac.7b01773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pablo Hernandez-Cerdan
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
- Riddet Insitute, Palmerston North, New Zealand
| | - Bradley W. Mansel
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Andrew Leis
- Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Leif Lundin
- RISE, Agrifood and Bioscience, Gothenburg, Sweden
| | - Martin A.K. Williams
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| |
Collapse
|
46
|
Fakra SC, Luef B, Castelle CJ, Mullin SW, Williams KH, Marcus MA, Schichnes D, Banfield JF. Correlative Cryogenic Spectromicroscopy to Investigate Selenium Bioreduction Products. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:503-512. [PMID: 26371540 DOI: 10.1021/acs.est.5b01409] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Accurate mapping of the composition and structure of minerals and associated biological materials is critical in geomicrobiology and environmental research. Here, we have developed an apparatus that allows the correlation of cryogenic transmission electron microscopy (cryo-TEM) and synchrotron hard X-ray microprobe (SHXM) data sets to precisely determine the distribution, valence state, and structure of selenium in biofilms sampled from a contaminated aquifer near Rifle, CO. Results were replicated in the laboratory via anaerobic selenate-reducing enrichment cultures. 16S rRNA analyses of field-derived biofilm indicated the dominance of Betaproteobacteria from the Comamonadaceae family and uncultivated members of the Simplicispira genus. The major product in field and culture-derived biofilms is ∼25-300 nm red amorphous Se0 aggregates of colloidal nanoparticles. Correlative analyses of the cultures provided direct evidence for the microbial dissimilatory reduction of Se(VI) to Se(IV) to Se0. Extended X-ray absorption fine-structure spectroscopy showed red amorphous Se0 with a first shell Se-Se interatomic distance of 2.339 ± 0.003 Å. Complementary scanning transmission X-ray microscopy revealed that these aggregates are strongly associated with a protein-rich biofilm matrix. These findings have important implications for predicting the stability and mobility of Se bioremediation products and understanding of Se biogeochemical cycling. The approach, involving the correlation of cryo-SHXM and cryo-TEM data sets from the same specimen area, is broadly applicable to biological and environmental samples.
Collapse
Affiliation(s)
- Sirine C Fakra
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Birgit Luef
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Cindy J Castelle
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Sean W Mullin
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Kenneth H Williams
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Matthew A Marcus
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Denise Schichnes
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| | - Jillian F Banfield
- Department of Earth and Planetary Science and ‡Department of Plant & Microbial Biology, University of California , Berkeley, California 94720, United States
- Advanced Light Source and ∥Earth Sciences Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States
| |
Collapse
|
47
|
Electron microscopic observations of prokaryotic surface appendages. J Microbiol 2017; 55:919-926. [DOI: 10.1007/s12275-017-7369-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 12/21/2022]
|
48
|
Mokwatlo SC, Nicol W. Structure and cell viability analysis of Actinobacillus succinogenes biofilms as biocatalysts for succinic acid production. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
49
|
Okamoto K, Miyazaki N, Song C, Maia FRNC, Reddy HKN, Abergel C, Claverie JM, Hajdu J, Svenda M, Murata K. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. Sci Rep 2017; 7:13291. [PMID: 29038566 PMCID: PMC5643343 DOI: 10.1038/s41598-017-13390-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/22/2017] [Indexed: 12/23/2022] Open
Abstract
The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter. These particles show significant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo-tomography (cryo-ET) and energy-filtered cryo-EM. We detected a previously undescribed low-density outer layer covering the tegument and a periodical structuring of the fibres in the striated apical cork. Energy-filtered Zernike phase-contrast cryo-EM images show distinct substructures inside the particles, implicating an internal compartmentalisation. The density of the interior volume of Pithovirus particles is three quarters lower than that of the Mimivirus. However, it is remarkably high given that the 600 kbp Pithovirus genome is only half the size of the Mimivirus genome and is packaged in a volume up to 100 times larger. These observations suggest that the interior is densely packed with macromolecules in addition to the genomic nucleic acid.
Collapse
Affiliation(s)
- Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
| | - Naoyuki Miyazaki
- National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan
| | - Chihong Song
- National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Hemanth K N Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Chantal Abergel
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, 13288, France
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, 13288, France.,Assistance Publique des Hôpitaux de Marseille. La Timone, 13005, Marseille, France
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.,Institute of Physics AS CR, v.v.i., Na Slovance 2, 18221, Prague 8, Czech Republic
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan.
| |
Collapse
|
50
|
Komorek R, Wei W, Yu X, Hill E, Yao J, Zhu Z, Yu XY. In Situ Characterization of Shewanella oneidensis MR1 Biofilms by SALVI and ToF-SIMS. J Vis Exp 2017. [PMID: 28872139 DOI: 10.3791/55944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial biofilms are surface-associated communities that are vastly studied to understand their self-produced extracellular polymeric substances (EPS) and their roles in environmental microbiology. This study outlines a method to cultivate biofilm attachment to the System for Analysis at the Liquid Vacuum Interface (SALVI) and achieve in situ chemical mapping of a living biofilm by time-of-flight secondary ion mass spectrometry (ToF-SIMS). This is done through the culturing of bacteria both outside and within the SALVI channel with our specialized setup, as well as through optical imaging techniques to detect the biofilm presence and thickness before ToF-SIMS analysis. Our results show the characteristic peaks of the Shewanella biofilm in its natural hydrated state, highlighting upon its localized water cluster environment, as well as EPS fragments, which are drastically different from the same biofilm's dehydrated state. These results demonstrate the breakthrough capability of SALVI that allows for in situ biofilm imaging with a vacuum-based chemical imaging instrument.
Collapse
Affiliation(s)
- Rachel Komorek
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory
| | - Wenchao Wei
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory
| | - Xiaofei Yu
- Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Eric Hill
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory
| | - Juan Yao
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory
| | - Zihua Zhu
- Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Xiao-Ying Yu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory;
| |
Collapse
|