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Xu M, Selvaraj GK, Lu H. Environmental sporobiota: Occurrence, dissemination, and risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161809. [PMID: 36702282 DOI: 10.1016/j.scitotenv.2023.161809] [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: 11/22/2022] [Revised: 01/03/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Spore-forming bacteria known as sporobiota are widespread in diverse environments from terrestrial and aquatic habitats to industrial and healthcare systems. Studies on sporobiota have been mainly focused on food processing and clinical fields, while a large amount of sporobiota exist in natural environments. Due to their persistence and capabilities of transmitting virulence factors and antibiotic resistant genes, environmental sporobiota could pose significant health risks to humans. These risks could increase as global warming and environmental pollution has altered the life cycle of sporobiota. This review summarizes the current knowledge of environmental sporobiota, including their occurrence, characteristics, and functions. An interaction network among clinical-, food-related, and environment-related sporobiota is constructed. Recent and effective methods for detecting and disinfecting environmental sporobiota are also discussed. Key problems and future research needs for better understanding and reducing the risks of environmental sporobiota and sporobiome are proposed.
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Affiliation(s)
- Min Xu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ganesh-Kumar Selvaraj
- Department of Microbiology, St. Peter's Institute of Higher Education and Research, Chennai 600054, Tamil Nadu, India.
| | - Huijie Lu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang, China.
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2
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Romanowicz KJ, Kling GW. Summer thaw duration is a strong predictor of the soil microbiome and its response to permafrost thaw in arctic tundra. Environ Microbiol 2022; 24:6220-6237. [PMID: 36135820 PMCID: PMC10092252 DOI: 10.1111/1462-2920.16218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023]
Abstract
Climate warming has increased permafrost thaw in arctic tundra and extended the duration of annual thaw (number of thaw days in summer) along soil profiles. Predicting the microbial response to permafrost thaw depends largely on knowing how increased thaw duration affects the composition of the soil microbiome. Here, we determined soil microbiome composition from the annually thawed surface active layer down through permafrost from two tundra types at each of three sites on the North Slope of Alaska, USA. Variations in soil microbial taxa were found between sites up to ~90 km apart, between tundra types, and between soil depths. Microbiome differences at a site were greatest across transitions from thawed to permafrost depths. Results from correlation analysis based on multi-decadal thaw surveys show that differences in thaw duration by depth were significantly, positively correlated with the abundance of dominant taxa in the active layer and negatively correlated with dominant taxa in the permafrost. Microbiome composition within the transition zone was statistically similar to that in the permafrost, indicating that recent decades of intermittent thaw have not yet induced a shift from permafrost to active-layer microbes. We suggest that thaw duration rather than thaw frequency has a greater impact on the composition of microbial taxa within arctic soils.
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Affiliation(s)
- Karl J Romanowicz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - George W Kling
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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3
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Gittins DA, Desiage PA, Morrison N, Rattray JE, Bhatnagar S, Chakraborty A, Zorz J, Li C, Horanszky O, Cramm MA, Bisiach F, Bennett R, Webb J, MacDonald A, Fowler M, Campbell DC, Hubert CRJ. Geological processes mediate a microbial dispersal loop in the deep biosphere. SCIENCE ADVANCES 2022; 8:eabn3485. [PMID: 36026445 PMCID: PMC9417182 DOI: 10.1126/sciadv.abn3485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy and survival at theoretical energy minima are hallmarks of microbial physiology in the subsurface, ecological processes such as dispersal and selection in the deep biosphere remain poorly understood. We investigated the biogeography of dispersing bacteria in the deep sea where upward hydrocarbon seepage was confirmed by acoustic imagery and geochemistry. Thermophilic endospores in the permanently cold seabed correlated with underlying seep conduits reveal geofluid-facilitated cell migration pathways originating in deep petroleum-bearing sediments. Endospore genomes highlight adaptations to life in anoxic petroleum systems and bear close resemblance to oil reservoir microbiomes globally. Upon transport out of the subsurface, viable thermophilic endospores reenter the geosphere by sediment burial, enabling germination and environmental selection at depth where new petroleum systems establish. This microbial dispersal loop circulates living biomass in and out of the deep biosphere.
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Affiliation(s)
- Daniel A. Gittins
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
- Corresponding author.
| | | | - Natasha Morrison
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Canada
| | - Jayne E. Rattray
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Srijak Bhatnagar
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | | | - Jackie Zorz
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Carmen Li
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Oliver Horanszky
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Margaret A. Cramm
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Francesco Bisiach
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Robbie Bennett
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Canada
| | - Jamie Webb
- Applied Petroleum Technology, Calgary, Canada
| | - Adam MacDonald
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Canada
| | | | - D. Calvin Campbell
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Canada
| | - Casey R. J. Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
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4
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Chakraborty A, Rattray JE, Drake SS, Matthews S, Li C, Jørgensen BB, Hubert CRJ. Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples. Front Microbiol 2022; 13:958417. [PMID: 36033870 PMCID: PMC9411986 DOI: 10.3389/fmicb.2022.958417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially mediated processes in a given habitat tend to be catalyzed by abundant populations that are ecologically adapted to exploit specific environmental characteristics. Typically, metabolic activities of rare populations are limited but may be stimulated in response to acute environmental stressors. Community responses to sudden changes in temperature and pressure can include suppression and activation of different populations, but these dynamics remain poorly understood. The permanently cold ocean floor hosts countless low-abundance microbes including endospores of thermophilic bacteria. Incubating sediments at high temperature resuscitates viable spores, causing the proliferation of bacterial populations. This presents a tractable system for investigating changes in a microbiome's community structure in response to dramatic environmental perturbations. Incubating permanently cold Arctic fjord sediments at 50°C for 216 h with and without volatile fatty acid amendment provoked major changes in community structure. Germination of thermophilic spores from the sediment rare biosphere was tracked using mass spectrometry-based metabolomics, radiotracer-based sulfate reduction rate measurements, and high-throughput 16S rRNA gene sequencing. Comparing community similarity at different intervals of the incubations showed distinct temporal shifts in microbial populations, depending on organic substrate amendment. Metabolite patterns indicated that amino acids and other sediment-derived organics were decomposed by fermentative Clostridia within the first 12–48 h. This fueled early and late phases of exponential increases in sulfate reduction, highlighting the cross-feeding of volatile fatty acids as electron donors for different sulfate-reducing Desulfotomaculia populations. The succession of germinated endospores triggered by sudden exposure to high temperature and controlled by nutrient availability offers a model for understanding the ecological response of dormant microbial communities following major environmental perturbations.
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Affiliation(s)
- Anirban Chakraborty
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- *Correspondence: Anirban Chakraborty
| | - Jayne E. Rattray
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Sienna S. Drake
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Stuart Matthews
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Bo Barker Jørgensen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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5
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Corona Ramírez A, Cailleau G, Fatton M, Dorador C, Junier P. Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco. Front Microbiol 2022; 13:826117. [PMID: 36687602 PMCID: PMC9847572 DOI: 10.3389/fmicb.2022.826117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/07/2022] [Indexed: 01/25/2023] Open
Abstract
The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.
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Affiliation(s)
- Andrea Corona Ramírez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mathilda Fatton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Cristina Dorador
- Department of Biotechnology, University of Antofagasta, Antofagasta, Chile
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland,*Correspondence: Pilar Junier,
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6
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Manirakiza B, Zhang S, Addo FG, Isabwe A, Nsabimana A. Exploring microbial diversity and ecological function of epiphytic and surface sediment biofilm communities in a shallow tropical lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:151821. [PMID: 34808175 DOI: 10.1016/j.scitotenv.2021.151821] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities in epiphytic biofilms and surface sediments play a vital role in the biogeochemical cycles of the major chemical elements in freshwater. However, little is known about the diversity, composition, and ecological functions of microbial communities in shallow tropical lakes dominated by aquatic macrophytes. In this study, epiphytic bacterial and eukaryotic biofilm communities on submerged and floating macrophytes and surface sediments were investigated in Lake Rumira, Rwanda in August and November 2019. High-throughput sequencing data revealed that members of the phyla, including Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, Chloroflexi, Bacteriodetes, Verrumicrobia, and Myxomycota, dominated bacterial communities, while the microeukaryotic communities were dominated by Unclassified (uncl) SAR(Stramenopiles, Alveolata, Rhizaria), Rotifers, Ascomycota, Gastrotricha, Platyhelminthes, Chloroplastida, and Arthropoda. Interestingly, the eukaryotic OTUs (operational taxonomic units) number and Shannon indices were significantly higher in sediments and epiphytic biofilms on Eicchornia crassipes than Ceratophyllum demersum (p < 0.05), while no differences were observed in bacterial OTUs number and Shannon values among substrates. Redundancy analysis (RDA) showed that water temperature, pH, dissolved oxygen (DO), total nitrogen (TN), and electrical conductivity (EC) were the most important abiotic factors closely related to the microbial community on C. demersum and E. crassipes. Furthermore, co-occurrence networks analysis (|r| > 0.7, p < 0.05) and functional prediction revealed more complex interactions among microbes on C. demersum than on E. crassipes and sediments, and those interactions include cross-feeding, parasitism, symbiosis, and predatism among organisms in biofilms. These results suggested that substrate-type and environmental factors were the strong driving forces of microbial diversity in epiphytic biofilms and surface sediments, thus shedding new insights into microbial community diversity in epiphytic biofilms and surface sediments and its ecological role in tropical lacustrine ecosystems.
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Affiliation(s)
- Benjamin Manirakiza
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China; University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
| | - Felix Gyawu Addo
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Antoine Nsabimana
- University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
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7
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Rattray JE, Chakraborty A, Li C, Elizondo G, John N, Wong M, Radović JR, Oldenburg TBP, Hubert CRJ. Sensitive quantification of dipicolinic acid from bacterial endospores in soils and sediments. Environ Microbiol 2020; 23:1397-1406. [PMID: 33264453 PMCID: PMC8048543 DOI: 10.1111/1462-2920.15343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 11/30/2020] [Indexed: 11/27/2022]
Abstract
Endospore-forming bacteria make up an important and numerically significant component of microbial communities in a range of settings including soils, industry, hospitals and marine sediments extending into the deep subsurface. Bacterial endospores are non-reproductive structures that protect DNA and improve cell survival during periods unfavourable for bacterial growth. An important determinant of endospores withstanding extreme environmental conditions is 2,6-pyridine dicarboxylic acid (i.e. dipicolinic acid, or DPA), which contributes heat resistance. This study presents an improved HPLC-fluorescence method for DPA quantification using a single 10-min run with pre-column Tb3+ chelation. Relative to existing DPA quantification methods, specific improvements pertain to sensitivity, detection limit and range, as well as the development of new free DPA and spore-specific DPA proxies. The method distinguishes DPA from intact and recently germinated spores, enabling responses to germinants in natural samples or experiments to be assessed in a new way. DPA-based endospore quantification depends on accurate spore-specific DPA contents, in particular, thermophilic spores are shown to have a higher DPA content, meaning that marine sediments with plentiful thermophilic spores may require spore number estimates to be revisited. This method has a wide range of potential applications for more accurately quantifying bacterial endospores in diverse environmental samples.
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Affiliation(s)
- Jayne E Rattray
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Anirban Chakraborty
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Gretta Elizondo
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Nisha John
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Michelle Wong
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
| | - Jagoš R Radović
- Department of Geoscience, University of Calgary, Calgary, T2N 1N4, Canada
| | | | - Casey R J Hubert
- Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
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8
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Nurul AAN, Danish-Daniel AM, Okomoda VT, Asma NA. Microbiota composition of captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839). Appl Microbiol Biotechnol 2020; 104:7391-7407. [PMID: 32676710 DOI: 10.1007/s00253-020-10781-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/02/2020] [Accepted: 07/07/2020] [Indexed: 01/09/2023]
Abstract
The Labroides dimidiatus is one of the most traded marine ornamental fishes worldwide, yet not much is known about the microflora associated with this fish. This study is designed to investigate the bacteria composition associated with captive L. dimidiatus and its surrounding aquarium water. The fish and carriage water were obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Bacteria present on the skin and in the stomach and the aquarium water were enumerated using culture-independent approaches and next-generation sequencing (NGS) technology. A total of 3,238,564 valid reads and 828 total operational taxonomic units (OTUs) were obtained from the three metagenomic libraries using NGS analysis. Of all the 15 phyla identified in this study, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most prevalent in all samples. Also, 170 families belonging to 36 bacteria classes were identified. Although many of the bacteria families were common in the skin, gut, and aquarium water (39%), about 26% of the families were exclusive to the aquarium water alone. Therefore, any substantial change in the structure and abundance of microbiota (especially pathogenic bacteria) reported in this study may serve as an early sign for disease infection in the species under captivity. KEY POINTS: • Proteobacteria was the most dominant. • The microbiota was either shared or exclusively in samples.
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Affiliation(s)
- Ahmad Ashyikin Noor Nurul
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | | | - Victor Tosin Okomoda
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Department of Fisheries and Aquaculture, University of Agriculture Makurdi, PMB, 2373, Makurdi, Benue State, Nigeria.
| | - Nur Ariffin Asma
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
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9
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Dead or alive: sediment DNA archives as tools for tracking aquatic evolution and adaptation. Commun Biol 2020; 3:169. [PMID: 32265485 PMCID: PMC7138834 DOI: 10.1038/s42003-020-0899-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
DNA can be preserved in marine and freshwater sediments both in bulk sediment and in intact, viable resting stages. Here, we assess the potential for combined use of ancient, environmental, DNA and timeseries of resurrected long-term dormant organisms, to reconstruct trophic interactions and evolutionary adaptation to changing environments. These new methods, coupled with independent evidence of biotic and abiotic forcing factors, can provide a holistic view of past ecosystems beyond that offered by standard palaeoecology, help us assess implications of ecological and molecular change for contemporary ecosystem functioning and services, and improve our ability to predict adaptation to environmental stress. Ellegaard et al. discuss the potential for using ancient environmental DNA (eDNA), combined with resurrection ecology, to analyse trophic interactions and evolutionary adaptation to changing environments. Their Review suggests that these techniques will improve our ability to predict genetic and phenotypic adaptation to environmental stress.
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10
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Diarrhoeal events can trigger long-term Clostridium difficile colonization with recurrent blooms. Nat Microbiol 2020; 5:642-650. [PMID: 32042128 DOI: 10.1038/s41564-020-0668-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/07/2020] [Indexed: 11/08/2022]
Abstract
Although Clostridium difficile is widely considered an antibiotic- and hospital-associated pathogen, recent evidence indicates that this is an insufficient depiction of the risks and reservoirs. A common thread that links all major risk factors of infection is their association with gastrointestinal disturbances, but this relationship to C. difficile colonization has never been tested directly. Here, we show that disturbances caused by diarrhoeal events trigger susceptibility to C. difficile colonization. Using survey data of the human gut microbiome, we detected C. difficile colonization and blooms in people recovering from food poisoning and Vibrio cholerae infections. Carriers remained colonized for year-long time scales and experienced highly variable patterns of C. difficile abundance, where increased shedding over short periods of 1-2 d interrupted week-long periods in which C. difficile was undetectable. Given that short shedding events were often linked to gastrointestinal disturbances, our results help explain why C. difficile is frequently detected as a co-infecting pathogen in patients with diarrhoea. To directly test the impact of diarrhoea on susceptibility to colonization, we developed a mouse model of variable disturbance intensity, which allowed us to monitor colonization in the absence of disease. As mice exposed to avirulent C. difficile spores ingested increasing quantities of laxatives, more individuals experienced C. difficile blooms. Our results indicate that the likelihood of colonization is highest in the days immediately following acute disturbances, suggesting that this could be an important window during which transmission could be interrupted and the incidence of infection lowered.
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11
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Liddicoat C, Sydnor H, Cando-Dumancela C, Dresken R, Liu J, Gellie NJC, Mills JG, Young JM, Weyrich LS, Hutchinson MR, Weinstein P, Breed MF. Naturally-diverse airborne environmental microbial exposures modulate the gut microbiome and may provide anxiolytic benefits in mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 701:134684. [PMID: 31704402 DOI: 10.1016/j.scitotenv.2019.134684] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 05/14/2023]
Abstract
Growing epidemiological evidence links natural green space exposure with a range of health benefits, including for mental health. Conversely, greater urbanisation associates with increased risk of mental health disorders. Microbiomes are proposed as an important but understudied link that may help explain many green space-human health associations. However, there remains a lack of controlled experimental evidence testing possible beneficial effects from passive exposure to natural biodiversity via airborne microbiota. Previous mouse model studies have used unrealistic environmental microbial exposures-including excessive soil and organic matter contact, feed supplements and injections-to demonstrate host microbiota, immune biomarker, and behavioural changes. Here, in a randomised controlled experiment, we demonstrate that realistic exposures to trace-level dust from a high biodiversity soil can change mouse gut microbiota, in comparison to dust from low biodiversity soil or no soil (control) (n = 54 total mice, comprising 3 treatments × 18 mice, with 9 females + 9 males per group). Furthermore, we found a nominal soil-derived anaerobic spore-forming butyrate-producer, Kineothrix alysoides, was supplemented to a greater extent in the gut microbiomes of high biodiversity treatment mice. Also, increasing relative abundance of this rare organism correlated with reduced anxiety-like behaviour in the most anxious mice. Our results point to an intriguing new hypothesis: that biodiverse soils may represent an important supplementary source of butyrate-producing bacteria capable of resupplying the mammalian gut microbiome, with potential for gut health and mental health benefits. Our findings have potential to inform cost-effective population health interventions through microbiome-conscious green space design and, ultimately, the mainstreaming of biodiversity into health care.
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Affiliation(s)
- Craig Liddicoat
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Harrison Sydnor
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Christian Cando-Dumancela
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Romy Dresken
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jiajun Liu
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia 5005, Australia; Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Nicholas J C Gellie
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jacob G Mills
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jennifer M Young
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia; College of Science and Engineering, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia 5005, Australia; Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mark R Hutchinson
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia 5005, Australia; Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Philip Weinstein
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Martin F Breed
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia; College of Science and Engineering, Flinders University, Bedford Park, South Australia 5042, Australia.
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12
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Cupit C, Lomstein BA, Kjeldsen KU. Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:352-360. [PMID: 30043505 DOI: 10.1111/1758-2229.12679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 07/09/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Bacterial endospores are highly abundant in marine sediments, but their taxonomic identity and ecology is largely unknown. We selectively extracted DNA from endospores and vegetative cells and sequenced 16S rRNA genes to characterize the composition of the endospore and vegetative Firmicutes communities in the sediment and water column of Aarhus Bay (Denmark). The endospore community in the sediment was dominated by the families Bacillaceae, Lachnospiraceae, Clostridiaceae and Ruminoccocaceae. These families were also represented in the vegetative community in the sediment and the endospore community in the water column. OTUs of high relative abundance in the endospore community were also represented in the vegetative Firmicutes community. Other OTUs were exclusively found in the endospore communities. This suggests that endospores accumulate in marine sediments due to passive deposition from the water column and sporulation of vegetative cells in the sediment. Some OTUs were detected in the endospore community of the water column and the vegetative community the sediment indicating that endospores deposited from the water column may germinate upon burial/deposition in the sediment. We provide novel insight into the composition of endospore communities in marine sediments and highlight their role in microbial dispersal and as a seed bank in subsurface sediments.
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Affiliation(s)
- Carina Cupit
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bente Aagaard Lomstein
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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15
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Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence. Appl Environ Microbiol 2019; 85:AEM.02646-18. [PMID: 30683748 PMCID: PMC6585489 DOI: 10.1128/aem.02646-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/21/2019] [Indexed: 01/31/2023] Open
Abstract
Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains. Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost. IMPORTANCE Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.
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Wörmer L, Hoshino T, Bowles MW, Viehweger B, Adhikari RR, Xiao N, Uramoto GI, Könneke M, Lazar CS, Morono Y, Inagaki F, Hinrichs KU. Microbial dormancy in the marine subsurface: Global endospore abundance and response to burial. SCIENCE ADVANCES 2019; 5:eaav1024. [PMID: 30801015 PMCID: PMC6382399 DOI: 10.1126/sciadv.aav1024] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/11/2019] [Indexed: 05/19/2023]
Abstract
Marine sediments host an unexpectedly large microbial biosphere, suggesting unique microbial mechanisms for surviving burial and slow metabolic turnover. Although dormancy is generally considered an important survival strategy, its specific role in subsurface sediments remains unclear. We quantified dormant bacterial endospores in 331 marine sediment samples from diverse depositional types and geographical origins. The abundance of endospores relative to vegetative cells increased with burial depth and endospores became dominant below 25 m, with an estimated population of 2.5 × 1028 to 1.9 × 1029 endospores in the uppermost kilometer of sediment and a corresponding biomass carbon of 4.6 to 35 Pg surpassing that of vegetative cells. Our data further identify distinct endospore subgroups with divergent resistance to burial and aging. Endospores may shape the deep biosphere by providing a core population for colonization of new habitats and/or through low-frequency germination to sustain slow growth in this environment.
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Affiliation(s)
- Lars Wörmer
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
- Corresponding author.
| | - Tatsuhiko Hoshino
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
| | | | - Bernhard Viehweger
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Rishi R. Adhikari
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Nan Xiao
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
| | - Go-ichiro Uramoto
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Center for Advanced Marine Core Research, Kochi University, Kochi 783-8502, Japan
| | - Martin Könneke
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
| | - Cassandre S. Lazar
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
- Department of Biological Sciences, Université du Québec à Montréal (UQAM), Montreal, Quebec H3C 3P8, Canada
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
| | - Fumio Inagaki
- Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi 783-8502, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama 236-0001, Japan
| | - Kai-Uwe Hinrichs
- MARUM—Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, 28359 Bremen, Germany
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Paul C, Filippidou S, Jamil I, Kooli W, House GL, Estoppey A, Hayoz M, Junier T, Palmieri F, Wunderlin T, Lehmann A, Bindschedler S, Vennemann T, Chain PSG, Junier P. Bacterial spores, from ecology to biotechnology. ADVANCES IN APPLIED MICROBIOLOGY 2018; 106:79-111. [PMID: 30798805 DOI: 10.1016/bs.aambs.2018.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The production of a highly specialized cell structure called a spore is a remarkable example of a survival strategy displayed by bacteria in response to challenging environmental conditions. The detailed analysis and description of the process of sporulation in selected model organisms have generated a solid background to understand the cellular processes leading to the formation of this specialized cell. However, much less is known regarding the ecology of spore-formers. This research gap needs to be filled as the feature of resistance has important implications not only on the survival of spore-formers and their ecology, but also on the use of spores for environmental prospection and biotechnological applications.
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Affiliation(s)
- Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sevasti Filippidou
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Isha Jamil
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Wafa Kooli
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mathilda Hayoz
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Tina Wunderlin
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Anael Lehmann
- Laboratory of stable isotope geochemistry, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Torsten Vennemann
- Laboratory of stable isotope geochemistry, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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Paul C, Bayrychenko Z, Junier T, Filippidou S, Beck K, Bueche M, Greub G, Bürgmann H, Junier P. Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater. PeerJ 2018; 6:e4989. [PMID: 29942682 PMCID: PMC6015491 DOI: 10.7717/peerj.4989] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/27/2018] [Indexed: 12/14/2022] Open
Abstract
Aquatic ecosystems serve as a dissemination pathway and a reservoir of both antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARG). In this study, we investigate the role of the bacterial sporobiota to act as a vector for ARG dispersal in aquatic ecosystems. The sporobiota was operationally defined as the resilient fraction of the bacterial community withstanding a harsh extraction treatment eliminating the easily lysed fraction of the total bacterial community. The sporobiota has been identified as a critical component of the human microbiome, and therefore potentially a key element in the dissemination of ARG in human-impacted environments. A region of Lake Geneva in which the accumulation of ARG in the sediments has been previously linked to the deposition of treated wastewater was selected to investigate the dissemination of tet(W) and sul1, two genes conferring resistance to tetracycline and sulfonamide, respectively. Analysis of the abundance of these ARG within the sporobiome (collection of genes of the sporobiota) and correlation with community composition and environmental parameters demonstrated that ARG can spread across the environment with the sporobiota being the dispersal vector. A highly abundant OTU affiliated with the genus Clostridium was identified as a potential specific vector for the dissemination of tet(W), due to a strong correlation with tet(W) frequency (ARG copy numbers/ng DNA). The high dispersal rate, long-term survival, and potential reactivation of the sporobiota constitute a serious concern in terms of dissemination and persistence of ARG in the environment.
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Affiliation(s)
- Christophe Paul
- Institute of Biology, Laboratory of Microbiology, University of Neuchatel, Neuchâtel, NE, Switzerland
| | - Zhanna Bayrychenko
- Institute of Biology, Laboratory of Microbiology, University of Neuchatel, Neuchâtel, NE, Switzerland
| | - Thomas Junier
- Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sevasti Filippidou
- Institute of Biology, Laboratory of Microbiology, University of Neuchatel, Neuchâtel, NE, Switzerland
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Matthieu Bueche
- Institute of Biology, Laboratory of Microbiology, University of Neuchatel, Neuchâtel, NE, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital Center, University of Lausanne, Lausanne, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Pilar Junier
- Institute of Biology, Laboratory of Microbiology, University of Neuchatel, Neuchâtel, NE, Switzerland
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Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota. ISME JOURNAL 2018; 12:2403-2416. [PMID: 29899513 DOI: 10.1038/s41396-018-0192-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/20/2018] [Accepted: 03/27/2018] [Indexed: 12/21/2022]
Abstract
Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endospores in situ and how sporulation varies across individuals and over time. Here we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.
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Thermophilic endospores associated with migrated thermogenic hydrocarbons in deep Gulf of Mexico marine sediments. ISME JOURNAL 2018; 12:1895-1906. [PMID: 29599524 PMCID: PMC6052102 DOI: 10.1038/s41396-018-0108-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/16/2018] [Accepted: 03/12/2018] [Indexed: 12/31/2022]
Abstract
Dormant endospores of thermophilic bacteria (thermospores) can be detected in cold marine sediments following high-temperature incubation. Thermospores in the cold seabed may be explained by a dispersal history originating in deep biosphere oil reservoir habitats where upward migration of petroleum fluids at hydrocarbon seeps transports viable cells into the overlying ocean. We assessed this deep-to-shallow dispersal hypothesis through geochemical and microbiological analyses of 111 marine sediments from the deep water Eastern Gulf of Mexico. GC-MS and fluorescence confirmed the unambiguous presence of thermogenic hydrocarbons in 71 of these locations, indicating seepage from deeply sourced petroleum in the subsurface. Heating each sediment to 50 °C followed by 16S rRNA gene sequencing revealed several thermospores with a cosmopolitan distribution throughout the study area, as well as thermospores that were more geographically restricted. Among the thermospores having a more limited distribution, 12 OTUs from eight different lineages were repeatedly detected in sediments containing thermogenic hydrocarbons. A subset of these were significantly correlated with hydrocarbons (p < 0.05) and most closely related to Clostridiales previously detected in oil reservoirs from around the world. This provides evidence of bacteria in the ocean being dispersed out of oil reservoirs, and suggests that specific thermospores may be used as model organisms for studying warm-to-cold transmigration in the deep sea.
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21
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Madueño L, Paul C, Junier T, Bayrychenko Z, Filippidou S, Beck K, Greub G, Bürgmann H, Junier P. A historical legacy of antibiotic utilization on bacterial seed banks in sediments. PeerJ 2018; 6:e4197. [PMID: 29312823 PMCID: PMC5756452 DOI: 10.7717/peerj.4197] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/05/2017] [Indexed: 12/31/2022] Open
Abstract
The introduction of antibiotics for both medical and non-medical purposes has had a positive effect on human welfare and agricultural output in the past century. However, there is also an important ecological legacy regarding the use of antibiotics and the consequences of increased levels of these compounds in the environment as a consequence of their use and disposal. This legacy was investigated by quantifying two antibiotic resistance genes (ARG) conferring resistance to tetracycline (tet(W)) and sulfonamide (sul1) in bacterial seed bank DNA in sediments. The industrial introduction of antibiotics caused an abrupt increase in the total abundance of tet(W) and a steady increase in sul1. The abrupt change in tet(W) corresponded to an increase in relative abundance from ca. 1960 that peaked around 1976. This pattern of accumulation was highly correlated with the abundance of specific members of the seed bank community belonging to the phylum Firmicutes. In contrast, the relative abundance of sul1 increased after 1976. This correlated with a taxonomically broad spectrum of bacteria, reflecting sul1 dissemination through horizontal gene transfer. The accumulation patterns of both ARGs correspond broadly to the temporal scale of medical antibiotic use. Our results show that the bacterial seed bank can be used to look back at the historical usage of antibiotics and resistance prevalence.
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Affiliation(s)
- Laura Madueño
- Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchâtel, NE, Switzerland
| | - Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchâtel, NE, Switzerland
| | - Thomas Junier
- Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zhanna Bayrychenko
- Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchâtel, NE, Switzerland
| | - Sevasti Filippidou
- Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchâtel, NE, Switzerland
| | - Karin Beck
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchatel, Neuchâtel, NE, Switzerland
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Hu A, Ju F, Hou L, Li J, Yang X, Wang H, Mulla SI, Sun Q, Bürgmann H, Yu CP. Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community. Environ Microbiol 2017; 19:4993-5009. [DOI: 10.1111/1462-2920.13942] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Feng Ju
- Department of Surface Waters-Research and Management; Eawag, Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum 6047 Switzerland
| | - Liyuan Hou
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Jiangwei Li
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Xiaoyong Yang
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Hongjie Wang
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Sikandar I. Mulla
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Qian Sun
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
| | - Helmut Bürgmann
- Department of Surface Waters-Research and Management; Eawag, Swiss Federal Institute of Aquatic Science and Technology; Kastanienbaum 6047 Switzerland
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion; Institute of Urban Environment Chinese Academy of Sciences; Xiamen 361021 China
- Graduate Institute of Environmental Engineering; National Taiwan University; Taipei 106 Taiwan
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Fecal microbiota of lambs fed purple prairie clover (Dalea purpurea Vent.) and alfalfa (Medicago sativa). Arch Microbiol 2017; 200:137-145. [PMID: 28864945 DOI: 10.1007/s00203-017-1427-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 06/30/2017] [Accepted: 08/22/2017] [Indexed: 12/18/2022]
Abstract
The present study assessed the effect of purple prairie clover (PPC) and PPC condensed tannins (CT) on the fecal microbiota of lambs using high-throughput 16S rRNA gene pyrosequencing. A total of 18 individual lambs were randomly divided into three groups and fed either green chop alfalfa (Alf), a 40:60 (DM basis; Mix) mixture of Alf and PPC, or Mix supplemented with polyethylene glycol (Mix-P) for 18 days. Fecal samples were collected on days 13 through 18 using digital rectal retrieval. The DNA of fecal samples was extracted and the microbial 16S rRNA gene amplicons were sequenced using 454 pyrosequencing. Regardless of diet, the bacterial community was dominated by Firmicutes and Bacteroidetes with many sequences unclassified at the genus level. Forage type and CT had no effect on the fecal microbial composition at the phylum level or on α-diversity. Compared to the Alf diet, the Mix diet reduced the relative abundance of Akkermansia (P = 0.03) and Asteroleplasma (P = 0.05). Fecal microbial populations in Alf and Mix-P clustered separately from each other when assessed using unweighted UniFrac (P < 0.05). These results indicate that PPC CT up to 36 g/kg DM in the diet had no major effect on fecal microbial flora at the phyla level and exerted only minor effects on the genera composition of fecal microbiota in lambs.
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Okpala GN, Chen C, Fida T, Voordouw G. Effect of Thermophilic Nitrate Reduction on Sulfide Production in High Temperature Oil Reservoir Samples. Front Microbiol 2017; 8:1573. [PMID: 28900416 PMCID: PMC5581841 DOI: 10.3389/fmicb.2017.01573] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/03/2017] [Indexed: 01/25/2023] Open
Abstract
Oil fields can experience souring, the reduction of sulfate to sulfide by sulfate-reducing microorganisms. At the Terra Nova oil field near Canada's east coast, with a reservoir temperature of 95°C, souring was indicated by increased hydrogen sulfide in produced waters (PW). Microbial community analysis by 16S rRNA gene sequencing showed the hyperthermophilic sulfate-reducing archaeon Archaeoglobus in Terra Nova PWs. Growth enrichments in sulfate-containing media at 55-70°C with lactate or volatile fatty acids yielded the thermophilic sulfate-reducing bacterium (SRB) Desulfotomaculum. Enrichments at 30-45°C in nitrate-containing media indicated the presence of mesophilic nitrate-reducing bacteria (NRB), which reduce nitrate without accumulation of nitrite, likely to N2. Thermophilic NRB (tNRB) of the genera Marinobacter and Geobacillus were detected and isolated at 30-50°C and 40-65°C, respectively, and only reduced nitrate to nitrite. Added nitrite strongly inhibited the isolated thermophilic SRB (tSRB) and tNRB and SRB could not be maintained in co-culture. Inhibition of tSRB by nitrate in batch and continuous cultures required inoculation with tNRB. The results suggest that nitrate injected into Terra Nova is reduced to N2 at temperatures up to 45°C but to nitrite only in zones from 45 to 65°C. Since the hotter zones of the reservoir (65-80°C) are inhabited by thermophilic and hyperthermophilic sulfate reducers, souring at these temperatures might be prevented by nitrite production if nitrate-reducing zones of the system could be maintained at 45-65°C.
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Affiliation(s)
- Gloria N. Okpala
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
| | - Chuan Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of TechnologyHarbin, China
| | - Tekle Fida
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
| | - Gerrit Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, CalgaryAB, Canada
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Reim A, Hernández M, Klose M, Chidthaisong A, Yuttitham M, Conrad R. Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand. Front Microbiol 2017; 8:785. [PMID: 28529503 PMCID: PMC5418361 DOI: 10.3389/fmicb.2017.00785] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Rice paddies in central Thailand are flooded either by irrigation (irrigated rice) or by rain (rain-fed rice). The paddy soils and their microbial communities thus experience permanent or arbitrary submergence, respectively. Since methane production depends on anaerobic conditions, we hypothesized that structure and function of the methanogenic microbial communities are different in irrigated and rain-fed paddies and react differently upon desiccation stress. We determined rates and relative proportions of hydrogenotrophic and aceticlastic methanogenesis before and after short-term drying of soil samples from replicate fields. The methanogenic pathway was determined by analyzing concentrations and δ13C of organic carbon and of CH4 and CO2 produced in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also determined the abundance (qPCR) of genes and transcripts of bacterial 16S rRNA, archaeal 16S rRNA and methanogenic mcrA (coding for a subunit of the methyl coenzyme M reductase) and the composition of these microbial communities by T-RFLP fingerprinting and/or Illumina deep sequencing. The abundances of genes and transcripts were similar in irrigated and rain-fed paddy soil. They also did not change much upon desiccation and rewetting, except the transcripts of mcrA, which increased by more than two orders of magnitude. In parallel, rates of CH4 production also increased, in rain-fed soil more than in irrigated soil. The contribution of hydrogenotrophic methanogenesis increased in rain-fed soil and became similar to that in irrigated soil. However, the relative microbial community composition on higher taxonomic levels was similar between irrigated and rain-fed soil. On the other hand, desiccation and subsequent anaerobic reincubation resulted in systematic changes in the composition of microbial communities for both Archaea and Bacteria. It is noteworthy that differences in the community composition were mostly detected on the level of operational taxonomic units (OTUs; 97% sequence similarity). The treatments resulted in change of the relative abundance of several archaeal OTUs. Some OTUs of Methanobacterium, Methanosaeta, Methanosarcina, Methanocella and Methanomassiliicoccus increased, while some of Methanolinea and Methanosaeta decreased. Bacterial OTUs within Firmicutes, Cyanobacteria, Planctomycetes and Deltaproteobacteria increased, while OTUs within other proteobacterial classes decreased.
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Affiliation(s)
- Andreas Reim
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Marcela Hernández
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany.,Centre for Biological Sciences, University of SouthamptonSouthampton, UK
| | - Melanie Klose
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Amnat Chidthaisong
- Joint Graduate School of Energy and Environment, King Mongkut's University of Technology ThonburiBangkok, Thailand
| | - Monthira Yuttitham
- Faculty of Environment and Resource Studies, Mahidol UniversitySalaya, Thailand
| | - Ralf Conrad
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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Fang H, Chen Y, Huang L, He G. Analysis of biofilm bacterial communities under different shear stresses using size-fractionated sediment. Sci Rep 2017; 7:1299. [PMID: 28465599 PMCID: PMC5431010 DOI: 10.1038/s41598-017-01446-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/30/2017] [Indexed: 12/21/2022] Open
Abstract
Microorganisms are ubiquitous in aqueous environments and are crucial for biogeochemical processes, but their community structures and functions remain poorly understood. In this paper, a rotating reactor was designed to study the effects of substrata and flow conditions on sediment bacterial communities using 16S rRNA gene sequencing, assaying three groups of size-fractionated sediments and three different levels of applied shear stress. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla of the microbial communities, with more anaerobic bacteria and opportunistic pathogens being detected under static water conditions, while more aerobic bacteria were detected under dynamic water flow conditions. Most of the top 10 genera were present in all the samples; however, there were significant differences in the species abundance. Paludibacter and Comamonadaceae_unclassified were the most abundant genera under static and dynamic conditions, respectively. Under static water conditions, the medium-grained sediment had the highest microbial diversity, followed by the fine and coarse sediments. Under dynamic water flow conditions, a higher flow velocity corresponded to a greater microbial diversity. Overall, there was no significant difference in the community richness or diversity between the static and dynamic water flow conditions. This study is beneficial for further understanding the heterogeneities of microbial communities in natural aquatic ecosystems.
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Affiliation(s)
- Hongwei Fang
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China
| | - Yishan Chen
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China
| | - Lei Huang
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China.
| | - Guojian He
- State Key Laboratory of Hydro-science and Engineering, Department of Hydraulic Engineering, Tsinghua University, Beijing, 100084, China
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Volpi M, Lomstein BA, Sichert A, Røy H, Jørgensen BB, Kjeldsen KU. Identity, Abundance, and Reactivation Kinetics of Thermophilic Fermentative Endospores in Cold Marine Sediment and Seawater. Front Microbiol 2017; 8:131. [PMID: 28220111 PMCID: PMC5292427 DOI: 10.3389/fmicb.2017.00131] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/18/2017] [Indexed: 11/23/2022] Open
Abstract
Cold marine sediments harbor endospores of fermentative and sulfate-reducing, thermophilic bacteria. These dormant populations of endospores are believed to accumulate in the seabed via passive dispersal by ocean currents followed by sedimentation from the water column. However, the magnitude of this process is poorly understood because the endospores present in seawater were so far not identified, and only the abundance of thermophilic sulfate-reducing endospores in the seabed has been quantified. We investigated the distribution of thermophilic fermentative endospores (TFEs) in water column and sediment of Aarhus Bay, Denmark, to test the role of suspended dispersal and determine the rate of endospore deposition and the endospore abundance in the sediment. We furthermore aimed to determine the time course of reactivation of the germinating TFEs. TFEs were induced to germinate and grow by incubating pasteurized sediment and water samples anaerobically at 50°C. We observed a sudden release of the endospore component dipicolinic acid immediately upon incubation suggesting fast endospore reactivation in response to heating. Volatile fatty acids (VFAs) and H2 began to accumulate exponentially after 3.5 h of incubation showing that reactivation was followed by a short phase of outgrowth before germinated cells began to divide. Thermophilic fermenters were mainly present in the sediment as endospores because the rate of VFA accumulation was identical in pasteurized and non-pasteurized samples. Germinating TFEs were identified taxonomically by reverse transcription, PCR amplification and sequencing of 16S rRNA. The water column and sediment shared the same phylotypes, thereby confirming the potential for seawater dispersal. The abundance of TFEs was estimated by most probable number enumeration, rates of VFA production, and released amounts of dipicolinic acid during germination. The surface sediment contained ∼105-106 inducible TFEs cm-3. TFEs thus outnumber thermophilic sulfate-reducing endospores by an order of magnitude. The abundance of cultivable TFEs decreased exponentially with sediment depth with a half-life of 350 years. We estimate that 6 × 109 anaerobic thermophilic endospores are deposited on the seafloor per m2 per year in Aarhus Bay, and that these thermophiles represent >10% of the total endospore community in the surface sediment.
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Affiliation(s)
- Marta Volpi
- Center for Geomicrobiology, Department of Bioscience, Aarhus UniversityAarhus, Denmark
| | | | | | | | | | - Kasper U. Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus UniversityAarhus, Denmark
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Ji Y, Angel R, Klose M, Claus P, Marotta H, Pinho L, Enrich-Prast A, Conrad R. Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. Environ Microbiol 2016; 18:5082-5100. [PMID: 27507000 DOI: 10.1111/1462-2920.13491] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/06/2016] [Indexed: 11/28/2022]
Abstract
Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity.
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Affiliation(s)
- Yang Ji
- Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science & Technology, Ningliu Road 219, Nanjing, 210044, China.,Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Peter Claus
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Humberto Marotta
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Graduated Program in Geosciences (Geochemistry), Graduated Program in Geography, Research Center on Biomass and Water Management (NAB/UFF), Sedimentary Environmental Processes Laboratory (LAPSA/UFF), International Laboratory of Global Change (LINC-Global), Fluminense Federal University (UFF), Niterói, Brazil
| | - Luana Pinho
- Department of Chemical Oceanography, Rio de Janeiro State University, Pavilhão João Lyra Filho, sala 4008 Bloco E, Rua São Francisco Xavier, 524, Maracanã-RJ, 20550-900, Brazil
| | - Alex Enrich-Prast
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Department of Environmental Change, Linköping University, Linköping, Sweden
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
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Wunderlin T, Ferrari B, Power M. Global and local-scale variation in bacterial community structure of snow from the Swiss and Australian Alps. FEMS Microbiol Ecol 2016; 92:fiw132. [PMID: 27297721 DOI: 10.1093/femsec/fiw132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2016] [Indexed: 11/13/2022] Open
Abstract
Seasonally, snow environments cover up to 50% of the land's surface, yet the microbial diversity and ecosystem functioning within snow, particularly from alpine regions are not well described. This study explores the bacterial diversity in snow using next-generation sequencing technology. Our data expand the global inventory of snow microbiomes by focusing on two understudied regions, the Swiss Alps and the Australian Alps. A total biomass similar to cell numbers in polar snow was detected, with 5.2 to 10.5 × 10(3) cells mL(-1) of snow. We found that microbial community structure of surface snow varied by country and site and along the altitudinal range (alpine and sub-alpine). The bacterial communities present were diverse, spanning 25 distinct phyla, but the six phyla Proteobacteria (Alpha- and Betaproteobacteria), Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Firmicutes, accounted for 72%-98% of the total relative abundance. Taxa such as Acidobacteriaceae and Methylocystaceae, associated with cold soils, may be part of the atmospherically sourced snow community, while families like Sphingomonadaceae were detected in every snow sample and are likely part of the common snow biome.
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Affiliation(s)
- Tina Wunderlin
- Department of Biological Sciences, Macquarie University, Sydney 2109, NSW, Australia Molecular Ecology, Institute for Sustainability Sciences, Agroscope, Zurich, Switzerland
| | - Belinda Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Randwick, Sydney 2052, NSW, Australia
| | - Michelle Power
- Department of Biological Sciences, Macquarie University, Sydney 2109, NSW, Australia
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30
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Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DG, Jørgensen BB, Stepanauskas R, Reinhardt R, Schramm A, Loy A, Adrian L. Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling. mBio 2016; 7:e00266-16. [PMID: 27143384 PMCID: PMC4959651 DOI: 10.1128/mbio.00266-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/05/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi The presence of genes encoding dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences were affiliated with the DEH Dsr clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH species. DEH-C11 also harbored genes encoding reductases for arsenate, dimethyl sulfoxide, and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate that this RdhA may not be a terminal reductase. The presence of other genes indicated that nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognized role in sulfur cycling and reveal the potential for expanded catabolic and respiratory functions among subsurface DEH. IMPORTANCE Sediments underlying our oceans are inhabited by microorganisms in cell numbers similar to those estimated to inhabit the oceans. Microorganisms in sediments consist of various diverse and uncharacterized groups that contribute substantially to global biogeochemical cycles. Since most subsurface microorganisms continue to evade cultivation, possibly due to very slow growth, we obtained and analyzed genomic information from a representative of one of the most widespread and abundant, yet uncharacterized bacterial groups of the marine subsurface. We describe several key features that may contribute to their widespread distribution, such as respiratory flexibility and the potential to use oxidized sulfur compounds, which are abundant in marine environments, as electron acceptors. Together, these data provide important information that can be used to assist in designing enrichment strategies or other postgenomic studies, while also improving our understanding of the diversity and distribution of dsrAB genes, which are widely used functional marker genes for sulfur-cycling microbes.
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Affiliation(s)
- Kenneth Wasmund
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Myriel Cooper
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Lars Schreiber
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Karen G Lloyd
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Brett J Baker
- Department of Marine Science, University of Texas-Austin, Marine Science Institute, Port Aransas, Texas, USA
| | - Dorthe G Petersen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | | | | | - Andreas Schramm
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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31
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More RP, Purohit HJ. The Identification of Discriminating Patterns from 16S rRNA Gene to Generate Signature for Bacillus Genus. J Comput Biol 2016; 23:651-61. [PMID: 27104769 DOI: 10.1089/cmb.2016.0002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The 16S ribosomal RNA (16S rRNA) gene has been widely used for the taxonomic classification of bacteria. A molecular signature is a set of nucleotide patterns, which constitute a regular expression that is specific to each particular taxon. Our main goal was to identify discriminating nucleotide patterns in 16S rRNA gene and then to generate signatures for taxonomic classification. To demonstrate our approach, we used the phylum Firmicutes as a model using representative taxa Bacilli (class), Bacillales (order), Bacillaceae (family), and Bacillus (genus), according to their dominance at each hierarchical taxonomic level. We applied combined composite vector and multiple sequence alignment approaches to generate gene-specific signatures. Further, we mapped all the patterns into the different hypervariable regions of 16S rRNA gene and confirmed the most appropriate distinguishing region as V3-V4 for targeted taxa. We also examined the evolution in discriminating patterns of signatures across taxonomic levels. We assessed the comparative classification accuracy of signatures with other methods (i.e., RDP Classifier, KNN, and SINA). Results revealed that the signatures for taxa Bacilli, Bacillales, Bacillaceae, and Bacillus could correctly classify isolate sequences with sensitivity of 0.99, 0.97, 0.94, and 0.89, respectively, and specificity close to 0.99. We developed signature-based software DNA Barcode Identification (DNA BarID) for taxonomic classification that is available at website http://www.neeri.res.in/DNA_BarID.htm . This pattern-based study provides a deeper understanding of taxon-specific discriminating patterns in 16S rRNA gene with respect to taxonomic classification.
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Affiliation(s)
- Ravi P More
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute , Nagpur, Maharashtra, India
| | - Hemant J Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute , Nagpur, Maharashtra, India
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32
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Wunderlin T, Junier T, Paul C, Jeanneret N, Junier P. Physical Isolation of Endospores from Environmental Samples by Targeted Lysis of Vegetative Cells. J Vis Exp 2016:e53411. [PMID: 26863128 DOI: 10.3791/53411] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Endospore formation is a survival strategy found among some bacteria from the phylum Firmicutes. During endospore formation, these bacteria enter a morpho-physiological resting state that enhances survival under adverse environmental conditions. Even though endospore-forming Firmicutes are one of the most frequently enriched and isolated bacterial groups in culturing studies, they are often absent from diversity studies based on molecular methods. The resistance of the spore core is considered one of the factors limiting the recovery of DNA from endospores. We developed a method that takes advantage of the higher resistance of endospores to separate them from other cells in a complex microbial community using physical, enzymatic and chemical lysis methods. The endospore-only preparation thus obtained can be used for re-culturing or to perform downstream analysis such as tailored DNA extraction optimized for endospores and subsequent DNA sequencing. This method, applied to sediment samples, has allowed the enrichment of endospores and after sequencing, has revealed a large diversity of endospore-formers in freshwater lake sediments. We expect that the application of this method to other samples will yield a similar outcome.
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Affiliation(s)
| | | | | | | | - Pilar Junier
- Laboratory of Microbiology, University of Neuchatel;
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33
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Ozgun H, Tao Y, Ersahin ME, Zhou Z, Gimenez JB, Spanjers H, van Lier JB. Impact of temperature on feed-flow characteristics and filtration performance of an upflow anaerobic sludge blanket coupled ultrafiltration membrane treating municipal wastewater. WATER RESEARCH 2015; 83:71-83. [PMID: 26141423 DOI: 10.1016/j.watres.2015.06.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 06/15/2015] [Accepted: 06/20/2015] [Indexed: 06/04/2023]
Abstract
The objective of this study was to assess the operational feasibility of an anaerobic membrane bioreactor (AnMBR), consisting of an upflow anaerobic sludge blanket (UASB) reactor coupled to an ultrafiltration membrane unit, at two operational temperatures (25°C and 15°C) for the treatment of municipal wastewater. The results showed that membrane fouling at 15°C was more severe than that at 25°C. Higher chemical oxygen demand (COD) and soluble microbial products (SMP) concentrations, lower mean particle diameter, and higher turbidity in the UASB effluent at lower temperature aggravated membrane fouling compared to the 25°C operation. However, the overall AnMBR treatment performance was not significantly affected by temperature, which was attributed to the physical membrane barrier. Cake resistance was found responsible for over 40% of the total fouling in both cases. However, an increase was observed in the contribution of pore blocking resistance at 15°C related to the larger amount of fine particles in the UASB effluent compared to 25°C. Based on the overall results, it is concluded that an AnMBR, consisting of a UASB coupled membrane unit, is not found technically feasible for the treatment of municipal wastewater at 15°C, considering the rapid deterioration of the filtration performance.
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Affiliation(s)
- Hale Ozgun
- Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600 GA Delft, The Netherlands; Istanbul Technical University, Civil Engineering Faculty, Environmental Engineering Department, Ayazaga Campus, Maslak, 34469 Istanbul, Turkey.
| | - Yu Tao
- Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600 GA Delft, The Netherlands; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Mustafa Evren Ersahin
- Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600 GA Delft, The Netherlands; Istanbul Technical University, Civil Engineering Faculty, Environmental Engineering Department, Ayazaga Campus, Maslak, 34469 Istanbul, Turkey
| | - Zhongbo Zhou
- Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600 GA Delft, The Netherlands; School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Juan B Gimenez
- Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600 GA Delft, The Netherlands; Departament d'Enginyeria Quimica, Escola Tecnica Superior d'Enginyeria, Universitat de Valencia, Avda. De la Universitat s/n, 46100 Burjassot, Valencia, Spain
| | - Henri Spanjers
- Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600 GA Delft, The Netherlands
| | - Jules B van Lier
- Department of Water Management, Section Sanitary Engineering, Delft University of Technology, PO Box 5048, 2600 GA Delft, The Netherlands
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Under-detection of endospore-forming Firmicutes in metagenomic data. Comput Struct Biotechnol J 2015; 13:299-306. [PMID: 25973144 PMCID: PMC4427659 DOI: 10.1016/j.csbj.2015.04.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/06/2015] [Accepted: 04/18/2015] [Indexed: 11/24/2022] Open
Abstract
Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methods of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group (spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches. Endospore formers were under-detected by profile analysis of sporulation genes in metagenomes. Endospore formers were absent even from those habitats known to harbor them. A tailored DNA extraction method improved detection in amplicon sequencing. Ameliorated DNA extraction did not improve shotgun classification. Endospore-formers represent an undetectable community fraction by metagenomic approaches.
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35
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O'Sullivan LA, Roussel EG, Weightman AJ, Webster G, Hubert CRJ, Bell E, Head I, Sass H, Parkes RJ. Survival of Desulfotomaculum spores from estuarine sediments after serial autoclaving and high-temperature exposure. THE ISME JOURNAL 2015; 9:922-33. [PMID: 25325382 PMCID: PMC4817712 DOI: 10.1038/ismej.2014.190] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/06/2014] [Accepted: 08/16/2014] [Indexed: 11/24/2022]
Abstract
Bacterial spores are widespread in marine sediments, including those of thermophilic, sulphate-reducing bacteria, which have a high minimum growth temperature making it unlikely that they grow in situ. These Desulfotomaculum spp. are thought to be from hot environments and are distributed by ocean currents. Their cells and spores upper temperature limit for survival is unknown, as is whether they can survive repeated high-temperature exposure that might occur in hydrothermal systems. This was investigated by incubating estuarine sediments significantly above (40-80 °C) maximum in situ temperatures (∼ 23 °C), and with and without prior triple autoclaving. Sulphate reduction occurred at 40-60 °C and at 60 °C was unaffected by autoclaving. Desulfotomaculum sp. C1A60 was isolated and was most closely related to the thermophilic D. kuznetsovii(T) (∼ 96% 16S rRNA gene sequence identity). Cultures of Desulfotomaculum sp. C1A60, D. kuznetsovii(T)and D. geothermicum B2T survived triple autoclaving while other related Desulfotomaculum spp. did not, although they did survive pasteurisation. Desulfotomaculum sp. C1A60 and D. kuznetsovii cultures also survived more extreme autoclaving (C1A60, 130 °C for 15 min; D. kuznetsovii, 135 °C for 15 min, maximum of 154 °C reached) and high-temperature conditions in an oil bath (C1A60, 130° for 30 min, D. kuznetsovii 140 °C for 15 min). Desulfotomaculum sp. C1A60 with either spores or predominantly vegetative cells demonstrated that surviving triple autoclaving was due to spores. Spores also had very high culturability compared with vegetative cells (∼ 30 × higher). Combined extreme temperature survival and high culturability of some thermophilic Desulfotomaculum spp. make them very effective colonisers of hot environments, which is consistent with their presence in subsurface geothermal waters and petroleum reservoirs.
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Affiliation(s)
- Louise A O'Sullivan
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
| | - Erwan G Roussel
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
| | - Andrew J Weightman
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
| | - Gordon Webster
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
| | - Casey RJ Hubert
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Emma Bell
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Ian Head
- School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Henrik Sass
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
| | - R John Parkes
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, Wales, UK
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