1
|
Brauer VS, Voskuhl L, Mohammadian S, Pannekens M, Haque S, Meckenstock RU. Imprints of ecological processes in the taxonomic core community: an analysis of naturally replicated microbial communities enclosed in oil. FEMS Microbiol Ecol 2024; 100:fiae074. [PMID: 38734895 PMCID: PMC11110866 DOI: 10.1093/femsec/fiae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/02/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
It is widely assumed that a taxonomic core community emerges among microbial communities from similar habitats because similar environments select for the same taxa bearing the same traits. Yet, a core community itself is no indicator of selection because it may also arise from dispersal and neutral drift, i.e. by chance. Here, we hypothesize that a core community produced by either selection or chance processes should be distinguishable. While dispersal and drift should produce core communities with similar relative taxon abundances, especially when the proportional core community, i.e. the sum of the relative abundances of the core taxa, is large, selection may produce variable relative abundances. We analyzed the core community of 16S rRNA gene sequences of 193 microbial communities occurring in tiny water droplets enclosed in heavy oil from the Pitch Lake, Trinidad and Tobago. These communities revealed highly variable relative abundances along with a large proportional core community (68.0 ± 19.9%). A dispersal-drift null model predicted a negative relationship of proportional core community and compositional variability along a range of dispersal probabilities and was largely inconsistent with the observed data, suggesting a major role of selection for shaping the water droplet communities in the Pitch Lake.
Collapse
Affiliation(s)
- Verena S Brauer
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, 45141 Essen, Germany
| | - Lisa Voskuhl
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Sadjad Mohammadian
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
| | - Mark Pannekens
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
- IWW Water Center, 45476 Mülheim an der Ruhr, Germany
| | - Shirin Haque
- Department of Physics, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Rainer U Meckenstock
- Aquatic Microbiology, Environmental Microbiology and Biotechnology, Faculty of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, 45141 Essen, Germany
| |
Collapse
|
2
|
Voskuhl L, Brusilova D, Brauer VS, Meckenstock RU. Inhibition of sulfate-reducing bacteria with formate. FEMS Microbiol Ecol 2022; 98:6510814. [PMID: 35040992 PMCID: PMC8831227 DOI: 10.1093/femsec/fiac003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/13/2021] [Accepted: 01/14/2022] [Indexed: 11/14/2022] Open
Abstract
Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally. Ion chromatography revealed very high formate concentrations around 2.37 mM in 21 out of 43 examined droplets. Since these concentrations were unexpectedly high, we performed growth experiments with the three sulfate-reducing type strains Desulfovibrio vulgaris, Desulfobacter curvatus, and Desulfococcus multivorans, and tested the effects of 2.5, 8 or 10 mM formate on sulfate reduction. Experiments demonstrated that 8 or 10 mM formate slowed down the growth rate of D. vulgaris and D. curvatus and the sulfate reduction rate of D. curvatus and D. multivorans. Concerning D. multivorans, increasing formate concentrations delayed the onsets of growth and sulfate reduction, which were even inhibited completely while formate was added constantly. Contrary to previous studies, D. multivorans was the only organism capable of formate consumption. Our study suggests that formate accumulates in the natural environment of the water droplets dispersed in oil and that such levels are very likely inhibiting sulfate-reducing microorganisms.
Collapse
Affiliation(s)
- L Voskuhl
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| | - D Brusilova
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| | - V S Brauer
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| | - R U Meckenstock
- University of Duisburg-Essen - Faculty of Chemistry - Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, Universitätsstr. 5, 45141 Essen, Germany
| |
Collapse
|
3
|
Voskuhl L, Akbari A, Müller H, Pannekens M, Brusilova D, Dyksma S, Haque S, Graupner N, Dunthorn M, Meckenstock RU, Brauer VS. Indigenous microbial communities in heavy oil show a threshold response to salinity. FEMS Microbiol Ecol 2021; 97:6447536. [PMID: 34864985 PMCID: PMC8684454 DOI: 10.1093/femsec/fiab157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/29/2021] [Indexed: 11/14/2022] Open
Abstract
Microbial degradation influences the quality of oil resources. The environmental factors that shape the composition of oil microbial communities are largely unknown because most samples from oil fields are impacted by anthropogenic oil production, perturbing the native ecosystem with exogenous fluids and microorganisms. We investigated the relationship between formation water geochemistry and microbial community composition in undisturbed oil samples. We isolated 43 microliter-sized water droplets naturally enclosed in the heavy oil of the Pitch Lake, Trinidad and Tobago. The water chemistry and microbial community composition within the same water droplet were determined by ion chromatography and 16S rRNA gene amplicon sequencing, respectively. The results revealed a high variability in ion concentrations and community composition between water droplets. Microbial community composition was mostly affected by the chloride concentration, which ranged from freshwater to brackish-sea water. Remarkably, microbial communities did not respond gradually to increasing chloride concentration but showed a sudden change to less diverse and uneven communities when exceeding a chloride concentration of 57.3 mM. The results reveal a threshold-regulated response of microbial communities to salinity, offering new insights into the microbial ecology of oil reservoirs.
Collapse
Affiliation(s)
- Lisa Voskuhl
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Ali Akbari
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Hubert Müller
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Mark Pannekens
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Darya Brusilova
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany.,German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Shirin Haque
- Faculty of Science and Technology, Department of Physics, The University of The West Indies, St. Augustine, Trinidad and Tobago
| | - Nadine Graupner
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Micah Dunthorn
- Eukaryotic Microbiology, Natural History Museum of Oslo, P.O. Box 1172, Blindern, Oslo 0318, Norway
| | - Rainer U Meckenstock
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| | - Verena S Brauer
- Environmental Microbiology and Biotechnology (EMB) - Aquatic Microbiology, University of Duisburg-Essen, Universitätsstr. 5, 45141 Essen, Germany
| |
Collapse
|