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Branco RHR, Meulepas RJW, Sekar P, van Veelen HPJ, Rijnaarts HHM, Sutton NB. Biostimulation with oxygen and electron donors supports micropollutant biodegradation in an experimentally simulated nitrate-reducing aquifer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172339. [PMID: 38608893 DOI: 10.1016/j.scitotenv.2024.172339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/16/2024] [Accepted: 04/07/2024] [Indexed: 04/14/2024]
Abstract
The availability of suitable electron donors and acceptors limits micropollutant natural attenuation in oligotrophic groundwater. This study investigated how electron donors with different biodegradability (humics, dextran, acetate, and ammonium), and different oxygen concentrations affect the biodegradation of 15 micropollutants (initial concentration of each micropollutant = 50 μg/L) in simulated nitrate reducing aquifers. Tests mimicking nitrate reducing field conditions showed no micropollutant biodegradation, even with electron donor amendment. However, 2,4-dichlorophenoxyacetic acid and mecoprop were biodegraded under (micro)aerobic conditions with and without electron donor addition. The highest 2,4-dichlorophenoxyacetic acid and mecoprop biodegradation rates and removal efficiencies were obtained under fully aerobic conditions with amendment of an easily biodegradable electron donor. Under microaerobic conditions, however, amendment with easily biodegradable dissolved organic carbon (DOC) inhibited micropollutant biodegradation due to competition between micropollutants and DOC for the limited oxygen available. Microbial community composition was dictated by electron acceptor availability and electron donor amendment, not by micropollutant biodegradation. Low microbial community richness and diversity led to the absence of biodegradation of the other 13 micropollutants (such as bentazon, chloridazon, and carbamazepine). Finally, adaptation and potential growth of biofilms interactively determined the location of the micropollutant removal zone relative to the point of amendment. This study provides new insight on how to stimulate in situ micropollutant biodegradation to remediate oligotrophic groundwaters as well as possible limitations of this process.
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Affiliation(s)
- Rita H R Branco
- Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, P.O. Box 1113, 8900 CC Leeuwarden, the Netherlands
| | - Roel J W Meulepas
- Wetsus, European Centre of Excellence for Sustainable Water Technology, P.O. Box 1113, 8900 CC Leeuwarden, the Netherlands
| | - Priyadharshini Sekar
- Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, P.O. Box 1113, 8900 CC Leeuwarden, the Netherlands
| | - H Pieter J van Veelen
- Wetsus, European Centre of Excellence for Sustainable Water Technology, P.O. Box 1113, 8900 CC Leeuwarden, the Netherlands
| | - Huub H M Rijnaarts
- Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands.
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Ascandari A, Aminu S, Safdi NEH, El Allali A, Daoud R. A bibliometric analysis of the global impact of metaproteomics research. Front Microbiol 2023; 14:1217727. [PMID: 37476667 PMCID: PMC10354264 DOI: 10.3389/fmicb.2023.1217727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
Background Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated. Methods Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores. Results A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1. Conclusion The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.
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Affiliation(s)
- AbdulAziz Ascandari
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Suleiman Aminu
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Nour El Houda Safdi
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid Daoud
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Harris RL, Vetter MCYL, van Heerden E, Cason E, Vermeulen JG, Taneja A, Kieft TL, DeCoste CJ, Laevsky GS, Onstott TC. FISH-TAMB, a Fixation-Free mRNA Fluorescent Labeling Technique to Target Transcriptionally Active Members in Microbial Communities. MICROBIAL ECOLOGY 2022; 84:182-197. [PMID: 34406445 PMCID: PMC9250922 DOI: 10.1007/s00248-021-01809-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Keystone species or ecological engineers are vital to the health of an ecosystem; however, often, their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, the fast hybridization time of as short as 15 min at target cells' growth temperature, and the omission of washing steps. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB's ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A (mcrA) expressed in (1) Escherichia coli containing a plasmid with a partial mcrA gene of the methanogen Methanosarcina barkeri (E. coli mcrA+); (2) M. barkeri; and (3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA and thus is a versatile addition to the molecular ecologist's toolkit, with potentially widespread application in the field of environmental microbiology.
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Affiliation(s)
- Rachel L Harris
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Maggie C Y Lau Vetter
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
- Laboratory of Extraterrestrial Ocean Systems, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, Hainan, China.
| | - Esta van Heerden
- Centre for Water Sciences and Management, North West University, Potchefstroom, South Africa
- iWater Pty Ltd, 5 Walter Sisulu Rd, Park West, Bloemfontein, 9301, South Africa
| | - Errol Cason
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- Department of Animal-, Wildlife- and Grassland Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - Jan-G Vermeulen
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- Department of Virology, University of the Free State, Bloemfontein, 9301, South Africa
| | - Anjali Taneja
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
- McCourt School of Public Policy, Georgetown University, Washington, DC, 20057, USA
| | - Thomas L Kieft
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Christina J DeCoste
- Flow Cytometry Resource Facility, Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Gary S Laevsky
- Confocal Imaging Facility, Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
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Weinstein DJ, Allen SE, Lau MCY, Erasmus M, Asalone KC, Walters-Conte K, Deikus G, Sebra R, Borgonie G, van Heerden E, Onstott TC, Bracht JR. The genome of a subterrestrial nematode reveals adaptations to heat. Nat Commun 2019; 10:5268. [PMID: 31754114 PMCID: PMC6872716 DOI: 10.1038/s41467-019-13245-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
The nematode Halicephalobus mephisto was originally discovered inhabiting a deep terrestrial aquifer 1.3 km underground. H. mephisto can thrive under conditions of abiotic stress including heat and minimal oxygen, where it feeds on a community of both chemolithotrophic and heterotrophic prokaryotes in an unusual ecosystem isolated from the surface biosphere. Here we report the comprehensive genome and transcriptome of this organism, identifying a signature of adaptation: an expanded repertoire of 70 kilodalton heat-shock proteins (Hsp70) and avrRpt2 induced gene 1 (AIG1) proteins. The expanded Hsp70 genes are transcriptionally induced upon growth under heat stress, and we find that positive selection is detectable in several members of this family. We further show that AIG1 may have been acquired by horizontal gene transfer (HGT) from a rhizobial fungus. Over one-third of the genes of H. mephisto are novel, highlighting the divergence of this nematode from other sequenced organisms. This work sheds light on the genomic basis of heat tolerance in a complete subterrestrial eukaryotic genome.
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Affiliation(s)
| | - Sarah E Allen
- Biology Department, American University, Washington, DC, 20016, USA
- Biology Department, Cornell University, Ithaca, NY, 14853, USA
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, No. 28, Luhuitou Road, Sanya, 572000, Hainan Province, P.R. China
| | - Mariana Erasmus
- UFS/TIA Saense Platform, Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
| | | | | | - Gintaras Deikus
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Esta van Heerden
- UFS/TIA Saense Platform, Department of Microbial, Biochemical, and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- North West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
| | - John R Bracht
- Biology Department, American University, Washington, DC, 20016, USA.
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Onstott T, Ehlmann B, Sapers H, Coleman M, Ivarsson M, Marlow J, Neubeck A, Niles P. Paleo-Rock-Hosted Life on Earth and the Search on Mars: A Review and Strategy for Exploration. ASTROBIOLOGY 2019; 19:1230-1262. [PMID: 31237436 PMCID: PMC6786346 DOI: 10.1089/ast.2018.1960] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/25/2019] [Indexed: 05/19/2023]
Abstract
Here we review published studies on the abundance and diversity of terrestrial rock-hosted life, the environments it inhabits, the evolution of its metabolisms, and its fossil biomarkers to provide guidance in the search for life on Mars. Key findings are (1) much terrestrial deep subsurface metabolic activity relies on abiotic energy-yielding fluxes and in situ abiotic and biotic recycling of metabolic waste products rather than on buried organic products of photosynthesis; (2) subsurface microbial cell concentrations are highest at interfaces with pronounced chemical redox gradients or permeability variations and do not correlate with bulk host rock organic carbon; (3) metabolic pathways for chemolithoautotrophic microorganisms evolved earlier in Earth's history than those of surface-dwelling phototrophic microorganisms; (4) the emergence of the former occurred at a time when Mars was habitable, whereas the emergence of the latter occurred at a time when the martian surface was not continually habitable; (5) the terrestrial rock record has biomarkers of subsurface life at least back hundreds of millions of years and likely to 3.45 Ga with several examples of excellent preservation in rock types that are quite different from those preserving the photosphere-supported biosphere. These findings suggest that rock-hosted life would have been more likely to emerge and be preserved in a martian context. Consequently, we outline a Mars exploration strategy that targets subsurface life and scales spatially, focusing initially on identifying rocks with evidence for groundwater flow and low-temperature mineralization, then identifying redox and permeability interfaces preserved within rock outcrops, and finally focusing on finding minerals associated with redox reactions and associated traces of carbon and diagnostic chemical and isotopic biosignatures. Using this strategy on Earth yields ancient rock-hosted life, preserved in the fossil record and confirmable via a suite of morphologic, organic, mineralogical, and isotopic fingerprints at micrometer scale. We expect an emphasis on rock-hosted life and this scale-dependent strategy to be crucial in the search for life on Mars.
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Affiliation(s)
- T.C. Onstott
- Department of Geosciences, Princeton University, Princeton, New Jersey, USA
- Address correspondence to: T.C. Onstott, Department of Geosciences, Princeton University,, Princeton, NJ 008544
| | - B.L. Ehlmann
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- B.L. Ehlmann, Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - H. Sapers
- Division of Geological & Planetary Sciences, California Institute of Technology, Pasadena, California, USA
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - M. Coleman
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- NASA Astrobiology Institute, Pasadena, California, USA
| | - M. Ivarsson
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - J.J. Marlow
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - A. Neubeck
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - P. Niles
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, Texas, USA
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New ecosystems in the deep subsurface follow the flow of water driven by geological activity. Sci Rep 2019; 9:3310. [PMID: 30824745 PMCID: PMC6397172 DOI: 10.1038/s41598-019-39699-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/30/2019] [Indexed: 11/17/2022] Open
Abstract
Eukarya have been discovered in the deep subsurface at several locations in South Africa, but how organisms reach the subsurface remains unknown. We studied river-subsurface fissure water systems and identified Eukarya from a river that are genetically identical for 18S rDNA. To further confirm that these are identical species one metazoan species recovered from the overlying river interbred successfully with specimen recovered from an underlying mine at −1.4 km. In situ seismic simulation experiments were carried out and show seismic activity to be a major force increasing the hydraulic conductivity in faults allowing organisms to create ecosystems in the deep subsurface. As seismic activity is a non-selective force we recovered specimen of algae and Insecta that defy any obvious other explanation at a depth of −3.4 km. Our results show there is a steady flow of surface organisms to the deep subsurface where some survive and adapt and others perish. As seismic activity is also present on other planets and moons in our solar system the mechanism elucidated here may be relevant for future search and selection of landing sites in planetary exploration.
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Stott M, Lueders T. Editorial: Deep life, kia ora! FEMS Microbiol Ecol 2018; 94:5101342. [DOI: 10.1093/femsec/fiy176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 09/03/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Matthew Stott
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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