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Zhang B, Yu W, Liang J, Yao X, Sun H, Iwata H, Guo J. Seasonal variation in structural and functional distribution of periphyton in a macrolide antibiotics-contaminated river. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123495. [PMID: 38342431 DOI: 10.1016/j.envpol.2024.123495] [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: 11/16/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/13/2024]
Abstract
Periphyton, a microbial assemblage of autotrophic and heterotrophic organisms, is vital to aquatic ecosystems. While exposure to macrolide antibiotics has been confirmed to reduce the biodiversity and damage the critical ecological functions in indoor microcosm bioassays, the distribution of periphyton along a macrolide antibiotic pollution gradient in a river has yet to be determined. Herein, we established the spatiotemporal distribution of five major macrolides, i.e., azithromycin (AZI), roxithromycin (ROX), erythromycin (ERY), clarithromycin (CLA), and anhydro erythromycin (ERY-H2O) in water and periphyton of Zao River (Xi'an, China), after which we evaluated the effects on the structures, photosynthetic activity, and carbon utilization capacity of periphyton in March, June, and September 2023. In contrast with the reference sites, the macrolides were identified in all sewage treatment plants (STPs) impacted sites with concentrations ranging from 0.05 to 2.18 μg/L in water and from not detected - 9.67 μg/g in periphyton. Regarding community structure, the occurrence of macrolides was negatively linked to FirmicutesExiguobacterium undae and Exiguobacterium sibiricum, CyanobacteriaOscillatoriales and Vischeria sp., and ChlorophytaMonostroma grevillei, Selenastrum sp. LU21 and Desmodesmus subspicatus. At the functional level, only the metabolism of phenolic acids was significantly decreased in river reach with high antibiotic levels in June, compared to the other five carbon sources that were not altered. The overall photosynthetic activity of periphytic photosystem II remained unchanged in both reference and STPs impacted groups throughout three seasons. Overall, the macrolides released from STPs were correlated with the altered periphytic structures in the river, whereas a similar trend was not detected for the community functions owing to the functional redundancy. A mesocosm experiments warrants further consideration to validate the field results.
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Affiliation(s)
- Baihuan Zhang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Wenqian Yu
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Jiayi Liang
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Xiunan Yao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Haotian Sun
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Hisato Iwata
- Center for Marine Environmental Studies, Ehime University, Bunkyo-cho 2-5, Matsuyama, Ehime prefecture, 790-8577, Japan
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China.
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2
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Groult B, St-Jean V, Lazar CS. Linking Groundwater to Surface Discharge Ecosystems: Archaeal, Bacterial, and Eukaryotic Community Diversity and Structure in Quebec (Canada). Microorganisms 2023; 11:1674. [PMID: 37512847 PMCID: PMC10384904 DOI: 10.3390/microorganisms11071674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely studied in marine environments, very little is known about the connection between underground and surface microbial communities in freshwater settings. Therefore, in this study, we used amplicon sequencing to analyze the archaeal, bacterial, and eukaryotic community diversity and structure in groundwater and surface water samples, spanning the vast regions of the Laurentides and Lanaudières in the Quebec province (Canada). Our results show significant differences between subsurface and surface taxa; with more fungi, Amoebozoa, and chemolithoautotrophic prokaryotes involved in nitrogen-, sulfur-, and iron-cycling dominating the underground samples; while algae, ciliates, methanogens, and Actinobacteria dominate the surface discharge waters. Microbial source tracking suggested that only a small portion of the microbial communities in the groundwater contributed to the surface discharge communities. However, many taxa were shared between both habitats, with a large range of functional diversity, likely explaining their survival in both subsurface and surface water ecosystems.
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Affiliation(s)
- Benjamin Groult
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada
| | - Vicky St-Jean
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada
| | - Cassandre Sara Lazar
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada
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3
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Couton M, Hürlemann S, Studer A, Alther R, Altermatt F. Groundwater environmental DNA metabarcoding reveals hidden diversity and reflects land-use and geology. Mol Ecol 2023. [PMID: 37067032 DOI: 10.1111/mec.16955] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023]
Abstract
Despite being the most important source of liquid freshwater on the planet, groundwater is severely threatened by climate change, agriculture, or industrial mining. It is thus extensively monitored for pollutants and declines in quantity. The organisms living in groundwater, however, are rarely the target of surveillance programmes and little is known about the fauna inhabiting underground habitats. The difficulties accessing groundwater, the lack of expertise, and the apparent scarcity of these organisms challenge sampling and prohibit adequate knowledge on groundwater fauna. Environmental DNA (eDNA) metabarcoding provides an approach to overcome these limitations but is largely unexplored. Here, we sampled water in 20 communal spring catchment boxes used for drinking water provisioning in Switzerland, with a high level of replication at both filtration and amplification steps. We sequenced a portion of the COI mitochondrial gene, which resulted in 4917 ASVs, yet only 3% of the reads could be assigned to a species, genus, or family with more than 90% identity. Careful evaluation of the unassigned reads corroborated that these sequences were true COI sequences belonging mostly to diverse eukaryotic groups, not present in the reference databases. Principal component analyses showed a strong correlation of the community composition with the surface land-use (agriculture vs. forest) and geology (fissured rock vs. unconsolidated sediment). While incomplete reference databases limit the assignment of taxa in groundwater eDNA metabarcoding, we showed that taxonomy-free approaches can reveal large hidden diversity and couple it with major land-use drivers, revealing their imprint on chemical and biological properties of groundwater.
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Affiliation(s)
- Marjorie Couton
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Samuel Hürlemann
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Angela Studer
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Roman Alther
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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4
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Retter A, Haas JC, Birk S, Stumpp C, Hausmann B, Griebler C, Karwautz C. From the Mountain to the Valley: Drivers of Groundwater Prokaryotic Communities along an Alpine River Corridor. Microorganisms 2023; 11:microorganisms11030779. [PMID: 36985351 PMCID: PMC10055094 DOI: 10.3390/microorganisms11030779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/08/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
Rivers are the “tip of the iceberg”, with the underlying groundwater being the unseen freshwater majority. Microbial community composition and the dynamics of shallow groundwater ecosystems are thus crucial, due to their potential impact on ecosystem processes and functioning. In early summer and late autumn, samples of river water from 14 stations and groundwater from 45 wells were analyzed along a 300 km transect of the Mur River valley, from the Austrian alps to the flats at the Slovenian border. The active and total prokaryotic communities were characterized using high-throughput gene amplicon sequencing. Key physico-chemical parameters and stress indicators were recorded. The dataset was used to challenge ecological concepts and assembly processes in shallow aquifers. The groundwater microbiome is analyzed regarding its composition, change with land use, and difference to the river. Community composition and species turnover differed significantly. At high altitudes, dispersal limitation was the main driver of groundwater community assembly, whereas in the lowland, homogeneous selection explained the larger share. Land use was a key determinant of the groundwater microbiome composition. The alpine region was more diverse and richer in prokaryotic taxa, with some early diverging archaeal lineages being highly abundant. This dataset shows a longitudinal change in prokaryotic communities that is dependent on regional differences affected by geomorphology and land use.
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Affiliation(s)
- Alice Retter
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | | | - Steffen Birk
- Institute of Earth Sciences, NAWI Graz Geocenter, University of Graz, 8010 Graz, Austria
| | - Christine Stumpp
- Institute of Soil Physics and Rural Water Management, University of Natural Resources and Life Sciences (BOKU), 1180 Wien, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Wien, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Wien, Austria
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
| | - Clemens Karwautz
- Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Wien, Austria
- Correspondence:
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Yan S, Ding N, Yao X, Song J, He W, Rehman F, Guo J. Effects of erythromycin and roxithromycin on river periphyton: Structure, functions and metabolic pathways. CHEMOSPHERE 2023; 316:137793. [PMID: 36640977 DOI: 10.1016/j.chemosphere.2023.137793] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Macrolides have been frequently detected in the surface waters worldwide, posing a threat to the aquatic microbes. Several studies have evaluated the ecotoxicological effects of macrolides on single algal and bacterial strains. However, without considering the species interaction in the aquatic microbial community, these results cannot be extrapolated to the field. Thus, the present study aimed to evaluate the effects of two macrolides (erythromycin and roxithromycin) on the structure, photosynthetic process, carbon utilization capacity, and the antibiotic metabolic pathways in river periphyton. The colonized periphyton was exposed to the graded concentration (0 μg/L (control), 0.5 μg/L (low), 5 μg/L (medium), 50 μg/L (high)) of ERY and ROX, respectively, for 7 days. Herein, high levels of ERY and ROX altered the community composition by reducing the relative abundance of Chlorophyta in the eukaryotic community. Also, the Shannon and Simpson diversity indexes of prokaryotes were reduced, although similar effects were seldomly detected in the low and medium groups. In contrast to the unchanged carbon utilization capacity, the PSII reaction center involved in the periphytic photosynthesis was significantly inhibited by macrolides at high levels. In addition, both antibiotics had been degraded by periphyton, with the removal rate of 51.63-66.87% and 41.85-48.27% for ERY and ROX, respectively, wherein the side chain and ring cleavage were the main degradation pathways. Overall, this study provides an insight into the structural and functional toxicity and degradation processes of macrolides in river periphyton.
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Affiliation(s)
- Shiwei Yan
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Ning Ding
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Xiunan Yao
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Jinxi Song
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China
| | - Wei He
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Fozia Rehman
- Interdisciplinary Research Center in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Pakistan
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China.
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6
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Perez‐Molphe‐Montoya E, Küsel K, Overholt WA. Redefining the phylogenetic and metabolic diversity of phylum Omnitrophota. Environ Microbiol 2022; 24:5437-5449. [DOI: 10.1111/1462-2920.16170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022]
Affiliation(s)
| | - Kirsten Küsel
- Institute of Biodiversity Friedrich Schiller University Jena Germany
- The German Center for Integrative Biodiversity Research (iDiv) Halle‐Jena‐ Leipzig Germany
| | - Will A. Overholt
- Institute of Biodiversity Friedrich Schiller University Jena Germany
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7
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Sanchez-Arcos C, Ueberschaar N, Pohnert G. Aquifer system and depth specific chemical patterns in fractured-rock groundwater from the Critical Zone revealed by untargeted LC-MS-based metabolomics. WATER RESEARCH 2022; 219:118566. [PMID: 35580391 DOI: 10.1016/j.watres.2022.118566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
In the Earth's Critical Zone, water plays an essential role as a collector and transporter of metabolites and their transformation products. It is generally believed that the chemical profiles of groundwater are strongly impacted by land use. However, predictors for the effects of above-ground natural and anthropogenic activities on below-ground chemistry are rare. We reasoned that comparing groundwater metabolomes from different land-use sites and depths can give insight into this coupling of above and below-ground processes in the Critical Zone. This study used an LC-MS-based untargeted metabolomic approach to identify links between groundwater metabolomes from monitoring wells in fractured carbonate-/siliciclastic alternations along a hillslope of the Hainich Critical Zone Exploratory (CZE) in Thuringia, Germany. Our results identify the land-use type, aquifer system, and sampling depth as critical factors determining the differences among groundwater metabolomes. We established five groundwater metabolic clusters and correlated these to the aquifer systems, hydrogeochemistry, and microbial community composition. Our untargeted metabolomic approach reveals the limited connectivity of groundwater chemical profiles with above-ground activities and illustrates how deep the input signals can travel.
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Affiliation(s)
- Carlos Sanchez-Arcos
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743, Jena, Germany
| | - Nico Ueberschaar
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743, Jena, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Lessingstrasse 8, D-07743, Jena, Germany.
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8
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Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome. Microbiol Spectr 2022; 10:e0043722. [PMID: 35699474 PMCID: PMC9431026 DOI: 10.1128/spectrum.00437-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce the excess particulate organic matter, including surface-derived microorganisms, thereby disturbing the groundwater microbiome. Some surface-derived bacteria will not survive this translocation, leading to an input of necromass to the groundwater. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time using a complementary protein-stable and DNA-stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within 4 days, accompanied by a strong decrease in Shannon diversity and a 10-fold increase in bacterial 16S rRNA gene copy numbers. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax, and Undibacterium dominated the microbial community within 2 days and were identified as key players in necromass degradation, based on a 13C incorporation of >90% in their peptides. Their proteomes comprised various proteins for uptake and transport functions and amino acid metabolization. After 4 and 8 days, the autotrophic and mixotrophic taxa Nitrosomonas, Limnohabitans, Paucibacter, and Acidovorax increased in abundance with a 13C incorporation between 0.5% and 23%. Likewise, eukaryotes assimilated necromass-derived carbon either directly or indirectly. Our data point toward a fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation. IMPORTANCE Subsurface microbiomes provide essential ecosystem services, like the generation of drinking water. These ecosystems are devoid of light-driven primary production, and microbial life is adapted to the resulting oligotrophic conditions. Modern groundwater is most vulnerable to anthropogenic and climatic impacts. Heavy rainfalls, which will increase with climate change, can result in high surface inputs into shallow aquifers by percolation or lateral flow. These inputs include terrestrial organic matter and surface-derived microbes that are not all capable to flourish in aquatic subsurface habitats. Here, we investigated the response of groundwater mesocosms to the addition of bacterial necromass, simulating event-driven surface input. We found that the groundwater microbiome responds with a rapid bloom of only a few primary degraders, followed by the activation of typical groundwater autotrophs and mixotrophs, as well as eukaryotes. Our results suggest that this multiphase strategy is essential to maintain the balance of the groundwater microbiome to provide ecosystem services.
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9
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Saccò M, Guzik MT, van der Heyde M, Nevill P, Cooper SJB, Austin AD, Coates PJ, Allentoft ME, White NE. eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153223. [PMID: 35063529 DOI: 10.1016/j.scitotenv.2022.153223] [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: 09/28/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.
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Affiliation(s)
- Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia.
| | - Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Mieke van der Heyde
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide 5000, SA, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Peterson J Coates
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, 1006, Dartmouth, Nova Scotia B2Y 4A2, Canada
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Nicole E White
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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10
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Zhu M, Li Y, Zhang W, Wang L, Wang H, Niu L, Hui C, Lei M, Wang L, Zhang H, Yang G. Determination of the direct and indirect effects of bend on the urban river ecological heterogeneity. ENVIRONMENTAL RESEARCH 2022; 207:112166. [PMID: 34619129 DOI: 10.1016/j.envres.2021.112166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
The ecological heterogeneity created by river bends benefits the diversity of microorganisms, which is vital for the pollutant degradation and overall river health. However, quantitative tools capable of determining the interactions among different trophic levels and species are lacking, and research regarding ecological heterogeneity has been limited to a few species. By integrating the multi-species-based index of biotic integrity (Mt-IBI) and the structure equation model (SEM), an interactions-based prediction modeling framework was established. Based on DNA metabarcoding, a multi-species (i.e., bacteria, protozoans, and metazoans) based index of biotic integrity including 309 candidate metrics was developed. After a three-step screening process, eight core metrics were obtained to assess the ecological heterogeneity, quantitatively. The Mt-IBI value, which ranged from 2.08 to 7.17, was calculated as the sum of each single core metric value. The Mt-IBI revealed that the ecological heterogeneity of concave banks was higher than other sites. According to the result of the SEM, D90 was the controlling factor (r = -0.779) of the ecological heterogeneity under the influence of the river bends. The bend-induced redistribution of sediment particle further influenced the concentrations of carbon, nitrogen, and sulphur. The nitrogen group (r = 0.668) also played an essential role in determining the ecological heterogeneity, follow by carbon group (r = 0.455). Furthermore, the alteration of niches would make a difference on the ecological heterogeneity. This multi-species interactions-based prediction modeling framework proposed a novel method to quantify ecological heterogeneity and provided insight into the enhancement of ecological heterogeneity in river bends.
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Affiliation(s)
- Mengjie Zhu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China.
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Linqiong Wang
- Key Laboratory of Marine Hazards Forecasting, Ministry of Natural Resources, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Haolan Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Cizhang Hui
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Mengting Lei
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
| | - Gang Yang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China
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11
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Bolstering fitness via CO 2 fixation and organic carbon uptake: mixotrophs in modern groundwater. THE ISME JOURNAL 2022; 16:1153-1162. [PMID: 34876683 PMCID: PMC8941145 DOI: 10.1038/s41396-021-01163-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/11/2021] [Accepted: 11/22/2021] [Indexed: 12/04/2022]
Abstract
Current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO2 fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically fixed carbon, the flux of CO2-derived carbon through various populations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here we implement novel Stable Isotope Cluster Analysis to render a time-resolved and quantitative evaluation of 13CO2-derived carbon flow through a groundwater community in microcosms stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not strict autotrophs, were the most abundant active organisms in groundwater microcosms. Species of Hydrogenophaga, Polaromonas, Dechloromonas, and other metabolically versatile mixotrophs drove the production and remineralization of organic carbon. Their activity facilitated the replacement of 43% and 80% of total microbial carbon stores in the groundwater microcosms with 13C in just 21 and 70 days, respectively. The mixotrophs employed different strategies for satisfying their carbon requirements by balancing CO2 fixation and uptake of available organic compounds. These different strategies might provide fitness under nutrient-limited conditions, explaining the great abundances of mixotrophs in other oligotrophic habitats, such as the upper ocean and boreal lakes.
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Surface Water Intrusion, Land Use Impacts, and Bacterial Community Composition in Shallow Groundwater Wells Supplying Potable Water in Sparsely Populated Areas of a Boreal Region. Microbiol Spectr 2021; 9:e0017921. [PMID: 34730413 PMCID: PMC8567237 DOI: 10.1128/spectrum.00179-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Rural communities often rely on groundwater for potable water supply. In this study, untreated groundwater samples from 28 shallow groundwater wells in Finland (<10 m deep and mostly supplying untreated groundwater to <200 users in rural areas) were assessed for physicochemical water quality, stable water isotopes, microbial water quality indicators, host-specific microbial source tracking (MST) markers, and bacterial community composition, activity, and diversity (using amplicon sequencing of the 16S rRNA gene and 16S rRNA). Indications of surface water intrusion were identified in five wells, and these indications were found to be negatively correlated, overall, with bacterial alpha diversity (based on amplicon sequencing of the 16S rRNA gene). High levels of turbidity, heterotrophs, and iron compromised water quality in two wells, with values up to 2.98 nephelometric turbidity units (NTU), 16,000 CFU/ml, and 2,300 μg/liter, respectively. Coliform bacteria and general fecal indicator Bacteroidales bacteria (GenBac3) were detected in 14 and 10 wells, respectively (albeit mostly at low levels), and correlations were identified between microbial, physicochemical, and environmental parameters, which may indicate impacts from nearby land use (e.g., agriculture, surface water, road salt used for deicing). Our results show that although water quality was generally adequate in most of the studied wells, the continued safe use of these wells should not be taken for granted. IMPORTANCE Standard physicochemical water quality analyses and microbial indicator analyses leave much of the (largely uncultured) complexity of groundwater microbial communities unexplored. This study combined these standard methods with additional analyses of stable water isotopes, bacterial community data, and environmental data about the surrounding areas to investigate the associations between physicochemical and microbial properties of 28 shallow groundwater wells in Finland. We detected impaired groundwater quality in some wells, identified potential land use impacts, and revealed indications of surface water intrusion which were negatively correlated with bacterial alpha diversity. The potential influence of surface water intrusion on groundwater wells and their bacterial communities is of particular interest and warrants further investigation because surface water intrusion has previously been linked to groundwater contamination, which is the primary cause of waterborne outbreaks in the Nordic region and one of the major causes in the United States and Canada.
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Blohm A, Kumar S, Knebl A, Herrmann M, Küsel K, Popp J, Frosch T. Activity and electron donor preference of two denitrifying bacterial strains identified by Raman gas spectroscopy. Anal Bioanal Chem 2021; 414:601-611. [PMID: 34297136 PMCID: PMC8748363 DOI: 10.1007/s00216-021-03541-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/26/2022]
Abstract
Human activities have greatly increased the input of reactive nitrogen species into the environment and disturbed the balance of the global N cycle. This imbalance may be offset by bacterial denitrification, an important process in maintaining the ecological balance of nitrogen. However, our understanding of the activity of mixotrophic denitrifying bacteria is not complete, as most research has focused on heterotrophic denitrification. The aim of this study was to investigate substrate preferences for two mixotrophic denitrifying bacterial strains, Acidovorax delafieldii and Hydrogenophaga taeniospiralis, under heterotrophic, autotrophic or mixotrophic conditions. This complex analysis was achieved by simultaneous identification and quantification of H2, O2, CO2, 14N2, 15N2 and 15N2O in course of the denitrification process with help of cavity-enhanced Raman spectroscopic (CERS) multi-gas analysis. To disentangle electron donor preferences for both bacterial strains, microcosm-based incubation experiments under varying substrate conditions were conducted. We found that Acidovorax delafieldii preferentially performed heterotrophic denitrification in the mixotrophic sub-experiments, while Hydrogenophaga taeniospiralis preferred autotrophic denitrification in the mixotrophic incubation. These observations were supported by stoichiometric calculations. The results demonstrate the prowess of advanced Raman multi-gas analysis to study substrate use and electron donor preferences in denitrification, based on the comprehensive quantification of complex microbial gas exchange processes.
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Affiliation(s)
- Annika Blohm
- Leibniz Institute of Photonic Technology, 07745, Jena, Germany
| | - Swatantar Kumar
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Andreas Knebl
- Leibniz Institute of Photonic Technology, 07745, Jena, Germany
| | - Martina Herrmann
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Kirsten Küsel
- Institute of Biodiversity, Friedrich Schiller University Jena, 07743, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology, 07745, Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
- Abbe Centre of Photonics, Friedrich Schiller University, 07743, Jena, Germany
| | - Torsten Frosch
- Leibniz Institute of Photonic Technology, 07745, Jena, Germany.
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany.
- Abbe Centre of Photonics, Friedrich Schiller University, 07743, Jena, Germany.
- Biophotonics and Biomedical Engineering Group, Technical University Darmstadt, Merckstraße 25, 64283, Darmstadt, Germany.
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Wang B, Huang J, Yang J, Jiang H, Xiao H, Han J, Zhang X. Bicarbonate uptake rates and diversity of RuBisCO genes in saline lake sediments. FEMS Microbiol Ecol 2021; 97:6149456. [PMID: 33629724 DOI: 10.1093/femsec/fiab037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 02/23/2021] [Indexed: 11/12/2022] Open
Abstract
There is limited knowledge of microbial carbon fixation rate, and carbon-fixing microbial abundance and diversity in saline lakes. In this study, the inorganic carbon uptake rates and carbon-fixing microbial populations were investigated in the surface sediments of lakes with a full range of salinity from freshwater to salt saturation. The results showed that in the studied lakes light-dependent bicarbonate uptake contributed substantially (>70%) to total bicarbonate uptake, while the contribution of dark bicarbonate uptake (1.35-25.17%) cannot be ignored. The light-dependent bicarbonate uptake rates were significantly correlated with pH and turbidity, while dark bicarbonate uptake rates were significantly influenced by dissolved inorganic carbon, pH, temperature and salinity. Carbon-fixing microbial populations using the Calvin-Benson-Bassham pathway were widespread in the studied lakes, and they were dominated by the cbbL and cbbM gene types affiliated with Cyanobacteria and Proteobacteria, respectively. The cbbL and cbbM gene abundance and population structures were significantly affected by different environmental variables, with the cbbL and cbbM genes being negatively correlated with salinity and organic carbon concentration, respectively. In summary, this study improves our knowledge of the abundance, diversity and function of carbon-fixing microbial populations in the lakes with a full range of salinity.
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Affiliation(s)
- Beichen Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jianrong Huang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China.,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Haiyi Xiao
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
| | - Jibin Han
- Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 81008, China
| | - Xiying Zhang
- Key Laboratory of Salt Lake Geology and Environment of Qinghai Province, Qinghai Institute of Salt Lakes, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Xining 81008, China
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Marxsen J, Rütz NK, Schmidt SI. Organic carbon and nutrients drive prokaryote and metazoan communities in a floodplain aquifer. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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