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Genitsaris S, Stefanidou N, Kourkoutmani P, Michaloudi E, Gros M, García-Gómez E, Petrović M, Ntziachristos L, Moustaka-Gouni M. Do coastal bacterioplankton communities hold the molecular key to the rapid biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) from shipping scrubber effluent? ENVIRONMENTAL RESEARCH 2025; 277:121563. [PMID: 40203979 DOI: 10.1016/j.envres.2025.121563] [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: 12/09/2024] [Revised: 04/01/2025] [Accepted: 04/06/2025] [Indexed: 04/11/2025]
Abstract
Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L-1) and a eutrophic (105.35 μg C L-1) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.
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Affiliation(s)
- Savvas Genitsaris
- Section of Ecology and Taxonomy, School of Biology, National and Kapodistrian University of Athens, Zografou Campus, 15784, Athens, Greece.
| | - Natassa Stefanidou
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Polyxeni Kourkoutmani
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece; Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Evangelia Michaloudi
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Meritxell Gros
- Catalan Institute for Water Research (ICRA), Girona, Spain; University of Girona (UdG), Girona, Spain
| | - Elisa García-Gómez
- Catalan Institute for Water Research (ICRA), Girona, Spain; University of Girona (UdG), Girona, Spain
| | - Mira Petrović
- Catalan Institute for Water Research (ICRA), Girona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Leonidas Ntziachristos
- Department of Mechanical Engineering, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Maria Moustaka-Gouni
- Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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2
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Roothans N, Pabst M, van Diemen M, Herrera Mexicano C, Zandvoort M, Abeel T, van Loosdrecht MCM, Laureni M. Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N 2O emissions during wastewater treatment. NATURE WATER 2025; 3:590-604. [PMID: 40417422 PMCID: PMC12098122 DOI: 10.1038/s44221-025-00430-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 03/20/2025] [Indexed: 05/27/2025]
Abstract
Nitrous oxide (N2O) is the third most important greenhouse gas and originates primarily from natural and engineered microbiomes. Effective emission mitigations are currently hindered by the largely unresolved ecophysiological controls of coexisting N2O-converting metabolisms in complex communities. To address this, we used biological wastewater treatment as a model ecosystem and combined long-term metagenome-resolved metaproteomics with ex situ kinetic and full-scale operational characterization over nearly 2 years. By leveraging the evidence independently obtained at multiple ecophysiological levels, from individual genetic potential to actual metabolism and emergent community phenotype, the cascade of environmental and operational triggers driving seasonal N2O emissions has ultimately been resolved. We identified nitrifier denitrification as the dominant N2O-producing pathway and dissolved O2 as the prime operational parameter, paving the way to the design and fostering of robust emission control strategies. This work exemplifies the untapped potential of multi-meta-omics in the mechanistic understanding and ecological engineering of microbiomes towards reducing anthropogenic impacts and advancing sustainable biotechnological developments.
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Affiliation(s)
- Nina Roothans
- Delft University of Technology, Delft, the Netherlands
| | - Martin Pabst
- Delft University of Technology, Delft, the Netherlands
| | | | | | | | - Thomas Abeel
- Delft University of Technology, Delft, the Netherlands
- Broad Institute of MIT and Harvard, Cambridge, MA USA
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3
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Broderick CM, Benucci GMN, Bachega LR, Miller GD, Evans SE, Hawkes CV. Long-term climate establishes functional legacies by altering microbial traits. THE ISME JOURNAL 2025; 19:wraf005. [PMID: 39804671 PMCID: PMC11805608 DOI: 10.1093/ismejo/wraf005] [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: 07/10/2024] [Revised: 11/12/2024] [Accepted: 01/10/2025] [Indexed: 02/09/2025]
Abstract
Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.
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Affiliation(s)
- Caitlin M Broderick
- W.K. Kellogg Biological Station, Michigan State University, 3700 Gull Lake Drive, Hickory Corners, MI 49060, United States
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Gian Maria Niccolò Benucci
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Luciana Ruggiero Bachega
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, United States
| | - Gabriel D Miller
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, United States
| | - Sarah E Evans
- W.K. Kellogg Biological Station, Michigan State University, 3700 Gull Lake Drive, Hickory Corners, MI 49060, United States
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, United States
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, United States
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4
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Noell SE, Abbaszadeh J, Richards H, Labat Saint Vincent M, Lee CK, Herbold CW, Stott MB, Cary SC, McDonald IR. Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms. Environ Microbiol 2025; 27:e70032. [PMID: 39871406 PMCID: PMC11772915 DOI: 10.1111/1462-2920.70032] [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: 10/14/2024] [Revised: 11/24/2024] [Accepted: 12/18/2024] [Indexed: 01/29/2025]
Abstract
Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.
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Affiliation(s)
- Stephen E. Noell
- Thermophile Research Unit, Te Aka Mātuatua, School of Science, Te Whare Wānanga o WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
- International Centre for Terrestrial Antarctic Research, Te Whare Wānanga o Waikato, University of WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
| | - Jaber Abbaszadeh
- Thermophile Research Unit, Te Aka Mātuatua, School of Science, Te Whare Wānanga o WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
- International Centre for Terrestrial Antarctic Research, Te Whare Wānanga o Waikato, University of WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
| | - Huw Richards
- Thermophile Research Unit, Te Aka Mātuatua, School of Science, Te Whare Wānanga o WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
- International Centre for Terrestrial Antarctic Research, Te Whare Wānanga o Waikato, University of WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
| | - Marie Labat Saint Vincent
- Thermophile Research Unit, Te Aka Mātuatua, School of Science, Te Whare Wānanga o WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
- International Centre for Terrestrial Antarctic Research, Te Whare Wānanga o Waikato, University of WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
- University de LilleLilleFrance
| | - Charles K. Lee
- Thermophile Research Unit, Te Aka Mātuatua, School of Science, Te Whare Wānanga o WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
- International Centre for Terrestrial Antarctic Research, Te Whare Wānanga o Waikato, University of WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
| | - Craig W. Herbold
- Te Kura Pūtaiao Koiora, School of Biological Sciences, Te Whare Wānanga o WaitahaUniversity of CanterburyChristchurchAotearoa‐New Zealand
| | - Matthew B. Stott
- Te Kura Pūtaiao Koiora, School of Biological Sciences, Te Whare Wānanga o WaitahaUniversity of CanterburyChristchurchAotearoa‐New Zealand
| | - S. Craig Cary
- Thermophile Research Unit, Te Aka Mātuatua, School of Science, Te Whare Wānanga o WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
- International Centre for Terrestrial Antarctic Research, Te Whare Wānanga o Waikato, University of WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
| | - Ian R. McDonald
- Thermophile Research Unit, Te Aka Mātuatua, School of Science, Te Whare Wānanga o WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
- International Centre for Terrestrial Antarctic Research, Te Whare Wānanga o Waikato, University of WaikatoUniversity of WaikatoHamiltonAotearoa‐New Zealand
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5
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Ding Y, Ma R, Zhang R, Zhang H, Zhang J, Li S, Zhang S. Increased antibiotic resistance gene abundance linked to intensive bacterial competition in the phyllosphere across an elevational gradient. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70042. [PMID: 39572861 PMCID: PMC11581953 DOI: 10.1111/1758-2229.70042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 10/24/2024] [Indexed: 11/24/2024]
Abstract
Antibiotic resistance genes (ARGs) are ancient and widespread in natural habitats, providing survival advantages for microbiomes under challenging conditions. In mountain ecosystems, phyllosphere bacterial communities face multiple stress conditions, and the elevational gradients of mountains represent crucial environmental gradients for studying biodiversity distribution patterns. However, the distribution patterns of ARGs in the phyllosphere along elevational gradients, and their correlation with bacterial community structures, remain poorly understood. Here, we applied metagenomic analyses to investigate the abundance and diversity of ARGs in 88 phyllosphere samples collected from Mount Tianmu, a national natural reserve. Our results showed that the abundance of ARGs in the phyllosphere increased along elevational gradients and was dominated by multidrug resistance and efflux pumps. The composition of bacterial communities, rather than plant traits or abiotic factors, significantly affected ARG abundance. Moreover, increased ARG abundance was correlated with greater phylogenetic overdispersion and a greater proportion of negative associations in the bacterial co-occurrence networks, suggesting that bacterial competition primarily shapes phyllosphere resistomes. These findings constitute a major advance in the biodiversity of phyllosphere resistomes along elevations, emphasizing the significant impact of bacterial community structure and assembly on ARG distribution, and are essential for understanding the emergence of ARGs.
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Affiliation(s)
- Yihui Ding
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Rui‐Ao Ma
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Ran Zhang
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Hongwei Zhang
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Jian Zhang
- School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Shaopeng Li
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Si‐Yu Zhang
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
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6
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Martin-Cuadrado AB, Rubio-Portillo E, Rosselló F, Antón J. The coral Oculina patagonica holobiont and its response to confinement, temperature, and Vibrio infections. MICROBIOME 2024; 12:222. [PMID: 39472959 PMCID: PMC11520598 DOI: 10.1186/s40168-024-01921-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 08/28/2024] [Indexed: 11/02/2024]
Abstract
BACKGROUND Extensive research on the diversity and functional roles of the microorganisms associated with reef-building corals has been promoted as a consequence of the rapid global decline of coral reefs attributed to climate change. Several studies have highlighted the importance of coral-associated algae (Symbiodinium) and bacteria and their potential roles in promoting coral host fitness and survival. However, the complex coral holobiont extends beyond these components to encompass other entities such as protists, fungi, and viruses. While each constituent has been individually investigated in corals, a comprehensive understanding of their collective roles is imperative for a holistic comprehension of coral health and resilience. RESULTS The metagenomic analysis of the microbiome of the coral Oculina patagonica has revealed that fungi of the genera Aspergillus, Fusarium, and Rhizofagus together with the prokaryotic genera Streptomyces, Pseudomonas, and Bacillus were abundant members of the coral holobiont. This study also assessed changes in microeukaryotic, prokaryotic, and viral communities under three stress conditions: aquaria confinement, heat stress, and Vibrio infections. In general, stress conditions led to an increase in Rhodobacteraceae, Flavobacteraceae, and Vibrionaceae families, accompanied by a decrease in Streptomycetaceae. Concurrently, there was a significant decline in both the abundance and richness of microeukaryotic species and a reduction in genes associated with antimicrobial compound production by the coral itself, as well as by Symbiodinium and fungi. CONCLUSION Our findings suggest that the interplay between microeukaryotic and prokaryotic components of the coral holobiont may be disrupted by stress conditions, such as confinement, increase of seawater temperature, or Vibrio infection, leading to a dysbiosis in the global microbial community that may increase coral susceptibility to diseases. Further, microeukaryotic community seems to exert influence on the prokaryotic community dynamics, possibly through predation or the production of secondary metabolites with anti-bacterial activity. Video Abstract.
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Affiliation(s)
| | - Esther Rubio-Portillo
- Dpt. Fisiología, Genética y Microbiología, University of Alicante, San Vicente del Raspeig, Spain.
| | - Francesc Rosselló
- Mathematics and Computer Science Dept, University of the Balearic Islands, Palma, Spain
- Balearic Islands Health Research Institute (IdISBa), Palma, Spain
| | - Josefa Antón
- Dpt. Fisiología, Genética y Microbiología, University of Alicante, San Vicente del Raspeig, Spain
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7
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Hernandez-Leyva AJ, Berna AZ, Liu Y, Rosen AL, Lint MA, Whiteside SA, Jaeger N, McDonough RT, Joardar N, Santiago-Borges J, Tomera CP, Luo W, John ARO, Kau AL. The breath volatilome is shaped by the gut microbiota. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.02.24311413. [PMID: 39132488 PMCID: PMC11312666 DOI: 10.1101/2024.08.02.24311413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The gut microbiota is widely implicated in host health and disease, inspiring translational efforts to implement our growing body of knowledge in clinical settings. However, the need to characterize gut microbiota by its genomic content limits the feasibility of rapid, point-of-care diagnostics. The microbiota produces a diverse array of xenobiotic metabolites that disseminate into tissues, including volatile organic compounds (VOCs) that may be excreted in breath. We hypothesize that breath contains gut microbe-derived VOCs that inform the composition and metabolic state of the microbiota. To explore this idea, we compared the breath volatilome and fecal gut microbiomes of 27 healthy children and found that breath VOC composition is correlated with gut microbiomes. To experimentally interrogate this finding, we devised a method for capturing exhaled breath from gnotobiotic mice. Breath volatiles are then profiled by gas-chromatography mass-spectrometry (GC-MS). Using this novel methodology, we found that the murine breath profile is markedly shaped by the composition of the gut microbiota. We also find that VOCs produced by gut microbes in pure culture can be identified in vivo in the breath of mice monocolonized with the same bacteria. Altogether, our studies identify microbe-derived VOCs excreted in breath and support a mechanism by which gut bacterial metabolism directly contributes to the mammalian breath VOC profiles.
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Affiliation(s)
- Ariel J. Hernandez-Leyva
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Amalia Z. Berna
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yang Liu
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anne L. Rosen
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michael A. Lint
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Samantha A. Whiteside
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Natalia Jaeger
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Current address: Department of Immunology, Augusta University, Augusta, GA 30912, USA
| | - Ryan T. McDonough
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Nikhilesh Joardar
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jesús Santiago-Borges
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Christopher P. Tomera
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Wentai Luo
- Department of Chemistry, Portland State University, Portland, OR 97201, USA
| | - Audrey R. Odom John
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew L. Kau
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
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8
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Liébana R, Viver T, Ramos-Barbero MD, Bustos-Caparros E, Urdiain M, López C, Amoozegar MA, Antón J, Rossello-Mora R. Extremely halophilic brine community manipulation shows higher robustness of microbiomes inhabiting human-driven solar saltern than naturally driven lake. mSystems 2024; 9:e0053824. [PMID: 38934645 PMCID: PMC11324034 DOI: 10.1128/msystems.00538-24] [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: 04/16/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Hypersaline ecosystems display taxonomically similar assemblages with low diversities and highly dense accompanying viromes. The ecological implications of viral infection on natural microbial populations remain poorly understood, especially at finer scales of diversity. Here, we sought to investigate the influence of changes in environmental physicochemical conditions and viral predation pressure by autochthonous and allochthonous viruses on host dynamics. For this purpose, we transplanted two microbiomes coming from distant hypersaline systems (solar salterns of Es Trenc in Spain and the thalassohaline lake of Aran-Bidgol lake in Iran), by exchanging the cellular fractions with the sterile-filtered accompanying brines with and without the free extracellular virus fraction. The midterm exposure (1 month) of the microbiomes to the new conditions showed that at the supraspecific taxonomic range, the assemblies from the solar saltern brine more strongly resisted the environmental changes and viral predation than that of the lake. The metagenome-assembled genomes (MAGs) analysis revealed an intraspecific transition at the ecotype level, mainly driven by changes in viral predation pressure, by both autochthonous and allochthonous viruses. IMPORTANCE Viruses greatly influence succession and diversification of their hosts, yet the effects of viral infection on the ecological dynamics of natural microbial populations remain poorly understood, especially at finer scales of diversity. By manipulating the viral predation pressure by autochthonous and allochthonous viruses, we uncovered potential phage-host interaction, and their important role in structuring the prokaryote community at an ecotype level.
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Affiliation(s)
- Raquel Liébana
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
| | - Tomeu Viver
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
- Department of
Molecular Ecology, Max Planck Institute for Marine
Microbiology, Bremen,
Germany
| | - María Dolores Ramos-Barbero
- Department of
Physiology, Genetics and Microbiology, University of
Alicante, Alicante,
Spain
- Department of
Genetics, Microbiology and Statistics, University of
Barcelona, Barcelona,
Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
| | - Mercedes Urdiain
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
| | - Cristina López
- Department of
Physiology, Genetics and Microbiology, University of
Alicante, Alicante,
Spain
| | - Mohammad Ali Amoozegar
- Extremophiles
Laboratory, Department of Microbiology, School of Biology and Center of
Excellence in Phylogeny of Living Organisms, College of Science,
University of Tehran,
Tehran, Iran
| | - Josefa Antón
- Department of
Physiology, Genetics and Microbiology, University of
Alicante, Alicante,
Spain
| | - Ramon Rossello-Mora
- Marine Microbiology
Group, Department of Animal and Microbial Biodiversity, Mediterranean
Institute for Advanced Studies (IMEDEA,
UIB-CSIC), Esporles,
Spain
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9
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Brown CL, Maile-Moskowitz A, Lopatkin AJ, Xia K, Logan LK, Davis BC, Zhang L, Vikesland PJ, Pruden A. Selection and horizontal gene transfer underlie microdiversity-level heterogeneity in resistance gene fate during wastewater treatment. Nat Commun 2024; 15:5412. [PMID: 38926391 PMCID: PMC11208604 DOI: 10.1038/s41467-024-49742-8] [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: 11/03/2023] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Activated sludge is the centerpiece of biological wastewater treatment, as it facilitates removal of sewage-associated pollutants, fecal bacteria, and pathogens from wastewater through semi-controlled microbial ecology. It has been hypothesized that horizontal gene transfer facilitates the spread of antibiotic resistance genes within the wastewater treatment plant, in part because of the presence of residual antibiotics in sewage. However, there has been surprisingly little evidence to suggest that sewage-associated antibiotics select for resistance at wastewater treatment plants via horizontal gene transfer or otherwise. We addressed the role of sewage-associated antibiotics in promoting antibiotic resistance using lab-scale sequencing batch reactors fed field-collected wastewater, metagenomic sequencing, and our recently developed bioinformatic tool Kairos. Here, we found confirmatory evidence that fluctuating levels of antibiotics in sewage are associated with horizontal gene transfer of antibiotic resistance genes, microbial ecology, and microdiversity-level differences in resistance gene fate in activated sludge.
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Affiliation(s)
- Connor L Brown
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA
| | | | | | - Kang Xia
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, USA
| | | | - Benjamin C Davis
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, USA
| | - Liqing Zhang
- Dept. of Computer Science, Virginia Tech, Blacksburg, USA
| | - Peter J Vikesland
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA.
| | - Amy Pruden
- Dept. of Civil and Environmental Engineering, Virginia Tech, Blacksburg, USA.
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10
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Medeiros W, Hidalgo K, Leão T, de Carvalho LM, Ziemert N, Oliveira V. Unlocking the biosynthetic potential and taxonomy of the Antarctic microbiome along temporal and spatial gradients. Microbiol Spectr 2024; 12:e0024424. [PMID: 38747631 PMCID: PMC11237469 DOI: 10.1128/spectrum.00244-24] [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: 01/25/2024] [Accepted: 04/19/2024] [Indexed: 06/06/2024] Open
Abstract
Extreme environments, such as Antarctica, select microbial communities that display a range of evolutionary strategies to survive and thrive under harsh environmental conditions. These include a diversity of specialized metabolites, which have the potential to be a source for new natural product discovery. Efforts using (meta)genome mining approaches to identify and understand biosynthetic gene clusters in Antarctica are still scarce, and the extent of their diversity and distribution patterns in the environment have yet to be discovered. Herein, we investigated the biosynthetic gene diversity of the biofilm microbial community of Whalers Bay, Deception Island, in the Antarctic Peninsula and revealed its distribution patterns along spatial and temporal gradients by applying metagenome mining approaches and multivariable analysis. The results showed that the Whalers Bay microbial community harbors a great diversity of biosynthetic gene clusters distributed into seven classes, with terpene being the most abundant. The phyla Proteobacteria and Bacteroidota were the most abundant in the microbial community and contributed significantly to the biosynthetic gene abundances in Whalers Bay. Furthermore, the results highlighted a significant correlation between the distribution of biosynthetic genes and taxonomic diversity, emphasizing the intricate interplay between microbial taxonomy and their potential for specialized metabolite production.IMPORTANCEThis research on antarctic microbial biosynthetic diversity in Whalers Bay, Deception Island, unveils the hidden potential of extreme environments for natural product discovery. By employing metagenomic techniques, the research highlights the extensive diversity of biosynthetic gene clusters and identifies key microbial phyla, Proteobacteria and Bacteroidota, as significant contributors. The correlation between taxonomic diversity and biosynthetic gene distribution underscores the intricate interplay governing specialized metabolite production. These findings are crucial for understanding microbial adaptation in extreme environments and hold significant implications for bioprospecting initiatives. The study opens avenues for discovering novel bioactive compounds with potential applications in medicine and industry, emphasizing the importance of preserving and exploring these polyextreme ecosystems to advance biotechnological and pharmaceutical research.
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Affiliation(s)
- William Medeiros
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, São Paulo, Brazil
- Interfaculty Institute of Microbiology, and Infection Medicine Institute for Bioinformatics and Medical Informatics, German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Kelly Hidalgo
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, São Paulo, Brazil
| | - Tiago Leão
- Chemistry Institute, São Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Lucas Miguel de Carvalho
- Center for Computing in Engineering and Sciences, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology, and Infection Medicine Institute for Bioinformatics and Medical Informatics, German Centre for Infection Research (DZIF), Tübingen, Germany
| | - Valeria Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology, and Agriculture (CPQBA), Universidade Estadual de Campinas (UNICAMP), Paulínia, São Paulo, Brazil
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11
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Rodríguez-Cruz UE, Castelán-Sánchez HG, Madrigal-Trejo D, Eguiarte LE, Souza V. Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila. Front Microbiol 2024; 15:1369263. [PMID: 38873164 PMCID: PMC11169877 DOI: 10.3389/fmicb.2024.1369263] [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: 01/11/2024] [Accepted: 05/03/2024] [Indexed: 06/15/2024] Open
Abstract
A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation).
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Affiliation(s)
- Ulises E. Rodríguez-Cruz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - David Madrigal-Trejo
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Estudios del Cuaternario de Fuego, Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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12
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Llorenç-Vicedo A, Lluesma Gomez M, Zeising O, Kleiner T, Freitag J, Martinez-Hernandez F, Wilhelms F, Martinez-Garcia M. New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves. mSphere 2024; 9:e0007324. [PMID: 38666797 PMCID: PMC11237435 DOI: 10.1128/msphere.00073-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/19/2024] [Indexed: 05/30/2024] Open
Abstract
The signs of climate change are undeniable, and the impact of these changes on ecosystem function heavily depends on the response of microbes that underpin the food web. Antarctic ice shelf is a massive mass of floating ice that extends from the continent into the ocean, exerting a profound influence on global carbon cycles. Beneath Antarctic ice shelves, marine ice stores valuable genetic information, where marine microbial communities before the industrial revolution are archived. Here, in this proof-of-concept, by employing a combination of single-cell technologiesand metagenomics, we have been able to sequence frozen microbial DNA (≈300 years old) stored in the marine ice core B15 collected from the Filchnner-Ronne Ice Shelf. Metagenomic data indicated that Proteobacteria and Thaumarchaeota (e.g., Nitrosopumilus spp.), followed by Actinobacteria (e.g., Actinomarinales), were abundant. Remarkably, our data allow us to "travel to the past" and calibrate genomic and genetic evolutionary changes for ecologically relevant microbes and functions, such as Nitrosopumilus spp., preserved in the marine ice (≈300 years old) with those collected recently in seawater under an ice shelf (year 2017). The evolutionary divergence for the ammonia monooxygenase gene amoA involved in chemolithoautotrophy was about 0.88 amino acid and 2.8 nucleotide substitution rate per 100 sites in a century, while the accumulated rate of genomic SNPs was 2,467 per 1 Mb of genome and 100 years. Whether these evolutionary changes remained constant over the last 300 years or accelerated during post-industrial periods remains an open question that will be further elucidated. IMPORTANCE Several efforts have been undertaken to predict the response of microbes under climate change, mainly based on short-term microcosm experiments under forced conditions. A common concern is that manipulative experiments cannot properly simulate the response of microbes to climate change, which is a long-term evolutionary process. In this proof-of-concept study with a limited sample size, we demonstrate a novel approach yet to be fully explored in science for accessing genetic information from putative past marine microbes preserved under Antarctic ice shelves before the industrial revolution. This potentially allows us estimating evolutionary changes as exemplified in our study. We advocate for gathering a more comprehensive Antarctic marine ice core data sets across various periods and sites. Such a data set would enable the establishment of a robust baseline, facilitating a better assessment of the potential effects of climate change on key genetic signatures of microbes.
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Affiliation(s)
- Aitana Llorenç-Vicedo
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Carretera San Vicente del Raspeig, Alicante, Spain
| | - Monica Lluesma Gomez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Carretera San Vicente del Raspeig, Alicante, Spain
| | - Ole Zeising
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaveng, Germany
| | - Thomas Kleiner
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaveng, Germany
| | - Johannes Freitag
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaveng, Germany
| | - Francisco Martinez-Hernandez
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
| | - Frank Wilhelms
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaveng, Germany
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Carretera San Vicente del Raspeig, San Vicente del Raspeig, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies (IMEM), University of Alicante, Carretera San Vicente del Raspeig, Alicante, Spain
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13
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He G, Chen G, Xie Y, Swift CM, Ramirez D, Cha G, Konstantinidis KT, Radosevich M, Löffler FE. Sustained bacterial N 2O reduction at acidic pH. Nat Commun 2024; 15:4092. [PMID: 38750010 PMCID: PMC11096178 DOI: 10.1038/s41467-024-48236-x] [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: 01/12/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
Nitrous oxide (N2O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N2O to dinitrogen (N2) is the major consumption process but microbial N2O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N2O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N2O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N2O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N2O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N2O reduction between pH 4.5 and 6, highlighting microbial N2O reduction potential in acidic soils.
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Affiliation(s)
- Guang He
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Gao Chen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Yongchao Xie
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Cynthia M Swift
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Diana Ramirez
- Department of Microbiology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Frank E Löffler
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
- Department of Microbiology, The University of Tennessee Knoxville, Knoxville, TN, 37996, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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14
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Gago JF, Viver T, Urdiain M, Ferreira E, Robledo P, Rossello-Mora R. Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode. Syst Appl Microbiol 2024; 47:126506. [PMID: 38640749 DOI: 10.1016/j.syapm.2024.126506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024]
Abstract
Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Elaine Ferreira
- The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain
| | - Pedro Robledo
- Unit of Geological and Mining Institute of Spain in Balearic Islands (IGME-CSIC), Palma de Mallorca, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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15
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Gallardo P, Izquierdo M, Viver T, Bustos-Caparros E, Piras D, Vidal RM, Harmsen HJ, Farfan MJ. A metagenomic approach to unveil the association between fecal gut microbiota and short-chain fatty acids in diarrhea caused by diarrheagenic Escherichia coli in children. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:116-127. [PMID: 38799407 PMCID: PMC11122282 DOI: 10.15698/mic2024.04.820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/12/2024] [Accepted: 02/23/2024] [Indexed: 05/29/2024]
Abstract
Diarrheagenic Escherichia coli (DEC) is the main cause of diarrhea in children under five years old. The virulence of DEC is tightly regulated by environmental signals influenced by the gut microbiota and its metabolites. Short-chain fatty acids (SCFAs) are the main metabolic product of anaerobic fermentation in the gut, but their role in DEC diarrhea has not yet been established. In this study, we determine the levels of acetate, propionate, and butyrate in stool samples from children with diarrhea caused by DEC, and we identify bacteria from the fecal gut microbiota associated with the production of SCFAs. The microbiota and SCFAs levels in stool samples obtained from 40 children with diarrhea and 43 healthy children were determined by 16S rRNA gene sequencing and HPLC, respectively. Additionally, shotgun metagenomics was used to identify metagenome-assembled genomes (MAGs) in a subgroup of samples. The results showed significantly higher levels of all SCFAs tested in diarrheal samples than in healthy controls. The abundance of Streptococcus sp., Limosilactobacillus, Blautia, Escherichia, Bacteroides, Megamonas, and Roseburia was higher in the DEC group than in healthy individuals. Functional analysis of bacteria and their main metabolic pathways made it possible to identify species MAGs that could be responsible for the detected SCFAs levels in DEC-positive diarrhea. In conclusion, based on our results and published data, we suggest that SCFAs may be important in the crosstalk between the microbiota and DEC pathogens in the gut.
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Affiliation(s)
- Pablo Gallardo
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Departamento de Cirugía y Pediatría Oriente, CICA Hospital Dr. Luis Calvo Mackenna, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mariana Izquierdo
- Departamento de Cirugía y Pediatría Oriente, CICA Hospital Dr. Luis Calvo Mackenna, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Dana Piras
- Departamento de Cirugía y Pediatría Oriente, CICA Hospital Dr. Luis Calvo Mackenna, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Roberto M. Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Hermie J.M. Harmsen
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mauricio J. Farfan
- Departamento de Cirugía y Pediatría Oriente, CICA Hospital Dr. Luis Calvo Mackenna, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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16
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Wilson NG, Hernandez-Leyva A, Schwartz DJ, Bacharier LB, Kau AL. The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma. FEMS MICROBES 2024; 5:xtae010. [PMID: 38560624 PMCID: PMC10981462 DOI: 10.1093/femsmc/xtae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Asthma is a common allergic airway disease that has been associated with the development of the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing of 95 stool samples from a cross-sectional cohort of 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in adults and children 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways, which have been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes (ARGs) in people with asthma. Several differentially abundant ARGs in the asthma cohort encode resistance to macrolide antibiotics, which are often prescribed to patients with asthma. Lastly, we found that ARG and virulence factor (VF) richness in the microbiome were correlated in both cohorts. ARG and VF pairs co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are coselected and maintained in the fecal microbiota of people with asthma. Overall, our results show functional alterations via LCFA biosynthetic genes and increases in antibiotic resistance genes in the gut microbiota of subjects with moderate-to-severe asthma and could have implications for asthma management and treatment.
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Affiliation(s)
- Naomi G Wilson
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, United States
| | - Ariel Hernandez-Leyva
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, United States
| | - Drew J Schwartz
- Division of Infectious Diseases, Department of Pediatrics and Center for Women’s Infectious Disease Research, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, United States
| | - Leonard B Bacharier
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Monroe Carell Jr Children’s Hospital at Vanderbilt University Medical Center, 2200 Children's Way, Nashville, TN 37232, United States
| | - Andrew L Kau
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO 63110, United States
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17
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Zhang L, Zhao H, Qin S, Hu C, Shen Y, Qu B, Bai Y, Liu B. Genome-Resolved Metagenomics and Denitrifying Strain Isolation Reveal New Insights into Microbial Denitrification in the Deep Vadose Zone. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2323-2334. [PMID: 38267389 DOI: 10.1021/acs.est.3c06466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
The heavy use of nitrogen fertilizer in intensive agricultural areas often leads to nitrate accumulation in subsurface soil and nitrate contamination in groundwater, which poses a serious risk to public health. Denitrifying microorganisms in the subsoil convert nitrate to gaseous forms of nitrogen, thereby mitigating the leaching of nitrate into groundwater. Here, we investigated denitrifying microorganisms in the deep vadose zone of a typical intensive agricultural area in China through microcosm enrichment, genome-resolved metagenomic analysis, and denitrifying bacteria isolation. A total of 1000 metagenome-assembled genomes (MAGs) were reconstructed, resulting in 98 high-quality, dereplicated MAGs that contained denitrification genes. Among them, 32 MAGs could not be taxonomically classified at the genus or species level, indicating that a broader spectrum of taxonomic groups is involved in subsoil denitrification than previously recognized. A denitrifier isolate library was constructed by using a strategy combining high-throughput and conventional cultivation techniques. Assessment of the denitrification characteristics of both the MAGs and isolates demonstrated the dominance of truncated denitrification. Functional screening revealed the highest denitrification activity in two complete denitrifiers belonging to the genus Pseudomonas. These findings greatly expand the current knowledge of the composition and function of denitrifying microorganisms in subsoils. The constructed isolate library provided the first pool of subsoil-denitrifying microorganisms that could facilitate the development of microbe-based technologies for nitrate attenuation in groundwater.
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Affiliation(s)
- Linqi Zhang
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Huicheng Zhao
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Shuping Qin
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Chunsheng Hu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Yanjun Shen
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Baoyuan Qu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Binbin Liu
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
- Xiong'an Institute of Innovation, Chinese Academy of Sciences, Xiong'an 071700, China
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18
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Behr JH, Kuhl-Nagel T, Sommermann L, Moradtalab N, Chowdhury SP, Schloter M, Windisch S, Schellenberg I, Maccario L, Sørensen SJ, Rothballer M, Geistlinger J, Smalla K, Ludewig U, Neumann G, Grosch R, Babin D. Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere. FEMS Microbiol Ecol 2024; 100:fiae003. [PMID: 38224956 PMCID: PMC10847717 DOI: 10.1093/femsec/fiae003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 01/17/2024] Open
Abstract
Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates and rhizosphere metabolites, physiological stress indicators, and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon, and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, and Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, and ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits, and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important.
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Affiliation(s)
- Jan Helge Behr
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Theresa Kuhl-Nagel
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Loreen Sommermann
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Narges Moradtalab
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Soumitra Paul Chowdhury
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis
(COMI), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Saskia Windisch
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Ingo Schellenberg
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Lorrie Maccario
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Michael Rothballer
- Institute of Network Biology
, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany
| | - Joerg Geistlinger
- Anhalt University of Applied Sciences, Department of Agriculture
, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Uwe Ludewig
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Günter Neumann
- University of Hohenheim, Institute of Crop Science (340 h), Fruwirthstraße 20, 70599 Stuttgart, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Doreen Babin
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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19
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Freeman CN, Russell JN, Yost CK. Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system. Microbiol Spectr 2024; 12:e0283223. [PMID: 38018980 PMCID: PMC10783093 DOI: 10.1128/spectrum.02832-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.
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Affiliation(s)
- Claire N. Freeman
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Chris K. Yost
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
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20
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Filippidou S, Price A, Spencer-Jones C, Scales A, Macey MC, Franchi F, Lebogang L, Cavalazzi B, Schwenzer SP, Olsson-Francis K. Diversity of Microbial Mats in the Makgadikgadi Salt Pans, Botswana. Microorganisms 2024; 12:147. [PMID: 38257974 PMCID: PMC10818877 DOI: 10.3390/microorganisms12010147] [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: 11/21/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
The Makgadikgadi Salt Pans are the remnants of a mega paleo-lake system in the central Kalahari, Botswana. Today, the Makgadikgadi Basin is an arid to semi-arid area receiving water of meteoric origin during the short, wet season. Large microbial mats, which support primary production, are formed due to desiccation during the dry season. This study aimed to characterise the microbial diversity of the microbial mats and the underlying sediment. The focus was the Ntwetwe Pan, located west of the Makgadikgadi Basin. Metagenomic analyses demonstrated that the mats consisted of a high relative abundance of Cyanobacteriota (synonym Cyanobacteria) (20.50-41.47%), Pseudomonadota (synonym Proteobacteria) (15.71 to 32.18%), and Actinomycetota (synonym Actinobacteria) (8.53-32.56%). In the underlying sediments, Pseudomonadota, Actinomycetota, and Euryarchaeota represented over 70% of the community. Localised fluctuations in water content and pH did not significantly affect the microbial diversity of the sediment or the mats.
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Affiliation(s)
- Sevasti Filippidou
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
- School of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alex Price
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Charlotte Spencer-Jones
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
- Department of Geography, Durham University, Durham DH1 3LE, UK
| | - Anthony Scales
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Michael C. Macey
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Fulvio Franchi
- Earth and Environmental Science Department, Botswana International University of Science and Technology, Palapye 10071, Botswana;
- School of Geosciences, University of the Witwatersrand, Johannesburg 2001, South Africa
| | - Lesedi Lebogang
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye 10071, Botswana;
| | - Barbara Cavalazzi
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, 40126 Bologna, Italy;
- Department of Geology, University of Johannesburg, Johannesburg 2006, South Africa
| | - Susanne P. Schwenzer
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
| | - Karen Olsson-Francis
- AstrobiologyOU, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; (S.F.); (A.P.); (C.S.-J.); (A.S.); (M.C.M.); (S.P.S.)
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21
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Miksch S, Orellana LH, Oggerin de Orube M, Vidal-Melgosa S, Solanki V, Hehemann JH, Amann R, Knittel K. Taxonomic and functional stability overrules seasonality in polar benthic microbiomes. THE ISME JOURNAL 2024; 18:wrad005. [PMID: 38365229 PMCID: PMC10811738 DOI: 10.1093/ismejo/wrad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 02/18/2024]
Abstract
Coastal shelf sediments are hot spots of organic matter mineralization. They receive up to 50% of primary production, which, in higher latitudes, is strongly seasonal. Polar and temperate benthic bacterial communities, however, show a stable composition based on comparative 16S rRNA gene sequencing despite different microbial activity levels. Here, we aimed to resolve this contradiction by identifying seasonal changes at the functional level, in particular with respect to algal polysaccharide degradation genes, by combining metagenomics, metatranscriptomics, and glycan analysis in sandy surface sediments from Isfjorden, Svalbard. Gene expressions of diverse carbohydrate-active enzymes changed between winter and spring. For example, β-1,3-glucosidases (e.g. GH30, GH17, GH16) degrading laminarin, an energy storage molecule of algae, were elevated in spring, while enzymes related to α-glucan degradation were expressed in both seasons with maxima in winter (e.g. GH63, GH13_18, and GH15). Also, the expression of GH23 involved in peptidoglycan degradation was prevalent, which is in line with recycling of bacterial biomass. Sugar extractions from bulk sediments were low in concentrations during winter but higher in spring samples, with glucose constituting the largest fraction of measured monosaccharides (84% ± 14%). In porewater, glycan concentrations were ~18-fold higher than in overlying seawater (1107 ± 484 vs. 62 ± 101 μg C l-1) and were depleted in glucose. Our data indicate that microbial communities in sandy sediments digest and transform labile parts of photosynthesis-derived particulate organic matter and likely release more stable, glucose-depleted residual glycans of unknown structures, quantities, and residence times into the ocean, thus modulating the glycan composition of marine coastal waters.
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Affiliation(s)
- Sebastian Miksch
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Luis H Orellana
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Monike Oggerin de Orube
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Silvia Vidal-Melgosa
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Vipul Solanki
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM MPG Bridge Group Marine Glycobiology, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
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22
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Roothans N, Gabriëls M, Abeel T, Pabst M, van Loosdrecht MCM, Laureni M. Aerobic denitrification as an N2O source from microbial communities. THE ISME JOURNAL 2024; 18:wrae116. [PMID: 38913498 PMCID: PMC11272060 DOI: 10.1093/ismejo/wrae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/26/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (>6.5 mg/L). N2O accounted for up to one-quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover-a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesised enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.
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Affiliation(s)
- Nina Roothans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Minke Gabriëls
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, van Mourik Broekmanweg 6, Delft 2628 XE, the Netherlands
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, United States
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Michele Laureni
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, the Netherlands
- Department of Water Management, Delft University of Technology, Stevinweg 1, 2628 CN Delft, the Netherlands
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23
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Ramos-Barbero MD, Aldeguer-Riquelme B, Viver T, Villamor J, Carrillo-Bautista M, López-Pascual C, Konstantinidis KT, Martínez-García M, Santos F, Rossello-Mora R, Antón J. Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains. THE ISME JOURNAL 2024; 18:wrae208. [PMID: 39579348 PMCID: PMC11631230 DOI: 10.1093/ismejo/wrae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 10/03/2024] [Accepted: 11/21/2024] [Indexed: 11/25/2024]
Abstract
Viruses shape microbial community structure and activity through the control of population diversity and cell abundances. Identifying and monitoring the dynamics of specific virus-host pairs in nature is hampered by the limitations of culture-independent approaches such as metagenomics, which do not always provide strain-level resolution, and culture-based analyses, which eliminate the ecological background and in-situ interactions. Here, we have explored the interaction of a specific "autochthonous" host strain and its viruses within a natural community. Bacterium Salinibacter ruber strain M8 was spiked into its environment of isolation, a crystallizer pond from a coastal saltern, and the viral and cellular communities were monitored for one month using culture, metagenomics, and microscopy. Metagenome sequencing indicated that the M8 abundance decreased sharply after being added to the pond, likely due to forces other than viral predation. However, the presence of M8 selected for two species of a new viral genus, Phoenicisalinivirus, for which 120 strains were isolated. During this experiment, an assemblage of closely related viral genomic variants was replaced by a single population with the ability to infect M8, a scenario which was compatible with the selection of a genomic variant from the rare biosphere. Further analysis implicated a viral genomic region putatively coding for a tail fiber protein to be responsible for M8 specificity. Our results indicate that low abundance viral genotypes provide a viral seed bank that allows for a highly specialized virus-host response within a complex ecological background.
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Affiliation(s)
- María Dolores Ramos-Barbero
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Diagonal 643. Annex. Floor 0, Barcelona E-08028, Spain
| | - Borja Aldeguer-Riquelme
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332, GA, United States
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles 07190, Spain
| | - Judith Villamor
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
| | - Miryam Carrillo-Bautista
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
| | - Cristina López-Pascual
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
| | | | - Manuel Martínez-García
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles 07190, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante 03690, Spain
- Multidisciplinary Institute of Environmental Studies Ramon Margalef, Alicante 03690, Spain
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24
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Ramos-Barbero MD, Gómez-Gómez C, Vique G, Sala-Comorera L, Rodríguez-Rubio L, Muniesa M. Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection. THE ISME JOURNAL 2024; 18:wrae192. [PMID: 39361891 PMCID: PMC11475920 DOI: 10.1093/ismejo/wrae192] [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: 05/02/2024] [Revised: 07/25/2024] [Accepted: 10/01/2024] [Indexed: 10/05/2024]
Abstract
The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical distribution around the globe of other members of the order Crassvirales remains unknown. To determine this, a recruitment analysis using 91 complete, non-redundant genomes of crAss-like phages in human and animal viromes revealed that only 13 crAss-like phages among the 91 phages analyzed were highly specific to humans, and p-crAssphage was not in this group. Investigations to elucidate whether any characteristic of the phages was responsible for their prevalence in humans showed that the 13 human crAss-like phages do not share a core genome. Phylogenomic analysis placed them in three independent families, indicating that within the Crassvirales group, human specificity is likely not a feature of a common ancestor but rather was introduced on separate/independent occasions in their evolutionary history. The 13 human crAss-like phages showed variable geographical distribution across human metagenomes worldwide, with some being more prevalent in certain countries than in others, but none being universally identified. The varied geographical distribution and the absence of a phylogenetic relationship among the human crAss-like phages are attributed to the emergence and dissemination of their bacterial host, the symbiotic human strains of Bacteroides, across various human populations occupying diverse ecological niches worldwide.
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Affiliation(s)
- María Dolores Ramos-Barbero
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 643, Prevosti Building, Floor 0. Barcelona E-08028, Spain
| | - Clara Gómez-Gómez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 643, Prevosti Building, Floor 0. Barcelona E-08028, Spain
| | - Gloria Vique
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 643, Prevosti Building, Floor 0. Barcelona E-08028, Spain
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 643, Prevosti Building, Floor 0. Barcelona E-08028, Spain
| | - Lorena Rodríguez-Rubio
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 643, Prevosti Building, Floor 0. Barcelona E-08028, Spain
| | - Maite Muniesa
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal, 643, Prevosti Building, Floor 0. Barcelona E-08028, Spain
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25
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Jesser KJ, Trueba G, Konstantinidis KT, Levy K. Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador. Gut Microbes 2023; 15:2281010. [PMID: 37992406 PMCID: PMC10730187 DOI: 10.1080/19490976.2023.2281010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/05/2023] [Indexed: 11/24/2023] Open
Abstract
A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea. The factors responsible for the development of diarrhea symptoms, or lack thereof, remain unclear. Here, we used DEC isolate genome and whole stool microbiome data from a case-control study of diarrhea in Ecuador to examine factors associated with diarrhea symptoms accompanying DEC carriage. We investigated i) pathogen abundance, ii) gut microbiome characteristics, and iii) strain-level pathogen characteristics from DEC infections with diarrhea symptoms (symptomatic infections) and without diarrhea symptoms (asymptomatic infections). We also included data from individuals with and without diarrhea who were not infected with DEC (uninfected cases and controls). i) E. coli relative abundance in the gut microbiome was highly variable, but higher on-average in individuals with symptomatic compared to asymptomatic DEC infections. Similarly, the number and relative abundances of virulence genes in the gut were higher in symptomatic than asymptomatic DEC infections. ii) Measures of microbiome diversity were similar regardless of diarrhea symptoms or DEC carriage. Proteobacterial families that have been described as pathobionts were enriched in symptomatic infections and uninfected cases, whereas potentially beneficial taxa, including the Bacteroidaceae and Bifidobacteriaceae, were more abundant in individuals without diarrhea. An analysis of high-level gene functions recovered in metagenomes revealed that genes that were differentially abundant by diarrhea and DEC infection status were more abundant in symptomatic than asymptomatic DEC infections. iii) DEC isolates from symptomatic versus asymptomatic individuals showed no significant differences in virulence or accessory gene content, and there was no phylogenetic signal associated with diarrhea symptoms. Together, these data suggest signals that distinguish symptomatic from asymptomatic DEC infections. In particular, the abundance of E. coli, the virulence gene content of the gut microbiome, and the taxa present in the gut microbiome have an apparent role.
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Affiliation(s)
- Kelsey J Jesser
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
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26
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Ke Y, Sun W, Liu S, Zhu Y, Yan S, Chen X, Xie S. Seasonal variations of biofilm C, N and S cycling genes in a pilot-scale chlorinated drinking water distribution system. WATER RESEARCH 2023; 247:120759. [PMID: 37897999 DOI: 10.1016/j.watres.2023.120759] [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: 08/04/2023] [Revised: 10/10/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023]
Abstract
Biofilms in drinking water distribution systems (DWDS) host diverse microorganisms. However, the functional attributes of DWDS biofilms and their associations with seasonality remain unclear. This study aims to characterize variations in the microbial metabolic traits of DWDS biofilms collected during different seasons, using a pilot-scale DWDS in dark under plug-flow conditions during one-year operation period. Network analysis was used to predict the functional gene hosts. The overall functional attributes determined by shotgun metagenomics exhibited significant differences among seasons. Genes associated with aromatic metabolism, fatty acid biosynthesis and degradation, and capsular extracellular polymeric substance (EPS) were significantly upregulated in summer owing to the higher temperatures and chlorine in the influent of the DWDS. Moreover, the pathways associated with nitrogen, sulfur, glycolysis, and tricarboxylic acid (TCA) cycling, as well as carbon fixation were reconstructed and displayed according to the sampling season. Nitrogen reduction pathways [dissimilatory nitrate reduction to ammonium (DNRA) 73 %, assimilatory nitrate reduction to ammonium (ANRA) 21 %] were identified in DWDS biofilms, but nitrogen oxidation pathways were not. Sulfur cycling were involved in diverse pathways and genes. Glycolysis and TCA cycling offered electron donors and energy sources for nitrogen and sulfur reduction in biofilms. Carbon fixation was observed in DWDS biofilms, with the predominant pathway for fixing carbon dioxide being the reductive citrate cycle (38 %). Constructed functional gene networks composed of carbon, nitrogen, and sulfur cycling-related genes demonstrated synergistic effects (Positive proportion: 63.52-71.09 %). In addition, from spring to autumn, the network complexity decreased and network modularity increased. The assembly mechanism of carbon, nitrogen and sulfur cycling-related genes was driven by stochastic processes for all samples. These results highlight the diverse functional genes in DWDS biofilms, their synergetic interrelationships, and the seasonality effect on functional attributes.
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Affiliation(s)
- Yanchu Ke
- School of Environment, Tsinghua University, Beijing 100084, China; State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Wenjun Sun
- School of Environment, Tsinghua University, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China.
| | - Shuming Liu
- School of Environment, Tsinghua University, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China
| | - Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuang Yan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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Font-Verdera F, Liébana R, Rossello-Mora R, Viver T. Impact of dilution on stochastically driven methanogenic microbial communities of hypersaline anoxic sediments. FEMS Microbiol Ecol 2023; 99:fiad146. [PMID: 37989854 PMCID: PMC10673710 DOI: 10.1093/femsec/fiad146] [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: 04/27/2023] [Revised: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023] Open
Abstract
Sediments underlying the solar salterns of S'Avall are anoxic hypersaline ecosystems dominated by anaerobic prokaryotes, and with the especial relevance of putative methanogenic archaea. Slurries from salt-saturated sediments, diluted in a gradient of salinity and incubated for > 4 years revealed that salt concentration was the major selection force that deterministically structured microbial communities. The dominant archaea in the original communities showed a decrease in alpha diversity with dilution accompanied by the increase of bacterial alpha diversity, being highest at 5% salts. Correspondingly, methanogens decreased and in turn sulfate reducers increased with decreasing salt concentrations. Methanogens especially dominated at 25%. Different concentrations of litter of Posidonia oceanica seagrass added as a carbon substrate, did not promote any clear relevant effect. However, the addition of ampicillin as selection pressure exerted important effects on the assemblage probably due to the removal of competitors or enhancers. The amended antibiotic enhanced methanogenesis in the concentrations ≤ 15% of salts, whereas it was depleted at salinities ≥ 20% revealing key roles of ampicillin-sensitive bacteria.
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Affiliation(s)
- Francisca Font-Verdera
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
| | - Raquel Liébana
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
- AZTI, Basque Research Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, 48395 Sukarrieta, Bizkaia, Spain
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
| | - Tomeu Viver
- Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marquès, 21, 07190 Esporles, Illes Balears, SPAIN
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
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Wegner CE, Stahl R, Velsko I, Hübner A, Fagernäs Z, Warinner C, Lehmann R, Ritschel T, Totsche KU, Küsel K. A glimpse of the paleome in endolithic microbial communities. MICROBIOME 2023; 11:210. [PMID: 37749660 PMCID: PMC10518947 DOI: 10.1186/s40168-023-01647-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/09/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards. RESULTS By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past. CONCLUSIONS Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.
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Affiliation(s)
- Carl-Eric Wegner
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Irina Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Alex Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, USA
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Robert Lehmann
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Thomas Ritschel
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geosciences, Friedrich Schiller University Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743, Jena, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany.
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29
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Hansen ZA, Vasco K, Rudrik JT, Scribner KT, Zhang L, Manning SD. Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts. Sci Rep 2023; 13:15524. [PMID: 37726374 PMCID: PMC10509190 DOI: 10.1038/s41598-023-42822-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/15/2023] [Indexed: 09/21/2023] Open
Abstract
Enteric pathogens cause widespread foodborne illness and are increasingly resistant to important antibiotics yet their ecological impact on the gut microbiome and resistome is not fully understood. Herein, shotgun metagenome sequencing was applied to stool DNA from 60 patients (cases) during an enteric bacterial infection and after recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) with greater resistome diversity than the follow-up samples (p < 0.001), while follow-ups had more diverse gut microbiota (p < 0.001). Although cases were primarily defined by genera Escherichia, Salmonella, and Shigella along with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and resistance genes for tetracyclines, macrolides, lincosamides, and streptogramins, and aminoglycosides. A host-tracking analysis revealed that Escherichia was the primary bacterial host of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamase (ESBL) genes were identified during infection, with some detectable upon recovery, highlighting the potential for gene transfer within the community. Because of the increasing incidence of disease caused by foodborne pathogens and their role in harboring and transferring resistance determinants, this study enhances our understanding of how enteric infections impact human gut ecology.
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Affiliation(s)
- Zoe A Hansen
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Karla Vasco
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - James T Rudrik
- Bureau of Laboratories, The Michigan Department of Health and Human Services, Lansing, MI, 48906, USA
| | - Kim T Scribner
- Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Lixin Zhang
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
- Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, 48824, USA
| | - Shannon D Manning
- Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.
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30
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Ke Y, Sun W, Chen X, Zhu Y, Guo X, Yan W, Xie S. Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:11430-11441. [PMID: 37478472 DOI: 10.1021/acs.est.3c01980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Understanding the biofilm microbiome and antibiotic resistome evolution in drinking water distribution systems (DWDSs) is crucial to ensure the safety of drinking water. We explored the 10 month evolution of the microbial community, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) co-existing with ARGs and pathogenic ARG hosts, and the ARG driving factors in DWDS biofilms using metagenomics assembly. Sampling season was critical in determining the microbial community and antibiotic resistome shift. Pseudomonas was the primary biofilm colonizer, and biofilms diversified more as the formation time increased. Most genera tended to cooperate to adapt to an oligotrophic environment with disinfectant stress. Biofilm microbial community and antibiotic resistome assembly were mainly determined by stochastic processes and changed with season. Metagenome assembly provided the occurrence and fates of MGEs co-existing with ARGs and ARG hosts in DWDS biofilms. The abundance of ARG- and MGE-carrying pathogen Stenotrophomonas maltophilia was high in summer. It primarily harbored the aph(3)-IIb, multidrug transporter, smeD, and metallo-beta-lactamase ARGs, which were transferred via recombination. The microbial community was the most crucial factor driving the antibiotic resistance shift. We provide novel insights about the evolution of pathogens and ARGs and their correlations in DWDS biofilms to ensure the safety of drinking water.
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Affiliation(s)
- Yanchu Ke
- School of Environment, Tsinghua University, Beijing 100084, China
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Wenjun Sun
- School of Environment, Tsinghua University, Beijing 100084, China
- Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ying Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Xu Guo
- Fangshan District Water Bureau, Beijing 102445, China
| | - Weixin Yan
- Beijing BiSheng United Water Company, Beijing 102400, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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31
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de Nies L, Galata V, Martin-Gallausiaux C, Despotovic M, Busi SB, Snoeck CJ, Delacour L, Budagavi DP, Laczny CC, Habier J, Lupu PC, Halder R, Fritz JV, Marques T, Sandt E, O'Sullivan MP, Ghosh S, Satagopam V, Krüger R, Fagherazzi G, Ollert M, Hefeng FQ, May P, Wilmes P. Altered infective competence of the human gut microbiome in COVID-19. MICROBIOME 2023; 11:46. [PMID: 36894986 PMCID: PMC9995755 DOI: 10.1186/s40168-023-01472-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. RESULTS We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls. CONCLUSIONS Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.
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Affiliation(s)
- Laura de Nies
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Valentina Galata
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camille Martin-Gallausiaux
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Milena Despotovic
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Susheel Bhanu Busi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Chantal J Snoeck
- Clinical and Applied Virology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Lea Delacour
- Luxembourg Centre for Systems Biomedicine, LCSB Operations, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Deepthi Poornima Budagavi
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Cédric Christian Laczny
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Janine Habier
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paula-Cristina Lupu
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Scientific Central Services, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Joëlle V Fritz
- Transversal Translation Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Taina Marques
- Translational Neuroscience Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Estelle Sandt
- Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Marc Paul O'Sullivan
- Translational Medicine Operations Hub, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Soumyabrata Ghosh
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Venkata Satagopam
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- Transversal Translation Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
- Translational Neuroscience Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Guy Fagherazzi
- Deep Digital Phenotyping Research Unit, Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Luxembourg
- Department of Dermatology and Allergy Centre, Odense University Hospital, Odense, Denmark
| | - Feng Q Hefeng
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Luxembourg
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Wilmes
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367, Belvaux, Luxembourg.
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32
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Zhang Z, Zhang L, Zhang G, Zhao Z, Wang H, Ju F. Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research. Microbiol Spectr 2023; 11:e0428222. [PMID: 36744896 PMCID: PMC10101064 DOI: 10.1128/spectrum.04282-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/18/2023] [Indexed: 02/07/2023] Open
Abstract
In the last decade, metagenomics has greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads raised mainly from the preparation of metagenomic DNA sequencing libraries and their impacts on metagenomic assembly and binning have never been brought to attention. Here, we explicitly investigated the effects of duplicate reads on metagenomic assemblies and binning based on analyses of five groups of representative metagenomes with distinct microbiome complexities. Our results showed that deduplication considerably increased the binning yields (by 3.5% to 80%) for most of the metagenomic data sets examined thanks to the improved contig length and coverage profiling of metagenome-assembled contigs, whereas it slightly decreased the binning yields of metagenomes with low complexity (e.g., human gut metagenomes). Specifically, 411 versus 397, 331 versus 317, 104 versus 88, and 9 versus 5 metagenome-assembled genomes (MAGs) were recovered from MEGAHIT assemblies of bioreactor sludge, surface water, lake sediment, and forest soil metagenomes, respectively. Noticeably, deduplication significantly reduced the computational costs of the metagenomic assembly, including the elapsed time (9.0% to 29.9%) and the maximum memory requirement (4.3% to 37.1%). Collectively, we recommend the removal of duplicate reads in metagenomes with high complexity before assembly and binning analyses, for example, the forest soil metagenomes examined in this study. IMPORTANCE Duplicated reads in shotgun metagenomes are usually considered technical artifacts. Their presence in metagenomes would theoretically not only introduce bias into the quantitative analysis but also result in mistakes in the coverage profile, leading to adverse effects on or even failures in metagenomic assembly and binning, as the widely used metagenome assemblers and binners all need coverage information for graph partitioning and assembly binning, respectively. However, this issue was seldom noticed, and its impacts on downstream essential bioinformatic procedures (e.g., assembly and binning) remained unclear. In this study, we comprehensively evaluated for the first time the implications of duplicate reads for the de novo assembly and binning of real metagenomic data sets by comparing the assembly qualities, binning yields, and requirements for computational resources with and without the removal of duplicate reads. It was revealed that deduplication considerably increased the binning yields of metagenomes with high complexity and significantly reduced the computational costs, including the elapsed time and the maximum memory requirement, for most of the metagenomes studied. These results provide empirical references for more cost-efficient metagenomic analyses in microbiome research.
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Affiliation(s)
- Zhiguo Zhang
- College of Environmental and Resources Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Lu Zhang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Guoqing Zhang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Ze Zhao
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Hui Wang
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
| | - Feng Ju
- Research Center for Industries of the Future, Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
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33
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Wilson NG, Hernandez-Leyva A, Schwartz DJ, Bacharier LB, Kau AL. The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522677. [PMID: 36711684 PMCID: PMC9882014 DOI: 10.1101/2023.01.03.522677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Asthma is a common allergic airway disease that develops in association with the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing of 95 stool samples from 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in children and adults 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways which have been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes (ARGs) in people with asthma. One differentially abundant ARG was a macrolide resistance marker, ermF, which significantly co-occurred with the Bacteroides fragilis toxin, suggesting a possible relationship between enterotoxigenic B. fragilis, antibiotic resistance, and asthma. Lastly, we found multiple virulence factor (VF) and ARG pairs that co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are co-selected and maintained in the fecal microbiota of people with asthma. Overall, our results show functional alterations via LCFA biosynthetic genes and increases in antibiotic resistance genes in the gut microbiota of subjects with moderate-to-severe asthma and could have implications for asthma management and treatment.
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Affiliation(s)
- Naomi G. Wilson
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ariel Hernandez-Leyva
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Drew J. Schwartz
- Division of Infectious Diseases, Department of Pediatrics and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Leonard B. Bacharier
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Monroe Carell Jr Children’s Hospital at Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew L. Kau
- Division of Allergy and Immunology, Department of Medicine and Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
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34
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Xu Y, You G, Yin J, Zhang M, Peng D, Xu J, Yang S, Hou J. Salt tolerance evolution facilitates antibiotic resistome in soil microbiota: Evidences from dissemination evaluation, hosts identification and co-occurrence exploration. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120830. [PMID: 36481466 DOI: 10.1016/j.envpol.2022.120830] [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: 08/10/2022] [Revised: 11/26/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Salinity is considered as one of the vital factors affecting the profiles of antibiotic resistance genes (ARGs) in soils, whereby its roles in shaping the antibiotic resistome were still poorly understood. Here, metagenomic analysis was conducted to track the ARGs distributions and dissemination in soils during salt accumulation and desalinization processes. Neutral-salt accumulation for 45 and 90 days significantly increased the relative abundances of ARGs and mobile genetic elements (MGEs) carrying antibiotic resistance contigs (ARCs). The ARGs within antibiotic efflux and target protection families primarily carried by Streptomyces, Nocardioides, Rhodanobacter and Monashia were largely enriched by salinity. The ARGs subtypes of the resistance-nodulation-division (RND) family, ATP-binding cassette (ABC) family, rRNA methyltransferase and other efflux were closely associated with MGEs, contributing to the enrichment of ARGs. Moreover, the ARGs subtypes and transposons were genetically linked with the salt-tolerance mechanisms of organic osmolyte transporters and K+ uptake proteins on the same ARC, demonstrating the coselection of ARGs and halotolerant genes. Furthermore, the antibiotic resistome could recover to a normal state after the prolonged incubation by alleviating salt stress. Nevertheless, the acquisition of ARGs by opportunistic pathogens after salt treatment was increased, serving to prioritize further efforts on the health risks correlated with resistance propagation and human exposure in saline soils.
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Affiliation(s)
- Yi Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098.
| | - Guoxiang You
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
| | - Jinbao Yin
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
| | - Mairan Zhang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098
| | - Dengyun Peng
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098
| | - Junzeng Xu
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China
| | - Shihong Yang
- College of Agricultural Science and Engineering, Hohai University, Nanjing, People's Republic of China, 210098; State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Hohai University, Nanjing 210098, PR China.
| | - Jun Hou
- Key Laboratory of Integrated Regulation and Resources Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, People's Republic of China, 210098
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Wright AT, Hudson LA, Garcia WL. Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes. Isr J Chem 2023. [DOI: 10.1002/ijch.202200099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Aaron T. Wright
- Department of Biology Baylor University Waco Texas 76798 USA
- Department of Chemistry and Biochemistry Baylor University Waco Texas 76798 USA
| | - LaRae A. Hudson
- Department of Biology Baylor University Waco Texas 76798 USA
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36
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Shen J, McFarland AG, Blaustein RA, Rose LJ, Perry-Dow KA, Moghadam AA, Hayden MK, Young VB, Hartmann EM. An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics. MICROBIOME 2022; 10:206. [PMID: 36457108 PMCID: PMC9716758 DOI: 10.1186/s40168-022-01412-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources. RESULTS The workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes. Video Abstract CONCLUSIONS: This workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.
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Affiliation(s)
- Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA.
| | - Alexander G McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Ryan A Blaustein
- Department of Nutrition and Food Science, University of Maryland, College Park, USA
| | - Laura J Rose
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Anahid A Moghadam
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
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Ayala-Muñoz D, Macalady JL, Sánchez-España J, Falagán C, Couradeau E, Burgos WD. Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake. THE ISME JOURNAL 2022; 16:2666-2679. [PMID: 36123522 PMCID: PMC9666448 DOI: 10.1038/s41396-022-01320-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022]
Abstract
Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.
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Affiliation(s)
- Diana Ayala-Muñoz
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA, 16802, USA.
| | - Jennifer L Macalady
- Department of Geosciences, The Pennsylvania State University, 211 Deike Building University Park, University Park, PA, 16802, USA
| | - Javier Sánchez-España
- Centro Nacional Instituto Geológico Minero de España (IGME), CSIC, Calera 1, 28760 Tres Cantos, Madrid, Spain
| | - Carmen Falagán
- School of Biological Sciences, University of Portsmouth, King Henry Building, King Henry 1st St., Portsmouth, PO1 2DY, UK
| | - Estelle Couradeau
- Department of Ecosystem Science and Management, The Pennsylvania State University, 50 ASI University Park, University Park, PA, 16802, USA
| | - William D Burgos
- Department of Civil and Environmental Engineering, The Pennsylvania State University, 212 Sackett Building, University Park, PA, 16802, USA.
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Wang L, Shen Z, Cheng X, Hwang JS, Guo Y, Sun M, Cao J, Liu R, Fang J. Metagenomic insights into the functions of microbial communities in sulfur-rich sediment of a shallow-water hydrothermal vent off Kueishan Island. Front Microbiol 2022; 13:992034. [DOI: 10.3389/fmicb.2022.992034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
Hydrothermal vent (HTV) systems are important habitats for understanding the biological processes of extremophiles on Earth and their relative contributions to material and energy cycles in the ocean. Current understanding on hydrothermal systems have been primarily focused on deep-sea HTVs, and little is known about the functions and metabolisms of microorganisms in shallow-water HTVs (SW-HTVs), which are distinguished from deep-sea HTVs by a depth limit of 200 m. In this study, we analyzed metagenomes of sulfur-rich sediment samples collected from a SW-HTV of Kueishan Island, located in a marginal sea of the western Pacific Ocean. Comparing with a previously published report of pelagic samples from the nearby sampling site, microbial communities in the SW-HTV sediments enriching with genes of both aerobic and anaerobic respiration inferred variable environments in the tested sediments. Abundant genes of energy metabolism encoding sulfur oxidation, H2 oxidation, and carbon fixation were detected from the sediment samples. Sixty-eight metagenome-assembled-genomes (MAGs) were reconstructed to further understand the metabolism and potential interactions between different microbial taxa in the SW-HTVs sediment. MAGs with the highest abundant were chemolithotrophic sulfur-oxidization bacteria, including Sulfurovum represented Campylobacteria involved sox multienzyme, sulfide oxidation genes and rTCA cycle, and Gammaproteobacteria involved dsr gene and CBB cycle. In addition, Desulfobacterota with the potential to participate in sulfur-disproportionating processes also had higher abundance than the sample’s overall mean value. The interaction of these bacterial groups allows the microbial communities to efficiently metabolize a large variety of sulfur compounds. In addition, the potential to use simple organic carbon, such as acetate, was found in chemolithotrophic Campylobacterial MAGs. Collectively, our results revealed the complexity of environmental conditions of the vent sediment and highlight the interactive relationships of the dominant microbial populations in driving sulfur cycles in the SW-HTV sediments off Kueishan Island.
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39
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Kim M, Rhee C, Wells M, Shin J, Lee J, Shin SG. Key players in syntrophic propionate oxidation revealed by metagenome-assembled genomes from anaerobic digesters bioaugmented with propionic acid enriched microbial consortia. Front Microbiol 2022; 13:968416. [DOI: 10.3389/fmicb.2022.968416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
Propionic acid (HPr) is frequently accumulated in anaerobic digesters due to its thermodynamically unfavorable degradation reaction. Here, we identify key players in HPr oxidation and organic overloading recovery from metagenome-assembled genomes (MAGs) recovered from anaerobic digesters inoculated with HPr-enriched microbial consortia before initiating organic overloading. Two independent HPr-enrichment cultures commonly selected two uncultured microorganisms represented with high relative abundance: Methanoculleus sp002497965 and JABUEY01 sp013314815 (a member of the Syntrophobacteraceae family). The relative abundance of JABUEY01 sp013314815 was 60 times higher in bioaugmented bioreactors compared to their unaugmented counterparts after recovery from organic overloading. Genomic analysis of JABUEY01 sp013314815 revealed its metabolic potential for syntrophic propionate degradation when partnered with hydrogenotrophic methanogens (e.g., Methanoculleus sp002497965) via the methylmalonyl-CoA pathway. Our results identified at least two key species that are responsible for efficient propionate removal and demonstrate their potential applications as microbial cocktails for stable AD operation.
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40
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Yi X, Liang JL, Su JQ, Jia P, Lu JL, Zheng J, Wang Z, Feng SW, Luo ZH, Ai HX, Liao B, Shu WS, Li JT, Zhu YG. Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes. THE ISME JOURNAL 2022; 16:2099-2113. [PMID: 35688988 PMCID: PMC9381775 DOI: 10.1038/s41396-022-01258-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 04/18/2023]
Abstract
Mining is among the human activities with widest environmental impacts, and mining-impacted environments are characterized by high levels of metals that can co-select for antibiotic resistance genes (ARGs) in microorganisms. However, ARGs in mining-impacted environments are still poorly understood. Here, we conducted a comprehensive study of ARGs in such environments worldwide, taking advantage of 272 metagenomes generated from a global-scale data collection and two national sampling efforts in China. The average total abundance of the ARGs in globally distributed studied mine sites was 1572 times per gigabase, being rivaling that of urban sewage but much higher than that of freshwater sediments. Multidrug resistance genes accounted for 40% of the total ARG abundance, tended to co-occur with multimetal resistance genes, and were highly mobile (e.g. on average 16% occurring on plasmids). Among the 1848 high-quality metagenome-assembled genomes (MAGs), 85% carried at least one multidrug resistance gene plus one multimetal resistance gene. These high-quality ARG-carrying MAGs considerably expanded the phylogenetic diversity of ARG hosts, providing the first representatives of ARG-carrying MAGs for the Archaea domain and three bacterial phyla. Moreover, 54 high-quality ARG-carrying MAGs were identified as potential pathogens. Our findings suggest that mining-impacted environments worldwide are underexplored hotspots of multidrug resistance genes.
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Affiliation(s)
- Xinzhu Yi
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jie-Liang Liang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Pu Jia
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jing-Li Lu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Jin Zheng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Zhang Wang
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Shi-Wei Feng
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
| | - Zhen-Hao Luo
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Hong-Xia Ai
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Bin Liao
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Wen-Sheng Shu
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China
- Guangdong Provincial Key Laboratory of Chemical Pollution, South China Normal University, Guangzhou, 510006, PR China
| | - Jin-Tian Li
- Institute of Ecological Science, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, PR China.
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
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41
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Ray AE, Zaugg J, Benaud N, Chelliah DS, Bay S, Wong HL, Leung PM, Ji M, Terauds A, Montgomery K, Greening C, Cowan DA, Kong W, Williams TJ, Hugenholtz P, Ferrari BC. Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. THE ISME JOURNAL 2022; 16:2547-2560. [PMID: 35933499 PMCID: PMC9561532 DOI: 10.1038/s41396-022-01298-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022]
Abstract
Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.
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42
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Capo E, Peterson BD, Kim M, Jones DS, Acinas SG, Amyot M, Bertilsson S, Björn E, Buck M, Cosio C, Elias DA, Gilmour C, Goñi Urriza MS, Gu B, Lin H, Liu YR, McMahon K, Moreau JW, Pinhassi J, Podar M, Puente-Sánchez F, Sánchez P, Storck V, Tada Y, Vigneron A, Walsh D, Vandewalle-Capo M, Bravo AG, Gionfriddo C. A consensus protocol for the recovery of mercury methylation genes from metagenomes. Mol Ecol Resour 2022; 23:190-204. [PMID: 35839241 PMCID: PMC10087281 DOI: 10.1111/1755-0998.13687] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/24/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022]
Abstract
Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-MATE (Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on co-assembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a co-assembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.
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Affiliation(s)
- Eric Capo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain.,Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Benjamin D Peterson
- Department of Bacteriology, University of Wisconsin at Madison, 53706, Madison, WI, USA
| | - Minjae Kim
- Natural Resource Ecology Laboratory, Colorado State University, 80523, Fort Collins, CO, USA
| | - Daniel S Jones
- Department of Earth and Environmental Science, New Mexico Institute of Mining and Technology, 87801, Socorro, NM, USA.,National Cave and Karst Research Institute, 88220, Carlsbad, NM, USA
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain
| | - Marc Amyot
- Department of Biological Sciences, University of Montréal, Montréal, QC, H3C 5J9, Canada
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, 90736, Umeå, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Claudia Cosio
- University of Reims Champagne-Ardenne, 51100, Reims, France
| | | | - Cynthia Gilmour
- Smithsonian Environmental Research Center, 21037, Edgewater, MD, USA
| | | | - Baohua Gu
- Oak Ridge National Lab, 37830, Oak Ridge, TN, USA
| | - Heyu Lin
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, 3010, Parkville, VIC, Australia
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Katherine McMahon
- Department of Bacteriology, University of Wisconsin at Madison, 53706, Madison, WI, USA
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, G12 8RZ, Glasgow, UK
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, 39231, Kalmar, Sweden
| | - Mircea Podar
- Oak Ridge National Lab, 37830, Oak Ridge, TN, USA
| | - Fernando Puente-Sánchez
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain
| | - Veronika Storck
- Department of Biological Sciences, University of Montréal, Montréal, QC, H3C 5J9, Canada
| | - Yuya Tada
- National Institute for Minamata Disease, Department of Environment and Public Health, Kumamoto, 867-0008, Japan
| | - Adrien Vigneron
- University of Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, 64000, France
| | - David Walsh
- Department of Biology, Concordia University, Montreal, Quebec H4BIR6, Canada
| | - Marine Vandewalle-Capo
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Andrea G Bravo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain
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Lee JY, Mitchell HD, Burnet MC, Wu R, Jenson SC, Merkley ED, Nakayasu ES, Nicora CD, Jansson JK, Burnum-Johnson KE, Payne SH. Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics. J Proteome Res 2022; 21:2023-2035. [PMID: 35793793 PMCID: PMC9361346 DOI: 10.1021/acs.jproteome.2c00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Metaproteomics has
been increasingly utilized for high-throughput
characterization of proteins in complex environments and has been
demonstrated to provide insights into microbial composition and functional
roles. However, significant challenges remain in metaproteomic data
analysis, including creation of a sample-specific protein sequence
database. A well-matched database is a requirement for successful
metaproteomics analysis, and the accuracy and sensitivity of PSM identification
algorithms suffer when the database is incomplete or contains extraneous
sequences. When matched DNA sequencing data of the sample is unavailable
or incomplete, creating the proteome database that accurately represents
the organisms in the sample is a challenge. Here, we leverage a de novo peptide sequencing approach to identify the sample
composition directly from metaproteomic data. First, we created a
deep learning model, Kaiko, to predict the peptide sequences from
mass spectrometry data and trained it on 5 million peptide–spectrum
matches from 55 phylogenetically diverse bacteria. After training,
Kaiko successfully identified organisms from soil isolates and synthetic
communities directly from proteomics data. Finally, we created a pipeline
for metaproteome database generation using Kaiko. We tested the pipeline
on native soils collected in Kansas, showing that the de novo sequencing model can be employed as an alternative and complementary
method to construct the sample-specific protein database instead of
relying on (un)matched metagenomes. Our pipeline identified all highly
abundant taxa from 16S rRNA sequencing of the soil samples and uncovered
several additional species which were strongly represented only in
proteomic data.
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Affiliation(s)
- Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Hugh D Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sarah C Jenson
- Signature Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Eric D Merkley
- Signature Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Samuel H Payne
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
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Fernández-López M, Sánchez-Reyes A, Barcelos C, Sidón-Ceseña K, Leite RB, Lago-Lestón A. Deep-Sea Sediments from the Southern Gulf of Mexico Harbor a Wide Diversity of PKS I Genes. Antibiotics (Basel) 2022; 11:antibiotics11070887. [PMID: 35884142 PMCID: PMC9311598 DOI: 10.3390/antibiotics11070887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
The excessive use of antibiotics has triggered the appearance of new resistant strains, which is why great interest has been taken in the search for new bioactive compounds capable of overcoming this emergency in recent years. Massive sequencing tools have enabled the detection of new microorganisms that cannot be cultured in a laboratory, thus opening the door to the search for new biosynthetic genes. The great variety in oceanic environments in terms of pressure, salinity, temperature, and nutrients enables marine microorganisms to develop unique biochemical and physiological properties for their survival, enhancing the production of secondary metabolites that can vary from those produced by terrestrial microorganisms. We performed a search for type I PKS genes in metagenomes obtained from the marine sediments of the deep waters of the Gulf of Mexico using Hidden Markov Models. More than 2000 candidate genes were detected in the metagenomes that code for type I PKS domains, while biosynthetic pathways that may code for other secondary metabolites were also detected. Our research demonstrates the great potential use of the marine sediments of the Gulf of Mexico for identifying genes that code for new secondary metabolites.
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Affiliation(s)
- Maikel Fernández-López
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca 62209, Mexico;
| | - Ayixon Sánchez-Reyes
- CONACYT-Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico;
| | - Clara Barcelos
- Posgrado de Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico; (C.B.); (K.S.-C.)
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
| | - Karla Sidón-Ceseña
- Posgrado de Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico; (C.B.); (K.S.-C.)
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
| | - Ricardo B. Leite
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal;
| | - Asunción Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana No. 3918, Zona Playitas, Ensenada 22860, Mexico
- Correspondence:
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Ren W, Zhong Y, Ding Y, Wu Y, Xu X, Zhou P. Mismatches in 16S rRNA Gene Primers: An Area Worth Further Exploring. Front Microbiol 2022; 13:888803. [PMID: 35770162 PMCID: PMC9234566 DOI: 10.3389/fmicb.2022.888803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Wenting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Yingwen Zhong
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Ding
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yuehong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - XueWei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources and Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
- *Correspondence: Peng Zhou
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Kim M, Kienast Y, Hatt JK, Kirby AE, Konstantinidis KT. Metagenomics indicate that public health risk may be higher from flooding following dry versus rainy periods. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:265-273. [PMID: 35112509 DOI: 10.1111/1758-2229.13047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Urban floodwater could lead to significant risk for public and environmental health from mobilization of microbial pathogens and overflow of wastewater treatment systems. Here, we attempted to assess this risk by obtaining metagenomic profiles of antibiotic resistance genes (ARGs), virulence factors (VFs) and pathogens present in floodwater samples collected in urban Atlanta, GA that were categorized in two distinct groups: floods that occurred after periods of drought and those after regular (seasonal) rain events. Even though no major (known) pathogens were present at the limit of detection of our sequencing effort (~3 Gbp/sample), we observed that floodwaters after drought showed a 2.5-fold higher abundance of both ARGs and VFs compared to floodwater after rainy days. These differences were mainly derived by several novel species of the Pseudomonas genus, which were more dominant in the former versus the latter samples and carried several genes to cope with osmotic stress in addition to ARGs and VFs. These results revealed that there are previously undescribed species that become mobilized after flooding events in the Southeast US urban settings and could represent an increased public health risk, especially after periods of drought, which warrants further attention.
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Affiliation(s)
- Minjae Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - Yvonne Kienast
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - Amy E Kirby
- Center for Global Safe Water, Sanitation, and Hygiene, Rollins School of Public Health, Emory University, Atlanta, GA, USA
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA, 30332, USA
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Irazoqui JM, Eberhardt MF, Adjad MM, Amadio AF. Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics. PeerJ 2022; 10:e12772. [PMID: 35310160 PMCID: PMC8929167 DOI: 10.7717/peerj.12772] [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: 07/13/2021] [Accepted: 12/19/2021] [Indexed: 01/07/2023] Open
Abstract
Wastewater stabilization ponds are a natural form of wastewater treatment. Their low operation and maintenance costs have made them popular, especially in developing countries. In these systems, effluents are retained for long periods of time, allowing the microbial communities present in the ponds to degrade the organic matter present, using both aerobic and anaerobic processes. Even though these systems are widespread in low income countries, there are no studies about the microorganisms present in them and how they operate. In this study, we analised the microbial communities of two serial full-scale stabilization ponds systems using whole genome shotgun sequencing. First, a taxonomic profiling of the reads was performed, to estimate the microbial diversity. Then, the reads of each system were assembled and binned, allowing the reconstruction of 110 microbial genomes. A functional analysis of the genomes allowed us to find how the main metabolic pathways are carried out, and we propose several organisms that would be key to this kind of environment, since they play an important role in these metabolic pathways. This study represents the first genome-centred approach to understand the metabolic processes in facultative ponds. A better understanding of these microbial communities and how they stabilize the effluents of dairy industries is necessary to improve them and to minimize the environmental impact of dairy industries wastewater.
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Affiliation(s)
- Jose M. Irazoqui
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
| | - Maria F. Eberhardt
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
| | - Maria M. Adjad
- Estacion Experimental Rafaela (INTA), Rafaela, Santa Fe, Argentina
| | - Ariel F. Amadio
- Instituto de Investigacion de la Cadena Lactea (INTA-CONICET), Rafaela, Santa Fe, Argentina
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Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool. Microorganisms 2022; 10:microorganisms10020441. [PMID: 35208895 PMCID: PMC8880012 DOI: 10.3390/microorganisms10020441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/29/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information. Here, we evaluated shotgun metagenomics to assess the detection of common enteric bacterial pathogens in stool. We sequenced 304 stool specimens from 285 patients alongside routine diagnostic testing for Salmonella spp., Campylobacter spp., Shigella spp., and shiga-toxin producing Escherichia coli. Five analytical approaches were assessed for pathogen detection: microbiome profiling, Kraken2, MetaPhlAn, SRST2, and KAT-SECT. Among analysis tools and databases compared, KAT-SECT analysis provided the best sensitivity and specificity for all pathogens tested compared to culture (91.2% and 96.2%, respectively). Where metagenomics detected a pathogen in culture-negative specimens, standard PCR was positive 85% of the time. The cost of metagenomics is approaching the current combined cost of PCR, reflex culture, and whole genome sequencing for pathogen detection and subtyping. As cost, speed, and analytics for single-approach metagenomics improve, it may be more routinely applied in clinical and public health laboratories.
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Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice. Microorganisms 2022; 10:microorganisms10020328. [PMID: 35208784 PMCID: PMC8879337 DOI: 10.3390/microorganisms10020328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono- and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice metagenomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 good- and high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations, either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The superimposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification.
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50
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Soto DF, Franzetti A, Gómez I, Huovinen P. Functional filtering and random processes affect the assembly of microbial communities of snow algae blooms at Maritime Antarctic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150305. [PMID: 34818790 DOI: 10.1016/j.scitotenv.2021.150305] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/04/2021] [Accepted: 09/08/2021] [Indexed: 05/10/2023]
Abstract
The increasing temperatures at the West Antarctic Peninsula (Maritime Antarctic) could lead to a higher occurrence of snow algal blooms which are ubiquitous events that change the snow coloration, reducing albedo and in turn exacerbating melting. However, there is a limited understanding of snow algae blooms biodiversity, composition, and their functional profiles, especially in one of the world's areas most affected by climate change. In this study we used 16S rRNA and 18S rRNA metabarcoding, and shotgun metagenomics to assess the diversity, composition, and functional potential of the snow algae blooms bacterial and eukaryotic communities at three different sites of Maritime Antarctic, between different colors of the algae blooms and between seasonal and semi-permanent snowfields. We tested the hypothesis that the functional potential of snow algae blooms is conserved despite a changing taxonomic composition. Furthermore, we determined taxonomic co-occurrence patterns of bacteria and eukaryotes and assessed the potential for the exchange of metabolites among bacterial taxa. Here, we tested the prediction that there are co-occurring taxa within snow algae whose biotic interactions are marked by the exchange of metabolites. Our results show that the composition of snow algae blooms vary significantly among sites. For instance, a higher abundance of fungi and protists were detected in Fildes Peninsula compared with Doumer Island and O'Higgins. Likewise, the composition varied between snow colors and snow types. However, the functional potential varied only among sampling sites with a higher abundance of genes involved in tolerance to environmental stress at O'Higgins. Co-occurrence patterns of dominant bacterial genera such as Pedobacter, Polaromonas, Flavobacterium and Hymenobacter were recorded, contrasting the absence of co-occurring patterns displayed by Chlamydomonadales algae with other eukaryotes. Finally, genome-scale metabolic models revealed that bacteria within snow algae blooms likely compete for resources instead of forming cooperative communities.
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Affiliation(s)
- Daniela F Soto
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Research Centre on Dynamics of High Latitude Marine Ecosystems (IDEAL), Valdivia, Chile.
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Milan, Italy
| | - Iván Gómez
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Research Centre on Dynamics of High Latitude Marine Ecosystems (IDEAL), Valdivia, Chile
| | - Pirjo Huovinen
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile; Research Centre on Dynamics of High Latitude Marine Ecosystems (IDEAL), Valdivia, Chile
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