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Liu G, Gu Z, Li B. Can the artificial exogenous addition really cause an increasing carbon emission driven by microbial community in grassland ecosystems? Front Microbiol 2024; 15:1421325. [PMID: 39027112 PMCID: PMC11255779 DOI: 10.3389/fmicb.2024.1421325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/21/2024] [Indexed: 07/20/2024] Open
Affiliation(s)
- Guanhong Liu
- Yinshanbeilu Grassland Eco-Hydrology National Observation and Research Station, China Institute of Water Resources and Hydropower Research, Beijing, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ze Gu
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Bingyi Li
- Hebei Normal University, Shijiazhuang, Hebei, China
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2
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Duran R, Cravo‐Laureau C. The hydrocarbon pollution crisis: Harnessing the earth hydrocarbon-degrading microbiome. Microb Biotechnol 2024; 17:e14526. [PMID: 39003601 PMCID: PMC11246598 DOI: 10.1111/1751-7915.14526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/02/2024] [Indexed: 07/15/2024] Open
Affiliation(s)
- Robert Duran
- Universite de Pau et Des Pays de l'Adour, E2S UPPA, CNRS, IPREMPauFrance
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3
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Ramljak A, Žučko J, Lučić M, Babić I, Morić Z, Fafanđel M, Furdek Turk M, Matijević S, Karpouzas D, Udiković-Kolić N, Petrić I. Microbial communities as indicators of marine ecosystem health: Insights from coastal sediments in the eastern Adriatic Sea. MARINE POLLUTION BULLETIN 2024; 205:116649. [PMID: 38944966 DOI: 10.1016/j.marpolbul.2024.116649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/27/2024] [Accepted: 06/21/2024] [Indexed: 07/02/2024]
Abstract
Considering the adaptability and responsiveness of microorganisms to environmental changes, their indicator potential is still not acknowledged in European directives. This comprehensive study examined the changes of microbial communities in sediments and a range of geochemical parameters from pristine and anthropogenically impacted coastal areas in the eastern Adriatic Sea. Various analytical methods found evidence of sediment contamination (high toxicity level, enrichments of metals, tributyltin) in certain areas, leading to the categorization of sediments based on the level of anthropogenic disturbance. Prokaryotes were identified as the most promising group of microbes for further research, with specific bacterial families (Rhodobacteraceae, Ectothiorhodospiraceae, Cyclobacteriaceae) and genera (Boseongicola, B2M28, Subgroup 23, Sva0485, Thiogranum) proposed as potential indicators of environmental status. Finally, predictive models were developed to identify key indicator variables for assessing anthropogenic impact in sediments. This research represents an essential step toward incorporating microbial communities into assessments of benthic environmental health.
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Affiliation(s)
- A Ramljak
- Division for Marine and Environmental Research, Ruder Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - J Žučko
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - M Lučić
- Division for Marine and Environmental Research, Ruder Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - I Babić
- Division for Marine and Environmental Research, Ruder Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Z Morić
- Department of Computer Science, Algebra University, Gradišćanska 24, 10000 Zagreb, Croatia
| | - M Fafanđel
- Center for Marine Research, Ruđer Bošković Institute, Giordano Paliaga 5, 52210 Rovinj, Croatia
| | - M Furdek Turk
- Division for Marine and Environmental Research, Ruder Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - S Matijević
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, 21000 Split, Croatia
| | - D Karpouzas
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41221 Larissa, Greece
| | - N Udiković-Kolić
- Division for Marine and Environmental Research, Ruder Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - I Petrić
- Division for Marine and Environmental Research, Ruder Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
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Barnett SE, Shade A. Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance. Ecol Lett 2024; 27:e14393. [PMID: 38430049 DOI: 10.1111/ele.14393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 03/03/2024]
Abstract
Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the 'whole' bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall structural resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.
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Affiliation(s)
- Samuel E Barnett
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Ashley Shade
- Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, Ecole Nationale Véterinaire de Lyon, Universite Claude Bernard Lyon 1, Villeurbanne, France
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Dosi A, Meziti A, Tounta E, Koemtzopoulos K, Komnenou A, Dendrinos P, Kormas K. Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation. Microbiol Spectr 2024; 12:e0280523. [PMID: 38084980 PMCID: PMC10783143 DOI: 10.1128/spectrum.02805-23] [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: 07/09/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.
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Affiliation(s)
- Aggeliki Dosi
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Eleni Tounta
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Kimon Koemtzopoulos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Anastasia Komnenou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Dendrinos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
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Jing J, Garbeva P, Raaijmakers JM, Medema MH. Strategies for tailoring functional microbial synthetic communities. THE ISME JOURNAL 2024; 18:wrae049. [PMID: 38537571 PMCID: PMC11008692 DOI: 10.1093/ismejo/wrae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/26/2024] [Indexed: 04/12/2024]
Abstract
Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.
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Affiliation(s)
- Jiayi Jing
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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7
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Shi J, Thakur MP. Climate extremes disrupt fungal-bacterial interactions. Nat Microbiol 2023; 8:2226-2229. [PMID: 38030901 DOI: 10.1038/s41564-023-01531-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Affiliation(s)
- Jingjing Shi
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Madhav P Thakur
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
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8
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Pinto R, Ansola G, Calvo L, Sáenz de Miera LE. High resilience of soil bacterial communities to large wildfires with an important stochastic component. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165719. [PMID: 37482359 DOI: 10.1016/j.scitotenv.2023.165719] [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: 04/17/2023] [Revised: 06/30/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Wildfires alter the structure and functioning of ecosystems through changes in their biotic and abiotic components. A deeper understanding recovery process concerning diverse communities and properties within these components can provide valuable insights into the ecological effects of wildfires. Therefore, it is appropriate to enhance our understanding of the resilience of bacterial communities after wildfires within Mediterranean ecosystems. In this research, soil bacterial community resilience was evaluated in three types of ecosystems for two fire severities, two years after a large wildfire in Mediterranean ecosystems. The resilience of the soil bacterial community refers to its ability to return to original state after disturbance. This capacity can be estimated by the study of its recovery over time. In this study we evaluated the resilience using the variables: alpha diversity, beta diversity and the changes in abundance of both OTUs (Operational Taxonomic Units) and principal bacterial taxa (phyla, classes or orders). Our results showed that resilience depends on fire severity and type of ecosystem. We studied three ecosystems with different stage in the secondary succession: low maturity shrublands and heathlands, and high maturity oak forests. In general, high resilience in the soil bacterial community was observed in heathlands under low and high fire severity conditions. The other two ecosystems were resilient only under low fire severity. Stochastic replacement of the abundance of the OTUs was observed in all three ecosystems, with a notable impact on oak forests, under during high-severity conditions.
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Affiliation(s)
- Rayo Pinto
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León. Campus de Vegazana s/n, CP: 24071 León, Spain.
| | - Gemma Ansola
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León. Campus de Vegazana s/n, CP: 24071 León, Spain.
| | - Leonor Calvo
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León. Campus de Vegazana s/n, CP: 24071 León, Spain.
| | - Luis E Sáenz de Miera
- Departamento de Biología Molecular, Universidad de León, Campus de Vegazana s/n, CP: 24071 León, Spain.
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Haney CH, Malone JG. Editorial overview: Unraveling microbiome complexity. Curr Opin Microbiol 2023; 75:102356. [PMID: 37421707 DOI: 10.1016/j.mib.2023.102356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2023]
Affiliation(s)
- Cara H Haney
- Department of Microbiology & Immunology, Faculty of Science, 1365 - 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada..
| | - Jacob G Malone
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, United Kingdom.
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