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Li J, Usman M, Arslan M, Gamal El-Din M. Molecular and microbial insights towards anaerobic biodegradation of anionic polyacrylamide in oil sands tailings. WATER RESEARCH 2024; 258:121757. [PMID: 38768520 DOI: 10.1016/j.watres.2024.121757] [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: 02/10/2024] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
Anionic polyacrylamide (A-PAM) is widely used as a flocculant in the management of oil sands tailings. Nevertheless, apprehensions arise regarding its potential biodegradation and environmental consequences within the context of oil sands tailings. Consequently, it is imperative to delve into the anaerobic biodegradation of A-PAM in oil sands tailings to gain a comprehensive understanding of its influence on tailings water quality. This work explored the dynamics of A-PAM biodegradation across concentrations: 50, 100, 250, 500, 1000, and 2000 mg/kg TS. The results showed a significant decrease in A-PAM concentration and molecular weight at lower concentrations (50 and 100 mg/kg TS) compared to higher ones, suggesting enhanced degradation efficiency. Likewise, the organic transformation and methane production exhibited dependency on A-PAM concentrations. The peak concentrations observed were 20.0 mg/L for volatile fatty acids (VFAs), 0.07 mg/L for acrylamide (AMD), and 8.9 mL for methane yield, with these maxima being recorded at 50 mg/kg TS. The biodegradation efficiency diminishes at higher concentrations of A-PAM, potentially due to the inhibitory effects of polyacrylic acid accumulation. A-PAM biodegradation under anaerobic condition did not contribute to acute toxicity or genotoxicity. SEM-EDS, FT-IR and XRD analyses further revealed that higher concentrations of A-PAM inhibited the biodegradation by altering floc structure and composition, thereby restricting the microbial activity. Major microorganisms, including Smithella, Candidatus_Cloacimonas, W5, XBB1006, and DMER64 were identified, highlighting A-PAM's dual role as a source of carbon and nitrogen under anaerobic conditions. The above findings from this research not only significantly advance understanding of A-PAM's environmental behavior but also contribute to the effective management practices in oil sands tailings.
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Affiliation(s)
- Jia Li
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Muhammad Usman
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Muhammad Arslan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada
| | - Mohamed Gamal El-Din
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Alberta, T6G 1H9, Canada.
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2
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Morales-Hidalgo M, Povedano-Priego C, Martinez-Moreno MF, Ojeda JJ, Jroundi F, Merroun ML. Long-term tracking of the microbiology of uranium-amended water-saturated bentonite microcosms: A mechanistic characterization of U speciation. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135044. [PMID: 38943881 DOI: 10.1016/j.jhazmat.2024.135044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Deep geological repositories (DGRs) stand out as one of the optimal options for managing high-level radioactive waste (HLW) such as uranium (U) in the near future. Here, we provide novel insights into microbial behavior in the DGR bentonite barrier, addressing potential worst-case scenarios such as waste leakage (e.g., U) and groundwater infiltration of electron rich donors in the bentonite. After a three-year anaerobic incubation, Illumina sequencing results revealed a bacterial diversity dominated by anaerobic and spore-forming microorganisms mainly from the phylum Firmicutes. Highly U tolerant and viable bacterial isolates from the genera Peribacillus, Bacillus, and some SRB such as Desulfovibrio and Desulfosporosinus, were enriched from U-amended bentonite. The results obtained by XPS and XRD showed that U was present as U(VI) and as U(IV) species. Regarding U(VI), we have identified biogenic U(VI) phosphates, U(UO2)·(PO4)2, located in the inner part of the bacterial cell membranes in addition to U(VI)-adsorbed to clays such as montmorillonite. Biogenic U(IV) species as uraninite may be produced as result of bacterial enzymatic U(VI) reduction. These findings suggest that under electron donor-rich water-saturation conditions, bentonite microbial community can control U speciation, immobilizing it, and thus enhancing future DGR safety if container rupture and waste leakage occurs.
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Affiliation(s)
- Mar Morales-Hidalgo
- Faculty of Science, Department of Microbiology, University of Granada, Granada, Spain.
| | | | | | - Jesus J Ojeda
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Fadwa Jroundi
- Faculty of Science, Department of Microbiology, University of Granada, Granada, Spain
| | - Mohamed L Merroun
- Faculty of Science, Department of Microbiology, University of Granada, Granada, Spain
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Seethalakshmi PS, Kumaresan TN, Vishnu Prasad Nair RU, Prathiviraj R, Seghal Kiran G, Selvin J. Comparative analysis of commercially available kits for optimal DNA extraction from bovine fecal samples. Arch Microbiol 2024; 206:314. [PMID: 38900289 DOI: 10.1007/s00203-024-04047-8] [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: 03/04/2024] [Revised: 05/19/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
In the field of metagenomic research, the choice of DNA extraction methods plays a pivotal yet often underestimated role in shaping the reliability and interpretability of microbial community data. This study delves into the impact of five commercially available DNA extraction kits on the analysis of bovine fecal microbiota. Recognizing the importance of accurate DNA extraction in elucidating microbial community dynamics, we systematically assessed DNA yield, quality, and microbial composition across these kits using 16S rRNA gene sequencing. Notably, the FastDNA spin soil kit yielded the highest DNA concentration, while significant variations in quality were observed across kits. Furthermore, differential abundance analysis revealed kit-specific biases that impacted taxa representation. Microbial richness and diversity were significantly influenced by the choice of extraction kit, with QIAamp DNA stool minikit, QIAamp Power Pro, and DNeasy PowerSoil outperforming the Stool DNA Kit. Principal-coordinate analysis revealed distinct clustering based on DNA isolation procedures, particularly highlighting the unique microbial community composition derived from the Stool DNA Kit. This study also addressed practical implications, demonstrating how kit selection influences the concentration of Gram-positive and Gram-negative bacterial taxa in samples. This research highlights the need for consideration of DNA extraction kits in metagenomic studies, offering valuable insights for researchers striving to advance the precision and depth of microbiota analyses in ruminants.
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Affiliation(s)
- P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - T N Kumaresan
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India
| | | | | | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Kalapet, Puducherry, 605014, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Kalapet, Puducherry, 605014, India.
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4
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Scales BS, Hassenrück C, Moldaenke L, Hassa J, Rückert-Reed C, Rummel C, Völkner C, Rynek R, Busche T, Kalinowski J, Jahnke A, Schmitt-Jansen M, Wendt-Potthoff K, Oberbeckmann S. Hunting for pigments in bacterial settlers of the Great Pacific Garbage Patch. Environ Microbiol 2024; 26:e16639. [PMID: 38899733 DOI: 10.1111/1462-2920.16639] [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: 07/07/2023] [Accepted: 04/30/2024] [Indexed: 06/21/2024]
Abstract
The Great Pacific Garbage Patch, a significant collection of plastic introduced by human activities, provides an ideal environment to study bacterial lifestyles on plastic substrates. We proposed that bacteria colonizing the floating plastic debris would develop strategies to deal with the ultraviolet-exposed substrate, such as the production of antioxidant pigments. We observed a variety of pigmentation in 67 strains that were directly cultivated from plastic pieces sampled from the Garbage Patch. The genomic analysis of four representative strains, each distinct in taxonomy, revealed multiple pathways for carotenoid production. These pathways include those that produce less common carotenoids and a cluster of photosynthetic genes. This cluster appears to originate from a potentially new species of the Rhodobacteraceae family. This represents the first report of an aerobic anoxygenic photoheterotrophic bacterium from plastic biofilms. Spectral analysis showed that the bacteria actively produce carotenoids, such as beta-carotene and beta-cryptoxanthin, and bacteriochlorophyll a. Furthermore, we discovered that the genetic ability to synthesize carotenoids is more common in plastic biofilms than in the surrounding water communities. Our findings suggest that plastic biofilms could be an overlooked source of bacteria-produced carotenoids, including rare forms. It also suggests that photoreactive molecules might play a crucial role in bacterial biofilm communities in surface water.
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Affiliation(s)
- Brittan S Scales
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Christiane Hassenrück
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Lynn Moldaenke
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | | | - Christoph Rummel
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Corinna Völkner
- Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Robby Rynek
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Annika Jahnke
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute for Environmental Research, RWTH Aachen University, Aachen, Germany
| | | | | | - Sonja Oberbeckmann
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
- Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
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Mellouk A, Mahmood T, Jlali M, Vieco-Saiz N, Michel V, Cozannet P, Ozbek S, Mercier Y, Devillard E, Consuegra J. Potential of guar gum as a leaky gut model in broilers: Digestibility, performance, and microbiota responses. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2024; 17:177-187. [PMID: 38779326 PMCID: PMC11109731 DOI: 10.1016/j.aninu.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 01/02/2024] [Accepted: 01/23/2024] [Indexed: 05/25/2024]
Abstract
Diet is a major modulator of animal resilience and its three pillars: host's immune response, gut microbiota, and intestinal barrier. In the present study, we endeavour to delineate a challenging condition aimed to degrade these pillars and elucidate its impact on broiler performance and nutrient digestibility. To attain this objective, we opted to use guar gum (GG) as a source of galactomannan. A series of three in vivo experiments were conducted employing conventional or semi-purified diets, supplemented with or without GG during the grower phase (14-28 d). Our findings demonstrate a substantial decline in animal performance metrics such as body weight (reduced by 29%, P < 0.001), feed intake (decreased by 12%, P < 0.001), and feed conversion ratio (up to 58% increase, P < 0.001) in the presence of GG at 2%. The supplementation of a semi-purified diet with incremental doses of GG resulted in a linear reduction (P < 0.001) in the apparent total tract digestibility of dry matter and apparent metabolisable energy. Additionally, a marked reduction in ileal endogenous losses, as well as apparent and standardised digestibility of all amino acids with varying proportions (P < 0.05), was observed. These alterations were accompanied by disrupted gut integrity assessed by fluorescein isothiocyanate-dextran (FITC-d) (P < 0.001) as well as an inflammatory status characterised by elevated levels of acute-phase proteins, namely orosomucoid and serum amyloid A in the sera (P = 0.03), and increased mRNA expression levels of IL-1, IL-6, IL-8, Inos, and K203 genes in the ileum, along with a decrease in IgA levels in the gut lumen (P < 0.05). Microbial ecology and activity were characterised by reduced diversity and richness (Shannon index, P = 0.005) in the presence of GG. Consequently, our results revealed diminished levels of short-chain fatty acids (P = 0.01) and their producer genera, such as Clostridium_XIVa and Blautia, in the gut caeca, coupled with excessive accumulation of lactate (17-fold increase, P < 0.01) in the presence of GG at 2%. In addition to providing a more comprehensive characterisation of the GG supplementation as a leaky gut model, our results substantiate a thorough understanding of the intricate adjustments and interplay between the intestinal barrier, immune response, and microbiota. Furthermore, they underscore the significance of feed components in modulating these dynamics.
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Affiliation(s)
| | | | | | - Nuria Vieco-Saiz
- Department of R&I in Monogastric Animal Nutrition, European Laboratory of Innovation Science & Expertise (ELISE), Adisseo France S.A.S., Saint Fons, France
| | - Virginie Michel
- Department of R&I in Monogastric Animal Nutrition, European Laboratory of Innovation Science & Expertise (ELISE), Adisseo France S.A.S., Saint Fons, France
| | - Pierre Cozannet
- Department of R&I in Monogastric Animal Nutrition, European Laboratory of Innovation Science & Expertise (ELISE), Adisseo France S.A.S., Saint Fons, France
| | - Sarper Ozbek
- Department of R&I in Monogastric Animal Nutrition, European Laboratory of Innovation Science & Expertise (ELISE), Adisseo France S.A.S., Saint Fons, France
| | - Yves Mercier
- Department of R&I in Monogastric Animal Nutrition, European Laboratory of Innovation Science & Expertise (ELISE), Adisseo France S.A.S., Saint Fons, France
| | - Estelle Devillard
- Department of R&I in Monogastric Animal Nutrition, European Laboratory of Innovation Science & Expertise (ELISE), Adisseo France S.A.S., Saint Fons, France
| | - Jessika Consuegra
- Department of R&I in Monogastric Animal Nutrition, European Laboratory of Innovation Science & Expertise (ELISE), Adisseo France S.A.S., Saint Fons, France
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Kalogiannis A, Vasiliadou IA, Tsiamis A, Galiatsatos I, Stathopoulou P, Tsiamis G, Stamatelatou K. Enhancement of Biodegradability of Chicken Manure via the Addition of Zeolite in a Two-Stage Dry Anaerobic Digestion Configuration. Molecules 2024; 29:2568. [PMID: 38893444 PMCID: PMC11173769 DOI: 10.3390/molecules29112568] [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: 04/29/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Leach bed reactors (LBRs) are dry anaerobic systems that can handle feedstocks with high solid content, like chicken manure, with minimal water addition. In this study, the chicken manure was mixed with zeolite, a novel addition, and packed in the LBR to improve biogas production. The resulting leachate was then processed in a continuous stirred tank reactor (CSTR), where most of the methane was produced. The supernatant of the CSTR was returned to the LBR. The batch mode operation of the LBR led to a varying methane production rate (MPR) with a peak in the beginning of each batch cycle when the leachate was rich in organic matter. Comparing the MPR in both systems, the peaks in the zeolite system were higher and more acute than in the control system, which was under stress, as indicated by the acetate accumulation at 2328 mg L-1. Moreover, the presence of zeolite in the LBR played a crucial role, increasing the overall methane yield from 0.142 (control experiment) to 0.171 NL CH4 per g of volatile solids of chicken manure entering the system at a solid retention time of 14 d. Zeolite also improved the stability of the system. The ammonia concentration increased gradually due to the little water entering the system and reached 3220 mg L-1 (control system) and 2730 mg L-1 (zeolite system) at the end of the experiment. It seems that zeolite favored the accumulation of the ammonia at a lower rate (14.0 mg L-1 d-1) compared to the control experiment (17.3 mg L-1 d-1). The microbial analysis of the CSTR fed on the leachate from the LBR amended with zeolite showed a higher relative abundance of Methanosaeta (83.6%) compared to the control experiment (69.1%). Both CSTRs established significantly different bacterial profiles from the inoculum after 120 days of operation (p < 0.05). Regarding the archaeal communities, there were no significant statistical differences between the CSTRs and the inoculum (p > 0.05).
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Affiliation(s)
- Achilleas Kalogiannis
- Department of Environmental Engineering, Democritus University of Thrace, Vas. Sofias 12, GR-67132 Xanthi, Greece; (A.K.); (I.A.V.)
| | - Ioanna A. Vasiliadou
- Department of Environmental Engineering, Democritus University of Thrace, Vas. Sofias 12, GR-67132 Xanthi, Greece; (A.K.); (I.A.V.)
- Department of Chemical Engineering, University of Western Macedonia, GR-50100 Kozani, Greece
| | - Athanasios Tsiamis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, GR-30131 Agrinio, Greece; (A.T.); (I.G.); (P.S.); (G.T.)
| | - Ioannis Galiatsatos
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, GR-30131 Agrinio, Greece; (A.T.); (I.G.); (P.S.); (G.T.)
| | - Panagiota Stathopoulou
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, GR-30131 Agrinio, Greece; (A.T.); (I.G.); (P.S.); (G.T.)
| | - George Tsiamis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Sustainable Agriculture, University of Patras, GR-30131 Agrinio, Greece; (A.T.); (I.G.); (P.S.); (G.T.)
| | - Katerina Stamatelatou
- Department of Environmental Engineering, Democritus University of Thrace, Vas. Sofias 12, GR-67132 Xanthi, Greece; (A.K.); (I.A.V.)
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Mondal S, Biswas B, Chowdhury R, Sengupta R, Mandal A, Kotal HN, Giri CK, Ghosh A, Saha S, Begam MM, Mukherjee C, Das I, Basak SK, Mitra Ghosh M, Ray K. Estuarine mangrove niches select cultivable heterotrophic diazotrophs with diverse metabolic potentials-a prospective cross-dialog for functional diazotrophy. Front Microbiol 2024; 15:1324188. [PMID: 38873137 PMCID: PMC11174608 DOI: 10.3389/fmicb.2024.1324188] [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: 10/19/2023] [Accepted: 05/10/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Biological nitrogen fixation (BNF), an unparalleled metabolic novelty among living microorganisms on earth, globally contributes ~88-101 Tg N year-1 to natural ecosystems, ~56% sourced from symbiotic BNF while ~22-45% derived from free-living nitrogen fixers (FLNF). The success of symbiotic BNF is largely dependent on its interaction with host-plant, however ubiquitous environmental heterotrophic FLNFs face many limitations in their immediate ecological niches to sustain unhindered BNF. The autotrophic FLNFs like cyanobacteria and oceanic heterotrophic diazotrophs have been well studied about their contrivances acclimated/adapted by these organisms to outwit the environmental constraints for functional diazotrophy. However, FLNF heterotrophs face more adversity in executing BNF under stressful estuarine/marine/aquatic habitats. Methods In this study a large-scale cultivation-dependent investigation was accomplished with 190 NCBI accessioned and 45 non-accessioned heterotrophic FLNF cultivable bacterial isolates (total 235) from halophilic estuarine intertidal mangrove niches of Indian Sundarbans, a Ramsar site and UNESCO proclaimed World Heritage Site. Assuming ~1% culturability of the microbial community, the respective niches were also studied for representing actual bacterial diversity via cultivation-independent next-generation sequencing of V3-V4 rRNA regions. Results Both the studies revealed a higher abundance of culturable Gammaproteobacteria followed by Firmicutes, the majority of 235 FLNFs studied belonging to these two classes. The FLNFs displayed comparable selection potential in media for free nitrogen fixers and iron-oxidizing bacteria, linking diazotrophy with iron oxidation, siderophore production, phosphorus solubilization, phosphorus uptake and accumulation as well as denitrification. Discussion This observation validated the hypothesis that under extreme estuarine mangrove niches, diazotrophs are naturally selected as a specialized multidimensional entity, to expedite BNF and survive. Earlier metagenome data from mangrove niches demonstrated a microbial metabolic coupling among C, N, P, S, and Fe cycling in mangrove sediments, as an adaptive trait, evident with the co-abundant respective functional genes, which corroborates our findings in cultivation mode for multiple interrelated metabolic potential facilitating BNF in a challenging intertidal mangrove environment.
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Affiliation(s)
- Sumana Mondal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Biswajit Biswas
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- Department of Microbiology, St. Xavier’s College (Autonomous), Kolkata, India
| | - Rajojit Chowdhury
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- Department of Botany, Sree Chaitanya College, Habra, India
| | - Rudranil Sengupta
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Anup Mandal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Hemendra Nath Kotal
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Chayan Kumar Giri
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Anjali Ghosh
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Subhajit Saha
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | - Mst Momtaj Begam
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- Department of Botany, Kalimpong College, Darjeeling, India
| | - Chandan Mukherjee
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
- School of Biological and Life Sciences, Galgotias University, Greater Noida, India
| | - Ipsita Das
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
| | | | | | - Krishna Ray
- Environmental Biotechnology Group, Department of Botany, West Bengal State University, Kolkata, India
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Vázquez-González L, Regueira-Iglesias A, Balsa-Castro C, Vila-Blanco N, Tomás I, Carreira MJ. PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome. BMC Bioinformatics 2024; 25:189. [PMID: 38745271 PMCID: PMC11092261 DOI: 10.1186/s12859-024-05805-7] [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: 11/29/2023] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND The selection of primer pairs in sequencing-based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We therefore propose PrimerEvalPy, a Python-based package designed to test the performance of any primer or primer pair against any sequencing database. The package calculates a coverage metric and returns the amplicon sequences found, along with information such as their average start and end positions. It also allows the analysis of coverage for different taxonomic levels. RESULTS As a case study, PrimerEvalPy was used to test the most commonly used primers in the literature against two oral 16S rRNA gene databases containing bacteria and archaea. The results showed that the most commonly used primer pairs in the oral cavity did not match those with the highest coverage. The best performing primer pairs were found for the detection of oral bacteria and archaea. CONCLUSIONS This demonstrates the importance of a coverage analysis tool such as PrimerEvalPy to find the best primer pairs for specific niches. The software is available under the MIT licence at https://gitlab.citius.usc.es/lara.vazquez/PrimerEvalPy .
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Affiliation(s)
- Lara Vázquez-González
- Centro Singular de Investigación en Tecnoloxías Intelixentes (CiTIUS), Universidade de Santiago de Compostela, Rúa de Jenaro de la Fuente Domínguez, E15782, Santiago de Compostela, Spain.
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain.
| | - Alba Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical Surgical Specialities, School of Medicine and Dentistry, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain
| | - Carlos Balsa-Castro
- Centro Singular de Investigación en Tecnoloxías Intelixentes (CiTIUS), Universidade de Santiago de Compostela, Rúa de Jenaro de la Fuente Domínguez, E15782, Santiago de Compostela, Spain
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical Surgical Specialities, School of Medicine and Dentistry, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain
| | - Nicolás Vila-Blanco
- Centro Singular de Investigación en Tecnoloxías Intelixentes (CiTIUS), Universidade de Santiago de Compostela, Rúa de Jenaro de la Fuente Domínguez, E15782, Santiago de Compostela, Spain
- Departamento de Electrónica e Computación, Escola Técnica Superior de Enxeñaría, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain
| | - Inmaculada Tomás
- Centro Singular de Investigación en Tecnoloxías Intelixentes (CiTIUS), Universidade de Santiago de Compostela, Rúa de Jenaro de la Fuente Domínguez, E15782, Santiago de Compostela, Spain.
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical Surgical Specialities, School of Medicine and Dentistry, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain.
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain.
| | - María J Carreira
- Centro Singular de Investigación en Tecnoloxías Intelixentes (CiTIUS), Universidade de Santiago de Compostela, Rúa de Jenaro de la Fuente Domínguez, E15782, Santiago de Compostela, Spain.
- Departamento de Electrónica e Computación, Escola Técnica Superior de Enxeñaría, Universidade de Santiago de Compostela, E15782, Santiago de Compostela, Spain.
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), E15706, Santiago de Compostela, Spain.
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Charalampous G, Fragkou E, Kalogerakis N, Antoniou E, Gontikaki E. Diversity links to functionality: Unraveling the impact of pressure disruption and culture medium on crude oil-enriched microbial communities from the deep Eastern Mediterranean Sea. MARINE POLLUTION BULLETIN 2024; 202:116275. [PMID: 38564821 DOI: 10.1016/j.marpolbul.2024.116275] [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: 10/31/2023] [Revised: 01/19/2024] [Accepted: 03/17/2024] [Indexed: 04/04/2024]
Abstract
Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS.
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Affiliation(s)
- Georgia Charalampous
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
| | - Efsevia Fragkou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Nicolas Kalogerakis
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece
| | - Eleftheria Antoniou
- School of Chemical and Environmental Engineering, Technical University of Crete, Chania, Greece; School of Mineral Resources Engineering, Technical University of Crete, Chania, Greece
| | - Evangelia Gontikaki
- Institute of Geoenergy, Foundation for Research and Technology Hellas, Chania, Greece.
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10
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Teh J, Biswas K, Waldvogel-Thurlow S, Broderick D, Clark ST, Johnston J, Wagner Mackenzie B, Douglas R. Paired qualitative and quantitative analysis of bacterial microcolonies in the tonsils of patients with tonsillar hyperplasia. Microbes Infect 2024; 26:105317. [PMID: 38452852 DOI: 10.1016/j.micinf.2024.105317] [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: 09/04/2023] [Revised: 02/03/2024] [Accepted: 02/29/2024] [Indexed: 03/09/2024]
Abstract
The discovery of bacterial microcolonies in tonsillar tissue of patients with tonsillar hyperplasia has raised the question of their role in provoking the local immune response. Tonsils collected from patients undergoing tonsillectomy were stained for three clinically relevant bacterial taxa and lymphocytes. The bacterial composition and abundance of microcolonies was investigated using a combination of laser-microdissection, amplicon sequencing and Droplet Digital polymerase chain reaction. Microcolonies were detected in most samples (32/35) with a high prevalence of Haemophilus influenzae (78% of samples). B and T cell lymphocytes were significantly higher in the epithelium adjacent to microcolonies compared to epithelium distal to microcolonies. Furthermore, significant positive and negative correlations were identified between bacterial taxa and lymphocytes. Genus Streptococcus, which includes Group A Streptococcus (traditionally described as the main pathogen of tonsillar hyperplasia), was found in low abundance in this study. These results suggest other potential pathogens may be involved in stimulating the local immune response leading to tonsillar hyperplasia.
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Affiliation(s)
- Jackson Teh
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand
| | - Kristi Biswas
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand.
| | - Sharon Waldvogel-Thurlow
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand
| | - David Broderick
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand
| | - Sita Tarini Clark
- Te Whatu Ora - Te Toka Tumai Auckland, Health New Zealand, Auckland, 1142, New Zealand
| | - James Johnston
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand; Te Whatu Ora - Te Toka Tumai Auckland, Health New Zealand, Auckland, 1142, New Zealand
| | - Brett Wagner Mackenzie
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand
| | - Richard Douglas
- Department of Surgery, School of Medicine, The University of Auckland, Auckland, 1023, New Zealand; Te Whatu Ora - Te Toka Tumai Auckland, Health New Zealand, Auckland, 1142, New Zealand
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11
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Lerdsittikul V, Apiratwarrasakul S, Atithep T, Withatanung P, Indrawattana N, Pumirat P, Chaiwattanarungruengpaisan S, Thongdee M. Isolation and characterisation of a novel Silviavirus bacteriophage promising antimicrobial agent against methicillin-resistant Staphylococcus aureus infections. Sci Rep 2024; 14:9251. [PMID: 38649443 PMCID: PMC11035597 DOI: 10.1038/s41598-024-59903-w] [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: 11/02/2023] [Accepted: 04/16/2024] [Indexed: 04/25/2024] Open
Abstract
The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) emphasises the urgent need for novel antimicrobial agents as alternatives to antibiotics. Bacteriophage therapy is one of the most promising antimicrobial strategies. Here, we isolated and comprehensively characterized a novel Staphylococcus phage, vB_SauM_VL10 (VL10), from urban sewage. The VL10 genome displays 141,746 bp of linear double-stranded DNA, containing 193 open reading frames and lacking tRNA, virulence, or antibiotic resistance genes. Phylogenetic analysis categorizes VL10 as a novel species within the Silviavirus genus, Twortvirinae subfamily. VL10 exhibits lytic behaviour characterized by efficient adsorption, a short latent period, and substantial burst size, with environmental stability. It demonstrates lytic activity against 79.06% of tested S. aureus strains, highlighting its species specificity. Additionally, VL10 effectively targets MRSA biofilms, reducing biomass and viable cells. In MRSA-infected G. mellonella larvae, VL10 enhances survival rates, supporting its potential for phage therapy applications. Moreover, the emergence of VL10-resistant S. aureus strains associated with fitness trade-offs, including reduced growth, biofilm formation, and virulence. Altogether, these findings emphasize VL10 as a promising candidate for developing therapeutic agents against MRSA infections, providing insights into phage biology and resistance dynamics.
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Affiliation(s)
- Varintip Lerdsittikul
- Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand.
| | - Sukanya Apiratwarrasakul
- Veterinary Diagnostic Center, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Thassanant Atithep
- Frontier Research Center, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Patoo Withatanung
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research and Excellence in Allergy and Immunology (SiALL), Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Somjit Chaiwattanarungruengpaisan
- The Monitoring Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Metawee Thongdee
- The Monitoring Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
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12
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Warashina T, Sato A, Hinai H, Shaikhutdinov N, Shagimardanova E, Mori H, Tamaki S, Saito M, Sanada Y, Sasaki Y, Shimada K, Dotsuta Y, Kitagaki T, Maruyama S, Gusev O, Narumi I, Kurokawa K, Morita T, Ebisuzaki T, Nishimura A, Koma Y, Kanai A. Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station. Appl Environ Microbiol 2024; 90:e0211323. [PMID: 38470121 PMCID: PMC11022576 DOI: 10.1128/aem.02113-23] [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: 11/22/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
A major incident occurred at the Fukushima Daiichi Nuclear Power Station following the tsunami triggered by the Tohoku-Pacific Ocean Earthquake in March 2011, whereby seawater entered the torus room in the basement of the reactor building. Here, we identify and analyze the bacterial communities in the torus room water and several environmental samples. Samples of the torus room water (1 × 109 Bq137Cs/L) were collected by the Tokyo Electric Power Company Holdings from two sampling points between 30 cm and 1 m from the bottom of the room (TW1) and the bottom layer (TW2). A structural analysis of the bacterial communities based on 16S rRNA amplicon sequencing revealed that the predominant bacterial genera in TW1 and TW2 were similar. TW1 primarily contained the genus Limnobacter, a thiosulfate-oxidizing bacterium. γ-Irradiation tests on Limnobacter thiooxidans, the most closely related phylogenetically found in TW1, indicated that its radiation resistance was similar to ordinary bacteria. TW2 predominantly contained the genus Brevirhabdus, a manganese-oxidizing bacterium. Although bacterial diversity in the torus room water was lower than seawater near Fukushima, ~70% of identified genera were associated with metal corrosion. Latent environment allocation-an analytical technique that estimates habitat distributions and co-detection analyses-revealed that the microbial communities in the torus room water originated from a distinct blend of natural marine microbial and artificial bacterial communities typical of biofilms, sludge, and wastewater. Understanding the specific bacteria linked to metal corrosion in damaged plants is important for advancing decommissioning efforts. IMPORTANCE In the context of nuclear power station decommissioning, the proliferation of microorganisms within the reactor and piping systems constitutes a formidable challenge. Therefore, the identification of microbial communities in such environments is of paramount importance. In the aftermath of the Fukushima Daiichi Nuclear Power Station accident, microbial community analysis was conducted on environmental samples collected mainly outside the site. However, analyses using samples from on-site areas, including adjacent soil and seawater, were not performed. This study represents the first comprehensive analysis of microbial communities, utilizing meta 16S amplicon sequencing, with a focus on environmental samples collected from the radioactive element-containing water in the torus room, including the surrounding environments. Some of the identified microbial genera are shared with those previously identified in spent nuclear fuel pools in countries such as France and Brazil. Moreover, our discussion in this paper elucidates the correlation of many of these bacteria with metal corrosion.
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Affiliation(s)
- Tomoro Warashina
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | | | - Nurislam Shaikhutdinov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Elena Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
- Life Improvement by Future Technologies (LIFT) Center, Skolkovo, Moscow, Russia
- Loginov Moscow Clinical Scientific Center, Moscow, Russia
| | | | - Satoshi Tamaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Motofumi Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | | | | | | | | | | | - Shigenori Maruyama
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Oleg Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
- Life Improvement by Future Technologies (LIFT) Center, Skolkovo, Moscow, Russia
- Intractable Disease Research Center, School of Medicine, Juntendo University, Tokyo, Japan
| | - Issay Narumi
- Faculty of Life Sciences, Toyo University, Oura-gun, Japan
| | | | - Teppei Morita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | | | | | | | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
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13
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McGrath AH, Lema K, Egan S, Wood G, Gonzalez SV, Kjelleberg S, Steinberg PD, Marzinelli EM. Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont. NPJ Biofilms Microbiomes 2024; 10:33. [PMID: 38553475 PMCID: PMC10980776 DOI: 10.1038/s41522-024-00503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
Host-associated microbiota are critical for eukaryotic host functioning, to the extent that hosts and their associated microbial communities are often considered "holobionts". Most studies of holobionts have focused on descriptive approaches or have used model systems, usually in the laboratory, to understand host-microbiome interactions. To advance our understanding of host-microbiota interactions and their wider ecological impacts, we need experimental frameworks that can explore causation in non-model hosts, which often have highly diverse microbiota, and in their natural ecological setting (i.e. in the field). We used a dominant habitat-forming seaweed, Hormosira banksii, to explore these issues and to experimentally test host-microbiota interactions in a non-model holobiont. The experimental protocols were aimed at trying to disentangle microbially mediated effects on hosts from direct effects on hosts associated with the methods employed to manipulate host-microbiota. This was done by disrupting the microbiome, either through removal/disruption using a combination of antimicrobial treatments, or additions of specific taxa via inoculations, or a combination of thew two. The experiments were done in mesocosms and in the field. Three different antibiotic treatments were used to disrupt seaweed-associated microbiota to test whether disturbances of microbiota, particularly bacteria, would negatively affect host performance. Responses of bacteria to these disturbances were complex and differed substantially among treatments, with some antibacterial treatments having little discernible effect. However, the temporal sequence of responses antibiotic treatments, changes in bacterial diversity and subsequent decreases in host performance, strongly suggested an effect of the microbiota on host performance in some treatments, as opposed to direct effects of the antibiotics. To further test these effects, we used 16S-rRNA-gene sequencing to identify bacterial taxa that were either correlated, or uncorrelated, with poor host performance following antibiotic treatment. These were then isolated and used in inoculation experiments, independently or in combination with the previously used antibiotic treatments. Negative effects on host performance were strongest where specific microbial antimicrobials treatments were combined with inoculations of strains that were correlated with poor host performance. For these treatments, negative host effects persisted the entire experimental period (12 days), even though treatments were only applied at the beginning of the experiment. Host performance recovered in all other treatments. These experiments provide a framework for exploring causation and disentangling microbially mediated vs. direct effects on hosts for ecologically important, non-model holobionts in the field. This should allow for better predictions of how these systems will respond to, and potentially mitigate, environmental disturbances in their natural context.
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Affiliation(s)
- Alexander Harry McGrath
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia.
- Sydney Institute of Marine Science, Mosman, NSW, Australia.
| | - Kimberley Lema
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Georgina Wood
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- UWA Oceans Institute & School of Biological Sciences, Indian Ocean Marine Research Centre, The University of Western Australia, Sydney, Australia
| | - Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth, and Environmental Science, University of New South Wales, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore, 637551, Singapore
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14
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Kumar V, Ameen F, Verma P. Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach. Front Microbiol 2024; 15:1350164. [PMID: 38529176 PMCID: PMC10961449 DOI: 10.3389/fmicb.2024.1350164] [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: 12/05/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.
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Affiliation(s)
- Vineet Kumar
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Pradeep Verma
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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15
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Martinez-Moreno MF, Povedano-Priego C, Mumford AD, Morales-Hidalgo M, Mijnendonckx K, Jroundi F, Ojeda JJ, Merroun ML. Microbial responses to elevated temperature: Evaluating bentonite mineralogy and copper canister corrosion within the long-term stability of deep geological repositories of nuclear waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170149. [PMID: 38242445 DOI: 10.1016/j.scitotenv.2024.170149] [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: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Deep Geological Repositories (DGRs) consist of radioactive waste contained in corrosion-resistant canisters, surrounded by compacted bentonite clay, and buried few hundred meters in a stable geological formation. The effects of bentonite microbial communities on the long-term stability of the repository should be assessed. This study explores the impact of harsh conditions (60 °C, highly-compacted bentonite, low water activity), and acetate:lactate:sulfate addition, on the evolution of microbial communities, and their effect on the bentonite mineralogy, and corrosion of copper material under anoxic conditions. No bentonite illitization was observed in the treatments, confirming its mineralogical stability as an effective barrier for future DGR. Anoxic incubation at 60 °C reduced the microbial diversity, with Pseudomonas as the dominant genus. Culture-dependent methods showed survival and viability at 60 °C of moderate-thermophilic aerobic bacterial isolates (e.g., Aeribacillus). Despite the low presence of sulfate-reducing bacteria in the bentonite blocks, we proved their survival at 30 °C but not at 60 °C. Copper disk's surface remained visually unaltered. However, in the acetate:lactate:sulfate-treated samples, sulfide/sulfate signals were detected, along with microbial-related compounds. These findings offer new insights into the impact of high temperatures (60 °C) on the biogeochemical processes at the compacted bentonite/Cu canister interface post-repository closure.
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Affiliation(s)
| | | | - Adam D Mumford
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Mar Morales-Hidalgo
- Faculty of Sciences, Department of Microbiology, University of Granada, Granada, Spain
| | | | - Fadwa Jroundi
- Faculty of Sciences, Department of Microbiology, University of Granada, Granada, Spain
| | - Jesus J Ojeda
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Mohamed L Merroun
- Faculty of Sciences, Department of Microbiology, University of Granada, Granada, Spain
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16
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Mousa WK, Abu-Izneid T, Salah-Tantawy A. High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change. FRONTIERS IN PLANT SCIENCE 2024; 15:1294173. [PMID: 38510442 PMCID: PMC10953687 DOI: 10.3389/fpls.2024.1294173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Introduction Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change. Methods This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region). Results Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions. Discussion Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.
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Affiliation(s)
- Walaa K. Mousa
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Tareq Abu-Izneid
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- Al Ain University (AAU) Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| | - Ahmed Salah-Tantawy
- Institute of Analytical and Environmental Sciences, College of Nuclear Science, National Tsing Hua University, Hsinchu, Taiwan
- Department of Zoology, Marine Science Division, College of Science, Al-Azhar University, Assiut, Egypt
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17
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Palma V, González-Pimentel JL, Jimenez-Morillo NT, Sauro F, Gutiérrez-Patricio S, De la Rosa JM, Tomasi I, Massironi M, Onac BP, Tiago I, González-Pérez JA, Laiz L, Caldeira AT, Cubero B, Miller AZ. Connecting molecular biomarkers, mineralogical composition, and microbial diversity from Mars analog lava tubes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169583. [PMID: 38154629 DOI: 10.1016/j.scitotenv.2023.169583] [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: 08/29/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023]
Abstract
Lanzarote (Canary Islands, Spain) is one of the best terrestrial analogs to Martian volcanology. Particularly, Lanzarote lava tubes may offer access to recognizably preserved chemical and morphological biosignatures valuable for astrobiology. By combining microbiological, mineralogical, and organic geochemistry tools, an in-depth characterization of speleothems and associated microbial communities in lava tubes of Lanzarote is provided. The aim is to untangle the underlying factors influencing microbial colonization in Earth's subsurface to gain insight into the possibility of similar subsurface microbial habitats on Mars and to identify biosignatures preserved in lava tubes unequivocally. The microbial communities with relevant representativeness comprise chemoorganotrophic, halophiles, and/or halotolerant bacteria that have evolved as a result of the surrounding oceanic environmental conditions. Many of these bacteria have a fundamental role in reshaping cave deposits due to their carbonatogenic ability, leaving behind an organic record that can provide evidence of past or present life. Based on functional profiling, we infer that Crossiella is involved in fluorapatite precipitation via urea hydrolysis and propose its Ca-rich precipitates as compelling biosignatures valuable for astrobiology. In this sense, analytical pyrolysis, stable isotope analysis, and chemometrics were conducted to characterize the complex organic fraction preserved in the speleothems and find relationships among organic families, microbial taxa, and precipitated minerals. We relate organic compounds with subsurface microbial taxa, showing that organic families drive the microbiota of Lanzarote lava tubes. Our data indicate that bacterial communities are important contributors to biomarker records in volcanic-hosted speleothems. Within them, the lipid fraction primarily consists of low molecular weight n-alkanes, α-alkenes, and branched-alkenes, providing further evidence that microorganisms serve as the origin of organic matter in these formations. The ongoing research in Lanzarote's lava tubes will help develop protocols, routines, and predictive models that could provide guidance on choosing locations and methodologies for searching potential biosignatures on Mars.
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Affiliation(s)
- Vera Palma
- HERCULES Laboratory, University of Évora, Évora, Portugal
| | | | | | - Francesco Sauro
- Department of Earth Sciences and Environmental Geology, University of Bologna, Italy
| | | | - José M De la Rosa
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain
| | - Ilaria Tomasi
- Geosciences Department, University of Padova, Padova, Italy
| | | | - Bogdan P Onac
- Karst Research Group, School of Geosciences, University of South Florida, Tampa, FL, USA; Emil G. Racoviță Institute, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Igor Tiago
- CFE-Center for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - José A González-Pérez
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain
| | - Ana T Caldeira
- HERCULES Laboratory, University of Évora, Évora, Portugal
| | - Beatriz Cubero
- Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain
| | - Ana Z Miller
- HERCULES Laboratory, University of Évora, Évora, Portugal; Instituto de Recursos Naturales y Agrobiologia de Sevilla (IRNAS-CSIC), Sevilla, Spain.
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18
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Lai JL, Li ZG, Han MW, Huang Y, Xi HL, Luo XG. Analysis of environmental biological effects and OBT accumulation potential of microalgae in freshwater systems exposed to tritium pollution. WATER RESEARCH 2024; 250:121013. [PMID: 38118252 DOI: 10.1016/j.watres.2023.121013] [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: 06/01/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/22/2023]
Abstract
The ecological risk of tritiated wastewater into the environment has attracted much attention. Assessing the ecological risk of tritium-containing pollution is crucial by studying low-activity tritium exposure's environmental and biological effects on freshwater micro-environment and the enrichment potential of organically bound tritium (OBT) in microalgae and aquatic plants. The impact of tritium-contaminated wastewater on the microenvironment of freshwater systems was analyzed using microcosm experiments to simulate tritium pollution in freshwater systems. Low activity tritium pollution (105 Bq/L) induced differences in microbial abundance, with Proteobacteria, Bacteroidota, and Desulfobacterota occupying important ecological niches in the water system. Low activity tritium (105-107 Bq/L) did not affect the growth of microalgae and aquatic plants, but OBT was significantly enriched in microalgae and two aquatic plants (Pistia stratiotes, Spirodela polyrrhiza), with the enrichment coefficients of 2.08-3.39 and 1.71-2.13, respectively. At the transcriptional level, low-activity tritium (105 Bq/L) has the risk of interfering with gene expression in aquatic plants. Four dominant cyanobacterial strains (Leptolyngbya sp., Synechococcus elongatus, Nostoc sp., and Anabaena sp.) were isolated and demonstrated good environmental adaptability to tritium pollution. Environmental factors can modify the tritium accumulation potential in cyanobacteria and microalgae, theoretically enhancing food chain transfer.
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Affiliation(s)
- Jin-Long Lai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China; State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Zhan-Guo Li
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Meng-Wei Han
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Yan Huang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Hai-Ling Xi
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
| | - Xue-Gang Luo
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.
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Vlasselaer L, Crauwels S, Lievens B, De Coninck B. Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms. FEMS Microbiol Ecol 2024; 100:fiae010. [PMID: 38317643 PMCID: PMC10872686 DOI: 10.1093/femsec/fiae010] [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: 08/18/2023] [Revised: 12/08/2023] [Accepted: 02/02/2024] [Indexed: 02/07/2024] Open
Abstract
Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.
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Affiliation(s)
- Liese Vlasselaer
- Plant Health and Protection Laboratory, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Sam Crauwels
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Willem de Croylaan 46, B-3001 Leuven, Belgium
| | - Bart Lievens
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Willem de Croylaan 46, B-3001 Leuven, Belgium
| | - Barbara De Coninck
- Plant Health and Protection Laboratory, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
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20
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Feng X, Cui X, Zhang LS, Ye C, Wang P, Zhong Y, Wu T, Zheng Z, He C. Sequencing of N 6-methyl-deoxyadenosine at single-base resolution across the mammalian genome. Mol Cell 2024; 84:596-610.e6. [PMID: 38215754 PMCID: PMC10872247 DOI: 10.1016/j.molcel.2023.12.021] [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: 10/17/2022] [Revised: 07/25/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Although DNA N6-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method, to measure 6mA at base resolution. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. We validated DR-6mA-seq through the successful mapping of the well-characterized G(6mA)TC motif in the E. coli DNA. As expected, when applying DR-6mA-seq to mammalian systems, we found that genomic DNA (gDNA) 6mA abundance is generally low in most mammalian tissues and cells; however, we did observe distinct gDNA 6mA sites in mouse testis and glioblastoma cells. DR-6mA-seq provides an enabling tool to detect 6mA at single-base resolution for a comprehensive understanding of DNA 6mA in eukaryotes.
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Affiliation(s)
- Xinran Feng
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xiaolong Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA; Department of Chemistry, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chang Ye
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Pingluan Wang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuhao Zhong
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Tong Wu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhong Zheng
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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21
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O'Brien AM, Laurich JR, Frederickson ME. Evolutionary consequences of microbiomes for hosts: impacts on host fitness, traits, and heritability. Evolution 2024; 78:237-252. [PMID: 37828761 DOI: 10.1093/evolut/qpad183] [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: 02/22/2022] [Revised: 08/30/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023]
Abstract
An organism's phenotypes and fitness often depend on the interactive effects of its genome (Ghost), microbiome (Gmicrobe), and environment (E). These G × G, G × E, and G × G × E effects fundamentally shape host-microbiome (co)evolution and may be widespread, but are rarely compared within a single experiment. We collected and cultured Lemnaminor (duckweed) and its associated microbiome from 10 sites across an urban-to-rural ecotone. We factorially manipulated host genotype and microbiome in two environments (low and high zinc, an urban aquatic stressor) in an experiment with 200 treatments: 10 host genotypes × 10 microbiomes × 2 environments. Host genotype explained the most variation in L.minor fitness and traits, while microbiome effects often depended on host genotype (G × G). Microbiome composition predicted G × G effects: when compared in more similar microbiomes, duckweed genotypes had more similar effects on traits. Further, host fitness increased and microbes grew faster when applied microbiomes more closely matched the host's field microbiome, suggesting some local adaptation between hosts and microbiota. Finally, selection on and heritability of host traits shifted across microbiomes and zinc exposure. Thus, we found that microbiomes impact host fitness, trait expression, and heritability, with implications for host-microbiome evolution and microbiome breeding.
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Affiliation(s)
- Anna M O'Brien
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Jason R Laurich
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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22
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Santillan E, Yasumaru F, Vethathirri RS, Thi SS, Hoon HY, Sian DCP, Wuertz S. Microbial community-based protein from soybean-processing wastewater as a sustainable alternative fish feed ingredient. Sci Rep 2024; 14:2620. [PMID: 38297061 PMCID: PMC10831065 DOI: 10.1038/s41598-024-51737-w] [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: 09/28/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
As the global demand for food increases, aquaculture plays a key role as the fastest growing animal protein sector. However, existing aquafeeds contain protein ingredients that are not sustainable under current production systems. We evaluated the use of microbial community-based single cell protein (SCP), produced from soybean processing wastewater, as a partial fishmeal protein substitute in juvenile Asian seabass (Lates calcarifer). A 24-day feeding trial was conducted with a control fishmeal diet and a 50% fishmeal replacement with microbial community-based SCP as an experimental group, in triplicate tanks containing 20 fish each. Both diets met the protein, essential amino acids (except for lysine), and fat requirements for juvenile Asian sea bass. The microbial composition of the SCP was dominated by the genera Acidipropionibacterium and Propioniciclava, which have potential as probiotics and producers of valuable metabolites. The growth performance in terms of percent weight gain, feed conversion ratio (FCR), specific growth rate (SGR), and survival were not significantly different between groups after 24 days. The experimental group had less variability in terms of weight gain and FCR than the control group. Overall, microbial community-based protein produced from soybean processing wastewater has potential as a value-added feed ingredient for sustainable aquaculture feeds.
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Affiliation(s)
- Ezequiel Santillan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Fanny Yasumaru
- Aquaculture Innovation Centre, Temasek Polytechnic, Singapore, 529757, Singapore
| | - Ramanujam Srinivasan Vethathirri
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Sara Swa Thi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Hui Yi Hoon
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Diana Chan Pek Sian
- Aquaculture Innovation Centre, Temasek Polytechnic, Singapore, 529757, Singapore.
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
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23
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Frank EM, Ahlinder J, Jephson T, Persson KM, Lindberg E, Paul CJ. Marine sediments are identified as an environmental reservoir for Escherichia coli: comparing signature-based and novel amplicon sequencing approaches for microbial source tracking. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167865. [PMID: 37863217 DOI: 10.1016/j.scitotenv.2023.167865] [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: 06/07/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/22/2023]
Abstract
Viable Escherichia coli were detected in sediments near a point of wastewater discharge in a marine coastal environment in Sweden. Since high concentrations were found in the sediments nearest the pipe, this suggested that treated wastewater effluent was the source of the microbes. In order to examine this hypothesis, different bioinformatics approaches were applied using 16S rRNA gene V3-V4 amplicon sequences from the sediments. Both signature-based source tracking using sequence libraries describing known sources of fecal water pollution (SourceTracker); and, a curated source tracking method, indicated that sediments were contaminated with wastewater. The results from the curated approach were independently confirmed using differential abundance analysis (DESeq2). A number of taxa originating from wastewater were identified which can be used to describe contamination of the sediments, and examine the spread of these specific taxa, even at low relative abundance, along the urban coast. Sequences of phylum Bacteroidetes (such as Bacteroides and Prevotella) and Firmicutes (such as Romboutsia) increased in sediments with higher concentrations of E. coli. In addition, sequences from Trichococcus are proposed as an indicator for treated wastewater. All three source tracking approaches, and the detection of viable E. coli, suggest that urban sediments can be a reservoir for indicator bacteria.
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Affiliation(s)
- Ellinor M Frank
- Water Resources Engineering, Department of Building and Environmental Technology, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden; Sweden Water Research, Ideon Science Park, Scheelevägen 15, SE-223 70 Lund, Sweden
| | - Jon Ahlinder
- FOI, Swedish Defense Research Agency, Cementvägen 20, SE-906 21 Umeå, Sweden
| | - Therese Jephson
- Sweden Water Research, Ideon Science Park, Scheelevägen 15, SE-223 70 Lund, Sweden
| | - Kenneth M Persson
- Water Resources Engineering, Department of Building and Environmental Technology, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden; Sweden Water Research, Ideon Science Park, Scheelevägen 15, SE-223 70 Lund, Sweden
| | - Elisabet Lindberg
- City of Helsingborg, Department of City Planning, Järnvägsgatan 22, SE-252 25 Helsingborg, Sweden
| | - Catherine J Paul
- Water Resources Engineering, Department of Building and Environmental Technology, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden; Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden.
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24
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Papazlatani C, Garbeva P, Huerta Lwanga E. Effect of microplastic pollution on the gut microbiome of anecic and endogeic earthworms. FEMS Microbiol Lett 2024; 371:fnae040. [PMID: 38849299 PMCID: PMC11232513 DOI: 10.1093/femsle/fnae040] [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: 12/18/2023] [Revised: 04/19/2024] [Accepted: 06/06/2024] [Indexed: 06/09/2024] Open
Abstract
Microplastic (MP) pollution constitutes an emerging type of pollution threatening both aquatic and terrestrial ecosystems. The impact on aquatic ecosystems has been extensively studied, but the effect on terrestrial ecosystems and their inhabitants is mostly underexplored. In this study, we explored the effect of MP pollution on gut bacterial microbiome of endogeic (Aporrectodea caliginosa) and anecic (Lumbricus terrestris) earthworms. The experiments were performed in sandy soil with 0.2% of low-density polyethylene MPs (LDPE MPs). We observed that the endogeic earthworms had 100% survival, while anecic earthworms survived 25 days in the control (i.e. in absence of MPs) and 21 days in the treatment with LDPE MPs. The main driver of shifts in the diversity and composition of the bacterial communities in the gut of tested earthworms was the lifestyle of the worms, followed by the presence of MPs. The bacterial microbiome diversity was significantly different among the two types of earthworms, and the highest bacterial diversity was found in the gut of the endogeic earthworms. The effect of MPs on gut bacterial microbiome was clearly observed in the changes in the relative abundance of several phyla and families of the bacterial communities in both types of earthworms, although it was most evident in the anecic earthworms. The Actinobacteriota, Proteobacteria, and Firmicutes were the main groups enhanced in the MP treatments, suggesting enrichment of the bacterial communities with potential plastic degraders.
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Affiliation(s)
- Christina Papazlatani
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands
| | - Esperanza Huerta Lwanga
- Soil Physics and Land Management Group, Wageningen University and Research, PO Box 47, 6708 PB Wageningen, The Netherlands
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Kaszecki E, Palberg D, Grant M, Griffin S, Dhanjal C, Capperauld M, Emery RJN, Saville BJ. Euglena mutabilis exists in a FAB consortium with microbes that enhance cadmium tolerance. Int Microbiol 2024:10.1007/s10123-023-00474-7. [PMID: 38167969 DOI: 10.1007/s10123-023-00474-7] [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: 10/19/2023] [Revised: 11/29/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Synthetic algal-fungal and algal-bacterial cultures have been investigated as a means to enhance the technological applications of the algae. This inclusion of other microbes has enhanced growth and improved stress tolerance of the algal culture. The goal of the current study was to investigate natural microbial consortia to gain an understanding of the occurrence and benefits of these associations in nature. The photosynthetic protist Euglena mutabilis is often found in association with other microbes in acidic environments with high heavy metal (HM) concentrations. This may suggest that microbial interactions are essential for the protist's ability to tolerate these extreme environments. Our study assessed the Cd tolerance of a natural fungal-algal-bacterial (FAB) association whereby the algae is E. mutabilis. RESULTS This study provides the first assessment of antibiotic and antimycotic agents on an E. mutabilis culture. The results indicate that antibiotic and antimycotic applications significantly decreased the viability of E. mutabilis cells when they were also exposed to Cd. Similar antibiotic treatments of E. gracilis cultures had variable or non-significant impacts on Cd tolerance. E. gracilis also recovered better after pre-treatment with antibiotics and Cd than did E. mutabilis. The recoveries were assessed by heterotrophic growth without antibiotics or Cd. In contrast, both Euglena species displayed increased chlorophyll production upon Cd exposure. PacBio full-length amplicon sequencing and targeted Sanger sequencing identified the microbial species present in the E. mutabilis culture to be the fungus Talaromyces sp. and the bacterium Acidiphilium acidophilum. CONCLUSION This study uncovers a possible fungal, algal, and bacterial relationship, what we refer to as a FAB consortium. The members of this consortium interact to enhance the response to Cd exposure. This results in a E. mutabilis culture that has a higher tolerance to Cd than the axenic E. gracilis. The description of this interaction provides a basis for explore the benefits of natural interactions. This will provide knowledge and direction for use when creating or maintaining FAB interactions for biotechnological purposes, including bioremediation.
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Affiliation(s)
- Emma Kaszecki
- Environmental and Life Science Graduate Program, Trent University, Peterborough, ON, Canada
| | - Daniel Palberg
- Environmental and Life Science Graduate Program, Trent University, Peterborough, ON, Canada
| | - Mikaella Grant
- Environmental and Life Science Graduate Program, Trent University, Peterborough, ON, Canada
| | - Sarah Griffin
- Forensic Science Department, Trent University, Peterborough, ON, Canada
| | - Chetan Dhanjal
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | - R J Neil Emery
- Environmental and Life Science Graduate Program, Trent University, Peterborough, ON, Canada
- Department of Biology, Trent University, Peterborough, ON, Canada
| | - Barry J Saville
- Environmental and Life Science Graduate Program, Trent University, Peterborough, ON, Canada.
- Forensic Science Department, Trent University, Peterborough, ON, Canada.
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26
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Newman-Portela AM, Krawczyk-Bärsch E, Lopez-Fernandez M, Bok F, Kassahun A, Drobot B, Steudtner R, Stumpf T, Raff J, Merroun ML. Biostimulation of indigenous microbes for uranium bioremediation in former U mine water: multidisciplinary approach assessment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7227-7245. [PMID: 38157180 PMCID: PMC10821841 DOI: 10.1007/s11356-023-31530-4] [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: 08/09/2023] [Accepted: 12/09/2023] [Indexed: 01/03/2024]
Abstract
Characterizing uranium (U) mine water is necessary to understand and design an effective bioremediation strategy. In this study, water samples from two former U-mines in East Germany were analysed. The U and sulphate (SO42-) concentrations of Schlema-Alberoda mine water (U: 1 mg/L; SO42-: 335 mg/L) were 2 and 3 order of magnitude higher than those of the Pöhla sample (U: 0.01 mg/L; SO42-: 0.5 mg/L). U and SO42- seemed to influence the microbial diversity of the two water samples. Microbial diversity analysis identified U(VI)-reducing bacteria (e.g. Desulfurivibrio) and wood-degrading fungi (e.g. Cadophora) providing as electron donors for the growth of U-reducers. U-bioreduction experiments were performed to screen electron donors (glycerol, vanillic acid, and gluconic acid) for Schlema-Alberoda U-mine water bioremediation purpose. Thermodynamic speciation calculations show that under experimental conditions, U(VI) is not coordinated to the amended electron donors. Glycerol was the best-studied electron donor as it effectively removed 99% of soluble U, 95% of Fe, and 58% of SO42- from the mine water, probably by biostimulation of indigenous microbes. Vanillic acid removed 90% of U, and no U removal occurred using gluconic acid.
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Affiliation(s)
- Antonio M Newman-Portela
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain.
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany.
| | - Evelyn Krawczyk-Bärsch
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Margarita Lopez-Fernandez
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
| | - Frank Bok
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Andrea Kassahun
- WISMUT GmbH, Jagdschänkenstraße 29, 09117, Chemnitz, Germany
| | - Björn Drobot
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Robin Steudtner
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Thorsten Stumpf
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Johannes Raff
- Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328, Dresden, Germany
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Science, University of Granada, Avda. Fuentenueva S/N, 18071, Granada, Spain
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Rayamajhee B, Willcox M, Sharma S, Mooney R, Petsoglou C, Badenoch PR, Sherchan S, Henriquez FL, Carnt N. Zooming in on the intracellular microbiome composition of bacterivorous Acanthamoeba isolates. ISME COMMUNICATIONS 2024; 4:ycae016. [PMID: 38500701 PMCID: PMC10945361 DOI: 10.1093/ismeco/ycae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/29/2023] [Accepted: 01/22/2024] [Indexed: 03/20/2024]
Abstract
Acanthamoeba, a free-living amoeba in water and soil, is an emerging pathogen causing severe eye infection known as Acanthamoeba keratitis. In its natural environment, Acanthamoeba performs a dual function as an environmental heterotrophic predator and host for a range of microorganisms that resist digestion. Our objective was to characterize the intracellular microorganisms of phylogenetically distinct Acanthamoeba spp. isolated in Australia and India through directly sequencing 16S rRNA amplicons from the amoebae. The presence of intracellular bacteria was further confirmed by in situ hybridization and electron microscopy. Among the 51 isolates assessed, 41% harboured intracellular bacteria which were clustered into four major phyla: Pseudomonadota (previously known as Proteobacteria), Bacteroidota (previously known as Bacteroidetes), Actinomycetota (previously known as Actinobacteria), and Bacillota (previously known as Firmicutes). The linear discriminate analysis effect size analysis identified distinct microbial abundance patterns among the sample types; Pseudomonas species was abundant in Australian corneal isolates (P < 0.007), Enterobacteriales showed higher abundance in Indian corneal isolates (P < 0.017), and Bacteroidota was abundant in Australian water isolates (P < 0.019). The bacterial beta diversity of Acanthamoeba isolates from keratitis patients in India and Australia significantly differed (P < 0.05), while alpha diversity did not vary based on the country of origin or source of isolation (P > 0.05). More diverse intracellular bacteria were identified in water isolates as compared with clinical isolates. Confocal and electron microscopy confirmed the bacterial cells undergoing binary fission within the amoebal host, indicating the presence of viable bacteria. This study sheds light on the possibility of a sympatric lifestyle within Acanthamoeba, thereby emphasizing its crucial role as a bunker and carrier of potential human pathogens.
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Affiliation(s)
- Binod Rayamajhee
- School of Optometry and Vision Science, Faculty of Medicine and Health, UNSW, Sydney, NSW 2052, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, Faculty of Medicine and Health, UNSW, Sydney, NSW 2052, Australia
| | - Savitri Sharma
- Jhaveri Microbiology Centre, Prof Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, L. V. Prasad Eye Institute (LVPEI), Hyderabad, 500034, India
| | - Ronnie Mooney
- School of Health and Life Sciences, University of the West of Scotland, Blantyre, PA1 2BE, United Kingdom
| | - Constantinos Petsoglou
- Sydney and Sydney Eye Hospital, South-Eastern Sydney Local Health District, Sydney, NSW 2000, Australia
- Save Sight Institute, University of Sydney, Sydney, NSW 2000, Australia
| | - Paul R Badenoch
- College of Medicine and Public Health, Flinders University, Adelaide, 5042, Australia
| | - Samendra Sherchan
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, United States
| | - Fiona L Henriquez
- School of Health and Life Sciences, University of the West of Scotland, Blantyre, PA1 2BE, United Kingdom
| | - Nicole Carnt
- School of Optometry and Vision Science, Faculty of Medicine and Health, UNSW, Sydney, NSW 2052, Australia
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28
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Nappi J, Goncalves P, Khan T, Majzoub ME, Grobler AS, Marzinelli EM, Thomas T, Egan S. Differential priority effects impact taxonomy and functionality of host-associated microbiomes. Mol Ecol 2023; 32:6278-6293. [PMID: 34995388 DOI: 10.1111/mec.16336] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 01/24/2023]
Abstract
Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.
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Affiliation(s)
- Jadranka Nappi
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Priscila Goncalves
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Tahsin Khan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Marwan E Majzoub
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Anna Sophia Grobler
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Ezequiel M Marzinelli
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Torsten Thomas
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
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29
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Langill T, Wójcik M, Vangronsveld J, Thijs S. Endophyte Community Changes in the Seeds of Eight Plant Species following Inoculation with a Multi-Endophytic Bacterial Consortium and an Individual Sphingomonas wittichii Strain Obtained from Noccaea caerulescens. PLANTS (BASEL, SWITZERLAND) 2023; 12:3660. [PMID: 37896123 PMCID: PMC10609953 DOI: 10.3390/plants12203660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
Noccaea caerulescens, a hyperaccumulator plant species known for its metal tolerance and accumulation abilities, harbours a microbiome of interest within its seed. These seed-associated bacteria, often referred to as seed endophytes, play a unique role in seed germination and plant growth and health. This work aimed to address how inoculating seeds of eight different plant species-Medicago sativa (alfalfa), Zea mays (corn), Raphanus sativus (radish), Helianthus annus (sunflower), Cucurbita pepo subsp. pepo (squash), Beta vulgaris subsp. cicla (rainbow chard), Arabidopsis thaliana (thale cress), and Noccaea caerulescens (penny cress)-with a bacterial consortium made from the seed endophytes of N. caerulescens would affect the seed microbiome of each test plant species, as well as inoculation with a strain of the bacterium Sphingomonas wittichii, which was previously isolated from seeds of N. caerulescens. Additionally, we aimed to offer preliminary plant tests in order to determine the best seed treatment plan for future research. The results showed that inoculation with the bacterial consortium held the most potential for increasing plant size (p < 0.001) and increasing germination rate (p < 0.05). The plant that responded best to inoculation was N. caerulescens (penny cress), likely because the microbes being introduced into the seed were not foreign. This paper also offers the first insight into the seed endophytes of Beta vulgaris subsp. cicla, highlighting an abundance of Proteobacteria, Firmicutes, and Actinobacteriota.
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Affiliation(s)
- Tori Langill
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium (J.V.)
| | - Małgorzata Wójcik
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium (J.V.)
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium (J.V.)
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Sofie Thijs
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium (J.V.)
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Lazarova S, Lozanova L, Neov B, Shumkova R, Balkanska R, Palova N, Salkova D, Radoslavov G, Hristov P. Composition and diversity of bacterial communities associated with honey bee foragers from two contrasting environments. BULLETIN OF ENTOMOLOGICAL RESEARCH 2023; 113:693-702. [PMID: 37545319 DOI: 10.1017/s0007485323000378] [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: 08/08/2023]
Abstract
The honey bee is associated with a diverse community of microbes (viruses, bacteria, fungi, and protists), commonly known as the microbiome. Here, we present data on honey bee microbiota from two localities having different surrounding landscapes - mountain (the Rhodope Mountains) and lowland (the Danube plain). The bacterial communities of abdomen of adult bees were studied using amplicon sequencing of the 16S rRNA gene. The composition and dominance structure and their variability within and between localities, alpha and beta diversity, and core and differential taxa were compared at different hierarchical levels (operational taxonomic units to phylum). Seven genera (Lactobacillus, Gilliamella, Bifidobacterium, Commensalibacter, Bartonella, Snodgrassella, and Frischella), known to include core gut-associated phylotypes or species clusters, dominated (92-100%) the bacterial assemblages. Significant variations were found in taxa distribution across both geographical regions and within each apiary. Lactobacillus (Firmicutes) prevailed significantly in the mountain locality followed by Gilliamella and Bartonella (Proteobacteria). Bacteria of four genera, core (Bartonella and Lactobacillus) and non-core (Pseudomonas and Morganella), dominated the bee-associated assemblages of the Danube plain locality. Several ubiquitous bacterial genera (e.g., Klebsiella, Serratia, and Providencia), some species known also as potential and opportunistic bee pathogens, had been found in the lowland locality. Beta diversity analyses confirmed the observed differences in the bacterial communities from both localities. The occurrence of non-core taxa contributes substantially to higher microbial richness and diversity in bees from the Danube plain locality. We assume that the observed differences in the microbiota of honey bees from both apiaries are due to a combination of factors specific for each region. The surrounding landscape features of both localities and related vegetation, anthropogenic impact and land use intensity, the beekeeping management practices, and bee health status might all contribute to observed differences in bee microbiota traits.
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Affiliation(s)
- Stela Lazarova
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Lyudmila Lozanova
- Department of Ecosystem Research, Environmental Risk Assessment and Conservation Biology, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Boyko Neov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Rositsa Shumkova
- Research Centre of Stockbreeding and Agriculture, Agricultural Academy, 4700 Smolyan, Bulgaria
| | - Ralitsa Balkanska
- Department 'Special Branches', Institute of Animal Science, Agricultural Academy, 2230 Kostinbrod, Bulgaria
| | - Nadezhda Palova
- Scientific Center of Agriculture, Agricultural Academy, Sredets 8300, Bulgaria
| | - Delka Salkova
- Department of Experimental Parasitology, Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Georgi Radoslavov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Peter Hristov
- Department of Animal Diversity and Resources, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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31
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Sułowicz S, Borymski S, Dulski M, Nowak A, Bondarczuk K, Markowicz A. Nanopesticide risk assessment based on microbiome profiling - Community structure and functional potential as biomarkers in captan@ZnO 35-45 nm and captan@SiO 220-30 nm treated orchard soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131948. [PMID: 37392645 DOI: 10.1016/j.jhazmat.2023.131948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/03/2023]
Abstract
Nanoformulation should minimise the usage of pesticides and limit their environmental footprint. The risk assessment of two nanopesticides with fungicide captan as an active organic substance and ZnO35-45 nm or SiO220-30 nm as nanocarriers was evaluated using the non-target soil microorganisms as biomarkers. The first time for that kind of nanopesticides next-generation sequencing (NGS) of bacterial 16 S rRNA and fungal ITS region and metagenomics functional predictions (PICRUST2) was made to study structural and functional biodiversity. During a 100-day microcosm study in soil with pesticide application history, the effect of nanopesticides was compared to pure captan and both nanocarriers. Nanoagrochemicals affected microbial composition, especially Acidobacteria-6 class, and alpha diversity, but the observed effect was generally more substantial for pure captan. As for beta diversity, the negative impact was detected only in response to captan and still observed on day 100. Fungal community in the orchard soil showed only a decrease in phylogenetic diversity in captan set-up since day 30. PICRUST2 analysis confirmed several times lower impact of nanopesticides considering the abundance of functional pathways and genes encoding enzymes. Furthermore, the overall data indicated that using SiO220-30 nm as a nanocarrier speeds up a recovery process compared to ZnO35-45 nm.
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Affiliation(s)
- Sławomir Sułowicz
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland.
| | - Sławomir Borymski
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
| | - Mateusz Dulski
- University of Silesia, Institute of Materials Engineering, Silesian Center for Education and Interdisciplinary Research, 75 Pulku Piechoty 1A, 41-500 Chorzow, Poland
| | - Anna Nowak
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
| | - Kinga Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Białystok, Jerzego Waszyngtona 13A, 15-269 Białystok, Poland
| | - Anna Markowicz
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland
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32
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Aitmanaitė L, Širmonaitis K, Russo G. Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap. Int J Mol Sci 2023; 24:13786. [PMID: 37762088 PMCID: PMC10531294 DOI: 10.3390/ijms241813786] [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: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The interaction between the microbial communities in the human body and the onset and progression of cancer has not been investigated until recently. The vast majority of the metagenomics research in this area has concentrated on the composition of microbiomes, attempting to link the overabundance or depletion of certain microorganisms to cancer proliferation, metastatic behaviour, and its resistance to therapies. However, studies elucidating the functional implications of the microbiome activity in cancer patients are still scarce; in particular, there is an overwhelming lack of studies assessing such implications directly, through analysis of the transcriptome of the bacterial community. This review summarises the contributions of metagenomics and metatranscriptomics to the knowledge of the microbial environment associated with several cancers; most importantly, it highlights all the advantages that metatranscriptomics has over metagenomics and suggests how such an approach can be leveraged to advance the knowledge of the cancer bacterial environment.
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Affiliation(s)
| | | | - Giancarlo Russo
- EMBL Partnership Institute for Gene Editing, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (L.A.); (K.Š.)
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33
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Muzny CA, Cerca N, Elnaggar JH, Taylor CM, Sobel JD, Van Der Pol B. State of the Art for Diagnosis of Bacterial Vaginosis. J Clin Microbiol 2023; 61:e0083722. [PMID: 37199636 PMCID: PMC10446871 DOI: 10.1128/jcm.00837-22] [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] [Indexed: 05/19/2023] Open
Abstract
Bacterial vaginosis (BV) is the most common cause of vaginal discharge among reproductive-age women. It is associated with multiple adverse health outcomes, including increased risk of acquisition of HIV and other sexually transmitted infections (STIs), in addition to adverse birth outcomes. While it is known that BV is a vaginal dysbiosis characterized by a shift in the vaginal microbiota from protective Lactobacillus species to an increase in facultative and strict anaerobic bacteria, its exact etiology remains unknown. The purpose of this minireview is to provide an updated overview of the range of tests currently used for the diagnosis of BV in both clinical and research settings. This article is divided into two primary sections: traditional BV diagnostics and molecular diagnostics. Molecular diagnostic assays, particularly 16S rRNA gene sequencing, shotgun metagenomic sequencing, and fluorescence in situ hybridization (FISH), are specifically highlighted, in addition to multiplex nucleic acid amplification tests (NAATs), given their increasing use in clinical practice (NAATs) and research studies (16S rRNA gene sequencing, shotgun metagenomic sequencing, and FISH) regarding the vaginal microbiota and BV pathogenesis. We also provide a discussion of the strengths and weaknesses of current BV diagnostic tests and discuss future challenges in this field of research.
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Affiliation(s)
- Christina A. Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nuno Cerca
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Braga, Portugal
| | - Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Jack D. Sobel
- Division of Infectious Diseases, Wayne State University, Detroit, Michigan, USA
| | - Barbara Van Der Pol
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
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34
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Na HS, Song Y, Yu Y, Chung J. Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies. Methods Protoc 2023; 6:71. [PMID: 37623922 PMCID: PMC10460062 DOI: 10.3390/mps6040071] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023] Open
Abstract
Recent advances in genomic technologies have enabled more in-depth study of the oral microbiome. In this study, we compared the amplicons generated by primers targeting different sites of the 16S rRNA gene found in the Human Oral Microbiome Database (HOMD). Six sets of primer targeting V1-V2, V1-V3, V3-V4, V4-V5, V5-V7 and V6-V8 regions of 16S rRNA were tested via in silico simulation. Primers targeting the V1-V2, V3-V4, and V4-V5 regions generated more than 90% of the original input sequences. Primers targeting the V1-V2 and V1-V3 regions exhibited a low number of mismatches and unclassified sequences at the taxonomic level, but there were notable discrepancies at the species level. Phylogenetic tree comparisons showed primers targeting the V1-V2 and V3-V4 regions showed performances similar to primers targeting the whole 16s RNA region in terms of separating total oral microbiomes and periodontopathogens. In an analysis of clinical oral samples, V1-V2 primers showed superior performance for identifying more taxa and had better resolution sensitivity for Streptococcus than V3-V4 primers. In conclusion, primers targeting the V1-V2 region of 16S rRNA showed the best performance for oral microbiome studies. In addition, the study demonstrates the need for careful PCR primer selections.
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Affiliation(s)
- Hee Sam Na
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea (Y.S.)
- Oral Genomics Research Center, Pusan National University, Yangsan 50612, Republic of Korea
- Dental Research Institute, BK21 PLUS Project, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
| | - Yuri Song
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea (Y.S.)
- Oral Genomics Research Center, Pusan National University, Yangsan 50612, Republic of Korea
| | - Yeuni Yu
- Interdisciplinary Program of Genomic Science, Pusan National University, Yangsan 50612, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Busan 46241, Republic of Korea
| | - Jin Chung
- Department of Oral Microbiology, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea (Y.S.)
- Oral Genomics Research Center, Pusan National University, Yangsan 50612, Republic of Korea
- Dental Research Institute, BK21 PLUS Project, School of Dentistry, Pusan National University, Yangsan 50612, Republic of Korea
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35
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Flocco CG, Methner A, Burkart F, Geppert A, Overmann J. Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects. Front Microbiol 2023; 14:1197837. [PMID: 37601377 PMCID: PMC10435870 DOI: 10.3389/fmicb.2023.1197837] [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: 03/31/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
Microbiological and biomolecular approaches to cultural heritage research have expanded the established research horizon from the prevalent focus on the cultural objects' conservation and human health protection to the relatively recent applications to provenance inquiry and assessment of environmental impacts in a global context of a changing climate. Standard microbiology and molecular biology methods developed for other materials, specimens, and contexts could, in principle, be applied to cultural heritage research. However, given certain characteristics common to several heritage objects-such as uniqueness, fragility, high value, and restricted access, tailored approaches are required. In addition, samples of heritage objects may yield low microbial biomass, rendering them highly susceptible to cross-contamination. Therefore, dedicated methodology addressing these limitations and operational hurdles is needed. Here, we review the main experimental challenges and propose a standardized workflow to study the microbiome of cultural heritage objects, illustrated by the exploration of bacterial taxa. The methodology was developed targeting the challenging side of the spectrum of cultural heritage objects, such as the delicate written record, while retaining flexibility to adapt and/or upscale it to heritage artifacts of a more robust constitution or larger dimensions. We hope this tailored review and workflow will facilitate the interdisciplinary inquiry and interactions among the cultural heritage research community.
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Affiliation(s)
- Cecilia G. Flocco
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Anika Methner
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Franziska Burkart
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Alicia Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ- German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
- Microbiology, Technical University of Braunschweig, Braunschweig, Germany
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36
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Lagunas B, Richards L, Sergaki C, Burgess J, Pardal AJ, Hussain RMF, Richmond BL, Baxter L, Roy P, Pakidi A, Stovold G, Vázquez S, Ott S, Schäfer P, Gifford ML. Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth. MICROBIOME 2023; 11:146. [PMID: 37394496 DOI: 10.1186/s40168-023-01592-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 06/05/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Despite the knowledge that the soil-plant-microbiome nexus is shaped by interactions amongst its members, very little is known about how individual symbioses regulate this shaping. Even less is known about how the agriculturally important symbiosis of nitrogen-fixing rhizobia with legumes is impacted according to soil type, yet this knowledge is crucial if we are to harness or improve it. We asked how the plant, soil and microbiome are modulated by symbiosis between the model legume Medicago truncatula and different strains of Sinorhizobium meliloti or Sinorhizobium medicae whose nitrogen-fixing efficiency varies, in three distinct soil types that differ in nutrient fertility, to examine the role of the soil environment upon the plant-microbe interaction during nodulation. RESULTS The outcome of symbiosis results in installment of a potentially beneficial microbiome that leads to increased nutrient uptake that is not simply proportional to soil nutrient abundance. A number of soil edaphic factors including Zn and Mo, and not just the classical N/P/K nutrients, group with microbial community changes, and alterations in the microbiome can be seen across different soil fertility types. Root endosphere emerged as the plant microhabitat more affected by this rhizobial efficiency-driven community reshaping, manifested by the accumulation of members of the phylum Actinobacteria. The plant in turn plays an active role in regulating its root community, including sanctioning low nitrogen efficiency rhizobial strains, leading to nodule senescence in particular plant-soil-rhizobia strain combinations. CONCLUSIONS The microbiome-soil-rhizobial dynamic strongly influences plant nutrient uptake and growth, with the endosphere and rhizosphere shaped differentially according to plant-rhizobial interactions with strains that vary in nitrogen-fixing efficiency levels. These results open up the possibility to select inoculation partners best suited for plant, soil type and microbial community. Video Abstract.
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Affiliation(s)
- Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Luke Richards
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Chrysi Sergaki
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jamie Burgess
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Rana M F Hussain
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Laura Baxter
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Proyash Roy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Anastasia Pakidi
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Gina Stovold
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Saúl Vázquez
- University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Nottingham, LE12 5RD, UK
| | - Sascha Ott
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Present Address: Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, 35392, Germany.
| | - Miriam L Gifford
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV47AL, UK.
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Martinez-Moreno MF, Povedano-Priego C, Morales-Hidalgo M, Mumford AD, Ojeda JJ, Jroundi F, Merroun ML. Impact of compacted bentonite microbial community on the clay mineralogy and copper canister corrosion: a multidisciplinary approach in view of a safe Deep Geological Repository of nuclear wastes. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131940. [PMID: 37390682 DOI: 10.1016/j.jhazmat.2023.131940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
Deep Geological Repository (DGR) is the preferred option for the final disposal of high-level radioactive waste. Microorganisms could affect the safety of the DGR by altering the mineralogical properties of the compacted bentonite or inducing the corrosion of the metal canisters. In this work, the impact of physicochemical parameters (bentonite dry density, heat shock, electron donors/acceptors) on the microbial activity, stability of compacted bentonite and corrosion of copper (Cu) discs was investigated after one-year anoxic incubation at 30 ºC. No-illitization in the bentonite was detected confirming its structural stability over 1 year under the experimental conditions. The microbial diversity analysis based on 16 S rRNA gene Next Generation Sequencing showed slight changes between the treatments with an increase of aerobic bacteria belonging to Micrococcaceae and Nocardioides in heat-shock tyndallized bentonites. The survival of sulfate-reducing bacteria (the main source of Cu anoxic corrosion) was demonstrated by the most probable number method. The detection of CuxS precipitates on the surface of Cu metal in the bentonite/Cu metal samples amended with acetate/lactate and sulfate, indicated an early stage of Cu corrosion. Overall, the outputs of this study help to better understand the predominant biogeochemical processes at the bentonite/Cu canister interface upon DGR closure.
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Affiliation(s)
| | | | - Mar Morales-Hidalgo
- Department of Microbiology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Adam D Mumford
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Jesus J Ojeda
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Fadwa Jroundi
- Department of Microbiology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Mohamed L Merroun
- Department of Microbiology, Faculty of Sciences, University of Granada, Granada, Spain
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Haveman NJ, Schuerger AC, Yu PL, Brown M, Doebler R, Paul AL, Ferl RJ. Advancing the automation of plant nucleic acid extraction for rapid diagnosis of plant diseases in space. FRONTIERS IN PLANT SCIENCE 2023; 14:1194753. [PMID: 37389293 PMCID: PMC10304293 DOI: 10.3389/fpls.2023.1194753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023]
Abstract
Human space exploration missions will continue the development of sustainable plant cultivation in what are obviously novel habitat settings. Effective pathology mitigation strategies are needed to cope with plant disease outbreaks in any space-based plant growth system. However, few technologies currently exist for space-based diagnosis of plant pathogens. Therefore, we developed a method of extracting plant nucleic acid that will facilitate the rapid diagnosis of plant diseases for future spaceflight applications. The microHomogenizer™ from Claremont BioSolutions, originally designed for bacterial and animal tissue samples, was evaluated for plant-microbial nucleic acid extractions. The microHomogenizer™ is an appealing device in that it provides automation and containment capabilities that would be required in spaceflight applications. Three different plant pathosystems were used to assess the versatility of the extraction process. Tomato, lettuce, and pepper plants were respectively inoculated with a fungal plant pathogen, an oomycete pathogen, and a plant viral pathogen. The microHomogenizer™, along with the developed protocols, proved to be an effective mechanism for producing DNA from all three pathosystems, in that PCR and sequencing of the resulting samples demonstrated clear DNA-based diagnoses. Thus, this investigation advances the efforts to automate nucleic acid extraction for future plant disease diagnosis in space.
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Affiliation(s)
- Natasha J. Haveman
- NASA Utilization & Life Sciences Office (UB-A), Kennedy Space Center, Merritt Island, FL, United States
| | - Andrew C. Schuerger
- Department of Plant Pathology, University of Florida, Space Life Science Lab, Merritt Island, FL, United States
| | - Pei-Ling Yu
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Mark Brown
- Claremont BioSolutions Limited Liability Company (LLC), Upland, CA, United States
| | - Robert Doebler
- Claremont BioSolutions Limited Liability Company (LLC), Upland, CA, United States
| | - Anna-Lisa Paul
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Robert J. Ferl
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
- University of Florida Office of Research, University of Florida, Gainesville, FL, United States
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Stevens BM, Creed TB, Reardon CL, Manter DK. Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil. Sci Rep 2023; 13:9323. [PMID: 37291169 PMCID: PMC10250467 DOI: 10.1038/s41598-023-36101-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Illumina MiSeq is the current standard for characterizing microbial communities in soil. The newer alternative, Oxford Nanopore Technologies MinION sequencer, is quickly gaining popularity because of the low initial cost and longer sequence reads. However, the accuracy of MinION, per base, is much lower than MiSeq (95% versus 99.9%). The effects of this difference in base-calling accuracy on taxonomic and diversity estimates remains unclear. We compared the effects of platform, primers, and bioinformatics on mock community and agricultural soil samples using short MiSeq, and short and full-length MinION 16S rRNA amplicon sequencing. For all three methods, we found that taxonomic assignments of the mock community at both the genus and species level matched expectations with minimal deviation (genus: 80.9-90.5%; species: 70.9-85.2% Bray-Curtis similarity); however, the short MiSeq with error correction (DADA2) resulted in the correct estimate of mock community species richness and much lower alpha diversity for soils. Several filtering strategies were tested to improve these estimates with varying results. The sequencing platform also had a significant influence on the relative abundances of taxa with MiSeq resulting in significantly higher abundances Actinobacteria, Chloroflexi, and Gemmatimonadetes and lower abundances of Acidobacteria, Bacteroides, Firmicutes, Proteobacteria, and Verrucomicrobia compared to the MinION platform. When comparing agricultural soils from two different sites (Fort Collins, CO and Pendleton, OR), methods varied in the taxa identified as significantly different between sites. At all taxonomic levels, the full-length MinION method had the highest similarity to the short MiSeq method with DADA2 correction with 73.2%, 69.3%, 74.1%, 79.3%, 79.4%, and 82.28% of the taxa at the phyla, class, order, family, genus, and species levels, respectively, showing similar patterns in differences between the sites. In summary, although both platforms appear suitable for 16S rRNA microbial community composition, biases for different taxa may make the comparison between studies problematic; and even with a single study (i.e., comparing sites or treatments), the sequencing platform can influence the differentially abundant taxa identified.
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Affiliation(s)
- Bo Maxwell Stevens
- Water Management and Systems Research Unit, USDA ARS, Fort Collins, CO, 80526, USA
| | - Tim B Creed
- Soil Management and Sugar Beet Research Unit, USDA ARS, Fort Collins, CO, 80526, USA
| | - Catherine L Reardon
- Columbia Plateau Conservation Research Center, USDA ARS, Adams, OR, 97810, USA
| | - Daniel K Manter
- Soil Management and Sugar Beet Research Unit, USDA ARS, Fort Collins, CO, 80526, USA.
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Vethathirri RS, Santillan E, Thi SS, Hoon HY, Wuertz S. Microbial community-based production of single cell protein from soybean-processing wastewater of variable chemical composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162241. [PMID: 36804981 DOI: 10.1016/j.scitotenv.2023.162241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/16/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
The use of food-processing wastewaters to produce microbial biomass-derived single cell protein (SCP) is a sustainable way to meet the global food demand. Microbial community-based approaches to SCP production have the potential benefits of lower costs and greater resource recovery compared to pure cultures, yet they have received scarce attention. Here, SCP production from soybean-processing wastewaters using their existent microbial communities was evaluated. Six sequencing batch reactors of 4.5-L working volume were operated at 30 °C for 34 d in cycles consisting of 3-h anaerobic and 9-h aerobic phases. Four reactors received no microbial inoculum and the remaining two were amended with 1.5 L of a mixed culture from a prior SCP production cycle. Reactors produced more SCP when fed with wastewaters of higher soluble total Kjeldahl nitrogen (sTKN) content. The protein yield in biomass ranged from 0.53 to 3.13 g protein/g sTKN, with a maximum protein content of 50 %. The average removal of soluble chemical oxygen demand (sCOD) and soluble total nitrogen (sTN) was 92 % and 73 %, respectively. Distinct microbial genera were enriched in all six bioreactors, with Azospirillum, Rhodobacter, Lactococcus, and Novosphingobium dominating. The study showed that constituents in soybean wastewater can be converted to SCP and demonstrated the effect of variable influent wastewater composition on SCP production.
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Affiliation(s)
- Ramanujam Srinivasan Vethathirri
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Ezequiel Santillan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore.
| | - Sara Swa Thi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Hui Yi Hoon
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
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De Wolfe TJ, Wright ES. Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis. BMC Microbiol 2023; 23:107. [PMID: 37076812 PMCID: PMC10114302 DOI: 10.1186/s12866-023-02851-8] [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: 09/26/2022] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles. RESULTS Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%). CONCLUSIONS Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.
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Affiliation(s)
- Travis J. De Wolfe
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 450 Technology Drive Rm. 426, Pittsburgh, PA 15219 USA
- Department of Pediatrics, BC Children’s Hospital Research Institute, University of British Columbia, 4480 Oak Street Rm. 208B, Vancouver, BC V6H 4E4 Canada
- Gut4Health, BC Children’s Hospital Research Institute, University of British Columbia, 950 West 28th Avenue Rm. 211, Vancouver, BC V5Z 4H4 Canada
| | - Erik S. Wright
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, 450 Technology Drive Rm. 426, Pittsburgh, PA 15219 USA
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Lemke M, DeSalle R. The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability. MICROBIAL ECOLOGY 2023; 85:781-795. [PMID: 36826587 PMCID: PMC10156817 DOI: 10.1007/s00248-023-02185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 05/04/2023]
Abstract
Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.
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Affiliation(s)
- Michael Lemke
- Department of Biology, University of Illinois at Springfield, Springfield, IL, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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Wang J, Yan Y, Si H, Li J, Zhao Y, Gao T, Pi J, Zhang R, Chen R, Chen W, Zheng Y, Jiang M. The effect of real-ambient PM2.5 exposure on the lung and gut microbiomes and the regulation of Nrf2. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114702. [PMID: 36950983 DOI: 10.1016/j.ecoenv.2023.114702] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/20/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
The influence of air pollution on human health has sparked widespread concerns across the world. Previously, we found that exposure to ambient fine particulate matter (PM2.5) in our "real-ambient exposure" system can result in reduced lung function. However, the mechanism of organ-specific toxicity is still not fully elucidated. The balance of the microbiome contributes to maintaining lung and gut health, but the changes in the microbiome under PM2.5 exposure are not fully understood. Recently, crosstalk between nuclear factor E2-related factor 2 (Nrf2) and the microbiome was reported. However, it is unclear whether Nrf2 affects the lung and gut microbiomes under PM2.5 exposure. In this study, wild-type (WT) and Nrf2-/- (KO) mice were exposed to filtered air (FA) and real ambient PM2.5 (PM) in the " real-ambient exposure" system to examine changes in the lung and gut microbiomes. Here, our data suggested microbiome dysbiosis in lung and gut of KO mice under PM2.5 exposure, and Nrf2 ameliorated the microbiome disorder. Our study demonstrated the detrimental impacts of PM2.5 on the lung and gut microbiome by inhaled exposure to air pollution and supported the protective role of Nrf2 in maintaining microbiome homeostasis under PM2.5 exposure.
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Affiliation(s)
- Jianxin Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Yongwei Yan
- Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Yellow Sea fisheries research institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, China
| | - Honglin Si
- School of Public Health, Qingdao University, Qingdao, China
| | - Jianyu Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Yanjie Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Tianlin Gao
- School of Public Health, Qingdao University, Qingdao, China
| | - Jingbo Pi
- School of Public Health, China Medical University, Shenyang, China
| | - Rong Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang, China
| | - Rui Chen
- School of Public Health, Capital Medical University, Beijing, China
| | - Wen Chen
- Department of Toxicology, School of Public Health, Sun Yaseen University, Guangzhou, China
| | - Yuxin Zheng
- School of Public Health, Qingdao University, Qingdao, China
| | - Menghui Jiang
- School of Public Health, Qingdao University, Qingdao, China.
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Regueira-Iglesias A, Vázquez-González L, Balsa-Castro C, Vila-Blanco N, Blanco-Pintos T, Tamames J, Carreira MJ, Tomás I. In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea. MICROBIOME 2023; 11:58. [PMID: 36949474 PMCID: PMC10035280 DOI: 10.1186/s40168-023-01481-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain. RESULTS A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) ≥75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively. CONCLUSIONS Given the three amplicon length categories (100-300, 301-600, and >600 base pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.
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Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), C/ Entrerrios s/n, 15872 Santiago de Compostela, Spain
| | - Lara Vázquez-González
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Rúa de Jenaro de la Fuente, s/n, 15705 Santiago de Compostela, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), C/ Entrerrios s/n, 15872 Santiago de Compostela, Spain
| | - Nicolás Vila-Blanco
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Rúa de Jenaro de la Fuente, s/n, 15705 Santiago de Compostela, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), C/ Entrerrios s/n, 15872 Santiago de Compostela, Spain
| | - Javier Tamames
- Microbiome Analysis Laboratory, Systems Biology Department, Centro Nacional de Biotecnología (CNB)-CSIC, Madrid, Spain
| | - Maria José Carreira
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Rúa de Jenaro de la Fuente, s/n, 15705 Santiago de Compostela, Spain
| | - Inmaculada Tomás
- Oral Sciences Research Group, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), C/ Entrerrios s/n, 15872 Santiago de Compostela, Spain
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Sajnaga E, Socała K, Kalwasińska A, Wlaź P, Waśko A, Jach ME, Tomczyk M, Wiater A. Response of murine gut microbiota to a prebiotic based on oligosaccharides derived via hydrolysis of fungal α-(1→3)-d-glucan: Preclinical trial study on mice. Food Chem 2023; 417:135928. [PMID: 36933426 DOI: 10.1016/j.foodchem.2023.135928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 02/04/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023]
Abstract
We investigated the modulating effect of α-(1→3)-glucooligosaccharides (GOS), i.e. a product of fungal α-(1→3)-d-glucan hydrolysis, on the gut microbiota composition. Mice were fed with a GOS-supplemented diet and two control diets for 21 days, and fecal samples were collected at 0, 1, and 3-week time points. The bacterial community composition was determined by 16S rRNA gene Illumina sequencing. The gut microbiota of the GOS-supplemented mice showed profound time-dependent changes in the taxonomic composition; however, we did not observe significant changes in α-diversity indices. The biggest number of genus abundance shifts after 1 week of the treatment was noticed between the group of the GOS-supplemented mice and the controls; however, the differences were still relevant after the 3-week treatment. The GOS-supplemented mice displayed higher abundance of Prevotella spp., with a concomitant decrease in the abundance of Escherichia-Shigella. Hence, GOS seems to be a promising candidate for a new prebiotic.
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Affiliation(s)
- Ewa Sajnaga
- Department of Biomedicine and Environmental Research, John Paul II Catholic University of Lublin, ul. Konstantynów 1J, 20-708 Lublin, Poland
| | - Katarzyna Socała
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Maria Curie-Skłodowska University, ul. Akademicka 19, 20-033 Lublin, Poland
| | - Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, ul. Lwowska 1, 87-100 Toruń, Poland
| | - Piotr Wlaź
- Department of Animal Physiology and Pharmacology, Institute of Biological Sciences, Maria Curie-Skłodowska University, ul. Akademicka 19, 20-033 Lublin, Poland
| | - Adam Waśko
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, ul. Skromna 8, 20-704 Lublin, Poland
| | - Monika Elżbieta Jach
- Department of Molecular Biology, John Paul II Catholic University of Lublin, ul. Konstantynów 1H, 20-708 Lublin, Poland
| | - Michał Tomczyk
- Department of Pharmacognosy, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2a, 15-230 Białystok, Poland
| | - Adrian Wiater
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, ul. Akademicka 19, 20-033 Lublin, Poland.
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Soil Inoculation and Blocker-Mediated Sequencing Show Effects of the Antibacterial T6SS on Agrobacterial Tumorigenesis and Gallobiome. mBio 2023; 14:e0017723. [PMID: 36877054 PMCID: PMC10128044 DOI: 10.1128/mbio.00177-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
The type VI secretion system (T6SS) is deployed by many proteobacteria to secrete effector proteins into bacterial competitors for competition or eukaryotic cells for pathogenesis. Agrobacteria, a group of soilborne phytopathogens causing crown gall disease on various plant species, deploy the T6SS to attack closely and distantly related bacterial species in vitro and in planta. Current evidence suggests that the T6SS is not essential for pathogenesis under direct inoculation, but it remains unknown whether the T6SS influences natural disease incidence or the microbial community within crown galls (i.e., the gallobiome). To address these two key questions, we established a soil inoculation method on wounded tomato seedlings that mimics natural infections and developed a bacterial 16S rRNA gene amplicon enrichment sequencing platform. By comparing the Agrobacterium wild-type strain C58 with two T6SS mutants, we demonstrate that the T6SS influences both disease occurrence and gallobiome composition. Based on multiple inoculation trials across seasons, all three strains induced tumors, but the mutants had significantly lower disease incidences. The season of inoculation played a more important role than the T6SS in shaping the gallobiome. The influence of the T6SS was evident in summer, during which two Sphingomonadaceae species and the family Burkholderiaceae were enriched in the gallobiome induced by the mutants. Further in vitro competition and colonization assays demonstrated the T6SS-mediated antagonism to a Sphingomonas sp. R1 strain isolated from tomato rhizosphere in this study. In conclusion, this work demonstrates that the Agrobacterium T6SS promotes tumorigenesis in infection processes and provides competitive advantages in gall-associated microbiota. IMPORTANCE The T6SS is widespread among proteobacteria and used for interbacterial competition by agrobacteria, which are soil inhabitants and opportunistic bacterial pathogens causing crown gall disease in a wide range of plants. Current evidence indicates that the T6SS is not required for gall formation when agrobacteria are inoculated directly on plant wounding sites. However, in natural settings, agrobacteria may need to compete with other bacteria in bulk soil to gain access to plant wounds and influence the microbial community inside crown galls. The role of the T6SS in these critical aspects of disease ecology have remained largely unknown. In this study, we successfully developed a soil inoculation method coupled with blocker-mediated enrichment of bacterial 16S rRNA gene amplicon sequencing, named SI-BBacSeq, to address these two important questions. We provided evidence that the T6SS promotes disease occurrence and influences crown gall microbiota composition by interbacterial competition.
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Anguita-Maeso M, Navas-Cortés JA, Landa BB. Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees. PLANTS (BASEL, SWITZERLAND) 2023; 12:912. [PMID: 36840260 PMCID: PMC9967459 DOI: 10.3390/plants12040912] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.
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Langill T, Jorissen LP, Oleńska E, Wójcik M, Vangronsveld J, Thijs S. Community Profiling of Seed Endophytes from the Pb-Zn Hyperaccumulator Noccaea caerulescens and Their Plant Growth Promotion Potential. PLANTS (BASEL, SWITZERLAND) 2023; 12:643. [PMID: 36771725 PMCID: PMC9920717 DOI: 10.3390/plants12030643] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Endophytes within plants are known to be crucial for plant fitness, and while their presence and functions in many compartments have been studied in depth, the research on seed endophytes is still limited. This work aimed to characterize the seed endophytic and rhizospheric bacterial community of two Noccaea caerulescens Pb-Zn hyperaccumulator populations, growing on two heavy-metal-polluted sites in Belgium. Cultured representatives were evaluated for their potential to enhance seed germination and root length of the model species Arabidopsis thaliana. The results indicated that the community structure within the seed is conserved between the two locations, comprising mainly of Proteobacteria (seeds), and Actinobacteria in the bulk soil. Root length of A. thaliana was significantly increased when inoculated with Sphingomonas vulcanisoli. The results of this paper offer insights into the importance of the selection of the core seed endophytic microbiome and highlight the precarious symbiotic relationship they have with the plant and seed.
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Affiliation(s)
- Tori Langill
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Lambert-Paul Jorissen
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Ewa Oleńska
- Faculty of Biology, University of Bialystok, 1J Ciołkowski, 15-245 Bialystok, Poland
| | - Małgorzata Wójcik
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Sofie Thijs
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
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Kueneman JG, Gillung J, Van Dyke MT, Fordyce RF, Danforth BN. Solitary bee larvae modify bacterial diversity of pollen provisions in the stem-nesting bee, Osmia cornifrons (Megachilidae). Front Microbiol 2023; 13:1057626. [PMID: 36699601 PMCID: PMC9868615 DOI: 10.3389/fmicb.2022.1057626] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
Microbes, including diverse bacteria and fungi, play an important role in the health of both solitary and social bees. Among solitary bee species, in which larvae remain in a closed brood cell throughout development, experiments that modified or eliminated the brood cell microbiome through sterilization indicated that microbes contribute substantially to larval nutrition and are in some cases essential for larval development. To better understand how feeding larvae impact the microbial community of their pollen/nectar provisions, we examine the temporal shift in the bacterial community in the presence and absence of actively feeding larvae of the solitary, stem-nesting bee, Osmia cornifrons (Megachilidae). Our results indicate that the O. cornifrons brood cell bacterial community is initially diverse. However, larval solitary bees modify the microbial community of their pollen/nectar provisions over time by suppressing or eliminating rare taxa while favoring bacterial endosymbionts of insects and diverse plant pathogens, perhaps through improved conditions or competitive release. We suspect that the proliferation of opportunistic plant pathogens may improve nutrient availability of developing larvae through degradation of pollen. Thus, the health and development of solitary bees may be interconnected with pollen bacterial diversity and perhaps with the propagation of plant pathogens.
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Affiliation(s)
- Jordan G. Kueneman
- Danforth Lab, Department of Entomology, Cornell University, Ithaca, NY, United States,*Correspondence: Jordan G. Kueneman, ✉
| | - Jessica Gillung
- Danforth Lab, Department of Entomology, Cornell University, Ithaca, NY, United States,Lyman Entomological Museum, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Maria T. Van Dyke
- Danforth Lab, Department of Entomology, Cornell University, Ithaca, NY, United States
| | - Rachel F. Fordyce
- Danforth Lab, Department of Entomology, Cornell University, Ithaca, NY, United States
| | - Bryan N. Danforth
- Danforth Lab, Department of Entomology, Cornell University, Ithaca, NY, United States
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SpPdp11 Administration in Diet Modified the Transcriptomic Response and Its Microbiota Associated in Mechanically Induced Wound Sparus aurata Skin. Animals (Basel) 2023; 13:ani13020193. [PMID: 36670734 PMCID: PMC9854838 DOI: 10.3390/ani13020193] [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: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Skin lesions are a frequent fact associated with intensive conditions affecting farmed fish. Knowing that the use of probiotics can improve fish skin health, SpPdp11 dietary administration has demonstrated beneficial effects for farmed fish, so its potential on the skin needs to be studied more deeply. The wounded specimens that received the diet with SpPdp11 showed a decrease in the abundance of Enterobacteriaceae, Photobacterium and Achromobacter related to bacterial biofilm formation, as well as the overexpression of genes involved in signaling mechanisms (itpr3), cell migration and differentiation (panxa, ttbk1a, smpd3, vamp5); and repression of genes related to cell proliferation (vstm4a, areg), consistent with a more efficient skin healing processes than that observed in the wounded control group. In addition, among the groups of damaged skin with different diets, Achromobacter, f_Ruminococcaceae, p_Bacteroidetes, Fluviicola and Flavobacterium genera with significant differences showed positive correlations with genes related to cell migration and negative correlations with inflammation and cell proliferation and may be the target of future studies.
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