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Zhong S, Feng JC, Chen X, Huang YJ, Wu XN, Zhang S. Exploring optimal incubation conditions and characteristics of methane oxidizing organisms in deep-sea environments. BIORESOURCE TECHNOLOGY 2024; 407:131084. [PMID: 39025372 DOI: 10.1016/j.biortech.2024.131084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/20/2024]
Abstract
Anaerobic methanotrophic archaea (ANME) play key roles in buffering the methane budget in the deep-sea environment. This study aimed to explore the optimal environmental conditions for ANME enrichment. The result showed that the sample at 10.5 MPa contained the largest copy numbers of methyl-coenzyme M reductase alpha subunit (mcrA) gene (1.1 × 106 copies/g) compared to any other pressures and the sample at 4 °C contained higher mcrA gene (1.6 × 106 copies/g) than other temperatures. The optimal enrichment pressure for ANME-2c is 10.5 MPa at 4 °C, with an optimal subsequent incubation for ANME-2c less than 211days. Moreover, the beta nearest taxon index was significantly correlated with the incubation time (P<0.05). Total inorganic carbon and sulfate ion were key environmental factors driving community construction. This study offers insights into how ANME-2c was enriched and how species coexist in shared habitats during enrichment.
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Affiliation(s)
- Song Zhong
- School of Ecology, Environmental, and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Jing-Chun Feng
- School of Ecology, Environmental, and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Guangzhou 511458, China.
| | - Xiao Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Yong-Ji Huang
- South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Xiao-Nan Wu
- School of Ecology, Environmental, and Resources, Guangdong University of Technology, Guangzhou 510006, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China.
| | - Si Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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Horváthová T, Lafuente E, Bartels J, Wallisch J, Vorburger C. Tolerance to environmental pollution in the freshwater crustacean Asellus aquaticus: A role for the microbiome. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13252. [PMID: 38783543 PMCID: PMC11116767 DOI: 10.1111/1758-2229.13252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.
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Affiliation(s)
- Terézia Horváthová
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Institute of Soil Biology and BiochemistryBiology Centre CASČeské BudějoviceCzechia
| | - Elvira Lafuente
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- Instituto Gulbenkian de CiênciaOeirasPortugal
| | | | | | - Christoph Vorburger
- Department of Aquatic EcologyEawagDübendorfSwitzerland
- D‐USYS, Department of Environmental Systems ScienceETH ZürichZürichSwitzerland
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3
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Rondon R, Cosseau C, Bergami E, Cárdenas CA, Pérez-Toledo C, Alvarez D, Aldridge J, Font A, Garrido I, Santa Cruz F, Perrois G, Balbi T, Corsi I, González-Aravena M. Exposure to nanoplastics and nanomaterials either single and combined affects the gill-associated microbiome of the Antarctic soft-shelled clam Laternula elliptica. MARINE ENVIRONMENTAL RESEARCH 2024; 198:106539. [PMID: 38718522 DOI: 10.1016/j.marenvres.2024.106539] [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: 12/04/2023] [Revised: 04/23/2024] [Accepted: 05/01/2024] [Indexed: 06/11/2024]
Abstract
Nanoplastics and engineering nanomaterials (ENMs) are contaminants of emerging concern (CECs), increasingly being detected in the marine environment and recognized as a potential threat for marine biota at the global level including in polar areas. Few studies have assessed the impact of these anthropogenic nanoparticles in the microbiome of marine invertebrates, however combined exposure resembling natural scenarios has been overlooked. The present study aimed to evaluate the single and combined effects of polystyrene nanoparticles (PS NP) as proxy for nanoplastics and nanoscale titanium dioxide (nano-TiO2) on the prokaryotic communities associated with the gill tissue of the Antarctic soft-shell clam Laternula elliptica, a keystone species of marine benthos Wild-caught specimens were exposed to two environmentally relevant concentrations of carboxylated PS NP (PS-COOH NP, ∼62 nm size) and nano-TiO2 (Aeroxide P25, ∼25 nm) as 5 and 50 μg/L either single and combined for 96h in a semi-static condition.Our findings show a shift in microbiome composition in gills of soft-shell clams exposed to PS NP and nano-TiO2 either alone and in combination with a decrease in the relative abundance of OTU1 (Spirochaetaceae). In addition, an increase of gammaproteobacterial OTUs affiliated to MBAE14 and Methylophagaceae (involved in ammonia denitrification and associated with low-quality water), and the OTU Colwellia rossensis (previously recorded in polluted waters) was observed. Our results suggest that nanoplastics and nano-TiO2 alone and in combination induce alterations in microbiome composition by promoting the increase of negative taxa over beneficial ones in the gills of the Antarctic soft-shell clam. An increase of two low abundance OTUs in PS-COOH NPs exposed clams was also observed. A predicted gene function analysis revealed that sugar, lipid, protein and DNA metabolism were the main functions affected by either PS-COOH NP and nano-TiO2 exposure. The molecular functions involved in the altered affiliated OTUs are novel for nano-CEC exposures.
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Affiliation(s)
- Rodolfo Rondon
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile.
| | - Céline Cosseau
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Elisa Bergami
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile; Millenium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | | | - Diego Alvarez
- Centro Asistencial Docente y de Investigación, Universidad de Magallanes, Punta Arenas, Chile
| | - Jacqueline Aldridge
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Punta Arenas, Chile
| | - Alejandro Font
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - Ignacio Garrido
- Centro de Investigaciones Dinámica de Ecosistemas Marinos de Altas Latitudes, Valdivia, Chile; Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | | | - Garance Perrois
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile; Tropical & Subtropical Research Center, Korea Institute of Ocean Science and Technology, Jeju, 63349, Republic of Korea
| | - Teresa Balbi
- Department of Earth Environment and Life Sciences, University of Genoa, Genoa, Italy
| | - Ilaria Corsi
- Department of Physical, Earth and Environmental Sciences, University of Siena, Siena, Italy
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Wang R, Bai B, Huang Y, Degen A, Mi J, Xue Y, Hao L. Yaks Are Dependent on Gut Microbiota for Survival in the Environment of the Qinghai Tibet Plateau. Microorganisms 2024; 12:1122. [PMID: 38930503 PMCID: PMC11205922 DOI: 10.3390/microorganisms12061122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
The yak (Poephagus grunniens) has evolved unique adaptations to survive the harsh environment of the Qinghai-Tibetan Plateau, while their gut microorganisms play a crucial role in maintaining the health of the animal. Gut microbes spread through the animal population not only by horizontal transmission but also vertically, which enhances microbial stability and inheritance between generations of the population. Homogenization of gut microbes in different animal species occurs in the same habitat, promoting interspecies coexistence. Using the yak as a model animal, this paper discusses the adaptive strategies under extreme environments, and how the gut microbes of the yak circulate throughout the Tibetan Plateau system, which not only affects other plateau animals such as plateau pikas, but can also have a profound impact on the health of people. By examining the relationships between yaks and their gut microbiota, this review offers new insights into the adaptation of yaks and their ecological niche on the Qinghai-Tibetan plateau.
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Affiliation(s)
- Runze Wang
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China; (R.W.); (B.B.)
| | - Binqiang Bai
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China; (R.W.); (B.B.)
| | - Yayu Huang
- PEGASE, INRAE, Institut Agro, 35590 Saint-Gilles, France;
| | - Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 8410500, Israel;
| | - Jiandui Mi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou 730000, China;
| | - Yanfeng Xue
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China; (R.W.); (B.B.)
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Wesseltoft JB, Danielsen CD, Andersen AM, de Jonge N, Olsen A, Rohde PD, Kristensen TN. Feeding Drosophila gut microbiomes from young and old flies modifies the microbiome. Sci Rep 2024; 14:7799. [PMID: 38565609 PMCID: PMC10987527 DOI: 10.1038/s41598-024-58500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/30/2024] [Indexed: 04/04/2024] Open
Abstract
It is becoming increasingly evident that the myriad of microbes in the gut, within cells and attached to body parts (or roots of plants), play crucial roles for the host. Although this has been known for decades, recent developments in molecular biology allow for expanded insight into the abundance and function of these microbes. Here we used the vinegar fly, Drosophila melanogaster, to investigate fitness measures across the lifetime of flies fed a suspension of gut microbes harvested from young or old flies, respectively. Our hypothesis was that flies constitutively enriched with a 'Young microbiome' would live longer and be more agile at old age (i.e. have increased healthspan) compared to flies enriched with an 'Old microbiome'. Three major take home messages came out of our study: (1) the gut microbiomes of young and old flies differ markedly; (2) feeding flies with Young and Old microbiomes altered the microbiome of recipient flies and (3) the two different microbial diets did not have any effect on locomotor activity nor lifespan of the recipient flies, contradicting our working hypothesis. Combined, these results provide novel insight into the interplay between hosts and their microbiomes and clearly highlight that the phenotypic effects of gut transplants and probiotics can be complex and unpredictable.
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Affiliation(s)
| | | | | | - Nadieh de Jonge
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anders Olsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Palle Duun Rohde
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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Stante M, Weiland-Bräuer N, von Hoyningen-Huene AJE, Schmitz RA. Marine bacteriophages disturb the associated microbiota of Aurelia aurita with a recoverable effect on host morphology. Front Microbiol 2024; 15:1356337. [PMID: 38533338 PMCID: PMC10964490 DOI: 10.3389/fmicb.2024.1356337] [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: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/28/2024] Open
Abstract
The concept of the metaorganism describes a multicellular host and its diverse microbial community, which form one biological unit with a combined genetic repertoire that significantly influences health and survival of the host. The present study delved into the emerging field of bacteriophage research within metaorganisms, focusing on the moon jellyfish Aurelia aurita as a model organism. The previously isolated Pseudomonas phage BSwM KMM1 and Citrobacter phages BSwM KMM2 - KMM4 demonstrated potent infectivity on bacteria present in the A. aurita-associated microbiota. In a host-fitness experiment, Baltic Sea subpopulation polyps were exposed to individual phages and a phage cocktail, monitoring polyp survival and morphology, as well as microbiome changes. The following effects were obtained. First, phage exposure in general led to recoverable malformations in polyps without affecting their survival. Second, analyses of the community structure, using 16S rRNA amplicon sequencing, revealed alterations in the associated microbial community in response to phage exposure. Third, the native microbiota is dominated by an uncultured likely novel Mycoplasma species, potentially specific to A. aurita. Notably, this main colonizer showed resilience through the recovery after initial declines, which aligned with abundance changes in Bacteroidota and Proteobacteria, suggesting a dynamic and adaptable microbial community. Overall, this study demonstrates the resilience of the A. aurita metaorganism facing phage-induced perturbations, emphasizing the importance of understanding host-phage interactions in metaorganism biology. These findings have implications for ecological adaptation and conservation in the rapidly changing marine environment, particularly regarding the regulation of blooming species and the health of marine ecosystems during ongoing environmental changes.
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Affiliation(s)
| | | | | | - Ruth Anne Schmitz
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
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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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Garcias-Bonet N, Roik A, Tierney B, García FC, Villela HDM, Dungan AM, Quigley KM, Sweet M, Berg G, Gram L, Bourne DG, Ushijima B, Sogin M, Hoj L, Duarte G, Hirt H, Smalla K, Rosado AS, Carvalho S, Thurber RV, Ziegler M, Mason CE, van Oppen MJH, Voolstra CR, Peixoto RS. Horizon scanning the application of probiotics for wildlife. Trends Microbiol 2024; 32:252-269. [PMID: 37758552 DOI: 10.1016/j.tim.2023.08.012] [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: 05/31/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023]
Abstract
The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.
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Affiliation(s)
- Neus Garcias-Bonet
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anna Roik
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Bremerhaven, Germany
| | - Braden Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Francisca C García
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Helena D M Villela
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ashley M Dungan
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia
| | - Kate M Quigley
- Minderoo Foundation, Perth, WA, Australia; James Cook University, Townsville, Australia
| | - Michael Sweet
- Aquatic Research Facility, Nature-based Solutions Research Centre, University of Derby, Derby, UK
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; University of Potsdam and Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs., Lyngby, Denmark
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Blake Ushijima
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Maggie Sogin
- Molecular Cell Biology, University of California, Merced, CA, USA
| | - Lone Hoj
- Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | - Gustavo Duarte
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; IMPG, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Heribert Hirt
- Center for Desert Agriculture (CDA), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Alexandre S Rosado
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Susana Carvalho
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Maren Ziegler
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative on Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Madeleine J H van Oppen
- School of Biosciences, The University of Melbourne, Parkville, VIC, Australia; Australian Institute of Marine Science, PMB 3, Townsville MC, Townsville, QLD 4810, Australia
| | | | - Raquel S Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Islam W, Zeng F, Ahmed Dar A, Sohail Yousaf M. Dynamics of soil biota and nutrients at varied depths in a Tamarix ramosissima-dominated natural desert ecosystem: Implications for nutrient cycling and desertification management. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120217. [PMID: 38340666 DOI: 10.1016/j.jenvman.2024.120217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 12/21/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
The underground community of soil organisms, known as soil biota, plays a critical role in terrestrial ecosystems. Different ecosystems exhibit varied responses of soil organisms to soil physical and chemical properties (SPCPs). However, our understanding of how soil biota react to different soil depths in naturally established population of salinity tolerant Tamarix ramosissima in desert ecosystems, remains limited. To address this, we employed High-Throughput Illumina HiSeq Sequencing to examine the population dynamics of soil bacteria, fungi, archaea, protists, and metazoa at six different soil depths (0-100 cm) in the naturally occurring T. ramosissima dominant zone within the Taklimakan desert of China. Our observations reveal that the alpha diversity of bacteria, fungi, metazoa, and protists displayed a linear decrease with the increase of soil depth, whereas archaea exhibited an inverse pattern. The beta diversity of soil biota, particularly metazoa, bacteria, and protists, demonstrated noteworthy associations with soil depths through Non-Metric Dimensional Scaling analysis. Among the most abundant classes of soil organisms, we observed Actinobacteria, Sordariomycetes, Halobacteria, Spirotrichea, and Nematoda for bacteria, fungi, archaea, protists, and metazoa, respectively. Additionally, we identified associations between the vertical distribution of dominant biotic communities and SPCPs. Bacterial changes were mainly influenced by total potassium, available phosphorus (AP), and soil water content (SWC), while fungi were impacted by nitrate (NO3-) and available potassium (AK). Archaea showed correlations with total carbon (TC) and AK thus suggesting their role in methanogenesis and methane oxidation, protists with AP and SWC, and metazoa with AP and pH. These correlations underscore potential connections to nutrient cycling and the production and consumption of greenhouse gases (GhGs). This insight establishes a solid foundation for devising strategies to mitigate nutrient cycling and GHG emissions in desert soils, thereby playing a pivotal role in the advancement of comprehensive approaches to sustainable desert ecosystem management.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, 848300, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Afzal Ahmed Dar
- Department of Building, Civil and Environmental Engineering, Concordia University, 1455 de Maisonneuve Blvd. W. Montreal, Quebec H3G1M8, Canada
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Zhou K, Zhang T, Chen XW, Xu Y, Zhang R, Qian PY. Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:467-485. [PMID: 37647612 DOI: 10.1146/annurev-marine-021623-093133] [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: 09/01/2023]
Abstract
Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts.
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Affiliation(s)
- Kun Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Ting Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Xiao-Wei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University (Xiang'an), Xiamen, Fujian, China
| | - Ying Xu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China;
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China;
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China;
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
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11
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Zhong S, Feng J, Kong J, Huang Y, Chen X, Zhang S. Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep. Microorganisms 2023; 11:3001. [PMID: 38138145 PMCID: PMC10745737 DOI: 10.3390/microorganisms11123001] [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: 10/18/2023] [Revised: 11/20/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We revealed the effect of methane seepage on co-occurrence networks and ecological niches of prokaryotic communities at the surface sediments and bottom seawater in the Haima cold seep. The results showed that methane seepage could cause the migration of Mn and Ba from the surface sediments to the overlying seawater, altering the elemental distribution at seepage sites (IS) compared with non-seepage sites (NS). Principal component analysis (PCA) showed that methane seepage led to closer distances of bacterial communities between surface sediments and bottom seawater. Co-occurrence networks indicated that methane seepage led to more complex interconnections at the surface sediments and bottom seawater. In summary, methane seepage caused bacterial communities in the surface sediments and bottom seawater to become more abundant and structurally complex. This study provides a comprehensive comparison of microbial profiles at the surface sediments and bottom seawater of cold seeps in the South China Sea (SCS), illustrating the impact of seepage on bacterial community dynamics.
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Affiliation(s)
- Song Zhong
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China;
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
| | - Jingchun Feng
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China;
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Jie Kong
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Yongji Huang
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Xiao Chen
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Si Zhang
- Research Centre of Ecology & Environment for Coastal Area and Deep Sea, Guangdong University of Technology, Guangzhou 510006, China; (J.K.); (Y.H.); (X.C.); (S.Z.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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12
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Islam W, Ullah A, Zeng F. Response of total belowground soil biota in Alhagi sparsifolia monoculture at different soil vertical profiles in desert ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:166027. [PMID: 37541502 DOI: 10.1016/j.scitotenv.2023.166027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
The soil organisms are extremely important for the land-based ecosystem. There is a growing interest in studying the variety and composition of the entire underground soil organism community at a large ecological scale. Soil organisms show different patterns in relation to soil physiochemical properties (SPPs) in various ecosystems. However, there is limited knowledge regarding their response to soil vertical profiles (SVPs) in monoculture of Alhagi sparsifolia, which is the primary shrub in the deserts of China, and is well-known for its contributions to sand dune stabilization, traditional Chinese medicine, and forage. Here, we investigated the population dynamics of soil bacteria, fungi, archaea, protists and metazoa across six different SVPs ranging from 0 to 100 cm in monoculture of A. sparsifolia, in its natural desert ecosystem. Our findings indicate that the soil biota communities displayed a declining pattern in the alpha diversity of bacteria, protists, and metazoa with an increase in soil depth. However, the opposite trend was observed for fungi and archaea. The beta diversity of soil biota was significantly affected by SVPs, particularly for metazoa, fungi and protists as revealed by Non-Metric Dimensional Scaling. The most prevalent soil bacterial, fungal, archaeal, protist, and metazoa classes were Actinobacteria, Sordariomycetes, Nitrososphaeria, Filosa-Sarcomonadea, and Nematoda, respectively. The correlation among vertical distribution of the most abundant biotic communities and variations in SPPs exhibited that the variations in total carbon (TC) and total nitrogen (TN) had the most significant influence on bacterial changes, while available potassium (AK) had an impact on fungi. Archaea were affected by TC and pH, protists by the C/N-Ratio and TP, and metazoa by TN, AK, and soil water capacity (SWC). Collectively, our findings provide a new perspective on the vertical distribution and distinct response patterns of soil biota in A. sparsifolia monoculture under natural desert ecosystem of China.
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Affiliation(s)
- Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Abd Ullah
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanjiang Zeng
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele 848300, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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13
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Petersen C, Hamerich IK, Adair KL, Griem-Krey H, Torres Oliva M, Hoeppner MP, Bohannan BJM, Schulenburg H. Host and microbiome jointly contribute to environmental adaptation. THE ISME JOURNAL 2023; 17:1953-1965. [PMID: 37673969 PMCID: PMC10579302 DOI: 10.1038/s41396-023-01507-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Most animals and plants have associated microorganisms, collectively referred to as their microbiomes, which can provide essential functions. Given their importance, host-associated microbiomes have the potential to contribute substantially to adaptation of the host-microbiome assemblage (the "metaorganism"). Microbiomes may be especially important for rapid adaptation to novel environments because microbiomes can change more rapidly than host genomes. However, it is not well understood how hosts and microbiomes jointly contribute to metaorganism adaptation. We developed a model system with which to disentangle the contributions of hosts and microbiomes to metaorganism adaptation. We established replicate mesocosms containing the nematode Caenorhabditis elegans co-cultured with microorganisms in a novel complex environment (laboratory compost). After approximately 30 nematode generations (100 days), we harvested worm populations and associated microbiomes, and subjected them to a common garden experiment designed to unravel the impacts of microbiome composition and host genetics on metaorganism adaptation. We observed that adaptation took different trajectories in different mesocosm lines, with some increasing in fitness and others decreasing, and that interactions between host and microbiome played an important role in these contrasting evolutionary paths. We chose two exemplary mesocosms (one with a fitness increase and one with a decrease) for detailed study. For each example, we identified specific changes in both microbiome composition (for both bacteria and fungi) and nematode gene expression associated with each change in fitness. Our study provides experimental evidence that adaptation to a novel environment can be jointly influenced by host and microbiome.
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Affiliation(s)
- Carola Petersen
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | - Inga K Hamerich
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | - Karen L Adair
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Hanne Griem-Krey
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | | | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | | | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany.
- Max-Planck Institute for Evolutionary Biology, Ploen, Germany.
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Angulo M, Guerra K, Arevalo P, Trujillo E, Monreal-Escalante E, Angulo C. Probiotic Potential of Bacillus sp. 62A Isolated from a Marine Extreme Environment. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10182-3. [PMID: 37889453 DOI: 10.1007/s12602-023-10182-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 10/28/2023]
Abstract
Antimicrobial resistance is an important health concern globally, and probiotics are considered an alternative to minimize it. The present study examined the in vitro probiotic characteristics and in vivo immunomodulatory potential of Bacillus sp. 62A - an extremophile bacterium. Bacillus sp. 62A was evaluated in vitro for its cytotoxicity, hemolytic activity, antibiotic susceptibility, and resistance to gastrointestinal conditions (bile salts, low pH, and intestinal adherence). Additionally, the immunomodulatory effect of Bacillus sp. 62A was studied in mice. The animals were supplemented daily with phosphate-buffered saline (control) and Bacillus sp. 62A at 1 × 108 colony forming units (CFU). Samples were taken on days 5 and 10. Isolated splenocytes were challenged with Escherichia coli for immunological analyses and immune-related gene expression. Serum and feces were collected for IgA and IgG determination. Bacillus sp. 62A did not show cytotoxicity, hemolytic activity, or resistance to antibiotics. Furthermore, the bacterium has autoaggregation and intestinal adhesion capacities and grows in the presence of bile salts and low pH. Bacillus supplementation in mice improved respiratory burst activity, nitric oxide production, and IL-1β and IL-6 gene expressions, mainly at 10 days. After E. coli challenge, Bacillus supplementation in mice induced an anti-inflammatory response through a decrease in immunological parameters and an increase in IL-10 gene expression. Moreover, serum IgA and IgG and fecal IgG augmented in supplemented mice. In conclusion, Bacillus sp. 62A has biosafe and immunomodulatory probiotic potential.
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Affiliation(s)
- Miriam Angulo
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.S. 23096, La Paz, Mexico
| | - Kevyn Guerra
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.S. 23096, La Paz, Mexico
- Tecnológico Nacional de México / Instituto Tecnológico de La Paz, Boulevard Forjadores 4720, 8 de Octubre Segunda sección, C.P. 23080, La Paz, Mexico
| | - Paola Arevalo
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.S. 23096, La Paz, Mexico
| | - Edgar Trujillo
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.S. 23096, La Paz, Mexico
| | - Elizabeth Monreal-Escalante
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.S. 23096, La Paz, Mexico
- Investigadora Por México-CONACYT, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.P. 23096, La Paz, Mexico
| | - Carlos Angulo
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Av. Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, C.S. 23096, La Paz, Mexico.
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15
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Landis SH, Piecyk A, Reitz M, Enzingmüller C, Schulenburg H, Bosch T, Dierking K, Deines P, Hunfeld-Häutle J, Rappaport K, Duscher T. Meet the Metaorganism: A web-based learning app for undergraduate and graduate biology students. Bioessays 2023; 45:e2300043. [PMID: 37522605 DOI: 10.1002/bies.202300043] [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: 03/02/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023]
Abstract
Meet the Metaorganism is a web-based learning app that combines three fundamental biological concepts (coevolution, community dynamics, and immune system) with latest scientific findings using the metaorganism as a central case study. In a transdisciplinary team of scientists, information designers, programmers, science communicators, and educators, we conceptualized and developed the app according to the latest didactic and scientific findings and aimed at setting new standards in visual design, digital knowledge transfer, and online education. A content management system allows continuous integration of new findings, which enables us to expand the app with the dynamics of the research field. Students can thus gain a close insight and connection to current research, and at the same time learn that knowledge is not static but grows dynamically. Especially in the realm of the easily accessible metaorganism research, visualization plays an essential role to keep complex processes understandable and memorable. Meet the Metaorganism is freely available online and can be accessed here: www.metaorganism.app.
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Affiliation(s)
- Susanne H Landis
- Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
- Science Communication Lab, Kiel, Germany
| | | | | | - Carolin Enzingmüller
- Chemistry Education, Leibniz Institute for Science and Mathematics Education at the University of Kiel, Kiel, Germany
| | | | - Thomas Bosch
- Zoological Institute, Kiel University, Kiel, Germany
| | - Katja Dierking
- Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | - Peter Deines
- Evolutionary Ecology and Genetics, Kiel University, Kiel, Germany
| | | | | | - Tom Duscher
- Science Communication Lab, Kiel, Germany
- Muthesius University of Fine Arts and Design, Kiel, Germany
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16
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Pinnow N, Chibani CM, Güllert S, Weiland-Bräuer N. Microbial community changes correlate with impaired host fitness of Aurelia aurita after environmental challenge. Anim Microbiome 2023; 5:45. [PMID: 37735458 PMCID: PMC10515101 DOI: 10.1186/s42523-023-00266-4] [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: 03/30/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
Climate change globally endangers certain marine species, but at the same time, such changes may promote species that can tolerate and adapt to varying environmental conditions. Such acclimatization can be accompanied or possibly even be enabled by a host's microbiome; however, few studies have so far directly addressed this process. Here we show that acute, individual rises in seawater temperature and salinity to sub-lethal levels diminished host fitness of the benthic Aurelia aurita polyp, demonstrated by up to 34% reduced survival rate, shrinking of the animals, and almost halted asexual reproduction. Changes in the fitness of the polyps to environmental stressors coincided with microbiome changes, mainly within the phyla Proteobacteria and Bacteroidota. The absence of bacteria amplified these effects, pointing to the benefit of a balanced microbiota to cope with a changing environment. In a future ocean scenario, mimicked by a combined but milder rise of temperature and salinity, the fitness of polyps was severely less impaired, together with condition-specific changes in the microbiome composition. Our results show that the effects on host fitness correlate with the strength of environmental stress, while salt-conveyed thermotolerance might be involved. Further, a specific, balanced microbiome of A. aurita polyps supports the host's acclimatization. Microbiomes may provide a means for acclimatization, and microbiome flexibility can be a fundamental strategy for marine animals to adapt to future ocean scenarios and maintain biodiversity and ecosystem functioning.
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Affiliation(s)
- Nicole Pinnow
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Cynthia M Chibani
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Simon Güllert
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
- Current address: Sysmex Inostics GmbH, Falkenried 88, 20251, Hamburg, Germany
| | - Nancy Weiland-Bräuer
- General Microbiology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
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De Filippis F, Bonelli M, Bruno D, Sequino G, Montali A, Reguzzoni M, Pasolli E, Savy D, Cangemi S, Cozzolino V, Tettamanti G, Ercolini D, Casartelli M, Caccia S. Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions. MICROBIOME 2023; 11:205. [PMID: 37705113 PMCID: PMC10500907 DOI: 10.1186/s40168-023-01649-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 07/16/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic waste management. Although many analyses based on 16S rRNA gene sequencing are available, an in-depth analysis of the insect gut microbiome to identify genes with plastic-degrading potential is still lacking. RESULTS In the present work, we aim to fill this gap using Black Soldier Fly (BSF) as insect model. BSF larvae have proven capability to efficiently bioconvert a wide variety of organic wastes but, surprisingly, have never been considered for plastic degradation. BSF larvae were reared on two widely used plastic polymers and shotgun metagenomics was exploited to evaluate if and how plastic-containing diets affect composition and functions of the gut microbial community. The high-definition picture of the BSF gut microbiome gave access for the first time to the genomes of culturable and unculturable microorganisms in the gut of insects reared on plastics and revealed that (i) plastics significantly shaped bacterial composition at species and strain level, and (ii) functions that trigger the degradation of the polymer chains, i.e., DyP-type peroxidases, multicopper oxidases, and alkane monooxygenases, were highly enriched in the metagenomes upon exposure to plastics, consistently with the evidences obtained by scanning electron microscopy and 1H nuclear magnetic resonance analyses on plastics. CONCLUSIONS In addition to highlighting that the astonishing plasticity of the microbiota composition of BSF larvae is associated with functional shifts in the insect microbiome, the present work sets the stage for exploiting BSF larvae as "bioincubators" to isolate microbial strains and enzymes for the development of innovative plastic biodegradation strategies. However, most importantly, the larvae constitute a source of enzymes to be evolved and valorized by pioneering synthetic biology approaches. Video Abstract.
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Affiliation(s)
- Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Marco Bonelli
- Department of Biosciences, University of Milan, Milan, Italy
| | - Daniele Bruno
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Aurora Montali
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marcella Reguzzoni
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Davide Savy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Silvana Cangemi
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Vincenza Cozzolino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Interdepartmental Research Centre of Nuclear Magnetic Resonance for the Environment, Agri-Food and New Materials (CERMANU), University of Naples Federico II, Portici, Italy
| | - Gianluca Tettamanti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
| | - Morena Casartelli
- Department of Biosciences, University of Milan, Milan, Italy.
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Portici, Italy.
| | - Silvia Caccia
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
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18
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Rotini A, Conte C, Winters G, Vasquez MI, Migliore L. Undisturbed Posidonia oceanica meadows maintain the epiphytic bacterial community in different environments. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:95464-95474. [PMID: 37548791 PMCID: PMC10482771 DOI: 10.1007/s11356-023-28968-x] [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: 02/03/2023] [Accepted: 07/20/2023] [Indexed: 08/08/2023]
Abstract
Seagrasses harbour different and rich epiphytic bacterial communities. These microbes may establish intimate and symbiotic relationships with the seagrass plants and change according to host species, environmental conditions, and/or ecophysiological status of their seagrass host. Although Posidonia oceanica is one of the most studied seagrasses in the world, and bacteria associated with seagrasses have been studied for over a decade, P. oceanica's microbiome remains hitherto little explored. Here, we applied 16S rRNA amplicon sequencing to explore the microbiome associated with the leaves of P. oceanica growing in two geomorphologically different meadows (e.g. depth, substrate, and turbidity) within the Limassol Bay (Cyprus). The morphometric (leaf area, meadow density) and biochemical (pigments, total phenols) descriptors highlighted the healthy conditions of both meadows. The leaf-associated bacterial communities showed similar structure and composition in the two sites; core microbiota members were dominated by bacteria belonging to the Thalassospiraceae, Microtrichaceae, Enterobacteriaceae, Saprospiraceae, and Hyphomonadaceae families. This analogy, even under different geomorphological conditions, suggest that in the absence of disturbances, P. oceanica maintains characteristic-associated bacterial communities. This study provides a baseline for the knowledge of the P. oceanica microbiome and further supports its use as a putative seagrass descriptor.
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Affiliation(s)
- Alice Rotini
- ISPRA Istituto Superiore per la Protezione e la Ricerca Ambientale, Via Vitaliano Brancati, 48, 00144, Rome, Italy
| | - Chiara Conte
- Department of Biology, Laboratory of Ecology and Ecotoxicology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Gidon Winters
- Dead Sea and Arava Science Center (DSASC), Masada National Park, 86910, Masada, Israel
- Eilat Campus, Ben-Gurion University of the Negev, Hatmarim Blv., 8855630, Eilat, Israel
| | - Marlen I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianos Str.t, 3036, Limassol, Cyprus
- European University of Technology, 30 Archbishop Kyprianos Str.t, 3036, Limassol, Cyprus
| | - Luciana Migliore
- Department of Biology, Laboratory of Ecology and Ecotoxicology, University of Rome Tor Vergata, 00133, Rome, Italy.
- eCampus University, Via Isimbardi 10, 22060, Novedrate, CO, Italy.
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Jensen N, Weiland-Bräuer N, Joel S, Chibani CM, Schmitz RA. The Life Cycle of Aurelia aurita Depends on the Presence of a Microbiome in Polyps Prior to Onset of Strobilation. Microbiol Spectr 2023; 11:e0026223. [PMID: 37378516 PMCID: PMC10433978 DOI: 10.1128/spectrum.00262-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Aurelia aurita's intricate life cycle alternates between benthic polyp and pelagic medusa stages. The strobilation process, a critical asexual reproduction mechanism in this jellyfish, is severely compromised in the absence of the natural polyp microbiome, with limited production and release of ephyrae. Yet, the recolonization of sterile polyps with a native polyp microbiome can correct this defect. Here, we investigated the precise timing necessary for recolonization as well as the host-associated molecular processes involved. We deciphered that a natural microbiota had to be present in polyps prior to the onset of strobilation to ensure normal asexual reproduction and a successful polyp-to-medusa transition. Providing the native microbiota to sterile polyps after the onset of strobilation failed to restore the normal strobilation process. The absence of a microbiome was associated with decreased transcription of developmental and strobilation genes as monitored by reverse transcription-quantitative PCR. Transcription of these genes was exclusively observed for native polyps and sterile polyps that were recolonized before the initiation of strobilation. We further propose that direct cell contact between the host and its associated bacteria is required for the normal production of offspring. Overall, our findings indicate that the presence of a native microbiome at the polyp stage prior to the onset of strobilation is essential to ensure a normal polyp-to-medusa transition. IMPORTANCE All multicellular organisms are associated with microorganisms that play fundamental roles in the health and fitness of the host. Notably, the native microbiome of the Cnidarian Aurelia aurita is crucial for the asexual reproduction by strobilation. Sterile polyps display malformed strobilae and a halt of ephyrae release, which is restored by recolonizing sterile polyps with a native microbiota. Despite that, little is known about the microbial impact on the strobilation process's timing and molecular consequences. The present study shows that A. aurita's life cycle depends on the presence of the native microbiome at the polyp stage prior to the onset of strobilation to ensure the polyp-to-medusa transition. Moreover, sterile individuals correlate with reduced transcription levels of developmental and strobilation genes, evidencing the microbiome's impact on strobilation on the molecular level. Transcription of strobilation genes was exclusively detected in native polyps and those recolonized before initiating strobilation, suggesting microbiota-dependent gene regulation.
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Affiliation(s)
- Nadin Jensen
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Nancy Weiland-Bräuer
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Shindhuja Joel
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Cynthia Maria Chibani
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| | - Ruth Anne Schmitz
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
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20
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Weiland-Bräuer N, Koutsouveli V, Langfeldt D, Schmitz RA. First insights into the Aurelia aurita transcriptome response upon manipulation of its microbiome. Front Microbiol 2023; 14:1183627. [PMID: 37637120 PMCID: PMC10448538 DOI: 10.3389/fmicb.2023.1183627] [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: 03/10/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction The associated diverse microbiome contributes to the overall fitness of Aurelia aurita, particularly to asexual reproduction. However, how A. aurita maintains this specific microbiome or reacts to manipulations is unknown. Methods In this report, the response of A. aurita to manipulations of its native microbiome was studied by a transcriptomics approach. Microbiome-manipulated polyps were generated by antibiotic treatment and challenging polyps with a non-native, native, and potentially pathogenic bacterium. Total RNA extraction followed by RNAseq resulted in over 155 million reads used for a de novo assembly. Results The transcriptome analysis showed that the antibiotic-induced change and resulting reduction of the microbiome significantly affected the host transcriptome, e.g., genes involved in processes related to immune response and defense mechanisms were highly upregulated. Similarly, manipulating the microbiome by challenging the polyp with a high load of bacteria (2 × 107 cells/polyp) resulted in induced transcription of apoptosis-, defense-, and immune response genes. A second focus was on host-derived quorum sensing interference as a potential defense strategy. Quorum Quenching (QQ) activities and the respective encoding QQ-ORFs of A. aurita were identified by functional screening a cDNA-based expression library generated in Escherichia coli. Corresponding sequences were identified in the transcriptome assembly. Moreover, gene expression analysis revealed differential expression of QQ genes depending on the treatment, strongly suggesting QQ as an additional defense strategy. Discussion Overall, this study allows first insights into A. aurita's response to manipulating its microbiome, thus paving the way for an in-depth analysis of the basal immune system and additional fundamental defense strategies.
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Affiliation(s)
| | - Vasiliki Koutsouveli
- GEOMAR Helmholtz Center for Ocean Research Kiel, Düsternbrooker Weg, Kiel, Germany
| | | | - Ruth A. Schmitz
- Institute of General Microbiology, Kiel University, Kiel, Germany
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21
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Yang Z, Lian Z, Liu L, Fang B, Li W, Jiao J. Cultivation strategies for prokaryotes from extreme environments. IMETA 2023; 2:e123. [PMID: 38867929 PMCID: PMC10989778 DOI: 10.1002/imt2.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/28/2023] [Indexed: 06/14/2024]
Abstract
The great majority of microorganisms are as-yet-uncultivated, mostly found in extreme environments. High-throughput sequencing provides data-rich genomes from single-cell and metagenomic techniques, which has enabled researchers to obtain a glimpse of the unexpected genetic diversity of "microbial dark matter." However, cultivating microorganisms from extreme environments remains essential for dissecting and utilizing the functions of extremophiles. Here, we provide a straightforward protocol for efficiently isolating prokaryotic microorganisms from different extreme habitats (thermal, xeric, saline, alkaline, acidic, and cryogenic environments), which was established through previous successful work and our long-term experience in extremophile resource mining. We propose common processes for extremophile isolation at first and then summarize multiple cultivation strategies for recovering prokaryotic microorganisms from extreme environments and meanwhile provide specific isolation tips that are always overlooked but important. Furthermore, we propose the use of multi-omics-guided microbial cultivation approaches for culturing these as-yet-uncultivated microorganisms and two examples are provided to introduce how these approaches work. In summary, the protocol allows researchers to significantly improve the isolation efficiency of pure cultures and novel taxa, which therefore paves the way for the protection and utilization of microbial resources from extreme environments.
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Affiliation(s)
- Zi‐Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Zheng‐Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Bao‐Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina
| | - Wen‐Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina
| | - Jian‐Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
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22
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Kiss A, Hariri Akbari F, Marchev A, Papp V, Mirmazloum I. The Cytotoxic Properties of Extreme Fungi's Bioactive Components-An Updated Metabolic and Omics Overview. Life (Basel) 2023; 13:1623. [PMID: 37629481 PMCID: PMC10455657 DOI: 10.3390/life13081623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 08/27/2023] Open
Abstract
Fungi are the most diverse living organisms on planet Earth, where their ubiquitous presence in various ecosystems offers vast potential for the research and discovery of new, naturally occurring medicinal products. Concerning human health, cancer remains one of the leading causes of mortality. While extensive research is being conducted on treatments and their efficacy in various stages of cancer, finding cytotoxic drugs that target tumor cells with no/less toxicity toward normal tissue is a significant challenge. In addition, traditional cancer treatments continue to suffer from chemical resistance. Fortunately, the cytotoxic properties of several natural products derived from various microorganisms, including fungi, are now well-established. The current review aims to extract and consolidate the findings of various scientific studies that identified fungi-derived bioactive metabolites with antitumor (anticancer) properties. The antitumor secondary metabolites identified from extremophilic and extremotolerant fungi are grouped according to their biological activity and type. It became evident that the significance of these compounds, with their medicinal properties and their potential application in cancer treatment, is tremendous. Furthermore, the utilization of omics tools, analysis, and genome mining technology to identify the novel metabolites for targeted treatments is discussed. Through this review, we tried to accentuate the invaluable importance of fungi grown in extreme environments and the necessity of innovative research in discovering naturally occurring bioactive compounds for the development of novel cancer treatments.
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Affiliation(s)
- Attila Kiss
- Agro-Food Science Techtransfer and Innovation Centre, Faculty for Agro, Food and Environmental Science, Debrecen University, 4032 Debrecen, Hungary;
| | - Farhad Hariri Akbari
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Andrey Marchev
- Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000 Plovdiv, Bulgaria
| | - Viktor Papp
- Department of Botany, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary;
| | - Iman Mirmazloum
- Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary
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Stante M, Weiland-Bräuer N, Repnik U, Werner A, Bramkamp M, Chibani CM, Schmitz RA. Four Novel Caudoviricetes Bacteriophages Isolated from Baltic Sea Water Infect Colonizers of Aurelia aurita. Viruses 2023; 15:1525. [PMID: 37515211 PMCID: PMC10383413 DOI: 10.3390/v15071525] [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: 06/14/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The moon jellyfish Aurelia aurita is associated with a highly diverse microbiota changing with provenance, tissue, and life stage. While the crucial relevance of bacteria to host fitness is well known, bacteriophages have often been neglected. Here, we aimed to isolate virulent phages targeting bacteria that are part of the A. aurita-associated microbiota. Four phages (Pseudomonas phage BSwM KMM1, Citrobacter phages BSwM KMM2-BSwM KMM4) were isolated from the Baltic Sea water column and characterized. Phages KMM2/3/4 infected representatives of Citrobacter, Shigella, and Escherichia (Enterobacteriaceae), whereas KMM1 showed a remarkably broad host range, infecting Gram-negative Pseudomonas as well as Gram-positive Staphylococcus. All phages showed an up to 99% adsorption to host cells within 5 min, short latent periods (around 30 min), large burst sizes (mean of 128 pfu/cell), and high efficiency of plating (EOP > 0.5), demonstrating decent virulence, efficiency, and infectivity. Transmission electron microscopy and viral genome analysis revealed that all phages are novel species and belong to the class of Caudoviricetes harboring a tail and linear double-stranded DNA (formerly known as Siphovirus-like (KMM3) and Myovirus-like (KMM1/2/4) bacteriophages) with genome sizes between 50 and 138 kbp. In the future, these isolates will allow manipulation of the A. aurita-associated microbiota and provide new insights into phage impact on the multicellular host.
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Affiliation(s)
- Melissa Stante
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
| | - Nancy Weiland-Bräuer
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
| | - Urska Repnik
- Central Microscopy Facility, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany;
| | - Almut Werner
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
| | - Marc Bramkamp
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
- Central Microscopy Facility, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany;
| | - Cynthia M. Chibani
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian Albrechts University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany; (M.S.); (N.W.-B.); (A.W.); (M.B.); (C.M.C.)
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Delva S, De Baets B, Baetens JM, De Clerck O, Stock W. No bacterial-mediated alleviation of thermal stress in a brown seaweed suggests the absence of ecological bacterial rescue effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162532. [PMID: 36870499 DOI: 10.1016/j.scitotenv.2023.162532] [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: 10/21/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
While microbiome alterations are increasingly proposed as a rapid mechanism to buffer organisms under changing environmental conditions, studies of these processes in the marine realm are lagging far behind their terrestrial counterparts. Here, we used a controlled laboratory experiment to examine whether the thermal tolerance of the brown seaweed Dictyota dichotoma, a common species in European coastal ecosystems, could be enhanced by the repeated addition of bacteria from its natural environment. Juvenile algae from three genotypes were subjected for two weeks to a temperature gradient, spanning almost the entire thermal range that can be tolerated by the species (11-30 °C). At the start of the experiment and again in the middle of the experiment, the algae were inoculated with bacteria from their natural environment or left untouched as a control. Relative growth rate was measured over the two-week period, and we assessed bacterial community composition prior to and at the end of the experiment. Since the growth of D. dichotoma over the full thermal gradient was not affected by supplementing bacteria, our results indicate no scope for bacterial-mediated stress alleviation. The minimal changes in the bacterial communities linked to bacterial addition, particularly at temperatures above the thermal optimum (22-23 °C), suggest the existence of a barrier to bacterial recruitment. These findings indicate that ecological bacterial rescue is unlikely to play a role in mitigating the effects of ocean warming on this brown seaweed.
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Affiliation(s)
- Soria Delva
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium; Research Unit Knowledge-Based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Bernard De Baets
- Research Unit Knowledge-Based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Jan M Baetens
- Research Unit Knowledge-Based Systems (KERMIT), Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Olivier De Clerck
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium.
| | - Willem Stock
- Phycology Research Group, Department of Biology, Ghent University, Krijgslaan 281-S8, 9000 Ghent, Belgium.
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25
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Dondjou DT, Diedhiou AG, Mbodj D, Mofini MT, Pignoly S, Ndiaye C, Diedhiou I, Assigbetse K, Manneh B, Laplaze L, Kane A. Rice developmental stages modulate rhizosphere bacteria and archaea co-occurrence and sensitivity to long-term inorganic fertilization in a West African Sahelian agro-ecosystem. ENVIRONMENTAL MICROBIOME 2023; 18:42. [PMID: 37198640 PMCID: PMC10193678 DOI: 10.1186/s40793-023-00500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/09/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rhizosphere microbial communities are important components of the soil-plant continuum in paddy field ecosystems. These rhizosphere communities contribute to nutrient cycling and rice productivity. The use of fertilizers is a common agricultural practice in rice paddy fields. However, the long-term impact of the fertilizers usage on the rhizosphere microbial communities at different rice developmental stages remains poorly investigated. Here, we examined the effects of long-term (27 years) N and NPK-fertilization on bacterial and archaeal community inhabiting the rice rhizosphere at three developmental stages (tillering, panicle initiation and booting) in the Senegal River Delta. RESULTS We found that the effect of long-term inorganic fertilization on rhizosphere microbial communities varied with the rice developmental stage, and between microbial communities in their response to N and NPK-fertilization. The microbial communities inhabiting the rice rhizosphere at panicle initiation appear to be more sensitive to long-term inorganic fertilization than those at tillering and booting stages. However, the effect of developmental stage on microbial sensitivity to long-term inorganic fertilization was more pronounced for bacterial than archaeal community. Furthermore, our data reveal dynamics of bacteria and archaea co-occurrence patterns in the rice rhizosphere, with differentiated bacterial and archaeal pivotal roles in the microbial inter-kingdom networks across developmental stages. CONCLUSIONS Our study brings new insights on rhizosphere bacteria and archaea co-occurrence and the long-term inorganic fertilization impact on these communities across developmental stages in field-grown rice. It would help in developing strategies for the successful manipulation of microbial communities to improve rice yields.
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Affiliation(s)
- Donald Tchouomo Dondjou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Abdala Gamby Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Daouda Mbodj
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Marie-Thérèse Mofini
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Sarah Pignoly
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Cheikh Ndiaye
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Issa Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
| | - Komi Assigbetse
- Laboratoire Mixte International Intensification Écologique Des Sols Cultivés en Afrique de L’Ouest (IESOL), Dakar, Sénégal
- Eco&Sols, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Baboucarr Manneh
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Africa Rice Center (AfricaRice), Saint-Louis, Senegal
| | - Laurent Laplaze
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA‑AGRISAN), UCAD, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Aboubacry Kane
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), Dakar, Sénégal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d’Excellence Africain « Environnement, Sociétés » (CEA-AGIR), UCAD, Santé, Dakar, Sénégal
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Huang Y, Feng JC, Kong J, Sun L, Zhang M, Huang Y, Tang L, Zhang S, Yang Z. Community assemblages and species coexistence of prokaryotes controlled by local environmental heterogeneity in a cold seep water column. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161725. [PMID: 36669671 DOI: 10.1016/j.scitotenv.2023.161725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/16/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
The distribution and heterogeneity characteristics of microbial communities in cold seep water columns are significant factors governing the efficiency of methane filtering and carbon turnover. However, this process is poorly understood. The diversity of vertically stratified microbial communities and the factors controlling the community assemblage process in the water column above the Haima cold seep were investigated in this study. The prokaryotic community diversities varied distinctly with vertical changes in hydrochemistry. Cyanobacteria dominated the light-transmitting layers and Proteobacteria dominated the deeper layers. With respect to microbial community assemblages and co-occurrence networks, stochastic processes were particularly important in shaping prokaryotic communities. In the shallow (≥85 m) and mesopelagic water columns (600-800 m), microbial community characteristics were affected by deterministic processes, reduced network connectivity, and modularity. Microbial community diversities and assemblage processes along a vertical profile were influenced by the vertical variations in pH, temperature, DIC, and nutrients. Stochastic processes may have facilitated the formation of complex co-occurrence networks. Briefly, the distribution of local environmental heterogeneity along the vertical dimension could drive unique microbial community assemblage and species coexistence patterns. This study provides new perspectives on how microorganisms adapt to the environment and build communities, and how species coexist in shared habitats.
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Affiliation(s)
- Yongji Huang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Jing-Chun Feng
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China.
| | - Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Liwei Sun
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Mingrui Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Yanyan Huang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Li Tang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
| | - Si Zhang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China
| | - Zhifeng Yang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, PR China
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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Shah AM, Bano I, Qazi IH, Matra M, Wanapat M. "The Yak"-A remarkable animal living in a harsh environment: An overview of its feeding, growth, production performance, and contribution to food security. Front Vet Sci 2023; 10:1086985. [PMID: 36814466 PMCID: PMC9940766 DOI: 10.3389/fvets.2023.1086985] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 02/05/2023] Open
Abstract
Yaks play an important role in the livelihood of the people of the Qinghai-Tibet Plateau (QTP) and contribute significantly to the economy of the different countries in the region. Yaks are commonly raised at high altitudes of ~ 3,000-5,400 m above sea level. They provide many important products, namely, milk, meat, fur, and manure, as well as social status, etc. Yaks were domesticated from wild yaks and are present in the remote mountains of the QTP region. In the summer season, when a higher quantity of pasture is available in the mountain region, yaks use their long tongues to graze the pasture and spend ~ 30-80% of their daytime grazing. The remaining time is spent walking, resting, and doing other activities. In the winter season, due to heavy snowfall in the mountains, pasture is scarce, and yaks face feeding issues due to pasture scarcity. Hence, the normal body weight of yaks is affected and growth retardation occurs, which consequently affects their production performance. In this review article, we have discussed the domestication of yaks, the feeding pattern of yaks, the difference between the normal and growth-retarded yaks, and also their microbial community and their influences. In addition, blood biochemistry, the compositions of the yaks' milk and meat, and reproduction are reported herein. Evidence suggested that yaks play an important role in the daily life of the people living on the QTP, who consume milk, meat, fur, use manure for fuel and land fertilizer purposes, and use the animals for transportation. Yaks' close association with the people's well-being and livelihood has been significant.
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Affiliation(s)
- Ali Mujtaba Shah
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand,Department of Livestock Production, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Sindh, Pakistan
| | - Iqra Bano
- Department of Veterinary Physiology and Biochemistry, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Sindh, Pakistan
| | - Izhar Hyder Qazi
- Department of Veterinary Anatomy, Histology, and Embryology, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Sindh, Pakistan
| | - Maharach Matra
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand
| | - Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand,*Correspondence: Metha Wanapat ✉
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Conte C, Apostolaki ET, Vizzini S, Migliore L. A Tight Interaction between the Native Seagrass Cymodocea nodosa and the Exotic Halophila stipulacea in the Aegean Sea Highlights Seagrass Holobiont Variations. PLANTS (BASEL, SWITZERLAND) 2023; 12:350. [PMID: 36679063 PMCID: PMC9863530 DOI: 10.3390/plants12020350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Seagrasses harbour bacterial communities with which they constitute a functional unit called holobiont that responds as a whole to environmental changes. Epiphytic bacterial communities rapidly respond to both biotic and abiotic factors, potentially contributing to the host fitness. The Lessepsian migrant Halophila stipulacea has a high phenotypical plasticity and harbours a highly diverse epiphytic bacterial community, which could support its invasiveness in the Mediterranean Sea. The current study aimed to evaluate the Halophila/Cymodocea competition in the Aegean Sea by analysing each of the two seagrasses in a meadow zone where these intermingled, as well as in their monospecific zones, at two depths. Differences in holobionts were evaluated using seagrass descriptors (morphometric, biochemical, elemental, and isotopic composition) to assess host changes, and 16S rRNA gene to identify bacterial community structure and composition. An Indicator Species Index was used to identify bacteria significantly associated with each host. In mixed meadows, native C. nodosa was shown to be affected by the presence of exotic H. stipulacea, in terms of both plant descriptors and bacterial communities, while H. stipulacea responded only to environmental factors rather than C. nodosa proximity. This study provided evidence of the competitive advantage of H. stipulacea on C. nodosa in the Aegean Sea and suggests the possible use of associated bacterial communities as an ecological seagrass descriptor.
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Affiliation(s)
- Chiara Conte
- PhD Program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, 00133 Rome, Italy
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Eugenia T. Apostolaki
- Institute of Oceanography, Hellenic Centre for Marine Research, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Salvatrice Vizzini
- Department of Earth and Marine Sciences, University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
- CoNISMa, National Interuniversity Consortium for Marine Sciences, Piazzale Flaminio 9, 00196 Roma, Italy
| | - Luciana Migliore
- Laboratory of Ecology and Ecotoxicology, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- eCampus University, Via Isimbardi 10, 22060 Novedrate (CO), Italy
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Bregman G, Lalzar M, Livne L, Bigal E, Zemah-Shamir Z, Morick D, Tchernov D, Scheinin A, Meron D. Preliminary study of shark microbiota at a unique mix-species shark aggregation site, in the Eastern Mediterranean Sea. Front Microbiol 2023; 14:1027804. [PMID: 36910211 PMCID: PMC9996248 DOI: 10.3389/fmicb.2023.1027804] [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: 08/25/2022] [Accepted: 01/16/2023] [Indexed: 02/25/2023] Open
Abstract
Sharks, as apex predators, play an essential ecological role in shaping the marine food web and maintaining healthy and balanced marine ecosystems. Sharks are sensitive to environmental changes and anthropogenic pressure and demonstrate a clear and rapid response. This designates them a "keystone" or "sentinel" group that may describe the structure and function of the ecosystem. As a meta-organism, sharks offer selective niches (organs) for microorganisms that can provide benefits for their hosts. However, changes in the microbiota (due to physiological or environmental changes) can turn the symbiosis into a dysbiosis and may affect the physiology, immunity and ecology of the host. Although the importance of sharks within the ecosystem is well known, relatively few studies have focused on the microbiome aspect, especially with long-term sampling. Our study was conducted at a site of coastal development in Israel where a mixed-species shark aggregation (November-May) is observed. The aggregation includes two shark species, the dusky (Carcharhinus obscurus) and sandbar (Carcharhinus plumbeus) which segregate by sex (females and males, respectively). In order to characterize the bacterial profile and examine the physiological and ecological aspects, microbiome samples were collected from different organs (gills, skin, and cloaca) from both shark species over 3 years (sampling seasons: 2019, 2020, and 2021). The bacterial composition was significantly different between the shark individuals and the surrounding seawater and between the shark species. Additionally, differences were apparent between all the organs and the seawater, and between the skin and gills. The most dominant groups for both shark species were Flavobacteriaceae, Moraxellaceae, and Rhodobacteraceae. However, specific microbial biomarkers were also identified for each shark. An unexpected difference in the microbiome profile and diversity between the 2019-2020 and 2021 sampling seasons, revealed an increase in the potential pathogen Streptococcus. The fluctuations in the relative abundance of Streptococcus between the months of the third sampling season were also reflected in the seawater. Our study provides initial information on shark microbiome in the Eastern Mediterranean Sea. In addition, we demonstrated that these methods were also able to describe environmental episodes and the microbiome is a robust measure for long-term ecological research.
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Affiliation(s)
- Goni Bregman
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Services Unit, University of Haifa, Haifa, Israel
| | - Leigh Livne
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Eyal Bigal
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Ziv Zemah-Shamir
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Danny Morick
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dan Tchernov
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Aviad Scheinin
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Dalit Meron
- Morris Kahn Marine Research Station, Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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Pei Y, Chen S, Diao X, Wang X, Zhou H, Li Y, Li Z. Deciphering the disturbance mechanism of BaP on the symbiosis of Montipora digitata via 4D-Proteomics approach. CHEMOSPHERE 2023; 312:137223. [PMID: 36372339 DOI: 10.1016/j.chemosphere.2022.137223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
The coral holobiont is mainly composed of coral polyps, zooxanthellae, and coral symbiotic microorganisms, which form the basis of coral reef ecosystems. In recent years, the severe degradation of coral reefs caused by climate warming and environmental pollution has aroused widespread concern. Benzo(a)pyrene (BaP) is a widely distributed pollutant in the environment. However, the underlying mechanisms of coral symbiosis destruction due to the stress of BaP are not well understood. In this study, diaPASEF proteomics and 16S rRNA amplicon pyrosequencing technology were used to reveal the effects of 50 μg/L BaP on Montipora digitate. Data analysis was performed from the perspective of the main symbionts of M. digitata (coral polyps, zooxanthellae, and coral symbiotic microorganisms). The results showed that BaP impaired cellular antioxidant capacity by disrupting the GSH/GSSG cycle, and sustained stress causes severe impairment of energy metabolism and protein degradation in coral polyps. In zooxanthellae, BaP downregulated the protein expression of SOD2 and mtHSP70, which then resulted in oxidative free radical accumulation and apoptosis. For coral symbiotic microorganisms, BaP altered the community structure of microorganisms and decreased immunity. Coral symbiotic microorganisms adapted to the stress of BaP by adjusting energy metabolism and enhancing extracellular electron transfer. BaP adversely affected the three main symbionts of M. digitata via different mechanisms. Decreased antioxidant capacity is a common cause of damages to coral polyps and zooxanthellae, whereas coral symbiotic microorganisms are able to appropriately adapt to oxidative stress. This study assessed the effects of BaP on corals from a symbiotic perspective, which is more comprehensive and reliable. At the same time, data from the study supports new directions for coral research and coral reef protection.
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Affiliation(s)
- Yuebin Pei
- School of Life Sciences, Hainan University, Haikou, 570228, China; State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China
| | - Shuai Chen
- School of Life Sciences, Hainan University, Haikou, 570228, China; State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China
| | - Xiaoping Diao
- State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China
| | - Xiaobing Wang
- School of Life Sciences, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China
| | - Hailong Zhou
- School of Life Sciences, Hainan University, Haikou, 570228, China; State Key Laboratory of South China Sea Marine Resource Utilisation, Hainan University, Haikou, 570228, China; One Health Institute, Hainan University, Haikou, Hainan, 570228, China.
| | - Yuanchao Li
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, 571126, China
| | - Zhiyong Li
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Correia Costa I, Amorim de Oliveira M, Wosnick N, Ann Hauser-Davis R, Siciliano S, Nunes JLS. Elasmobranch-associated microbiota: a scientometric literature review. PeerJ 2022; 10:e14255. [PMID: 36345481 PMCID: PMC9636872 DOI: 10.7717/peerj.14255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Elasmobranchs provide greatly relevant ecosystem services for the balance of the environments in which they are inserted. In recent decades, sharp population declines have been reported for many species in different regions worldwide, making this taxonomic group currently one of the most threatened with extinction. This scenario is almost entirely due to excessive fishing pressure, but any contributing factor that may cause additional mortality to populations must be mapped and monitored. In a fast-changing world, emerging marine pollution associated with climate change display the potential to increase the spread of infectious agents. These can, in turn, lead to mortality events, both directly and indirectly, by reducing immune responses and the physical and nutritional condition of affected individuals. In this context, the present study aimed to analyze data concerning elasmobranch-associated microbiota, identifying study trends and knowledge gaps in order to direct future studies on this topic of growing relevance for the health of wild populations, as well as individuals maintained in captivity, considering the zoonotic potential of these microorganisms.
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Affiliation(s)
- Ivana Correia Costa
- Laboratório de Organismos Aquáticos, Universidade Federal do Maranhão, São Luís, Maranhão, Brazil
| | - Mariene Amorim de Oliveira
- Laboratório de Genética e Biologia Molecular, Universidade Federal do Maranhão, São Luís, Maranhão, Brazil
| | - Natascha Wosnick
- Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Rachel Ann Hauser-Davis
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Salvatore Siciliano
- Departamento de Ciências Biológicas, Escola Nacional de Saúde Pública/FIOCRUZ, Rio de Janeiro, Brazil
| | - Jorge Luiz Silva Nunes
- Laboratório de Organismos Aquáticos, Universidade Federal do Maranhão, São Luís, Maranhão, Brazil
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Aagaard A, Liu S, Tregenza T, Braad Lund M, Schramm A, Verhoeven KJF, Bechsgaard J, Bilde T. Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola. Mol Ecol 2022; 31:5765-5783. [PMID: 36112081 PMCID: PMC9827990 DOI: 10.1111/mec.16696] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 02/06/2023]
Abstract
Understanding the role of genetic and nongenetic variants in modulating phenotypes is central to our knowledge of adaptive responses to local conditions and environmental change, particularly in species with such low population genetic diversity that it is likely to limit their evolutionary potential. A first step towards uncovering the molecular mechanisms underlying population-specific responses to the environment is to carry out environmental association studies. We associated climatic variation with genetic, epigenetic and microbiome variation in populations of a social spider with extremely low standing genetic diversity. We identified genetic variants that are associated strongly with environmental variation, particularly with average temperature, a pattern consistent with local adaptation. Variation in DNA methylation in many genes was strongly correlated with a wide set of climate parameters, thereby revealing a different pattern of associations than that of genetic variants, which show strong correlations to a more restricted range of climate parameters. DNA methylation levels were largely independent of cis-genetic variation and of overall genetic population structure, suggesting that DNA methylation can work as an independent mechanism. Microbiome composition also correlated with environmental variation, but most strong associations were with precipitation-related climatic factors. Our results suggest a role for both genetic and nongenetic mechanisms in shaping phenotypic responses to local environments.
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Affiliation(s)
- Anne Aagaard
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Shenglin Liu
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Tom Tregenza
- Centre for Ecology & Conservation, School of BiosciencesUniversity of ExeterPenryn CampusUK
| | - Marie Braad Lund
- Section for Microbiology, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Andreas Schramm
- Section for Microbiology, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Koen J. F. Verhoeven
- Terrestrial Ecology DepartmentNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Jesper Bechsgaard
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
| | - Trine Bilde
- Section for Genetics, Ecology & Evolution, Department of BiologyAarhus UniversityAarhus CDenmark
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Biodiversity and Bioprospecting of Fungal Endophytes from the Antarctic Plant Colobanthus quitensis. J Fungi (Basel) 2022; 8:jof8090979. [PMID: 36135704 PMCID: PMC9504944 DOI: 10.3390/jof8090979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 12/14/2022] Open
Abstract
Microorganisms from extreme environments are considered as a new and valuable reservoir of bioactive molecules of biotechnological interest and are also utilized as tools for enhancing tolerance to (a)biotic stresses in crops. In this study, the fungal endophytic community associated with the leaves of the Antarctic angiosperm Colobanthus quitensis was investigated as a new source of bioactive molecules. We isolated 132 fungal strains and taxonomically annotated 26 representative isolates, which mainly belonged to the Basidiomycota division. Selected isolates of Trametes sp., Lenzites sp., Sistotrema sp., and Peniophora sp. displayed broad extracellular enzymatic profiles; fungal extracts from some of them showed dose-dependent antitumor activity and inhibited the formation of amyloid fibrils of α-synuclein and its pathological mutant E46K. Selected fungal isolates were also able to promote secondary root development and fresh weight increase in Arabidopsis and tomato and antagonize the growth of pathogenic fungi harmful to crops. This study emphasizes the ecological and biotechnological relevance of fungi from the Antarctic ecosystem and provides clues to the bioprospecting of Antarctic Basidiomycetes fungi for industrial, agricultural, and medical applications.
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35
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Sudan S, Zhan X, Li J. A Novel Probiotic Bacillus subtilis Strain Confers Cytoprotection to Host Pig Intestinal Epithelial Cells during Enterotoxic Escherichia coli Infection. Microbiol Spectr 2022; 10:e0125721. [PMID: 35736372 PMCID: PMC9430607 DOI: 10.1128/spectrum.01257-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/26/2022] [Indexed: 01/13/2023] Open
Abstract
Enteric infections caused by enterotoxic Escherichia coli (ETEC) negatively impact the growth performance of piglets during weaning, resulting in significant economic losses for the producers. With the ban on antibiotic usage in livestock production, probiotics have gained a lot of attention as a potential alternative. However, strain specificity and limited knowledge on the host-specific targets limit their efficacy in preventing ETEC-related postweaning enteric infections. We recently isolated and characterized a novel probiotic Bacillus subtilis bacterium (CP9) that demonstrated antimicrobial activity. Here, we report anti-ETEC properties of CP9 and its impact on metabolic activity of swine intestinal epithelial (IPEC-J2) cells. Our results showed that pre- or coincubation with CP9 protected IPEC-J2 cells from ETEC-induced cytotoxicity. CP9 significantly attenuated ETEC-induced inflammatory response by reducing ETEC-induced nitric oxide production and relative mRNA expression of the Toll-like receptors (TLRs; TLR2, TLR4, and TLR9), proinflammatory tumor necrosis factor alpha, interleukins (ILs; IL-6 and IL-8), augmenting anti-inflammatory granulocyte-macrophage colony-stimulating factor and host defense peptide mucin 1 (MUC1) mRNA levels. We also show that CP9 significantly (P < 0.05) reduced caspase-3 activity, reinstated cell proliferation and increased relative expression of tight junction genes, claudin-1, occludin, and zona occludens-1 in ETEC-infected cells. Finally, metabolomic analysis revealed that CP9 exposure induced metabolic modulation in IPEC J2 cells with the greatest impact seen in alanine, aspartate, and glutamate metabolism; pyrimidine metabolism; nicotinate and nicotinamide metabolism; glutathione metabolism; the citrate cycle (TCA cycle); and arginine and proline metabolism. Our study shows that CP9 incubation attenuated ETEC-induced cytotoxicity in IPEC-J2 cells and offers insight into potential application of this probiotic for ETEC infection control. IMPORTANCE ETEC remains one of the leading causes of postweaning diarrhea and mortality in swine production. Due to the rising concerns with the antibiotic use in livestock, alternative interventions need to be developed. In this study, we analyzed the cytoprotective effect of a novel probiotic strain in combating ETEC infection in swine intestinal cells, along with assessing its mechanism of action. To our knowledge, this is also the first study to analyze the metabolic impact of a probiotic on intestinal cells. Results from this study should provide effective cues in developing a probiotic intervention for ameliorating ETEC infection and improving overall gut health in swine production.
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Affiliation(s)
- Sudhanshu Sudan
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Xiaoshu Zhan
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
| | - Julang Li
- Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada
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36
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Cziesielski MJ, Liew YJ, Cui G, Aranda M. Increased incompatibility of heterologous algal symbionts under thermal stress in the cnidarian-dinoflagellate model Aiptasia. Commun Biol 2022; 5:760. [PMID: 35902758 PMCID: PMC9334593 DOI: 10.1038/s42003-022-03724-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 07/15/2022] [Indexed: 11/09/2022] Open
Abstract
Rising ocean temperatures are increasing the rate and intensity of coral mass bleaching events, leading to the collapse of coral reef ecosystems. To better understand the dynamics of coral-algae symbioses, it is critical to decipher the role each partner plays in the holobiont's thermotolerance. Here, we investigated the role of the symbiont by comparing transcriptional heat stress responses of anemones from two thermally distinct locations, Florida (CC7) and Hawaii (H2) as well as a heterologous host-symbiont combination composed of CC7 host anemones inoculated with the symbiont Breviolum minutum (SSB01) from H2 anemones (CC7-B01). We find that oxidative stress and apoptosis responses are strongly influenced by symbiont type, as further confirmed by caspase-3 activation assays, but that the overall response to heat stress is dictated by the compatibility of both partners. Expression of genes essential to symbiosis revealed a shift from a nitrogen- to a carbon-limited state only in the heterologous combination CC7-B01, suggesting a bioenergetic disruption of symbiosis during stress. Our results indicate that symbiosis is highly fine-tuned towards particular partner combinations and that heterologous host-symbiont combinations are metabolically less compatible under stress. These results are essential for future strategies aiming at increasing coral resilience using heterologous thermotolerant symbionts.
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Affiliation(s)
- Maha J Cziesielski
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.,Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Yi Jin Liew
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.,Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.,CSIRO Health & Biosecurity, North Ryde, NSW, Australia
| | - Guoxin Cui
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.,Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Manuel Aranda
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia. .,Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Siro G, Pipite A, Christi K, Srinivasan S, Subramani R. Marine Actinomycetes Associated with Stony Corals: A Potential Hotspot for Specialized Metabolites. Microorganisms 2022; 10:microorganisms10071349. [PMID: 35889068 PMCID: PMC9319285 DOI: 10.3390/microorganisms10071349] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 07/02/2022] [Indexed: 02/05/2023] Open
Abstract
Microbial secondary metabolites are an important source of antibiotics currently available for combating drug-resistant pathogens. These important secondary metabolites are produced by various microorganisms, including Actinobacteria. Actinobacteria have a colossal genome with a wide array of genes that code for several bioactive metabolites and enzymes. Numerous studies have reported the isolation and screening of millions of strains of actinomycetes from various habitats for specialized metabolites worldwide. Looking at the extent of the importance of actinomycetes in various fields, corals are highlighted as a potential hotspot for untapped secondary metabolites and new bioactive metabolites. Unfortunately, knowledge about the diversity, distribution and biochemistry of marine actinomycetes compared to hard corals is limited. In this review, we aim to summarize the recent knowledge on the isolation, diversity, distribution and discovery of natural compounds from marine actinomycetes associated with hard corals. A total of 11 new species of actinomycetes, representing nine different families of actinomycetes, were recovered from hard corals during the period from 2007 to 2022. In addition, this study examined a total of 13 new compounds produced by five genera of actinomycetes reported from 2017 to 2022 with antibacterial, antifungal and cytotoxic activities. Coral-derived actinomycetes have different mechanisms of action against their competitors.
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Affiliation(s)
- Galana Siro
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
| | - Atanas Pipite
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
- Correspondence: (A.P.); or (S.S.)
| | - Ketan Christi
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 01797, Korea
- Correspondence: (A.P.); or (S.S.)
| | - Ramesh Subramani
- School of Agriculture, Geography, Environment, Ocean and Natural Sciences (SAGEONS), The University of the South Pacific, Laucala Campus, Suva, Fiji; (G.S.); (K.C.); (R.S.)
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Microbiota mediated plasticity promotes thermal adaptation in the sea anemone Nematostella vectensis. Nat Commun 2022; 13:3804. [PMID: 35778405 PMCID: PMC9249911 DOI: 10.1038/s41467-022-31350-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
At the current rate of climate change, it is unlikely that multicellular organisms will be able to adapt to changing environmental conditions through genetic recombination and natural selection alone. Thus, it is critical to understand alternative mechanisms that allow organisms to cope with rapid environmental changes. Here, we use the sea anemone Nematostella vectensis, which has evolved the capability of surviving in a wide range of temperatures and salinities, as a model to investigate the microbiota as a source of rapid adaptation. We long-term acclimate polyps of Nematostella to low, medium, and high temperatures, to test the impact of microbiota-mediated plasticity on animal acclimation. Using the same animal clonal line, propagated from a single polyp, allows us to eliminate the effects of the host genotype. The higher thermal tolerance of animals acclimated to high temperature can be transferred to non-acclimated animals through microbiota transplantation. The offspring fitness is highest from F0 females acclimated to high temperature and specific members of the acclimated microbiota are transmitted to the next generation. These results indicate that microbiota plasticity can contribute to animal thermal acclimation and its transmission to the next generation may represent a rapid mechanism for thermal adaptation. This study shows that sea anemones acclimated to high temperatures exhibit increased resistance to thermal stress and that this improved fitness can be transferred by microbiome transplantation. These results indicate that plasticity mediated by the microbiota might be an important factor facilitating thermal adaptations in animals.
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39
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The adaptive strategies of yaks to live in the Asian highlands. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 9:249-258. [PMID: 35600551 PMCID: PMC9092367 DOI: 10.1016/j.aninu.2022.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/20/2021] [Accepted: 02/25/2022] [Indexed: 11/23/2022]
Abstract
The yak (Bos grunniens), an indigenous herbivore raised at altitudes between 3,000 and 5,000 m above sea level, is closely linked to more than 40 ethnic communities and plays a vital role in the ecological stability, livelihood security, socio-economic development, and ethnic cultural traditions in the Asian highlands. They provide the highlanders with meat, milk, fibres, leather and dung (fuel). They are also used as pack animals to transport goods, for travel and ploughing, and are important in many religious and traditional ceremonies. The Asian highlands are known for an extremely, harsh environment, namely low air temperature and oxygen content and high ultraviolet light and winds. Pasture availability fluctuates greatly, with sparse pasture of poor quality over the long seven-month cold winter. After long-term natural and artificial selections, yaks have adapted excellently to the harsh conditions: 1) by genomics, with positively selected genes involved in hypoxia response and energy metabolism; 2) anatomically, including a short tongue with a weak sense of taste, and large lung and heart; 3) physiologically, by insensitivity to hypoxic pulmonary vasoconstriction, maintaining foetal haemoglobin throughout life, and low heart rate and heat production in the cold season; 4) behaviourlly, by efficient grazing and selecting forbs with high nutritional contents; 5) by low nitrogen and energy requirements for maintenance and low methane emission and nitrogen excretion, namely, ‘Low-Carbon’ and ‘Nitrogen-Saving’ traits; 6) by harboring unique rumen microbiota with a distinct maturation pattern, that has co-evolved with host metabolism. This review aims to provide an overview of the comprehensive adaptive strategies of the yak to the severe conditions of the highlands. A better understanding of these strategies that yaks employ to adapt to the harsh environment could be used in improving their production, breeding and management, and gaining benefits in ecosystem service and a more resilient livelihood to climate change in the Asian highlands.
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40
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Carrier TJ, Maldonado M, Schmittmann L, Pita L, Bosch TCG, Hentschel U. Symbiont transmission in marine sponges: reproduction, development, and metamorphosis. BMC Biol 2022; 20:100. [PMID: 35524305 PMCID: PMC9077847 DOI: 10.1186/s12915-022-01291-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.
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Affiliation(s)
- Tyler J Carrier
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
- Zoological Institute, University of Kiel, Kiel, Germany.
| | - Manuel Maldonado
- Department of Marine Ecology, Center for Advanced Studies of Blanes (CEAB-CSIC), Girona, Spain
| | | | - Lucía Pita
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | | | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Zoological Institute, University of Kiel, Kiel, Germany
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41
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Eco-Evolutionary Dynamics of the Human-Gut Microbiota Symbiosis in a Changing Nutritional Environment. Evol Biol 2022. [DOI: 10.1007/s11692-022-09569-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractThe operational harmony between living beings and their circumstances, their ever-changing environment, is a constitutive condition of their existence. Nutrition and symbiosis are two essential aspects of this harmony. Disruption of the symbiosis between host and gut microbiota, the so-called dysbiosis, as well as the inadequate diet from which it results, contribute to the etiology of immunometabolic disorders. Research into the development of these diseases is highly influenced by our understanding of the evolutionary roots of metabolic functioning, thereby considering that chronic non-communicable diseases arise from an evolutionary mismatch. However, the lens has been mostly directed toward energy availability and metabolism, but away from our closest environmental factor, the gut microbiota. Thus, this paper proposes a narrative thread that places symbiosis in an evolutionary perspective, expanding the traditional framework of humans’ adaptation to their food environment.
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Chen J, Liu H, Bai Y, Qi J, Qi W, Liu H, Peng J, Qu J. Mixing regime shapes the community assembly process, microbial interaction and proliferation of cyanobacterial species Planktothrix in a stratified lake. J Environ Sci (China) 2022; 115:103-113. [PMID: 34969441 DOI: 10.1016/j.jes.2021.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 06/14/2023]
Abstract
Lake mixing influences aquatic chemical properties and microbial community composition, and thus, we hypothesized that it would alter microbial community assembly and interaction. To clarify this issue, we explored the community assembly processes and cooccurrence networks in four seasons at two depths (epilimnion and hypolimnion) in a mesotrophic and stratified lake (Chenghai Lake), which formed stratification in the summer and turnover in the winter. During the stratification period, the epilimnion and hypolimnion went through contrary assembly processes but converged to similar assembly patterns in the mixing period. In a highly homogeneous selection environment, species with low niche breadth were filtered, resulting in decreased species richness. Water mixing in the winter homogenized the environment, resulting in a simpler microbial cooccurrence network. Interestingly, we observed a high abundance of the cyanobacterial genus Planktothrix in the winter, probably due to nutrient redistribution and Planktothrix adaptivity to the winter environment in which mixing played important roles. Our study provides deeper fundamental insights into how environmental factors influence microbial community structure through community assembly processes.
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Affiliation(s)
- Junwen Chen
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huacong Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jing Qi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weixiao Qi
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jianfeng Peng
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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43
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Moubayed NM, Al Houri HJ, Bukhari SI. Turbinaria ornata and its associated epiphytic Bacillus sp. A promising molecule supplier to discover new natural product approaches. Saudi J Biol Sci 2022; 29:2532-2540. [PMID: 35531156 PMCID: PMC9072896 DOI: 10.1016/j.sjbs.2021.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/11/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022] Open
Abstract
Marine ecosystems are highly dependent on macroalgea in providing food and shelter for aquatic organisms, interacting with many bacteria and mostly producing secondary metabolites of potent therapeutic antibacterial property. Screening of marine microbial secondary metabolites of valuable biotechnological and therapeutical applications are now extensively studied. In this study, Bacillus spp. identified by DNA sequencing and found associated with Turbinaria ornata, was screened and characterized for its cell free supernatant (CFS) possible antimicrobial and antibiofilm applications. Among the 7 microbial isolates tested, CFS greatly affected Bacillus subitilis (12 mm) and inhibited equally the yeast isolates Candida albicans, Candida tropicalis and Candida glabrata (10 mm) and had no or negligible effect on S.aureus, E.coli, P. aeruginosa. As for the CFS antibiofilm activity, no difference was revealed from the positive control. Algal crude extracts (methanol, acetone and aqueous), on the other hand, were similarly tested for their antimicrobial activity against the seven microbial isolates, where highest activity was observed with the aqueous crude extract against Staphylococcus aureus(10 mm) and Pseudomonas aeruginosa (9 mm) compared to the negligible effects of methanol and acetone crude extracts. Chemical analysis was performed to reveal the major constituents of both crude algal extracts and Bacillus spp. CFS. FTIR spectrum of the bacterial CFS indicated the presence of bacteriocin as the major lipopeptide responsible for its biological activity. Whereas, methanol and water crude algal extract GC-MS spectra revealed different chemical groups of various combined therapeutical activity mainly Naphthalene, amino ethane-sulfonic acid, pyrlene, Biotin and mercury chloromethyl correspondingly. Thus, the present study, demonstrated the moderate activity of both crude algal extract and the bacterial CFS, however, further investigations are needed for a better biological activity.
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Affiliation(s)
- Nadine M.S. Moubayed
- Botany and Microbiology Department, Science College, Female Campus, King Saud University, Riyadh 11495, Saudi Arabia
| | - Hadeel J. Al Houri
- Botany and Microbiology Department, Science College, Female Campus, King Saud University, Riyadh 11495, Saudi Arabia
| | - Sarah I. Bukhari
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Sefrji FO, Marasco R, Michoud G, Seferji KA, Merlino G, Daffonchio D. Insights Into the Cultivable Bacterial Fraction of Sediments From the Red Sea Mangroves and Physiological, Chemotaxonomic, and Genomic Characterization of Mangrovibacillus cuniculi gen. nov., sp. nov., a Novel Member of the Bacillaceae Family. Front Microbiol 2022; 13:777986. [PMID: 35250919 PMCID: PMC8894767 DOI: 10.3389/fmicb.2022.777986] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/28/2022] [Indexed: 12/28/2022] Open
Abstract
Mangrove forests are dynamic and productive ecosystems rich in microbial diversity; it has been estimated that microbial cells in the mangrove sediments constitute up to 91% of the total living biomass of these ecosystems. Despite in this ecosystem many of the ecological functions and services are supported and/or carried out by microorganisms (e.g., nutrient cycling and eukaryotic-host adaptation), their diversity and function are overlooked and poorly explored, especially for the oligotrophic mangrove of the Red Sea coast. Here, we investigated the cultivable fraction of bacteria associated with the sediments of Saudi Arabian Red Sea mangrove forest by applying the diffusion-chamber-based approach in combination with oligotrophic medium and long incubation time to allow the growth of bacteria in their natural environment. Cultivation resulted in the isolation of numerous representatives of Isoptericola (n = 51) and Marinobacter (n = 38), along with several less abundant and poorly study taxa (n = 25) distributed across ten genera. Within the latest group, we isolated R1DC41T, a novel member of the Bacillaceae family in the Firmicutes phylum. It showed 16S rRNA gene similarity of 94.59–97.36% with closest relatives of Rossellomorea (which was formerly in the Bacillus genus), Domibacillus, Bacillus, and Jeotgalibacillus genera. Based on the multilocus sequence analysis (MLSA), R1DC41T strain formed a separated branch from the listed genera, representing a novel species of a new genus for which the name Mangrovibacillus cuniculi gen. nov., sp. nov. is proposed. Genomic, morphological, and physiological characterizations revealed that R1DC41T is an aerobic, Gram-stain-variable, rod-shaped, non-motile, endospore-forming bacterium. A reduced genome and the presence of numerous transporters used to import the components necessary for its growth and resistance to the stresses imposed by the oligotrophic and salty mangrove sediments make R1DC41T extremely adapted to its environment of origin and to the competitive conditions present within.
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45
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Ecological and Biotechnological Relevance of Mediterranean Hydrothermal Vent Systems. MINERALS 2022. [DOI: 10.3390/min12020251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Marine hydrothermal systems are a special kind of extreme environments associated with submarine volcanic activity and characterized by harsh chemo-physical conditions, in terms of hot temperature, high concentrations of CO2 and H2S, and low pH. Such conditions strongly impact the living organisms, which have to develop adaptation strategies to survive. Hydrothermal systems have attracted the interest of researchers due to their enormous ecological and biotechnological relevance. From ecological perspective, these acidified habitats are useful natural laboratories to predict the effects of global environmental changes, such as ocean acidification at ecosystem level, through the observation of the marine organism responses to environmental extremes. In addition, hydrothermal vents are known as optimal sources for isolation of thermophilic and hyperthermophilic microbes, with biotechnological potential. This double aspect is the focus of this review, which aims at providing a picture of the ecological features of the main Mediterranean hydrothermal vents. The physiological responses, abundance, and distribution of biotic components are elucidated, by focusing on the necto-benthic fauna and prokaryotic communities recognized to possess pivotal role in the marine ecosystem dynamics and as indicator species. The scientific interest in hydrothermal vents will be also reviewed by pointing out their relevance as source of bioactive molecules.
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46
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Abstract
Microbial communities associated with deep-sea animals are critical to the establishment of novel biological communities in unusual environments. Over the past few decades, rapid exploration of the deep sea has enabled the discovery of novel microbial communities, some of which form symbiotic relationships with animal hosts. Symbiosis in the deep sea changes host physiology, behavior, ecology, and evolution over time and space. Symbiont diversity within a host is often aligned with diverse metabolic pathways that broaden the environmental niche for the animal host. In this review, we focus on microbiomes and obligate symbionts found in different deep-sea habitats and how they facilitate survival of the organisms that live in these environments. In addition, we discuss factors that govern microbiome diversity, host specificity, and biogeography in the deep sea. Finally, we highlight the current limitations of microbiome research and draw a road map for future directions to advance our knowledge of microbiomes in the deep sea. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Eslam O Osman
- Biology Department, Eberly College, Pennsylvania State University, State College, Pennsylvania, USA; .,Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Biology Lab, Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Alexis M Weinnig
- Biology Department, Temple University, Philadelphia, Pennsylvania, USA
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47
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Dubé CE, Ziegler M, Mercière A, Boissin E, Planes S, Bourmaud CAF, Voolstra CR. Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition. Nat Commun 2021; 12:6402. [PMID: 34737272 PMCID: PMC8568919 DOI: 10.1038/s41467-021-26543-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/04/2021] [Indexed: 02/07/2023] Open
Abstract
Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.
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Affiliation(s)
- C. E. Dubé
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia ,grid.23856.3a0000 0004 1936 8390Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, G1V 0A6 Canada
| | - M. Ziegler
- grid.8664.c0000 0001 2165 8627Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, 35392 Giessen, Germany ,grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia
| | - A. Mercière
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - E. Boissin
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - S. Planes
- grid.11136.340000 0001 2192 5916PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860 Perpignan, France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. A. -F. Bourmaud
- grid.11642.300000 0001 2111 2608UMR 9220 ENTROPIE, UR-IRD-CNRS-UNC-IFREMER, Université de La Réunion, 15 Avenue René Cassin, CS 92003, 97744 Saint-Denis Cedex, La Réunion France ,Laboratoire d’Excellence “CORAIL”, 98729 Papetoai, Moorea French Polynesia
| | - C. R. Voolstra
- grid.45672.320000 0001 1926 5090Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, 23955 Saudi Arabia ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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48
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Wale M, Daffonchio D, Fusi M, Marasco R, Garuglieri E, Diele K. The Importance of Larval Stages for Considering Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization. Front Microbiol 2021; 12:770245. [PMID: 34721372 PMCID: PMC8555880 DOI: 10.3389/fmicb.2021.770245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- Matthew Wale
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Daniele Daffonchio
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marco Fusi
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
| | - Ramona Marasco
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Elisa Garuglieri
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Karen Diele
- School of Applied Sciences, Edinburgh Napier University, Edinburgh, United Kingdom
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49
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Prediction of Genes That Function in Methanogenesis and CO 2 Pathways in Extremophiles. Microorganisms 2021; 9:microorganisms9112211. [PMID: 34835337 PMCID: PMC8621995 DOI: 10.3390/microorganisms9112211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 12/04/2022] Open
Abstract
Gaet’ale (GAL) and Mud’ara (MUP) are two hypersaline ponds located in the Danakil Depression recharged by underground water from the surrounding highlands. These two ponds have different pH, salinity, and show variation in the concentration of many ionic components. Metagenomic analysis concludes that GAL is dominated by bacteria as in the case of the other hypersaline and acidic ponds in the Danakil Depression. However, Archaea dominated the ponds of MUP. In the current study, the application of SEED and KEGG helped to map the ordered steps of specific enzyme catalyzed reaction in converting CO2 into cell products. We predict that highly efficient and light-independent carbon fixation involving phosphoenolpyruvate carboxylase takes place in MUP. On the contrary, genes encoding enzymes involved in hydrogenotrophic and acetoclastic methanogenesis appeared solely in ponds of GAL, implying the biological source of the hazardous methane gas in that environment. Based on the investigation of the sources of the genes of interest, it is clear that cooperative interactions between members of the two communities and syntrophic metabolism is the main strategy adapted to utilize inorganic carbon as a carbon source in both MUP and GAL. This insight can be used to design biotechnological applications of microbial communities in production of methane biogas or to minimize CO2 emissions.
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Horizontal gene transfer-mediated bacterial strain variation affects host fitness in Drosophila. BMC Biol 2021; 19:187. [PMID: 34565363 PMCID: PMC8474910 DOI: 10.1186/s12915-021-01124-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
Background How microbes affect host fitness and environmental adaptation has become a fundamental research question in evolutionary biology. To better understand the role of microbial genomic variation for host fitness, we tested for associations of bacterial genomic variation and Drosophila melanogaster offspring number in a microbial Genome Wide Association Study (GWAS). Results We performed a microbial GWAS, leveraging strain variation in the genus Gluconobacter, a genus of bacteria that are commonly associated with Drosophila under natural conditions. We pinpoint the thiamine biosynthesis pathway (TBP) as contributing to differences in fitness conferred to the fly host. While an effect of thiamine on fly development has been described, we show that strain variation in TBP between bacterial isolates from wild-caught D. melanogaster contributes to variation in offspring production by the host. By tracing the evolutionary history of TBP genes in Gluconobacter, we find that TBP genes were most likely lost and reacquired by horizontal gene transfer (HGT). Conclusion Our study emphasizes the importance of strain variation and highlights that HGT can add to microbiome flexibility and potentially to host adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01124-y.
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