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Ferreira MJ, Sierra-Garcia IN, Louvado A, Gomes NCM, Figueiredo S, Patinha C, Pinto DCGA, Cremades J, Silva H, Cunha Â. Domestication shapes the endophytic microbiome and metabolome of Salicornia europaea. J Appl Microbiol 2023; 134:lxad178. [PMID: 37587019 DOI: 10.1093/jambio/lxad178] [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: 05/25/2023] [Revised: 07/20/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
AIMS We aim at understanding the effect of domestication on the endophytic microbiome and metabolome of Salicornia europaea and collecting evidence on the potential role of microbial populations and metabolites in the adaptation of plants to different ecological contexts (wild vs crops). METHODS AND RESULTS Samples were collected from a natural salt marsh (wild) and an intensive crop field (crop). High-throughput sequencing of the 16S rRNA gene, gas chromatography-mass spectrometry (GC-MS) and ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) were used to analyze the endophytic bacterial communities and the metabolite profiles of S. europaea roots, respectively. The elemental analysis of the plant shoots was performed by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS).Overall, significant differences were found between the microbiome of wild and cultivated plants. The later showed a higher relative abundance of the genera Erythrobacter, Rhodomicrobium, and Ilumatobacter than wild plants. The microbiome of wild plants was enriched in Marinobacter, Marixanthomonas, and Thalassospira. The metabolite profile of crop plants revealed higher amounts of saturated and non-saturated fatty acids and acylglycerols. In contrast, wild plants contained comparatively more carbohydrates and most macroelements (i.e. Na, K, Mg, and Ca). CONCLUSIONS There is a strong correlation between plant metabolites and the endosphere microbiome of S. europaea. In wild populations, plants were enriched in carbohydrates and the associated bacterial community was enriched in genes related to primary metabolic pathways such as nitrogen metabolism and carbon fixation. The endosphere microbiome of crop plants was predicted to have higher gene counts related to pathogenesis. Crop plants also exhibited higher amounts of azelaic acid, an indicator of exposure to phytopathogens.
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Affiliation(s)
- Maria J Ferreira
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - I Natalia Sierra-Garcia
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - António Louvado
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Sandro Figueiredo
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Carla Patinha
- Department of Geosciences & Geobiotec, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Diana C G A Pinto
- LAQV-REQUIMTE & Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Javier Cremades
- Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071 A Coruña, Spain
| | - Helena Silva
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Ângela Cunha
- Department of Biology & Center for Environmental and Marine Studies (CESAM), University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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Massé A, Detang J, Duval C, Duperron S, Woo AC, Domart-Coulon I. Bacterial Microbiota of Ostreobium, the Coral-Isolated Chlorophyte Ectosymbiont, at Contrasted Salinities. Microorganisms 2023; 11:1318. [PMID: 37317290 DOI: 10.3390/microorganisms11051318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies in reefs of contrasted salinities. Here, we analyzed their bacterial community's composition and plasticity in response to salinity. Multiple cultures of Pocillopora coral-isolated Ostreobium strains from two distinct rbcL lineages representative of IndoPacific environmental phylotypes were pre-acclimatized (>9 months) to three ecologically relevant reef salinities: 32.9, 35.1, and 40.2 psu. Bacterial phylotypes were visualized for the first time at filament scale by CARD-FISH in algal tissue sections, within siphons, at their surface or in their mucilage. Ostreobium-associated microbiota, characterized by bacterial 16S rDNA metabarcoding of cultured thalli and their corresponding supernatants, were structured by host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae or Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on Ostreobium lineage, and shifted Rhizobiales' abundances in response to the salinity increase. A small core microbiota composed of seven ASVs (~1.5% of thalli ASVs, 19-36% cumulated proportions) was persistent across three salinities in both genotypes, with putative intracellular Amoebophilaceae and Rickettsiales_AB1, as well as Hyphomonadaceae and Rhodospirillaceae also detected within environmental (Ostreobium-colonized) Pocillopora coral skeletons. This novel knowledge on the taxonomic diversity of Ostreobium bacteria paves the way to functional interaction studies within the coral holobiont.
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Affiliation(s)
- Anaïs Massé
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Juliette Detang
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Charlotte Duval
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Sébastien Duperron
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Anthony C Woo
- Pôle Analyse de Données UAR 2700 2AD, Muséum National d'Histoire Naturelle (MNHN), 43 Rue Cuvier, 75005 Paris, France
| | - Isabelle Domart-Coulon
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
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Chen Y, Zhuang Z, Liu J, Wang Z, Guo Y, Chen A, Chen B, Zhao W, Niu J. Effects of Hermetia illucens larvae meal on the Pacific white shrimp (Litopenaeus vannamei) revealed by innate immunity and 16S rRNA gene sequencing analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101080. [PMID: 37141643 DOI: 10.1016/j.cbd.2023.101080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/30/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
The larvae of the black soldier fly, Hermetia illucens, are now attracting attention and becoming promising sources for aquafeed ingredient due to the nutritious substance. However, the introduction of a novel ingredient into the recipe may have unpredictable effects on the innate immune function and gut bacteria composition of crustaceans. Therefore, the present study aimed to evaluate how dietary black soldier fly larvae meal (BSFLM) affected the antioxidant ability, innate immunity and gut microbiome of shrimp (Litopenaeus vannamei) fed with a practical diet, including the gene expression of Toll and immunodeficiency (IMD) pathways. Six experimental diets were formulated by replacing gradient levels of fish meal (0 %, 10 %, 20 %, 30 %, 40 % and 50 %) based on a commercial shrimp diet. Four replicates of shrimp were fed different diets three times daily for 60 days. Growth performance linearly decreased with increasing BSFLM inclusion. Results of antioxidative enzyme activities and gene expression suggested that low dietary BSFLM levels activated the antioxidant capacity of shrimp, while dietary BSFLM levels up to 100 g/kg may induce oxidative stress and inhibit glutathione peroxidase activity. Although traf6, toll1, dorsal and relish were significantly upregulated in different BSFLM groups, the expression of tak1 was significantly downregulated in groups containing BSFLM, implying the immune susceptibility may be weakened. Gut flora analysis indicated dietary BSFLM altered both beneficial and opportunistic pathogenic bacterial abundance, with low levels of dietary BSFLM increased the abundance of bacteria that may contribute to carbohydrate utilization, while high levels of dietary BSFLM may cause intestinal disease and low intestinal immune response. To conclude, 60-80 g/kg of dietary BSFLM showed no adverse effects on the growth, antioxidant capacity and gut flora of shrimp, which was the adequate level in shrimp diet. While 100 g/kg dietary BSFLM may induce oxidative stress and potentially weaken the innate immunity of shrimp.
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Affiliation(s)
- Yongkang Chen
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Zhenxiao Zhuang
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Jieping Liu
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Ziqiao Wang
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Yucai Guo
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Anqi Chen
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Baoyang Chen
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Wei Zhao
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China.
| | - Jin Niu
- State key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory for Aquatic Economic Animals and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, Guangdong Province, PR China.
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Structural Comparison of a Promiscuous and a Highly Specific Sucrose 6 F-Phosphate Phosphorylase. Int J Mol Sci 2019; 20:ijms20163906. [PMID: 31405215 PMCID: PMC6720575 DOI: 10.3390/ijms20163906] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/17/2022] Open
Abstract
In family GH13 of the carbohydrate-active enzyme database, subfamily 18 contains glycoside phosphorylases that act on α-sugars and glucosides. Because their phosphorolysis reactions are effectively reversible, these enzymes are of interest for the biocatalytic synthesis of various glycosidic compounds. Sucrose 6F-phosphate phosphorylases (SPPs) constitute one of the known substrate specificities. Here, we report the characterization of an SPP from Ilumatobacter coccineus with a far stricter specificity than the previously described promiscuous SPP from Thermoanaerobacterium thermosaccharolyticum. Crystal structures of both SPPs were determined to provide insight into their similarities and differences. The residues responsible for binding the fructose 6-phosphate group in subsite +1 were found to differ considerably between the two enzymes. Furthermore, several variants that introduce a higher degree of substrate promiscuity in the strict SPP from I. coccineus were designed. These results contribute to an expanded structural knowledge of enzymes in subfamily GH13_18 and facilitate their rational engineering.
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Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01563-15. [PMID: 26769942 PMCID: PMC4714123 DOI: 10.1128/genomea.01563-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacteria belonging to the family Acidimicrobiaceae are frequently encountered in heavy metal-contaminated acidic environments. However, their phylogenetic and metabolic diversity is poorly resolved. We present draft genome sequences of two novel and phylogenetically distinct Acidimicrobiaceae members assembled from an acid mine drainage biofilm metagenome.
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Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez‐Valera F. Key roles for freshwater
A
ctinobacteria revealed by deep metagenomic sequencing. Mol Ecol 2014; 23:6073-90. [DOI: 10.1111/mec.12985] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Rohit Ghai
- Evolutionary Genomics Group Departamento de Producción Vegetal y Microbiología Universidad Miguel Hernández San Juan de Alicante 03550 Alicante Spain
| | - Carolina Megumi Mizuno
- Evolutionary Genomics Group Departamento de Producción Vegetal y Microbiología Universidad Miguel Hernández San Juan de Alicante 03550 Alicante Spain
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia Burjassot E‐46100 Valencia Spain
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia Burjassot E‐46100 Valencia Spain
| | - Francisco Rodriguez‐Valera
- Evolutionary Genomics Group Departamento de Producción Vegetal y Microbiología Universidad Miguel Hernández San Juan de Alicante 03550 Alicante Spain
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