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McLean AHC, Godfray HCJ, Ellers J, Henry LM. Host relatedness influences the composition of aphid microbiomes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:808-816. [PMID: 31573138 PMCID: PMC6900097 DOI: 10.1111/1758-2229.12795] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/08/2019] [Accepted: 09/14/2019] [Indexed: 05/10/2023]
Abstract
Animals are host to a community of microbes, collectively referred to as their microbiome, that can play a key role in their hosts' biology. The bacterial endosymbionts of insects have a particularly strong influence on their hosts, but despite their importance we still know little about the factors that influence the composition of insect microbial communities. Here, we ask: what is the relative importance of host relatedness and host ecology in structuring symbiont communities of diverse aphid species? We used next-generation sequencing to compare the microbiomes of 46 aphid species with known host plant affiliations. We find that relatedness between aphid species is the key factor explaining the microbiome composition, with more closely related aphid species housing more similar bacterial communities. Endosymbionts dominate the microbial communities, and we find a novel bacterium in the genus Sphingopyxis that is associated with numerous aphid species feeding exclusively on trees. The influence of ecology was less pronounced than that of host relatedness. Our results suggest that co-adaptation between insect species and their facultative symbionts is a more important determinant of symbiont species presence in aphids than shared ecology of hosts.
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Affiliation(s)
| | | | - Jacintha Ellers
- Animal Ecology, Department of Ecological ScienceVU University AmsterdamAmsterdamThe Netherlands
| | - Lee M. Henry
- Department of ZoologyUniversity of OxfordOxfordUK
- Animal Ecology, Department of Ecological ScienceVU University AmsterdamAmsterdamThe Netherlands
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Song J, Zhang J, Kang S, Zhang H, Yuan J, Zeng C, Zhang F, Huang Y. Analysis of microbial diversity in apple vinegar fermentation process through 16s rDNA sequencing. Food Sci Nutr 2019; 7:1230-1238. [PMID: 31024696 PMCID: PMC6475731 DOI: 10.1002/fsn3.944] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 11/08/2022] Open
Abstract
Based on SPME-GC-MS analysis, it could be found that the production of acetic acid, phenethyl acetate, and isoamyl acetate gradually increased in the apple vinegar fermentation broth with the fermentation time. Consequently, in order to systematically explore the dynamic changes of microbial diversity and metabolites in the process of apple vinegar fermentation, 16S rDNA were sequenced and analyzed in this work. The present results showed that bacterial diversity was rich and exhibited a certain variation during the dynamic fermentation process of apple vinegar. Furthermore, Lactococcus and Oenococcus were the predominant bacteria in the pre-fermentation (alcoholic fermentation) of apple vinegar, while the dominant bacteria in the middle and late fermentation stages (acetic acid fermentation) were Lactococcus and Acetobacter. In addition, during the whole fermentation process of apple vinegar, Lactococcus was the most dominant bacteria, Oenococcus was the unique species in the stage of alcohol fermentation, and Acetobacter increased rapidly in the stage of acetic acid fermentation. In conclusion, our finding provided a theoretical basis for the processing technology of apple vinegar fermentation, and a theory evidence for the safety and health assessment of apple vinegar.
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Affiliation(s)
- Juan Song
- Agricultural Product Storage and Processing Research InstituteGansu Academy of Agricultural SciencesLanzhouChina
| | - Ji‐Hong Zhang
- Agricultural Product Storage and Processing Research InstituteGansu Academy of Agricultural SciencesLanzhouChina
| | - San‐Jiang Kang
- Agricultural Product Storage and Processing Research InstituteGansu Academy of Agricultural SciencesLanzhouChina
| | - Hai‐Yan Zhang
- Agricultural Product Storage and Processing Research InstituteGansu Academy of Agricultural SciencesLanzhouChina
| | - Jing Yuan
- Agricultural Product Storage and Processing Research InstituteGansu Academy of Agricultural SciencesLanzhouChina
| | - Chao‐Zhen Zeng
- Agricultural Product Storage and Processing Research InstituteGansu Academy of Agricultural SciencesLanzhouChina
| | - Fang Zhang
- Agricultural Product Storage and Processing Research InstituteGansu Academy of Agricultural SciencesLanzhouChina
| | - Yu‐Long Huang
- Agricultural Product Storage and Processing Research InstituteGansu Academy of Agricultural SciencesLanzhouChina
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Santos-Garcia D, Juravel K, Freilich S, Zchori-Fein E, Latorre A, Moya A, Morin S, Silva FJ. To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies. Front Microbiol 2018; 9:2254. [PMID: 30319574 PMCID: PMC6167482 DOI: 10.3389/fmicb.2018.02254] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/04/2018] [Indexed: 02/05/2023] Open
Abstract
Insect lineages feeding on nutritionally restricted diets such as phloem sap, xylem sap, or blood, were able to diversify by acquiring bacterial species that complement lacking nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all of their host's nutritional requirements, driving the acquisition of additional symbiotic species. Phloem-feeding members of the insect family Aleyrodidae (whiteflies) established an obligate relationship with Candidatus Portiera aleyrodidarum, which provides its hots with essential amino acids and carotenoids. In addition, many whitefly species harbor additional endosymbionts which may potentially further supplement their host's diet. To test this hypothesis, genomes of several endosymbionts of the whiteflies Aleurodicus dispersus, Aleurodicus floccissimus and Trialeurodes vaporariorum were analyzed. In addition to Portiera, all three species were found to harbor one Arsenophonus and one Wolbachia endosymbiont. A comparative analysis of Arsenophonus genomes revealed that although all three are capable of synthesizing B vitamins and cofactors, such as pyridoxal, riboflavin, or folate, their genomes and phylogenetic relationship vary greatly. Arsenophonus of A. floccissimus and T. vaporariorum belong to the same clade, and display characteristics of facultative endosymbionts, such as large genomes (3 Mb) with thousands of genes and pseudogenes, intermediate GC content, and mobile genetic elements. In contrast, Arsenophonus of A. dispersus belongs to a different lineage and displays the characteristics of a primary endosymbiont-a reduced genome (670 kb) with ~400 genes, 32% GC content, and no mobile genetic elements. However, the presence of 274 pseudogenes suggests that this symbiotic association is more recent than other reported primary endosymbionts of hemipterans. The gene repertoire of Arsenophonus of A. dispersus is completely integrated in the symbiotic consortia, and the biosynthesis of most vitamins occurs in shared pathways with its host. In addition, Wolbachia endosymbionts have also retained the ability to produce riboflavin, flavin adenine dinucleotide, and folate, and may make a nutritional contribution. Taken together, our results show that Arsenophonus hold a pivotal place in whitefly nutrition by their ability to produce B vitamins.
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Affiliation(s)
- Diego Santos-Garcia
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Diego Santos-Garcia
| | - Ksenia Juravel
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shiri Freilich
- Institute of Plant Sciences, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat-Yishai, Israel
| | - Einat Zchori-Fein
- Department of Entomology, Newe-Ya'ar Research Center, Agricultural Research Organization, Volcani Center, Ramat-Yishai, Israel
| | - Amparo Latorre
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
| | - Shai Morin
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Francisco J. Silva
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
- Francisco J. Silva
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Franzini PZN, Ramond JB, Scholtz CH, Sole CL, Ronca S, Cowan DA. The Gut Microbiomes of Two Pachysoma MacLeay Desert Dung Beetle Species (Coleoptera: Scarabaeidae: Scarabaeinae) Feeding on Different Diets. PLoS One 2016; 11:e0161118. [PMID: 27532606 PMCID: PMC4988786 DOI: 10.1371/journal.pone.0161118] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/29/2016] [Indexed: 12/13/2022] Open
Abstract
Micro-organisms inhabiting animal guts benefit from a protected and nutrient-rich environment while assisting the host with digestion and nutrition. In this study we compare, for the first time, the bacterial and fungal gut communities of two species of the small desert dung beetle genus Pachysoma feeding on different diets: the detritivorous P. endroedyi and the dry-dung-feeding P. striatum. Whole-gut microbial communities from 5 individuals of each species were assessed using 454 pyrosequencing of the bacterial 16S rRNA gene and fungal ITS gene regions. The two bacterial communities were significantly different, with only 3.7% of operational taxonomic units shared, and displayed intra-specific variation. The number of bacterial phyla present within the guts of P. endroedyi and P. striatum individuals ranged from 6-11 and 4-7, respectively. Fungal phylotypes could only be detected within the gut of P. striatum. Although the role of host phylogeny in Pachysoma microbiome assembly remains unknown, evidence presented in this study suggests that host diet may be a deterministic factor.
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Affiliation(s)
- Philippa Z. N. Franzini
- Centre for Microbial Ecology and Genomics, Genomic Research Institute, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Genomic Research Institute, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Clarke H. Scholtz
- Scarab Research Group, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Catherine L. Sole
- Scarab Research Group, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Sandra Ronca
- Centre for Microbial Ecology and Genomics, Genomic Research Institute, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Genomic Research Institute, Department of Genetics, University of Pretoria, Pretoria, South Africa
- * E-mail:
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Raina HS, Singh A, Popli S, Pandey N, Rajagopal R. Infection of Bacterial Endosymbionts in Insects: A Comparative Study of Two Techniques viz PCR and FISH for Detection and Localization of Symbionts in Whitefly, Bemisia tabaci. PLoS One 2015; 10:e0136159. [PMID: 26287997 PMCID: PMC4546005 DOI: 10.1371/journal.pone.0136159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial endosymbionts have been associated with arthropods and large number of the insect species show interaction with such bacteria. Different approaches have been used to understand such symbiont- host interactions. The whitefly, Bemisia tabaci, a highly invasive agricultural pest, harbors as many as seven different bacterial endosymbionts. These bacterial endosymbionts are known to provide various nutritional, physiological, environmental and evolutionary benefits to its insect host. In this study, we have tried to compare two techniques, Polymerase chain reaction (PCR) and Flourescence in situ Hybridisation (FISH) commonly used for identification and localization of bacterial endosymbionts in B. tabaci as it harbors one of the highest numbers of endosymbionts which have helped it in becoming a successful global invasive agricultural pest. The amplified PCR products were observed as bands on agarose gel by electrophoresis while the FISH samples were mounted on slides and observed under confocal microscope. Analysis of results obtained by these two techniques revealed the advantages of FISH over PCR. On a short note, performing FISH, using LNA probes proved to be more sensitive and informative for identification as well as localization of bacterial endosymbionts in B. tabaci than relying on PCR. This study would help in designing more efficient experiments based on much reliable detection procedure and studying the role of endosymbionts in insects.
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Affiliation(s)
- Harpreet Singh Raina
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Ambika Singh
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Sonam Popli
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Neeti Pandey
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Raman Rajagopal
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
- * E-mail:
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