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Gook DH, Jung M, Kim S, Lee DH. Species diversity of environmentally-transmitted bacteria colonizing Riptortus pedestris (Hemiptera: Alydidae) and symbiotic effects of the most dominant bacteria. Sci Rep 2023; 13:15166. [PMID: 37704685 PMCID: PMC10499786 DOI: 10.1038/s41598-023-42419-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023] Open
Abstract
Riptortus pedestris (Hemiptera: Alydidae) establish endosymbiosis with specific bacteria from extremely diverse microbiota in soil. To better understand ecology and evolution of the symbiosis, it is important to characterize bacterial species diversity colonizing R. pedestris and evaluate their symbiotic effects. Nonetheless, previous research was limited to a few bacteria strains such as Caballeronia insecticola. In this study, second-instar nymphs were provided with field soils and reared to adult. Then, bacteria colonizing the midgut M4 region of R. pedestris were analyzed for bacterial species identification based on the 16S rRNA gene. First, a total of 15 bacterial species were detected belonging to Burkholderiaceae. Most of R. pedestris were found to harbor single bacterial species, whereas several insects harbored at most two bacterial species simultaneously. Among the total insects harboring single bacterial species, 91.2% harbored genus Caballeronia. The most dominant species was C. jiangsuensis, not previously documented for symbiotic associations with R. pedestris. Second, in laboratory conditions, C. jiangsuensis significantly enhanced the development, body size, and reproductive potentials of R. pedestris, compared to individuals with no symbiotic bacteria. These results add novel information to better understand symbiotic bacteria community establishing in R. pedestris and symbiotic effects on the host insects.
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Affiliation(s)
- Do-Hun Gook
- Department of Life Sciences, Gachon University, Seongnam-daero 1342, Seongnam-si, Gyeonggi-do, South Korea
| | - Minhyung Jung
- Department of Life Sciences, Gachon University, Seongnam-daero 1342, Seongnam-si, Gyeonggi-do, South Korea
| | - Soowan Kim
- Department of Life Sciences, Gachon University, Seongnam-daero 1342, Seongnam-si, Gyeonggi-do, South Korea
| | - Doo-Hyung Lee
- Department of Life Sciences, Gachon University, Seongnam-daero 1342, Seongnam-si, Gyeonggi-do, South Korea.
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González Plaza JJ, Hradecký J. The tropical cookbook: Termite diet and phylogenetics—Over geographical origin—Drive the microbiome and functional genetic structure of nests. Front Microbiol 2023; 14:1089525. [PMID: 36998409 PMCID: PMC10043212 DOI: 10.3389/fmicb.2023.1089525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/13/2023] [Indexed: 03/15/2023] Open
Abstract
Termites are key decomposers of dead plant material involved in the organic matter recycling process in warm terrestrial ecosystems. Due to their prominent role as urban pests of timber, research efforts have been directed toward biocontrol strategies aimed to use pathogens in their nest. However, one of the most fascinating aspects of termites is their defense strategies that prevent the growth of detrimental microbiological strains in their nests. One of the controlling factors is the nest allied microbiome. Understanding how allied microbial strains protect termites from pathogen load could provide us with an enhanced repertoire for fighting antimicrobial-resistant strains or mining for genes for bioremediation purposes. However, a necessary first step is to characterize these microbial communities. To gain a deeper understanding of the termite nest microbiome, we used a multi-omics approach for dissecting the nest microbiome in a wide range of termite species. These cover several feeding habits and three geographical locations on two tropical sides of the Atlantic Ocean known to host hyper-diverse communities. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, a taxonomical profile for bacteria and fungi through amplicon sequencing, and further diving into the genetic repertoire through a metagenomic sequencing approach. Naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We investigated the apparent differences in terms of bacterial community structure and discovered that feeding habits and phylogenetic relatedness had a greater influence than geographical location. The phylogenetic relatedness among nests' hosts influences primarily bacterial communities, while diet influences fungi. Finally, our metagenomic analysis revealed that the gene content provided both soil-feeding genera with similar functional profiles, while the wood-feeding genus showed a different one. Our results indicate that the nest functional profile is largely influenced by diet and phylogenetic relatedness, irrespective of geographical location.
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Bizuti DTG, Robin A, Soares TM, Moreno¹ VS, Almeida DRA, Andreote FD, Casagrande JC, Guillemot J, Herrmann L, Melis J, Perim JEL, Medeiros SDS, Sorrini TB, Brancalion PHS. Multifunctional soil recovery during the restoration of Brazil's Atlantic Forest after bauxite mining. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Denise T. G. Bizuti
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Agnès Robin
- CIRADUMR Eco&Sols Piracicaba Brazil
- Eco&SolsUniversité de MontpellierCIRADINRAIRD Montpellier SupAgro, Montpellier France
- Department of Soil Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Thaís M. Soares
- Center for Nuclear Energy in Agriculture University of São Paulo Piracicaba Brazil
| | | | - Danilo R. A. Almeida
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Fernando D. Andreote
- Department of Soil Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - José Carlos Casagrande
- Department of Natural Resources and Environmental Protection Federal University of São Carlos Araras Brazil
| | - Joannès Guillemot
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
- CIRADUMR Eco&Sols Piracicaba Brazil
- Eco&SolsUniversité de MontpellierCIRADINRAIRD Montpellier SupAgro, Montpellier France
| | - Laetitia Herrmann
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT‐Asia)Common Microbial Biotechnology Platform (CMBP) Hanoi Vietnam
| | - Juliano Melis
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Júlia E. L. Perim
- Department of Soil Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Simone D. S. Medeiros
- Department of Informatics and Statistics Federal University of Santa Catarina Florianópolis Brazil
| | - Taísi B. Sorrini
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Pedro H. S. Brancalion
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
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Manikkam R, Imchen M, Kaari M, Angamuthu V, Venugopal G, Thangavel S, Joseph J, Ramasamy B, Kumavath R. Metagenomic insights unveil the dominance of undescribed Actinobacteria in pond ecosystem of an Indian shrine. Meta Gene 2020. [DOI: 10.1016/j.mgene.2019.100639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Long-Term Effects of Periodical Fires on Archaeal Communities from Brazilian Cerrado Soils. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2019; 2019:6957210. [PMID: 30833827 PMCID: PMC6369511 DOI: 10.1155/2019/6957210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/11/2018] [Accepted: 11/18/2018] [Indexed: 12/29/2022]
Abstract
The Cerrado biome corresponds to an extensive area of Brazil and is considered a biodiversity hotspot. Frequent fires are a natural feature in this biome and have influences on vegetation structure and composition. However, continuous anthropogenic actions are promoting changes in fire frequency and seasonality. Despite the high biodiversity of the Cerrado, little is known about its microbiome, with few publications describing some aspects of the bacterial and fungal communities found on this biome and almost no references about archaea. In this study, we describe the archaeal diversity in Cerrado sensu stricto soils, comparing the archaeal communities from soils of an area long protected from fires to one exposed to biennial fires, using both 16S rRNA and amoA genes as molecular markers. Almost all 16S rRNA sequences from both studied areas were affiliated with I.1b and 1.1c Thaumarchaeota, groups commonly detected in terrestrial environments. A higher relative abundance of I.1b thaumarchaeal subgroup was detected in the frequently burned area even though no statistically significant differences were observed in archaeal 16S rRNA richness and diversity between the investigated areas. Many ammonia-oxidizing archaea (AOA) are affiliated with this group, which is consistent with the higher amoA diversity and OTU numbers detected in the area periodically burned. Taken together, our results suggest that, although total archaeal community richness and diversity do not seem to greatly differ between the investigated conditions, alterations in wood cover and vegetation structure caused by frequent fires likely cause long-term effects in AOA diversity in Cerrado soils.
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Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2018; 2018:9319345. [PMID: 30410420 PMCID: PMC6206559 DOI: 10.1155/2018/9319345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/22/2018] [Indexed: 11/18/2022]
Abstract
Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. The relative abundances of different species showed great changes in bacteria and archaea, and the number of dominant species in bacteria was much higher than that in archaea. Compared to archaea, the community compositions of bacteria were more abundant and the changes were more significant. Meanwhile, bacteria and archaea had large differences in compositions between water and soil. The microbial richness in water was significantly higher than that in soil. Simultaneously, soil had a significant enrichment effect on some microbial flora.
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Valorization of passion fruit peel by-product: Xylanase production and its potential as bleaching agent for kraft pulp. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.07.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Imchen M, Kumavath R, Barh D, Azevedo V, Ghosh P, Viana M, Wattam AR. Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems. Sci Rep 2017; 7:8859. [PMID: 28821820 PMCID: PMC5562921 DOI: 10.1038/s41598-017-09254-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 07/26/2017] [Indexed: 02/06/2023] Open
Abstract
In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples. The ocean samples were predominantly Archaea, with Euryarchaeota as the dominant phylum. Principal component and functional analyses grouped the samples isolated from forests, including those from disparate mangrove forests and the tropical rain forest, from the ocean. Our findings show similar patterns in samples were isolated from forests, and these were distinct from the ocean sediment isolates. The taxonomic structure was maintained to the level of class, and functional analysis of the genes present also displayed these similarities. Our report for the first time shows the richness of microbial diversity in the Kerala coast and its differences with tropical rain forest and ocean microbiome.
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Affiliation(s)
- Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Periye, Padanakkad P.O, Kasaragod, Kerala, 671314, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Periye, Padanakkad P.O, Kasaragod, Kerala, 671314, India.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, 721172, India.,Xcode Life Sciences, 3D Eldorado, 112 Nungambakkam High Road, Nungambakkam, Chennai, Tamil Nadu, 600034, India.,Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia, 23284, USA
| | - Marcus Viana
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Alice R Wattam
- Biocomplexity Institute, Virginia Tech University, Blacksburg, Virginia, 24061, USA.
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Archaea in Natural and Impacted Brazilian Environments. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:1259608. [PMID: 27829818 PMCID: PMC5086508 DOI: 10.1155/2016/1259608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/08/2016] [Indexed: 11/26/2022]
Abstract
In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.
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