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Higuita Palacio MF, Montoya OI, Saldamando CI, García-Bonilla E, Junca H, Cadavid-Restrepo GE, Moreno-Herrera CX. Dry and Rainy Seasons Significantly Alter the Gut Microbiome Composition and Reveal a Key Enterococcus sp. (Lactobacillales: Enterococcaceae) Core Component in Spodoptera frugiperda (Lepidoptera: Noctuidae) Corn Strain From Northwestern Colombia. JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:6420650. [PMID: 34734290 PMCID: PMC8567080 DOI: 10.1093/jisesa/ieab076] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Indexed: 06/13/2023]
Abstract
Spodoptera frugiperda is a polyphagous pest of several crops of economic importance. Nowadays, the insect is broadly distributed in America and, recently, in Africa, Asia, and Australia. The species has diverged into corn and rice strains. The role of the gut microbiota in insect physiology is relevant due to its participation in crucial functions. However, knowledge of seasonal variations that alter the gut microbiome in pests is limited. Gut microbiome composition between the dry and rainy seasons was analyzed with cultured and uncultured approaches in S. frugiperda corn strain larvae collected at Northwest Colombia, as seasonal microbiome changes might fluctuate due to environmental changes. On the basis of culture-dependent methods, results show well-defined microbiota with bacterial isolates belonging to Enterococcus, Klebsiella (Enterobacteriales: Enterobacteriaceae), Enterobacter (Enterobacterales: Enterobacteriaceae), and Bacillus (Bacillales: Bacillaceae) genera. The community composition displayed a low bacterial diversity across all samples. The core community detected with uncultured methods was composed of Enterococcus, Erysipelatoclostridium (Erysipelotrichales: Erysipelotrichaceae), Rasltonia (Burkholderiales: Burkholderiaceae), and Rhizobium (Hyphomicrobiales: Rhizobiaceae) genera, and Enterobacteriaceae family members. Significant differences in microbiome diversity were observed between the two seasons. The relative abundance of Erysipelatoclostridium was high in the dry season, while in the phylotype ZOR0006 (Erysipelotrichales: Erysipelotrichaceae) and Tyzzerella (Lachnospirales: Lachnospiraceae) genus, the relative abundance was high in the rainy season. The overall low gut bacterial diversity observed in the S. frugiperda corn strain suggests a strong presence of antagonist activity as a selection factor possibly arising from the host, the dominant bacterial types, or the material ingested. Targeting the stability and predominance of this core microbiome could be an additional alternative to pest control strategies, particularly in this moth.
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Affiliation(s)
- Marlon Felipe Higuita Palacio
- Grupo de Microbiodiversidad y Bioprospección, Facultad de Ciencias, Laboratorio de Biología Celular y Molecular, Universidad Nacional de Colombia Sede Medellín, Calle 59 A No. 63-20, 050003 Medellín, Colombia
| | - Olga I Montoya
- Grupo de Microbiodiversidad y Bioprospección, Facultad de Ciencias, Laboratorio de Biología Celular y Molecular, Universidad Nacional de Colombia Sede Medellín, Calle 59 A No. 63-20, 050003 Medellín, Colombia
| | - Clara I Saldamando
- Grupo de Biotecnología Vegetal UNALMED-CIB, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Calle 59A No. 63-20, Medellín, Colombia
| | - Erika García-Bonilla
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Division of Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, 250008 Chía, Colombia
| | - Howard Junca
- RG Microbial Ecology: Metabolism, Genomics & Evolution, Division of Ecogenomics & Holobionts, Microbiomas Foundation, LT11A, 250008 Chía, Colombia
| | - Gloria E Cadavid-Restrepo
- Grupo de Microbiodiversidad y Bioprospección, Facultad de Ciencias, Laboratorio de Biología Celular y Molecular, Universidad Nacional de Colombia Sede Medellín, Calle 59 A No. 63-20, 050003 Medellín, Colombia
| | - Claudia Ximena Moreno-Herrera
- Grupo de Microbiodiversidad y Bioprospección, Facultad de Ciencias, Laboratorio de Biología Celular y Molecular, Universidad Nacional de Colombia Sede Medellín, Calle 59 A No. 63-20, 050003 Medellín, Colombia
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Rozadilla G, Clemente JM, McCarthy CB. HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets. Bio Protoc 2020; 10:e3679. [PMID: 33659350 PMCID: PMC7842381 DOI: 10.21769/bioprotoc.3679] [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: 10/11/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 11/02/2022] Open
Abstract
Data generated by metagenomic and metatranscriptomic experiments is both enormous and inherently noisy. When using taxonomy-dependent alignment-based methods to classify and label reads, the first step consists in performing homology searches against sequence databases. To obtain the most information from the samples, nucleotide sequences are usually compared to various databases (nucleotide and protein) using local sequence aligners such as BLASTN and BLASTX. Nevertheless, the analysis and integration of these results can be problematic because the outputs from these searches usually show inconsistencies, which can be notorious when working with RNA-seq. Moreover, and to the best of our knowledge, existing tools do not criss-cross and integrate information from the different homology searches, but provide the results of each analysis separately. We developed the HoSeIn workflow to intersect the information from these homology searches, and then determine the taxonomic and functional profile of the sample using this integrated information. The workflow is based on the assumption that the sequences that correspond to a certain taxon are composed of: sequences that were assigned to the same taxon by both homology searches; sequences that were assigned to that taxon by one of the homology searches but returned no hits in the other one.
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Affiliation(s)
- Gaston Rozadilla
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Jorgelina Moreiras Clemente
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Christina B. McCarthy
- Centro Regional de Estudios Genómicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- Departamento de Informática y Tecnología, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Buenos Aires, Argentina
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Han X, Lu C, Geib SM, Zheng J, Wu S, Zhang F, Liang G. Characterization of Dendrolimus houi Lajonquiere (Lepidoptera: Lasiocampidae) Transcriptome across All Life Stages. INSECTS 2019; 10:insects10120442. [PMID: 31835398 PMCID: PMC6956129 DOI: 10.3390/insects10120442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/28/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022]
Abstract
Dendrolimus houi Lajonquiere is a phytophagous caterpillar infesting many economically important coniferous tree species in China, causing serious economic and ecological environment losses. Based on previous research, it has one generation per year in South China and East China in contrast to two generations per year in Yunnan province in southwestern China. The species is potentially resilient to climatic extremes in these regions with the eggs and 1st instar larvae surviving in the winter (5 °C), older instar larvae and pupae surviving high temperatures in the summer (35 °C), suggesting some temperature stress tolerance during different developmental stages. However, little is known in this species at the genetic and genomic level. In this study, we used high throughput sequencing to obtain transcriptome data from different developmental stages (eggs, 1st-3rd instar larvae, 4th-5th instar larvae, 6th-7th instar larvae, pupae, male and female adults), which were collected from Fujian province. In total, we obtained approximately 90 Gb of data, from which 33,720 unigenes were assembled and 17,797 unigenes were annotated. We furtherly analyzed the differentially expressed genes (DGEs) across all stages, the largest number between the eggs and 1st instar larvae stage and gene expression varied significantly in different developmental stages. Furthermore, 4138 SSR genes and 114,977 SNP loci were screened from transcriptome data. This paper will be a foundation for further study towards improved integrated pest management strategies for this species.
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Affiliation(s)
- Xiaohong Han
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
| | - Ciding Lu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
| | - Scott M. Geib
- Daniel K. Inouye US Pacific Basin Agricultural Research Center, USDA-ARS, 64 Nowelo, St.; Hilo, HI 96720, USA;
| | - Junxian Zheng
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
| | - Songqing Wu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
- Provincial Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Feiping Zhang
- Provincial Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Guanghong Liang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
- Provincial Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Correspondence: ; Tel.: +86-0591-8385-1475
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