scholarly journals Diversity of fall armyworm, Spodoptera frugiperda and their gut bacterial community in Kenya

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8701 ◽  
Author(s):  
Joseph Gichuhi ◽  
Subramanian Sevgan ◽  
Fathiya Khamis ◽  
Johnnie Van den Berg ◽  
Hannalene du Plessis ◽  
...  
Keyword(s):  
Spodoptera Frugiperda ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Fall Armyworm ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Metarhizium Rileyi ◽  
Rice Strain ◽  
Fungal Entomopathogen ◽  
Bacterial Groups

Background The invasive fall armyworm, Spodoptera frugiperda (J.E. Smith) is a polyphagous pest that causes widespread damage particularly to maize and sorghum in Africa. The microbiome associated with S. frugiperda could play a role in the insects’ success and adaptability. However, bacterial communities in S. frugiperda remain poorly studied. Methods We investigated the composition, abundance and diversity of microbiomes associated with larval and adult specimens of S. frugiperda collected from four maize growing regions in Kenya through high throughput sequencing of the bacterial 16S rRNA gene. The population structure of S. frugiperda in Kenya was assessed through amplification of the mitochondrial cytochrome oxidase subunit I gene. Results We identified Proteobacteria and Firmicutes as the most dominant bacterial phyla and lesser proportions of Bacteroidetes and Actinobacteria. We also observed differences in bacterial microbiome diversity between larvae and adults that are a likely indication that some prominent larval bacterial groups are lost during metamorphosis. However, several bacterial groups were found in both adults and larvae suggesting that they are transmitted across developmental stages. Reads corresponding to several known entomopathogenic bacterial clades as well as the fungal entomopathogen, Metarhizium rileyi, were observed. Mitochondrial DNA haplotyping of the S. frugiperda population in Kenya indicated the presence of both “Rice” and “Corn” strains, with a higher prevalence of the “Rice” strain.

scholarly journals Diversity of fall armyworm, Spodoptera frugiperda and their gut bacterial community in Kenya

2019 ◽  
Author(s):  
Joseph Gichuhi ◽  
Sevgan Subramanian ◽  
Fathiya M. Khamis ◽  
Johnnie Van den Berg ◽  
Hannalene du Plessis ◽  
...  
Keyword(s):  
Spodoptera Frugiperda ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Fall Armyworm ◽  
Rrna Gene ◽  
Metarhizium Rileyi ◽  
Rice Strain ◽  
Bacterial Microbiome ◽  
Abundance And Diversity ◽  
Bacterial Groups

AbstractThe invasive fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a polyphagous pest that causes widespread damage particularly to maize and sorghum in Africa. The microbiome associated with S. frugiperda could play a role in their success and adaptability. However, these bacterial communities remain poorly studied, especially for S. frugiperda in Africa. We investigated the composition, abundance and diversity of microbiomes associated with larval and adult specimens of S. frugiperda collected from four maize growing regions in Kenya through high throughput sequencing of bacterial 16S rRNA gene. We identified Proteobacteria and Firmicutes as the most dominant phyla and lesser proportions of Bacteroidetes and Actinobacteria. We also observed differences in bacterial microbiome diversity between larvae and adults that are a likely indication that some prominent larval bacterial groups are lost during metamorphosis. Several bacterial groups were found in both adults and larvae suggesting that they are transmitted across developmental stages. Reads corresponding to several known entomopathogenic bacterial clades as well as the non-bacterial entomopathogen, Metarhizium rileyi (Farl.) Kepler, Rehner & Humber (2014), were observed. Mitochondrial DNA haplotyping of the S. frugiperda population in Kenya indicated the presence of both ‘Rice’ and ‘Corn’ strains, with a higher prevalence of the ‘Rice’ strain. Insights into the microbiota may ultimately provide alternative avenues for controlling of this pest.

scholarly journals Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

2021 ◽  
Vol 17 ◽  
pp. 117693432199635
Author(s):  
Daoxin Liu ◽  
Pengfei Song ◽  
Jingyan Yan ◽  
Haijing Wang ◽  
Zhenyuan Cai ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Bacterial Phyla ◽  
In Captivity ◽  
Relative Abundances ◽  
Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

scholarly journals Occurrence and molecular identification of an invasive rice strain of fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) from Sindh, Pakistan, using mitochondrial cytochrome c oxidase I gene sequences

2021 ◽  
Author(s):  
Sumaira Yousaf ◽  
Abdul Rehman ◽  
Mariyam Masood ◽  
Kazam Ali ◽  
Nazia Suleman
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Spodoptera Frugiperda ◽  
Fall Armyworm ◽  
Coi Gene ◽  
Invasive Pest ◽  
Mitochondrial Cytochrome ◽  
Cytochrome C Oxidase I ◽  
Gene Sequences ◽  
Rice Strain

AbstractThe fall armyworm (FAW), an invasive pest of maize, is an emerging threat in Southern Asia after America and Europe. Recently, this notorious pest has also been found in different areas of Pakistan. To assess its presence in Pakistan, a survey was carried out in the provinces of Punjab, Sindh, and Khyber Pakhtunkhwa during May–October 2019. We observed the highest incidence of FAW in Sindh with maximum impact in districts Tando-Allahyar and Hyderabad. These samples were identified as Spodoptera frugiperda on the morphological and taxonomical bases. However, morphological identification of this pest is very difficult at early larval instars. Here, we use the mitochondrial cytochrome c oxidase I (COI) gene region for the precise identification of larva of this invasive pest at species level. Two different regions of COI gene (COI-5′ and COI-3′) were used as molecular markers for the identification of this species. DNA sequence similarity searches of the obtained COI gene sequences (NCBI GenBank Accession Nos. MW241537, MW241538, MW349515, MW349516, MW349493 and MW349494) revealed that genetically it is more than 99% identical to S. frugiperda. The phylogenetic analysis indicated it as the rice-strain (R-strain). Both 3′- and 5′-fragment tree topologies showed that the collected samples of the FAW species belong to the R-strain. To the best of our knowledge, this is the first report providing molecular evidence for the existence of R-strain of S. frugiperda that was found feeding on maize crop in Sindh, Pakistan, using COI gene sequences as a marker.

scholarly journals Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rafael J. Vivero ◽  
Marcela Villegas-Plazas ◽  
Gloria E. Cadavid-Restrepo ◽  
Claudia Ximena Moreno Herrera ◽  
Sandra I. Uribe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Sand Fly ◽  
Human Populations ◽  
Rrna Gene ◽  
Remarkable Feature ◽  
Core Microbiome ◽  
Bacterial Phyla ◽  
Wide Range

AbstractPhlebotomine sand flies are remarkable vectors of several etiologic agents (virus, bacterial, trypanosomatid Leishmania), posing a heavy health burden for human populations mainly located at developing countries. Their intestinal microbiota is involved in a wide range of biological and physiological processes, and could exclude or facilitate such transmission of pathogens. In this study, we investigated the Eubacterial microbiome from digestive tracts of Lu. evansi adults structure using 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq) obtained from digestive tracts of Lu. evansi adults. The samples were collected at two locations with high incidence of the disease in humans: peri-urban and forest ecosystems from the department of Sucre, Colombia. 289,068 quality-filtered reads of V4 region of 16S rRNA gene were obtained and clustered into 1,762 operational taxonomic units (OTUs) with 97% similarity. Regarding eubacterial diversity, 14 bacterial phyla and 2 new candidate phyla were found to be consistently associated with the gut microbiome content. Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla in all the samples and the core microbiome was particularly dominated by Methylobacterium genus. Methylobacterium species, are known to have mutualistic relationships with some plants and are involved in shaping the microbial community in the phyllosphere. As a remarkable feature, OTUs classified as Wolbachia spp. were found abundant on peri-urban ecosystem samples, in adult male (OTUs n = 776) and unfed female (OTUs n = 324). Furthermore, our results provide evidence of OTUs classified as Cardinium endosymbiont in relative abundance, notably higher with respect to Wolbachia. The variation in insect gut microbiota may be determined by the environment as also for the type of feeding. Our findings increase the richness of the microbiota associated with Lu. evansi. In this study, OTUs of Methylobacterium found in Lu. evansi was higher in engorged females, suggesting that there are interactions between microbes from plant sources, blood nutrients and the parasites they transmit during the blood intake.

scholarly journals Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

2015 ◽  
Vol 12 (13) ◽  
pp. 10233-10269 ◽  
Author(s):  
J. Comte ◽  
C. Lovejoy ◽  
S. Crevecoeur ◽  
W. F. Vincent
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Keystone Species ◽  
Small World ◽  
Rrna Gene ◽  
Permafrost Degradation ◽  
Bacterial Phyla ◽  
Organic Carbon Concentration ◽  
Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

scholarly journals Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

2016 ◽  
Vol 13 (1) ◽  
pp. 175-190 ◽  
Author(s):  
J. Comte ◽  
C. Lovejoy ◽  
S. Crevecoeur ◽  
W. F. Vincent
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Permafrost Degradation ◽  
Food Web Structure ◽  
Bacterial Phyla ◽  
Organic Carbon Concentration ◽  
Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north–south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This “small world network” property would render the communities more robust to environmental change but vulnerable to the loss of microbial “keystone species”. These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

scholarly journals Genomic Diversity in a Population of Spodoptera frugiperda Nucleopolyhedrovirus

2020 ◽  
Author(s):  
Tomás Masson ◽  
María Laura Fabre ◽  
Matias Luis Pidre ◽  
José María Niz ◽  
Marcelo Facundo Berretta ◽  
...  
Keyword(s):  
Spodoptera Frugiperda ◽  
High Throughput Sequencing ◽  
Biological Control Agent ◽  
Fall Armyworm ◽  
Control Agent ◽  
Genomic Diversity ◽  
List Type ◽  
Structural Variants ◽  
Single Nucleotide Variants ◽  
Coding Regions

AbstractSpodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) represents a strong candidate to develop environmental-friendly pesticides against the fall armyworm (Spodoptera frugiperda), a widespread pest that poses a severe threat to different crops around the world. However, little is known regarding the genomic diversity present inside SfMNPV isolates and how it shapes the interactions between virus and host. Here, the genomic diversity present inside an isolate of SfMNPV was explored using high-throughput sequencing for the first time. We identified 704 intrahost single nucleotide variants, from which 184 are nonsynonymous mutations distributed among 82 different coding sequences. We detected several structural variants affecting SfMNPV genome, including two previously reported deletions inside the egt region. A comparative analysis between polymorphisms present in different SfMNPV isolates and our intraisolate diversity data suggests that coding regions with higher genetic diversity are associated with oral infectivity or unknown functions. In this context, through molecular evolution studies we provide evidence of diversifying selection acting on sf29, a putative collagenase which could contribute to the oral infectivity of SfMNPV. Overall, our results contribute to deepen our understanding of the coevolution between SfMNPV and the fall armyworm and will be useful to improve the applicability of this virus as a biological control agent.HighlightsWe characterized the genomic diversity within a population of SfMNPV.Coding regions with higher genetics diversity are associated with oral infectivity or unknown functions.Several structural variants contribute to the genomic diversity of SfMNPV.Sf29, a putative collagenase, shows signs of adaptive evolution.

scholarly journals Fall armyworm Spodoptera frugiperda : An invasive pest of Maize Omprakash Navik* and Jagadeesh Patil

2019 ◽  
Vol 34 (01) ◽  
Author(s):  
Omprakash Navik ◽  
Jagadeesh Patil
Keyword(s):  
Spodoptera Frugiperda ◽  
Tamil Nadu ◽  
Entomopathogenic Nematode ◽  
Fall Armyworm ◽  
Invasive Pest ◽  
Management Approach ◽  
Maize Crop ◽  
Larval Stages ◽  
Metarhizium Rileyi ◽  
Favorable Conditions

Fall armyworm, Spodoptera frugiperda (J.E. Smith) is an invasive pest of maize and first time reported in July 2018 from Karnataka, India. Presently, this pest has made havoc on maize crop in Karnataka, Tamil Nadu, Maharashtra, Telangana, Andhra Pradesh, Odisha, West Bengal and Chhattisgarh. This pest is an American origin and polyphagous in nature feeds on more than 80 plant species. It prefers to feed on maize crop, however in the absence of maize it feeds on sugarcane, sorghum, rice, cabbage, soybean, onion, tomato, potato and cotton. Life cycle of this pest completes within 32 to 46 days on maize under the favorable conditions. First two instars of S. frugiperda feed on the leaves and later instars moves inside the leaf whorl and starts feeding by leaving frass around the damaged area. For the management of this pest, an adaptation of integrated pest management approach is needed. Integrating, bioagents like egg parasistoids, Trichogramma pretiosum and Telenomus sp. and for larval stages by entompathogenic fungi Metarhizium anisopliae, Nomuraea rileyi (=Metarhizium rileyi, bacteria, (Bt) and entomopathogenic nematode, Heterorhabditis indica are useful options. However, need based application of insecticides like emamectin benzoate can be used for successful management of this pest.

Gene Expression Differences Between Developmental Stages of the Fall Armyworm (Spodoptera frugiperda)

2021 ◽  
Vol 40 (4) ◽  
pp. 580-588
Author(s):  
Lei Wang ◽  
Qiao Yang ◽  
Ruixiang Tang ◽  
Xu Liu ◽  
Zhenxin Fan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spodoptera Frugiperda ◽  
Developmental Stages ◽  
Fall Armyworm
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