scholarly journals Comparison of the bacterial abundance and diversity in the Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae) between both sexes

2019 ◽  
Author(s):  
Chunhui Guo ◽  
Xin Peng ◽  
Xialin Zheng ◽  
Xiaoyun Wang ◽  
Ruirui Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Illumina Miseq ◽  
Invasive Pest ◽  
Operational Taxonomic Units ◽  
Adult Females ◽  
Comprehensive Comparison ◽  
Leptocybe Invasa ◽  
Sex Regulation ◽  
Abundance And Diversity ◽  
Dominant Bacteria

Background. Insects harbor a myriad of microorganisms, many of which can affect the sex ratio and manipulate the reproduction of the host. Leptocybe invasa is an invasive pest that causes serious damage to eucalyptus plantations, and both female-biased sex ratios and thelytokous parthenogenesis in L. invasa contribute to the rapid invasion and fast growth of the population. However, the interior bacterial composition and abundance of L. invasa and the differences between both sexes remain unclear. Results. The Illumina MiSeq platform was used to compare the composition of the bacterial community in adult females and males by sequencing with variation in the V3-V4 region of the 16S ribosomal DNA gene. The results showed that 1320 operational taxonomic units (OTUs) were obtained in total. These OTUs were annotated into 24 phyla, 71 classes, 130 orders, 245 families and 501 genera. At the genus level, the dominant bacteria in females and males was Rickettsia and Rhizobium, respectively. Conclusion. The bacteria living in L. invasa adult females and males had high diversity. There were differences in the bacterial community in L. invasa between both sexes, and the bacterial diversity in male adults was more abundant than that in female adults. This study presents a comprehensive comparison of bacterial communities living in L. invasa between sexes, which plays a significant role in reproductive strategy, sex regulation and the invasive mechanism of L. invasa and provides a basis for follow-up studies on the coevolution and interaction between L. invasa and its predominant bacteria.

scholarly journals Comparison of the bacterial abundance and diversity in the Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae) between both sexes

2019 ◽  
Author(s):  
Chunhui Guo ◽  
Xin Peng ◽  
Xialin Zheng ◽  
Xiaoyun Wang ◽  
Ruirui Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Illumina Miseq ◽  
Invasive Pest ◽  
Operational Taxonomic Units ◽  
Adult Females ◽  
Comprehensive Comparison ◽  
Leptocybe Invasa ◽  
Sex Regulation ◽  
Abundance And Diversity ◽  
Dominant Bacteria

Background. Insects harbor a myriad of microorganisms, many of which can affect the sex ratio and manipulate the reproduction of the host. Leptocybe invasa is an invasive pest that causes serious damage to eucalyptus plantations, and both female-biased sex ratios and thelytokous parthenogenesis in L. invasa contribute to the rapid invasion and fast growth of the population. However, the interior bacterial composition and abundance of L. invasa and the differences between both sexes remain unclear. Results. The Illumina MiSeq platform was used to compare the composition of the bacterial community in adult females and males by sequencing with variation in the V3-V4 region of the 16S ribosomal DNA gene. The results showed that 1320 operational taxonomic units (OTUs) were obtained in total. These OTUs were annotated into 24 phyla, 71 classes, 130 orders, 245 families and 501 genera. At the genus level, the dominant bacteria in females and males was Rickettsia and Rhizobium, respectively. Conclusion. The bacteria living in L. invasa adult females and males had high diversity. There were differences in the bacterial community in L. invasa between both sexes, and the bacterial diversity in male adults was more abundant than that in female adults. This study presents a comprehensive comparison of bacterial communities living in L. invasa between sexes, which plays a significant role in reproductive strategy, sex regulation and the invasive mechanism of L. invasa and provides a basis for follow-up studies on the coevolution and interaction between L. invasa and its predominant bacteria.

scholarly journals Comparison of bacterial diversity and abundance between sexes of Leptocybe invasa Fisher & La Salle (Hymenoptera: Eulophidae) from China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8411
Author(s):  
Chunhui Guo ◽  
Xin Peng ◽  
Xialin Zheng ◽  
Xiaoyun Wang ◽  
Ruirui Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Small Body ◽  
Bacterial Community Composition ◽  
Illumina Miseq ◽  
Invasive Pest ◽  
Comprehensive Comparison ◽  
Leptocybe Invasa ◽  
Dominant Bacteria

Background Insects harbor a myriad of microorganisms, many of which can affect the sex ratio and manipulate the reproduction of the host. Leptocybe invasa is an invasive pest that causes serious damage to eucalyptus plantations, and the thelytokous parthenogenesis, low temperature resistance, protection in galls, generation overlap and small body of L. invasa contribute to its rapid invasion and population growth. However, the endosymbiotic bacterial composition, abundance and sex differences of L. invasa remain unclear. Therefore, this research aimed to identify the bacterial communities in L. invasa adults and compare them between the sexes of L. invasa lineage B. Results The Illumina MiSeq platform was used to compare bacterial community composition between females and males of L. invasa by sequencing the V3–V4 region of the 16S ribosomal RNA gene. A total of 1,320 operational taxonomic units (OTUs) were obtained. These OTUs were subdivided into 24 phyla, 71 classes, 130 orders, 245 families and 501 genera. At the genus level, the dominant bacteria in females and males were Rickettsia and Rhizobium, respectively. Conclusion The endosymbiotic bacteria of L. invasa females and males were highly diverse. There were differences in the bacterial community of L. invasa between sexes, and the bacterial diversity in male specimens was greater than that in female specimens. This study presents a comprehensive comparison of bacterial communities in L. invasa and these data will provide an overall view of the bacterial community in both sexes of L. invasa with special attention on sex-related bacteria.

scholarly journals 16S rRNA–Based Analysis Reveals Differences in the Bacterial Community Present in Tissues of Choromytilus chorus (Mytilidae, Bivalvia) Grown in an Estuary and a Bay in Southern Chile

Diversity ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 209
Author(s):  
Tamara Valenzuela ◽  
Joaquin I. Riling ◽  
Giovanni Larama ◽  
Jacquelinne J. Acuña ◽  
Marco Campos ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Venn Diagram ◽  
Linear Discriminant ◽  
Operational Taxonomic Units ◽  
Marine Bivalves ◽  
Diagram Analysis

Microbiota associated with bivalves have drawn considerable attention because studies have suggested their relevance to the fitness and growth of marine bivalves. Although the mussel Choromytilus chorus is a valuable resource for Chilean aquaculture and fisheries, its microbiota is still unknown. In this study, the composition and predicted functions of the bacterial community in tissues of C. chorus specimens grown in an estuary (Nehuentue) and a bay (Hueihue) were investigated. Using 16S rRNA genes as targets, the bacterial abundance in tissues was estimated by quantitative PCR and sequenced via Illumina MiSeq. The abundances of bacteria ranged from 103 to 105 copies of 16S rRNA genes g−1 tissue. In the Nehuentue estuary, the bacterial communities in the tissues were dominated by the Tenericutes phylum, whereas the Tenericutes and Proteobacteria phyla dominated in mussels from Hueihue Bay. Higher numbers of operational taxonomic units (OTUs) were observed in tissues from the Nehuentue Estuary than in those from Hueihue Bay. Differences in bacterial community compositions in tissues between both locations were confirmed by nonmetric multidimensional scaling (nMDS) and Venn diagram analysis. In addition, linear discriminant analysis effect size (LEfSe) revealed that the Mollicutes class and Actynomycetales order were key phylotypes in tissues from the Nehuentue Estuary and Hueihue Bay, respectively. Our analysis also predicted a high abundance of sequences assigned to heterotrophy; however, relatively high functional diversity was also found in tissues from Hueihue Bay. This work represents our first attempt to elucidate the C. chorus microbiota in contrasting Chilean aquatic environments.

scholarly journals Rhizosphere Bacterial Community Characteristics over Different Years of Sugarcane Ratooning in Consecutive Monoculture

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Xiaoning Gao ◽  
Zilin Wu ◽  
Rui Liu ◽  
Jiayun Wu ◽  
Qiaoying Zeng ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Illumina Miseq ◽  
Miseq Sequencing ◽  
Community Characteristics ◽  
Dynamic Changes ◽  
Operational Taxonomic Units ◽  
Total Bacterial Community ◽  
Rhizosphere Bacterial Community ◽  
Rhizosphere Bacterial Communities

To understand dynamic changes in rhizosphere microbial community in consecutive monoculture, Illumina MiSeq sequencing was performed to evaluate the V3-V4 region of 16S rRNA in the rhizosphere of newly planted and three-year ratooning sugarcane and to analyze the rhizosphere bacterial communities. A total of 126,581 and 119,914 valid sequences were obtained from newly planted and ratooning sugarcane and annotated with 4445 and 4620 operational taxonomic units (OTUs), respectively. Increased bacterial community abundance was found in the rhizosphere of ratooning sugarcane when compared with the newly planted sugarcane. The dominant bacterial taxa phyla were similar in both sugarcane groups. Proteobacteria accounted for more than 40% of the total bacterial community, followed by Acidobacteria and Actinobacteria. The abundance of Actinobacteria was higher in the newly planted sugarcane, whereas the abundance of Acidobacteria was higher in the ratooning sugarcane. Our study showed that Sphingomonas, Bradyrhizobium, Bryobacter, and Gemmatimonas were dominant genera. Moreover, the richness and diversity of the rhizosphere bacterial communities slightly increased and the abundance of beneficial microbes, such as Bacillus, Pseudomonas, and Streptacidiphilus, in ratooning sugarcane were more enriched. With the consecutive monoculture of sugarcane, the relative abundance of functional groups related to energy metabolism, glycan biosynthesis, metabolism, and transcription were overrepresented in ratooning sugarcane. These findings could provide the way for promoting the ratooning ability of sugarcane by improving the soil bacterial community.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 569
Author(s):  
Chakriya Sansupa ◽  
Sara Fareed Mohamed Wahdan ◽  
Terd Disayathanoowat ◽  
Witoon Purahong
Keyword(s):  
Bacterial Community ◽  
Forest Soil ◽  
Culture Media ◽  
Enrichment Culture ◽  
Sequence Similarity ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Soil Samples ◽  
Enrichment Cultures ◽  
Total Community

This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

Diversity of halophilic bacteria isolated from Rambla Salada, Murcia (Spain)

2014 ◽  
Vol 60 (12) ◽  
pp. 839-846 ◽  
Author(s):  
Rocío Luque ◽  
Victoria Béjar ◽  
Emilia Quesada ◽  
Inmaculada Llamas
Keyword(s):  
Bacterial Community ◽  
Halophilic Bacteria ◽  
Operational Taxonomic Units ◽  
Sequence Identity ◽  
Abundant Genus ◽  
Phenotypic Tests ◽  
Sampling Season ◽  
V3 Region ◽  
Rrna Sequences ◽  
16S Rrna Sequences

In this study we analyzed the diversity of the halophilic bacteria community from Rambla Salada during the years 2006 and 2007. We collected a total of 364 strains, which were then identified by means of phenotypic tests and by the hypervariable V1–V3 region of the 16S rRNA sequences (around 500 bp). The ribosomal data showed that the isolates belonged to Proteobacteria (72.5%), Firmicutes (25.8%), Actinobacteria (1.4%), and Bacteroidetes (0.3%) phyla, with Gammaproteobacteria the predominant class. Halomonas was the most abundant genus (41.2% isolates) followed by Marinobacter (12.9% isolates) and Bacillus (12.6% isolates). In addition, 9 strains showed <97% sequence identity with validly described species and may well represent new taxa. The diversity of the bacterial community analyzed with the DOTUR package determined 139 operational taxonomic units at 3% genetic distance level. Rarefaction curves and diversity indexes demonstrated that our collection of isolates adequately represented all the bacterial community at Rambla Salada that can be grown under the conditions used in this work. We found that the sampling season influenced the composition of the bacterial community, and bacterial diversity was higher in 2007; this fact could be related to lower salinity at this sampling time.

scholarly journals Treatment nonresponse in children receiving silver diamine fluoride for caries: A pilot study

2020 ◽  
Author(s):  
Ryan Richard Ruff ◽  
Bidisha Paul ◽  
Maria A Sierra ◽  
Fangxi Xu ◽  
Yasmi Crystal ◽  
...  
Keyword(s):  
Pilot Study ◽  
Bacterial Species ◽  
Illumina Miseq ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Lasso Regression ◽  
Silver Diamine Fluoride ◽  
Operational Taxonomic Units ◽  
Acid Tolerant ◽  
Nonsurgical Therapy

AbstractObjectives: Silver diamine fluoride (SDF) is a nonsurgical therapy for the arrest and prevention of dental caries with demonstrated clinical efficacy. Approximately 20% of children receiving SDF fail to respond to treatment. The objective of this study was to develop a predictive model of treatment nonresponse using machine learning. Methods: An observational pilot study (N=20) consisting of children with and without active decay and who did and did not respond to silver diamine fluoride provided salivary samples and plaque from infected and contralateral sites. 16S rRNA genes from samples were amplified and sequenced on an Illumina Miseq and analyzed using QIIME. The association between operational taxonomic units and treatment nonresponse was assessed using lasso regression and artificial neural networks. Results: Bivariate group comparisons of bacterial abundance indicate a number of genera were significantly different between nonresponders and those who responded to SDF therapy. No differences were found between nonresponders and caries-active subjects. Prevotella pallens and Veillonella denticariosi were retained in full lasso models and combined with clinical variables in a six-input multilayer perceptron. Discussion: The acidogenic and acid-tolerant nature of retained bacterial species may overcome the antimicrobial effects of SDF. Further research to validate the model in larger external samples is needed.

scholarly journals Diversity Analysis of Endophytic Bacterial Community in Two Citrus Cultivars With Different Resistance to Citrus Canker

2021 ◽  
Author(s):  
Bing Liu ◽  
Jiahao Lai ◽  
Simeng Wu ◽  
Junxi Jiang ◽  
Weigang Kuang
Keyword(s):  
Bacterial Community ◽  
Endophytic Bacteria ◽  
Citrus Canker ◽  
Navel Orange ◽  
Xanthomonas Citri ◽  
Canker Disease ◽  
Satsuma Mandarin ◽  
Endophytic Bacterial Community ◽  
Dominant Bacteria ◽  
The Relationship

Abstract The selective infection of Xanthomonas citri pv. citri to citrus cultivars is universally known, but it is not clarified whether there is a relationship between endophytic bacteria and the resistance of host variety to canker disease. In order to explore the relationship, Satsuma mandarin and Newhall navel orange were collected respectively as samples of resistant or susceptible cultivars to citrus canker disease, and endophytic bacterial community of two citrus cultivars were analyzed by using a next-generation, Illumina-based sequencing approach. Simultaneously, the seasonal dynamics of endophytic bacterial community and dominant genera were analyzed. The results showed that there were four dominant groups including Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes in all samples at phylum level. Endophytic bacteria were the most abundant in spring samples, then in summer and autumn samples. There were some differences between endophytic bacterial community of resistant citrus and that of susceptible citrus to canker disease, and the endophytic bacteria of Satsuma mandarin are more abundant than that of Newhall navel orange. According to the analysis of dominant bacteria in two citrus cultivars, it was found that some endophytic bacteria with antagonistic characteristics existed universally in all samples, although the dominant bacteria in different seasonal sample were different. However, in Newhall navel orange of susceptible citrus to canker disease, there were not only some bacteria against Xanthomonas citri pv. citri, but also some cooperative bacteria of canker occurrence like Stenotrophomonas.

Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures

1999 ◽  
Vol 65 (4) ◽  
pp. 1721-1730 ◽  
Author(s):  
Allison E. McCaig ◽  
L. Anne Glover ◽  
James I. Prosser
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Sequence Similarity ◽  
Soil Samples ◽  
Operational Taxonomic Units ◽  
16S Ribosomal Dna ◽  
Pcr Products ◽  
Evenness Indices ◽  
Low Coverage

ABSTRACT Bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16S ribosomal DNA (rDNA) sequence analysis of DNAs extracted from triplicate soil plots. PCR products were cloned, and 45 to 48 clones from each of the six libraries were partially sequenced. Phylogenetic analysis of the resultant 275 clone sequences indicated that there was considerable variation in abundance in replicate unfertilized, unimproved soil samples and fertilized, improved soil samples but that there were no significant differences in the abundance of any phylogenetic group. Several clone sequences were identical in the 16S rDNA region analyzed, and the clones comprised eight pairs of duplicate clones and two sets of triplicate clones. Many clones were found to be most closely related to environmental clones obtained in other studies, although three clones were found to be identical to culturable species in databases. The clones were clustered into operational taxonomic units at a level of sequence similarity of >97% in order to quantify diversity. In all, 34 clusters containing two or more sequences were identified, and the largest group contained nine clones. A number of diversity, dominance, and evenness indices were calculated, and they all indicated that diversity was high, reflecting the low coverage of rDNA libraries achieved. Differences in diversity between sample types were not observed. Collector’s curves, however, indicated that there were differences in the underlying community structures; in particular, there was reduced diversity of organisms of the α subdivision of the class Proteobacteria (α-proteobacteria) in improved soils.

Sign in / Sign up

Export Citation Format

Share Document