Next generation sequencing, insect microbiomes, and the confounding effect of Wolbachia: a case study using Drosophila suzukii Matsumura (Diptera: Drosophilidae)

Wilches, Diana; Coghlin, Paul C.; Floate, Kevin D.

doi:10.1139/cjz-2020-0260

Cited by 12 publications

(13 citation statements)

References 57 publications

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“…However, co-variation results from individual fly lines with different levels of genetic diversity more clearly show that the tipping point between community resilience and functional redundancy and communities suffering from more stochastic microbe-microbe associations, and hence reduced functional redundancy, relates more to bottleneck treatment effects than genetic variation within bottleneck treatment. This interpretation is affected by whether lines with high relative abundance of Wolbachia was included or not, as Wolbachia can affect both host fitness and the presence/abundances of other microbial taxa [ 40 , 69 – 71 ] (see also Fig H in S1 Text ).…”

Section: Discussionmentioning

confidence: 99%

“…The demultiplexed paired-end reads were quality filtered, assembled to make consensus amplicon reads, clustered into ASVs, and taxonomically assigned using a custom workflow AmpProc version 5.1.0.beta2.11.1 ( https://github.com/eyashiro/AmpProc ), which relies on USEARCH version 11.0.66_i86linux64 [ 82 ] sequenced reads processing and FastTree version 2.1.10 [ 83 ] for tree building. When present in insects, the endosymbiont Wolbachia can affect host fitness and/or the presence/abundance of other microbial taxa, complicating interpretation of results [ 40 , 69 – 71 ]. Therefore, we removed six lines with a relative Wolbachia abundance >85%.…”

Section: Methodsmentioning

confidence: 99%

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Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness

et al. 2022

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It is becoming increasingly clear that microbial symbionts influence key aspects of their host’s fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome diversity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial diversity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness

et al. 2022

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“…The extremely high abundance of sequences identified as Wolbachia in our samples (~92% overall abundance) could be introducing a potential confounding effect in the estimation of relative abundances for the actual gut-associated bacterial taxa. This possible issue was recently analyzed by Wilches et al [56] using the spotted-wing drosophila (Drosophila suzukii) as a case of study when NGS is applied to investigate the microbiome in Wolbachia-infected insect samples. The authors detected large discrepancies in the measures of alpha and beta diversity, as well as in the relative abundances of several bacteria taxa in the microbiome between Wolbachia-infected fly samples (mean abundance of 98.8% for Wolbachia sequences) and non-infected.…”

Section: Discussionmentioning

confidence: 99%

Diversity of bacterial symbionts associated with the tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) revealed by high-throughput 16S rRNA sequencing.

Navarro-Escalante¹,

Benavides²,

Acevedo³

2022

Preprint

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Insects and microbes have developed complex symbiotic relationships that evolutively and ecologically play beneficial roles for both, the symbiont and the host. In most Hemiptera insects, bacterial symbionts offer mainly nutritional, defense and reproductive roles and have promoted the adaptive radiation of several hemipteran phytophagous lineages. The tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) is a polyphagous herbivore considered an important insect pest for several economically-relevant tropical crops; however, information about the composition of its bacterial microbiota was missing. In this study, we describe the diversity and structure of the bacterial microbiota in the nymph and adult life stages of M. velezangeli using Illumina high-throughput sequencing of 16S ribosomal RNA gene amplicons (meta-barcoding). We found that both insect life stages share a similar microbiota in terms of bacterial diversity and community structure. The intracellular symbiont Wolbachia (~92%) dominated the overall microbiome composition in these life stages, followed by the potential gut-associated bacteria genera Romboutsia (1.8%), Ignavibacterium (0.8%) and Clostridium (0.70%) as the top most abundant taxa. The persistent presence of bacterial genera Romboutsia , Ignavibacterium, Clostridium, Paracoccus, Allobaculum, Methylobacterium, Sediminibacterium, Faecalibaculum, Faecalibacterium, Collinsella, Rothia and Sphingomonas suggest these are members of the core microbiota and could play important biological roles for M. velezangeli . This data opens new questions and avenues to better understand the contribution of symbiotic bacteria in the biological performance of this insect pest.

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“…This interpretation is affected by whether lines with high relative abundance of Wolbachia was included or not, as Wolbachia can affect both host fitness and the presence/abundances of other microbial taxa (see Supplementary Fig. S9; Simhadri et al 2017;Audsley et al 2018;Duan et al 2020;Wilches et al 2021).…”

Section: Discussionmentioning

confidence: 99%

“…) for tree building. When present in insects, the endosymbiont Wolbachia can affect host fitness and/or the presence/abundance of other microbial taxa, complicating interpretation of results (Simhadri et al 2017;Audsley et al 2018;Duan et al 2020;Wilches et al 2021). Therefore, we removed six lines with a relative Wolbachia abundance >85 %.…”

mentioning

confidence: 99%

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness

Oersted

Yashiro

Hoffmann

et al. 2021

Preprint

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It is becoming increasingly clear that microbial symbionts influence key aspects of their host's fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Fitness consequences of such reductions are normally interpreted in terms of a loss of genetic variation and increase in inbreeding depression due to a loss of heterozygosity. However, fitness effects might also be mediated through microbiome diversity, e.g. if functionally important microbes are lost. Here we utilise Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks increased with higher host genetic variation, and 5) reduced microbial diversity is associated with weaker evolutionary responses in stressful environments. These findings suggest that population bottlenecks reduce hologenomic variation (in combined host and microbial genomes). Thus while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations.

show abstract

Next generation sequencing, insect microbiomes, and the confounding effect of Wolbachia: a case study using Drosophila suzukii Matsumura (Diptera: Drosophilidae)

Cited by 12 publications

References 57 publications

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness

Diversity of bacterial symbionts associated with the tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) revealed by high-throughput 16S rRNA sequencing.

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness

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