Methods for the Extraction of Endosymbionts from the Whitefly Bemisia tabaci

Summary

Here, we present a protocol to isolate endosymbionts from the whitefly Bemisia tabaci through dissection and filtration. After amplification, the DNA samples are suitable for subsequent sequencing and study of the mutualism between endosymbionts and whitefly.

Abstract

Bacterial symbionts form an intimate relationship with their hosts and confer advantages to the hosts in most cases. Genomic information is critical to study the functions and evolution of bacterial symbionts in their host. As most symbionts cannot be cultured in vitro, methods to isolate an adequate quantity of bacteria for genome sequencing are very important. In the whitefly Bemisia tabaci, a number of endosymbionts have been identified and are predicted to be of importance in the development and reproduction of the pests through multiple approaches. However, the mechanism underpinning the associations remains largely unknown. The obstacle partially comes from the fact that the endosymbionts in whitefly, mostly restrained in bacteriocytes, are hard to separate from the host cells. Here we report a step-by-step protocol for the identification, extraction and purification of endosymbionts from the whitefly B. tabaci mainly by dissection and filtration. Endosymbiont samples prepared by this method, although still a mixture of different endosymbiont species, are suitable for subsequent genome sequencing and analysis of the possible roles of endosymbionts in B. tabaci. This method may also be used to isolate endosymbionts from other insects.

Introduction

Bacteria forming an intimate symbiotic relationship with relative hosts are widespread in arthropods¹. The endosymbionts have been demonstrated to affect aspects of hosts, such as nutrition metabolism, reproduction, responses to environmental stresses^2,3,4 etc., in almost every developmental stage⁵. However, the mechanism underpinning the associations still remains largely unknown. Genomics is of priority and importance when studying the potential functions and roles of bacteria. Some fundamental information, i.e. the taxonomic status, functional genes, metabolism pathways, secretion systems, can be inferred from genome sequences, which sheds lights on the potential roles of symbionts in symbiosis. With the development of high-throughput sequencing, a vast number of bacterial genomes have been sequenced with diverse functions revealed⁶.

Endosymbionts are of vital importance in hemipterans, such as aphids⁷, bedbugs⁸, psyllids⁹, brown planthoppers¹⁰ and cicadas¹¹. For instance, Buchnera in aphids, as the obligate symbiont, has been demonstrated to be involved in essential amino acids biosynthesis, along with the genes from aphid genome¹². Furthermore, transcriptional regulation of Buchnera is also revealed¹³. In psyllids, Carsonella is sequenced and ranked the smallest bacterial genome ever found¹⁴. All these hallmarks of endosymbionts are based and inferred from the genome sequences. Because these endosymbionts cannot be cultured in vitro, several approaches have been applied to isolate adequate bacteria for sequencing. In aphids, endosymbionts are extracted through centrifugation and filtration, and subjected to further genomic and transcriptomic analysis⁵. In brown planthoppers, endosymbionts are sequenced along with the whole insect genome¹⁰.

Whitefly B. tabaci is a species complex containing more than 35 morphologically indistinguishable species (cryptic species), among which, two invasive species have invaded all over the world and caused tremendous harm to agricultural production¹⁵. Of note, endosymbionts within the B. tabaci species have shown importance in the development of the pests¹⁶. To date, eight endosymbionts have been identified in the whitefly, including the obligate symbiont, Candidatus Portiera aleyrodidarum, and seven secondary symbionts Hamiltonella, Rickettsia, Arsenophonus, Cardinium, Wolbachia, Fritschea and Hemipteriphilus defined^17,18.

Unlike the hemipterans described previously, the whitefly B. tabaci is an extremely tiny insect only 1 mm in length. Most endosymbionts are confined to bacteriocytes¹⁹ (specialized cells containing symbionts, which further form bacteriome in B. tabaci). In addition, these endosymbionts cannot be cultured in vitro. The only way to obtain endosymbionts from B. tabaci is to dissect the bacteriome out. However, there is difficulty in the dissection. First, the fragile bacteriome always links with other tissues of the whitefly, which is hard to separate. Secondly, the tiny size of the whitefly limits the isolation of enough bacteriome. Thirdly, endosymbionts cluster in the bacteriome, making it extremely complicated to acquire a single species of bacterium.

Here, we report a simple and inexpensive protocol to isolate whitefly endosymbionts for subsequent metagenome sequencing. Through dissection, purification and amplification, adequate endosymbiont DNA could be obtained and the species of bacteria could be confirmed. The described protocol can be used similarly in other arthropods.

Protocol

1. Whitefly Rearing and Cryptic Species Identification

1. Maintain the whitefly species on cotton Gossypium hirsutum (Malvaceae) (cv. Zhe-Mian 1973) in cages under standard conditions of 27 ± 1 °C, 70 ± 10% humidity and 14 h light: 10 h dark regime.
2. Collect an individual adult whitefly and homogenize in 30 µL of lysis buffer (10 mM Tris, pH 8.4, 50 mM KCl, 0.45% [wt/vol] Tween-20, 0.2% [wt/vol] gelatin, 0.45% [vol/vol] Nonidet P 40, 60 g/mL Proteinase K).
3. Incubate the homogenate at 65 °C for 1 h and then 100 °C for 10 min.
   NOTE: The incubation time at 65 °C can be increased if necessary. The incubation time at 100 °C should be critically controlled to sufficiently inactivate Proteinase K and avoid DNA damage.
4. Perform polymerase chain reaction (PCR) using whitefly DNA (acquired in section 1.3) based on mitochondrial cytochrome oxidase I primers.
   COI-F: 5'-TTGATTTTTTGGTCATCCAGAAGT-3'
   COI-R: 5'-TAATATGGCAGATTAGTGCATTGGA-3'
   1. Perform the PCR reactions in a final volume of 25 µL containing 1 U of Taq DNA polymerase, 2.5 µL 10x Buffer, 0.2 mM dNTP, 0.2 mM of each primer and 2 µL of whitefly DNA.
   2. Use the following PCR procedure conditions: initial denaturation 95 °C for 3 min followed by 35 cycles of 95 °C for 45 s (denaturation), 50 °C for 45 s (annealing) and 72 °C for 1 min (extension) and another 10 min at 72 °C for further extension.
5. Clean the PCR amplified product using a DNA gel extraction kit with the recommended protocol.
6. Sequence the purified DNA samples with a DNA sample sequencing system following the manufacturer's instruction.
7. Analyze the sequences using the Basic Local Alignment Search Tool (BLAST) to identify the cryptic species of whitefly and avoid contamination of other species.

2. Endosymbiont Identification and Localization

1. Perform PCR on the whitefly DNA (acquired in Step 1.3) to amplify the specific genes of each endosymbiont within the whitefly (the PCR recipe is described in section 1.4, and PCR procedures and primers are listed in Table 1).
2. Subject the amplified sample to agarose gel electrophoresis according to previously published protocol²⁰ (1% agarose gel, Tris-acetate-EDTA as running buffer, voltage 5 V/cm) to identify the specific gene of each bacterium.
3. Recover and sequence each band to determine the bacterial species within whitefly (see sections 1.5-1.7).
4. Perform fluorescence in situ hybridizations (FISH) on whiteflies to identify the location of endosymbionts according to previously published protocol¹⁹.
   NOTE: Increase the concentration of the fluorescent probes if necessary.

3. Transmission Electron Microscopy (TEM)

1. Immerse and fix whiteflies in phosphate buffer (0.1 M, pH 7.0) containing 2.5% [vol/vol] glutaraldehyde for 4 h.
2. Wash the samples in phosphate buffer (0.1 M, pH 7.0) three times, 15 min each time.
3. Immerse and fix the samples again in phosphate buffer (0.1 M, pH 7.0) containing 1% [wt/vol] OsO₄ for 2 h.
4. Dehydrate the samples by a graded series of ethanol (30%, 50%, 70%, 80%, 90%, 95% and 100%), 15 min each time.
5. Transfer and immerse the samples into 100% acetone for 20 min.
6. Place the samples in mixture of 100% acetone and 100% Spurr resin (1:1) for 1 h at room temperature.
7. Transfer the samples to mixture of 100% acetone and 100% Spurr resin (1:3) for 3 h at room temperature.
8. Transfer and immerse the samples into 100% Spurr resin (incubated at 70 °C) for more than 9 h.
9. Section the whitefly samples by using a microtome.
10. Stain the ultra-thin films (acquired in section 3.9) by immersion in absolute uranyl acetate for 5-10 min, followed by immersion in 50% alkaline lead citrate for another 5-10 min.
    NOTE: The volumes of reagents utilized in section 3.1-3.10 depend on the samples. Make sure the samples are immersed in the reagents.
11. Observe samples under transmission electron microscopy (15,000X) to determine the localization, shape and size of bacteria for further use (see section 4.6).

4. Whitefly Bacteriome Dissection and Purification

1. Add 100 µL of 1x PBS solution onto a microscope slide. Pick some 3^rd or 4^th instar nymphs from cotton leaves and immerse them into the PBS solution.
2. Use fine entomological needles under a stereomicroscope and pull the bacteriomes out from the whitefly body.
   1. Gently cut a hole on one side of the nymph, and slightly press the other side to let the bacteriomes out.
3. Mount a 20 µL microloader (with the leading end cut to meet the size of bacteriome) on a 0.5-10 µL pipette. Extract the individual bacteriome out of the PBS solution into the microloader.
4. Wash the bacteriome to eliminate the contamination of other whitefly tissues by pipetting the bacteriome into the PBS solution and extracting the bacteriome. Repeat three times.
5. Immediately pipette the washed bacteriome into a centrifuge tube containing 60 µL of 1x PBS solution.
6. Syringe-filter the assembled bacteriome through a 5 µm filter membrane (determined by sizes of bacteria and nucleus of bacteriocyte in whitefly). Repeat multiple times to move the mixed liquid through the filter membrane thoroughly.
   NOTE: To achieve a better result of amplification and sequencing, assemble over 100 bacteriomes. Wet the filter membrane first by using 1x PBS solution to decrease the loss of bacteria binding to the membrane.

5. Amplification of Endosymbiont Genomes

1. Amplify the filtrate (mainly containing endosymbionts of the whitefly) using a DNA amplification kit by the recommended protocol with some modification.
   1. Choose the recommended protocol of amplification of genomic DNA from blood or cells and prepare buffer D2 for subsequent experiment.
   2. Directly add 1.5 µL of filtrate (see section 4.6) to the centrifuge tube, followed by 1.5 µL of the Buffer D2 and mix well.
   3. Incubate on ice for 10 min and add 1.5 µL of the stop solution.
   4. Add 15 µL of the reaction buffer and 1 µL of the DNA polymerase and mix gently.
   5. Incubate the mixture at 30 °C for 16 h, followed by 3 min at 65 °C.
2. Perform PCR directly on the amplified filtrate (dilute the amplified samples if necessary) by using specific primers designed for bacteria to confirm the bacteria species (see section 2.1).
3. Conduct PCR to confirm whether there is contamination of host genome by using whitefly gene beta-Actin and EF1 primers according to previously published method²¹ (the PCR recipe is described in section 1.4).

6. Endosymbiont Metagenome Sequencing

1. Subject the amplified filtrate to a spectrophotometer and a fluorometer (according to the manufacturer's instructions) before sequencing to test the quality of samples and whether the samples meet the criteria for sequencing.
2. Subject the amplified to a genome sequencer according to the manufacturer's instructions.

Results

The Middle East Asia Minor 1 (MEAM1) species of the B. tabaci complex was taken as an example here for description. Cotton for rearing whiteflies and several developmental stages of whiteflies are shown in Figure 1 including a cotton plant, adult whitefly and the 1^st, 2^nd and 4^th instar nymphs of whitefly (the 3^rd instar nymph looks similarly as the 4^th instar nymph). It was obvious that the 4

Discussion

Since the endosymbionts within whiteflies cannot be cultured in vitro, dissection and assembling bacteriocytes is an effective way to obtain enough genetic material of endosymbionts. Before dissection, the species of whitefly and endosymbionts involved should be explicitly confirmed. The whitefly B. tabaci is a species complex with more than 35 morphologically indistinguishable species and different cryptic species may contain different endosymbionts. Portiera is uniformly harbored as an obliga...

Materials

Name	Company	Catalog Number	Comments
Taq DNA polymerase	Takara	R001A	including rTaq, 10×Buffer and dNTP
Gel DNA extraction kit	Qiagen	28704
DNA sample sequencing system	ABI	ABI-3730XL
Microtome	Leica	EM UC7
Transmission electron microscopy	Hitachi	H-7650 TEM
Stereo microscope	Zeiss	Stemi 2000-C
20 μL microloader	Eppendorf	F2771951
Filter holder	Millipore	SX0001300
Filter membrane filter	Millipore	SMWP001300	5.0 μm SMWP
REPLI-g UltraFast Mini Kit	Qiagen	150033	DNA amlification kit
NanoDrop	Thermo Scientific	NanoDrop 2000
Qubit Fluorometer	Thermo Fisher Scientific	Q33216
Genome Sequencer	Illumina	Hiseq 2000