Application of 16S rDNA-DGGE to examine the microbial ecology associated with a social wasp Vespula germanica

Characterization of the gut microbes of greater wax moth (Galleria mellonella Linnaeus) shows presence of potential polymer degraders

Greater wax moth (GWM), Galleria mellonella (Lepidoptera: Pyralidae), is a highly destructive honey bee pest prevalent throughout the world. It is considered as a major factor to the alarming decline in honey bee population. GWM destroys active honey combs as it feeds on the beeswax and lays eggs in bee hives, and the primary food of their larva is beeswax. Beeswax is a polymer composed mainly of saturated and unsaturated, linear and complex monoesters, and hydrocarbons. The most frequent bond in beeswax is ethene (CH₂-CH₂) which is also found in the common plastic polyethylene. As wax-digestion is not a common animal character, we hypothesized about a possible role of GWM gut microflora in the process; which could possibly degrade polyethylene-like polymers as well. This study was aimed to identify the GWM gut microflora via culture-dependant approach. We characterized several bacterial species based on the culture characteristics, Gram-reaction, and various biochemical tests. Sequencing of 16S-rDNA revealed nine bacterial and one microalgal species from GWM gut. The bacterial species included Gram-positive Exiguobacterium aestuarii, Bacillus circulans, Microbacterium zaea, Microbacterium sp. and Enterococcus faecalis; Gram-negative Agrobacterium sp., Sphingomonas pseudosanguinis, Sphingobium yanoikuyae and Acinetobacter radioresistens; the microalgae was Picochlorum oklahomensis. Some of them have been previously reported to degrade polycyclic aromatic hydrocarbon, low-density polyethylene, and 2-methylphenanthrene. Meanwhile, the microalga, P. oklahomensis, was reported to steal bacterial genes to adapt with abiotic stresses. Further investigation is necessary to explore the precise details about polymer degrading capabilities of these microbes; nevertheless, this study builds a foundation for elaborate and advanced future research.

Microbiome of the wasp Vespula pensylvanica in native and invasive populations, and associations with Moku virus

Invasive species present a worldwide concern as competition and pathogen reservoirs for native species. Specifically, the invasive social wasp, Vespula pensylvanica, is native to western North America and has become naturalized in Hawaii, where it exerts pressures on native arthropod communities as a competitor and predator. As invasive species may alter the microbial and disease ecology of their introduced ranges, there is a need to understand the microbiomes and virology of social wasps. We used 16S rRNA gene sequencing to characterize the microbiome of V. pensylvanica samples pooled by colony across two geographically distinct ranges and found that wasps generally associate with taxa within the bacterial genera Fructobacillus, Fructilactobacillus, Lactococcus, Leuconostoc, and Zymobacter, and likely associate with environmentally-acquired bacteria. Furthermore, V. pensylvanica harbors-and in some cases were dominated by-many endosymbionts including Wolbachia, Sodalis, Arsenophonus, and Rickettsia, and were found to contain bee-associated taxa, likely due to scavenging on or predation upon honey bees. Next, we used reverse-transcriptase quantitative PCR to assay colony-level infection intensity for Moku virus (family: Iflaviridae), a recently-described disease that is known to infect multiple Hymenopteran species. While Moku virus was prevalent and in high titer, it did not associate with microbial diversity, indicating that the microbiome may not directly interact with Moku virus in V. pensylvanica in meaningful ways. Collectively, our results suggest that the invasive social wasp V. pensylvanica associates with a simple microbiome, may be infected with putative endosymbionts, likely acquires bacterial taxa from the environment and diet, and is often infected with Moku virus. Our results suggest that V. pensylvanica, like other invasive social insects, has the potential to act as a reservoir for bacteria pathogenic to other pollinators, though this requires experimental demonstration.

Diel pattern in the structure and function of the gut microbial community in Lymantria dispar asiatica (Lepidoptera: Lymantriidae) larvae

In the present study, diel pattern in gut microbial communities in insects were evaluated. Lymantria dispar asiatica fourth instar larvae (72 ± 2 hr after molting) at noon (LdD) and midnight (LdN) were used for a comparative analysis of the gut microbial community. Ten bacterial operational taxonomic units (OTUs) were shared between LdD and LdN samples. One bacterial OTU was specific to LdD. The dominant gut microbes were OTU72 in LdD and OTU75 in LdN. A linear discriminant analysis effect size cladogram suggested that ten bacterial OTUs maintain significant differences in relative abundances between LdD and LdN. These results agreed with the discrete ellipses between LdD and LdN in principal coordinates analysis plots. Additionally, using phylogenetic investigation of communities by reconstruction of unobserved states, the gut microbial community was assigned to 23 functional terms, among which 22 exhibited significant differences between LdD and LdN. To conclude, the present study documented a diel pattern in the gut microbial community of L. dispar asiatica larvae.

Influence of dietary aconitine and nicotine on the gut microbiota of two lepidopteran herbivores

The gut microbiota plays an important role in pheromone production, pesticide degradation, vitamin synthesis, and pathogen prevention in the host animal. Therefore, similar to gut morphology and digestive enzyme activity, the gut microbiota may also get altered under plant defensive compound-induced stress. To test this hypothesis, Dendrolimus superans larvae were fed either aconitine- or nicotine-treated fresh leaves of Larix gmelinii, and Lymantria dispar larvae were fed either aconitine- or nicotine-treated fresh leaves of Salix matsudana. Subsequently, the larvae were sampled 72hr after diet administration and DNA extracted from larval enteric canals were employed for gut microbial 16S ribosomal RNA gene sequencing (338 F and 806 R primers). The sequence analysis revealed that dietary nicotine and aconitine influenced the dominant bacteria in the larval gut and determined their abundance. Moreover, the effect of either aconitine or nicotine on D. superans and L. dispar larvae had a greater dependence on insect species than on secondary plant metabolites. These findings further our understanding of the interaction between herbivores and host plants and the coevolution of plants and insects.

Tracing insect pests: is there new potential in molecular techniques?

Insects are amongst the greatest pests of agriculture, horticulture and forestry worldwide, inflicting damage and economic costs both directly and by transmitting plant viruses. Many kinds of insects are now resistant or cross-resistant to pesticides. Tracking studies have become very important for combatting insect pests and for better understanding their biology (eg insect population dynamics, movements, feeding behaviour and other ecological interactions). A wide variety of tracing approaches have been used including discriminative, tracer and molecular methods. The perfect technique for insect tracking is the technique that harmonizes with insects' 'normal' biology. Furthermore, the technique should be environmentally safe, cost-effective and easy to use. This paper reviews the current techniques used for insect traceability, documents the advantages and drawbacks of each method, and puts special focus on molecular techniques, including PCR-denaturing gradient gel electrophoresis as a new and promising traceability tool that could provide insects with a unique biological barcode and thus make it possible to trace their movements.

Ambient temperature-mediated enzymic activities and intestinal microflora in Lymantria dispar larvae

To understand how ambient temperature affect the gypsy moth larvae, and provide a theoretical basis for pest control in different environments. Fourth instar gypsy moth larvae were incubating for 3 hr at 15℃, 20℃, 25℃, 30℃, 35℃, and 40℃, respectively. Afterward, digestive and antioxidant enzyme activities, total antioxidant capacity, and intestinal microflora community were analyzed to reveal how the caterpillars respond to ambient temperature stress. Results showed that both digestive and antioxidant enzymes were regulated by the ambient temperature. The optimum incubation temperatures of protease, amylase, trehalase, and lipase in gypsy moth larvae were 30℃, 25℃, and 20℃, respectively. When the incubation temperature was deviated optimum temperatures, digestive enzyme activities would be downregulated depending on the extent of temperature stress. In addition, glutathione S-transferase, peroxidase, catalase, and polyphenol oxidase would be activated under a sufferable temperature stress, but superoxide dismutase and carboxylesterase (CarE) would be inhibited. In addition, results showed that the top two abundant phyla were Proteobacteria and Firmicutes. The phylum Firmicutes abundance was decreased and phylum Proteobacteria abundance was increased by ambient temperature stress. Moreover, it suggested that gypsy moth caterpillars at different ambient temperature mainly differed from each other by Escherichia-Shigella and Bifidobacterium in control, Acinetobacter in T15, and Lactobacillus in T40, respectively.

Community analysis of gut microbiota in hornets, the largest eusocial wasps, Vespa mandarinia and V. simillima

Gut microbiota are important for various aspects of host physiology, and its composition is generally influenced by both intrinsic and extrinsic contexts of the host. Social bee gut microbiota composition is simple and highly stable hypothesized to be due to their unique food habit and social interactions. Here, we focused on hornets, the largest of the eusocial wasps – Vespa mandarinia and V. simillima. Unlike the well-studied honey bees, adult hornets are generally herbivorous but also hunt insects for broods, a unique behavior which could influence their gut microbiota. Analysis of the gut microbiome using 16S rRNA gene sequencing revealed that the two species have simple gut microbiota, composed of seven or eight consistently maintained ‘core’ operational taxonomic units (OTUs). While the two Vespa species shared some OTUs, the structures of their gut communities differed. Phylogenetic analysis indicated association of core OTUs with host diet. Intriguingly, prey honey bee gut microbes were detected in the V. simillima gut (and to a lesser extent in V. mandarinia), suggesting migration of microorganisms from the prey gut. This is the first report uncovering gut microbiome in hornets, giving additional insight into how food habit affects gut microbiota of social insects.

Metagenomic analysis reveals changes of the Drosophila suzukii microbiota in the newly colonized regions

The spotted wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a highly polyphagous pest of a wide variety of wild or cultivated berry and stone fruit. Originating from Southeast Asia, it has recently invaded a wide range of regions in Europe and North America. It is well known that insect microbiotas may significantly influence several aspects of the host biology and play an important role in invasive species introduction into new areas. However, in spite of the great economic importance of D. suzukii, a limited attention has been given so far to its microbiota. In this study, we present the first in-depth characterization of gut bacterial diversity from field (native and invasive range) and lab-reared populations of this insect. The gut bacterial communities of field insects were dominated, regardless of their origin, by 2 families of the phylum Proteobacteria: Acetobacteraceae and Enterobacteriaceae, while Firmicutes, mainly represented by the family Staphylococcaceae, prevailed in lab-reared population. Locality was the most significant factor in shaping the microbiota of wild flies. Moreover, a negative correlation between diversity and abundance of Enterobacteriaceae and the time elapsed since the establishment of D. suzukii in a new region was observed. Altogether our results indicate that habitat, food resources as well as the colonization phase of a new region contribute to shape the bacterial communities of the invasive species which, in turn, by evolving more quickly, could influence host adaptation in a new environment.

Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua

The insect gut has been the house of many taxonomically and physiologically diverse groups of microbial colonizers as symbionts and commensals, which are evolving to support the physiological requirement of insects. Lepidoptera is one of the important family of class hexapoda, comprising agriculture insect pest Spodoptera litura and Spilosoma obliqua. Information on gut microbiota and their functional role in these insects was meager to elucidate the wide-ranging survivalist mechanisms. In this context, we analyzed the composition, diversity and functional role of gut bacteria in S. litura and S. obliqua collected from soybean and sunflower crops, respectively, using Next Generation Sequencing of 16S rRNA. A total of 3427 and 206 Operation Taxonomic Units (OTUs) were identified in S. litura and S. obliqua gut metagenome, respectively. Highest number of sequences were annotated to unclassified bacteria (34%), followed by Proteobacteria (27%), and Chlorobi (14%) in S. litura, while S. obliqua has significant representation of Firmicutes (48%), followed by Bacteroidetes (20%), and unclassified bacteria (11%). Functionality of both metagenomes revealed, high abundance of ammonia oxidizers (20.1 58.0%) followed by relative abundance of detoxifying processes - dehalogenation (17.4-41.2%) and aromatic hydrocarbons degradation (1.1-3.1%). This study highlights the significance of the inherent microbiome of two defoliators in shaping the metagenome for nutrition and detoxifying the chemical molecules, and opens an avenue for exploring role of insect gut bacteria in host selection, metabolic endurance of insecticides and synergistic or agonistic mechanisms inside gut of insects feeding on insect-resistant biotech crops.

Yeasts Harbored by Vespine Wasps in the Pacific Northwest

The ecological role of social wasps has been extensively studied, but little is known about symbiotic relationships of these wasps with microbes. Recently, it was shown that vespid wasps in Europe carry yeasts, predominantly Saccharomyces cerevisiae, in their gastrointestinal (GI) tract. Interestingly, this niche allowed for sexual recombination of yeasts to occur and the formation of novel hybrid species. Our goals were 1) to survey the GI tract of eusocial wasps in the Pacific Northwest for the presence of yeasts and 2) to compare the diversity of such yeasts to that described for wasps in Europe. The GI tracts of 19 individual wasps from five species were plated, and 27 yeast-like colonies were identified to the species level. Yeasts in the genera Lachancea and Hanseniaspora each comprised ∼30% of the isolates; ∼25% were identified as Metschnikowia spp., with the remaining 10% belonging to Rhodotorula. Four bacterial isolates were identified as Escherichia coli, Enterococcus faecalis, and two isolates of Stenotrophomonas maltophilia. Yeasts were present at all life stages of the wasps except for two unfed gynes of Dolichovespula maculata (L.) that contained only bacteria. The presence of a particular yeast species was not correlated with any wasp species. Furthermore, S. cerevisiae was not found in any wasp species. This highlights an interesting difference in the life cycle of both S. cerevisiae and wasps in Europe and the Pacific Northwest, and prompts further studies on the interactions of these microbes with their host wasps.

Characterization of the Microbial Communities in the Ant Lion Euroleon coreanus (Okamoto) (Neuroptera: Myrmeleontidae)

Euroleon coreanus (Okamoto) is widely distributed in China, and the larval stage can be treated as traditional Chinese medicine. However, the host-bacterium relationship remains unexplored, as there is a lack of knowledge on the microbial community of ant lions. Hence, in the current study, we explored the microbial community of the larval ant lion E. coreanus using Illumina MiSeq sequencing. Results indicated that a total of 10 phyla, 126 genera, and 145 species were characterized from the second instars of E. coreanus, and most of the microbes were classified in the phylum Proteobacteria. Cronobacter muytjensii was the most abundant species characterized in the whole body and gut of E. coreanus, and the unclassified species in the genera Brevundimonas and Lactobacillus were relatively more abundant in the head and carcass. In addition, no Wolbachia-like bacteria were detected, whereas bacteria like Francisella tularensis subsp. Holarctica OSU18 and unclassified Rickettsiella were first identified in ant lion E. coreanus.

Isolation and Characterization of α-Endosulfan Degrading Bacteria from the Microflora of Cockroaches

Extensive applications of organochlorine pesticides like endosulfan have led to the contamination of soil and environments. Five different bacteria were isolated from cockroaches living in pesticide contaminated environments. According to morphological, physiological, biochemical properties, and total cellular fatty acid profile by Fatty Acid Methyl Esters (FAMEs), the isolates were identified as Pseudomonas aeruginosa G1, Stenotrophomonas maltophilia G2, Bacillus atrophaeus G3, Citrobacter amolonaticus G4 and Acinetobacter lwoffii G5. This is the first study on the bacterial flora of Blatta orientalis evaluated for the biodegradation of α-endosulfan. After 10 days of incubation, the biodegradation yields obtained from P. aeruginosa G1, S. maltophilia G2, B. atrophaeus G3, C. amolonaticus G4 and A. lwoffii G5 were 88.5% , 85.5%, 64.4%, 56.7% and 80.2%, respectively. As a result, these bacterial strains may be utilized for biodegradation of endosulfan polluted soil and environments.

Pyrosequencing reveals a shift in symbiotic bacteria populations across life stages of Bactrocera dorsalis

Bactrocera dorsalis is one of the most economically important fruit flies around the world. In this study, 454 pyrosequencing was used to identify the bacteria associated with different developmental stages of B. dorsalis. At ≥ 97% nucleotide similarity, total reads could be assigned to 172 Operational Taxonomic Units belonging to six phyla. Proteobacteria dominated in immature stages while Firmicutes dominated in adult stages. The most abundant families were Enterococcaceae and Comamondaceae. The genus Comamonas was most abundant in pupae whereas completely absent in adults. Some identified species had low sequence similarity to reported species indicating the possibility of novel taxa. However, a majority sequence reads were similar to sequences previously identified to be associated with Bactrocera correcta, suggesting a characteristic microbial fauna for this insect genus. The type and abundance of different bacterial groups varied across the life stages of B. dorsalis. Selection pressure exerted by the host insect as a result of its habitat and diet choices could be the reason for the observed shift in the bacteria groups. These findings increase our understanding of the intricate symbiotic relationships between bacteria and B. dorsalis and provide clues to develop potential biocontrol techniques against this fruit fly.

No evidence of enemy release in pathogen and microbial communities of common wasps (Vespula vulgaris) in their native and introduced range

When invasive species move to new environments they typically experience population bottlenecks that limit the probability that pathogens and parasites are also moved. The invasive species may thus be released from biotic interactions that can be a major source of density-dependent mortality, referred to as enemy release. We examined for evidence of enemy release in populations of the common wasp (Vespula vulgaris), which attains high densities and represents a major threat to biodiversity in its invaded range. Mass spectrometry proteomic methods were used to compare the microbial communities in wasp populations in the native (Belgium and England) and invaded range (Argentina and New Zealand). We found no evidence of enemy release, as the number of microbial taxa was similar in both the introduced and native range. However, some evidence of distinctiveness in the microbial communities was observed between countries. The pathogens observed were similar to a variety of taxa observed in honey bees. These taxa included Nosema, Paenibacillus, and Yersina spp. Genomic methods confirmed a diversity of Nosema spp., Actinobacteria, and the Deformed wing and Kashmir bee viruses. We also analysed published records of bacteria, viruses, nematodes and fungi from both V. vulgaris and the related invader V. germanica. Thirty-three different microorganism taxa have been associated with wasps including Kashmir bee virus and entomophagous fungi such as Aspergillus flavus. There was no evidence that the presence or absence of these microorganisms was dependent on region of wasp samples (i.e. their native or invaded range). Given the similarity of the wasp pathogen fauna to that from honey bees, the lack of enemy release in wasp populations is probably related to spill-over or spill-back from bees and other social insects. Social insects appear to form a reservoir of generalist parasites and pathogens, which makes the management of wasp and bee disease difficult.

Molecular phylogenetic profiling of gut-associated bacteria in larvae and adults of flesh flies

Flesh flies of the genus Sarcophaga (Diptera: Sarcophagidae) are carrion-breeding, necrophagous insects important in medical and veterinary entomology as potential transmitters of pathogens to humans and animals. Our aim was to analyse the diversity of gut-associated bacteria in wild-caught larvae and adult flesh flies using culture-dependent and culture-independent methods. Analysis of 16S rRNA gene sequences from cultured isolates and clone libraries revealed bacteria affiliated to Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes in the guts of larval and adult flesh flies. Bacteria cultured from larval and adult flesh fly guts belonged to the genera Acinetobacter, Bacillus, Budvicia, Citrobacter, Dermacoccus, Enterococcus, Ignatzschineria, Lysinibacillus, Myroides, Pasteurella, Proteus, Providencia and Staphylococcus. Phylogenetic analysis showed clone sequences of the genera Aeromonas, Bacillus, Bradyrhizobium, Citrobacter, Clostridium, Corynebacterium, Ignatzschineria, Klebsiella, Pantoea, Propionibacterium, Proteus, Providencia, Serratia, Sporosarcina, Weissella and Wohlfahrtiimonas. Species of clinically significant genera such as Ignatzschineria and Wohlfahrtiimonas spp. were detected in both larvae and adult flesh flies. Sequence analysis of 16S rRNA gene libraries supported culture-based results and revealed the presence of additional bacterial taxa. This study determined the diversity of gut microbiota in flesh flies, which will bolster the ability to assess microbiological risk associated with the presence of these flies. The present data thereby establish a platform for a much larger study.

Genomic and proteomic characterization of bacteriocin-producing Leuconostoc mesenteroides strains isolated from raw camel milk in two southwest Algerian arid zones

Information on the microbiology of camel milk is very limited. In this work, the genetic characterization and proteomic identification of 13 putative producing bacteriocin Leuconostoc strains exhibiting antilisterial activity and isolated from camel milk were performed. DNA sequencing of the 13 selected strains revealed high homology among the 16S rRNA genes for all strains. In addition, 99% homology with Leuconostoc mesenteroides was observed when these sequences were analysed by the BLAST tool against other sequences from reference strains deposited in the Genbank. Furthermore, the isolates were characterized by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDITOF MS) which allowed for the identification of 2 mass peaks 6242 m/z and 5118 m/z that resulted to be specific to the species L. mesenteroides. Remarkably, the phyloproteomic tree provided more intraspecific information of L. mesenteroides than phylogenetic analysis. Accordingly, phyloproteomic analysis grouped L. mesenteroides strains into different subbranches, while all L. mesenteroides isolates were grouped in the same branch according to phylogenetic analysis. This study represents, to our knowledge, the first report on the use of MALDI-TOF MS on the identification of LAB isolated from camel milk.

Comparative analysis of the composition of intestinal bacterial communities in Dastarcus helophoroides fed different diets

The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides.

Comparative analysis of the composition of intestinal bacterial communities in Dastarcus helophoroides fed different diets

The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides.

Analyzing arthropods for the presence of bacteria

Bacteria within arthropods can be identified using culture-independent methods. This unit describes protocols for surface sterilization of arthropods, DNA extraction of whole bodies and tissues, touchdown PCR amplification using 16S rDNA general bacteria primers, and profiling the bacterial community using denaturing gradient gel electrophoresis.

Novel Rickettsiella bacterium in the leafhopper Orosius albicinctus (Hemiptera: Cicadellidae)

Bacteria in the genus Rickettsiella (Coxiellaceae), which are mainly known as arthropod pathogens, are emerging as excellent models to study transitions between mutualism and pathogenicity. The current report characterizes a novel Rickettsiella found in the leafhopper Orosius albicinctus (Hemiptera: Cicadellidae), a major vector of phytoplasma diseases in Europe and Asia. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to survey the main symbionts of O. albicinctus, revealing the obligate symbionts Sulcia and Nasuia, and the facultative symbionts Arsenophonus and Wolbachia, in addition to Rickettsiella. The leafhopper Rickettsiella is allied with bacteria found in ticks. Screening O. albicinctus from the field showed that Rickettsiella is highly prevalent, with over 60% of individuals infected. A stable Rickettsiella infection was maintained in a leafhopper laboratory colony for at least 10 generations, and fluorescence microscopy localized bacteria to accessory glands of the female reproductive tract, suggesting that the bacterium is vertically transmitted. Future studies will be needed to examine how Rickettsiella affects host fitess and its ability to vector phytopathogens.

Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications

Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH) enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host diet, and suggested that this relationship could be exploited for the discovery of symbionts and biocatalysts useful for biorefinery applications.

Composition and diversity analysis of the gut bacterial community of the Oriental armyworm, Mythimna separata, determined by culture-independent and culture-dependent techniques

The intestinal bacteria community structure and diversity of the Oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae), was studied by analysis of a 16S rDNA clone library, denaturing gradient gel electrophoresis,and culture-dependent techniques. The 16S rDNA clone library revealed a bacterial community diversity comprising Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes and Proteobacteria, among which Escherichia coli (Migula) (Enterobacteriales: Enterobacteriaceae) was the dominant bacteria. The intestinal bacteria isolated by PCR-denaturing gradient gel electrophoresis were classified to Firmicutes, Proteobacteria, and Gracilicutes, and E. coli was again the dominant bacteria. The culture-dependent technique showed that the intestinal bacteria belonged to Firmicutes and Actinobacteria, and Staphylococcus was the dominant bacteria. The intestinal bacteria of M. separata were widely distributed among the groups Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes, Proteobacteria, and Gracilicutes. 16S rDNA clone library, denaturing gradient gel electrophoresis, and culture-dependent techniques should be integrated to obtain precise results in terms of the microbial community and its diversity.

Diversity of the chlorite dismutase gene in low and high organic carbon rhizosphere soil colonized by perchlorate-reducing bacteria

Chlorite dismutase (cld) is an essential enzyme in the biodegradation of perchlorate. The objective of this study was to determine the change in sequence diversity of the cld gene, and universal bacterial 16S rRNA genes, in soil samples under varying conditions of organic carbon, bioaugmentation, and plant influence. The cld gene diversity was not different between high organic carbon (HOC) and low organic carbon (LOC) soil. Combining results from HOC and LOC soil, diversity of the cld gene was decreased in soil that had been bioaugmented or planted. However, with both bioaugmentation and planting the cld diversity was not decreased. These observations were repeated when focusing on LOC soil. However, in HOC soil the cld diversity was not affected by reactor treatment. General bacterial diversity as measured with 16S rRNA was significantly greater in HOC soil than in LOC soil, but no significant difference was observed between reference soil and planted or bioaugmented soil. Different sequences of the cld gene occur in different species of microorganisms. In LOC soil, combining bioaugmentation and planting results in a highly diverse population of perchlorate degraders. This diverse population will be more resilient and is desirable where perchlorate reduction is a critical remediation process. Supplemental materials are available for this article. Go to the publisher's online edition of International Journal of Phytoremediation to view the supplemental file.

Bacillus subtillis RTSBA6 6.00, a new strain isolated from gut of Helicoverpa armigera (Lepidoptera: Noctuidae) produces chymotrypsin-like proteases

Exploring bacterial communities with proteolytic activity from the gut of the Helicoverpa armigera (Hubner) (Lepidoptera: Noctuidae) insect pests was the purpose of this study. As initial efforts to achieve this goal here we report the isolation of new Bacillus subtillis RTSBA6 6.00 strain from the gut of H. armigera and demonstrated as proteases producer. Zymographic analysis revealed 12 proteolytic bands with apparent molecular weights ranging from 20 to 185 kDa. Although some activity was detected at acidic pH, the major activity was observed at slight alkaline pH (7.8). The optimum temperature was found to be 35 °C with complete loss of activity at 70 °C. All proteases were completely inactivated by PMSF (phenylmethylsulfonyl fluoride) and TPCK (N-tosyl-l-phenylalanine chloromethyl ketone), suggesting that proteases secreted by B. subtillis RTSBA6 6.00 belong to serine proteases class with chymotrypsin-like activity. The occurrence of protease producing bacterial community in the gut of the H. armigera advocates its probable assistance to insect in proteinaceous food digestion and adaptation to protease inhibitors of host plants.

Comparison of the diversity of the bacterial communities in the intestinal tract of adult Bactrocera dorsalis from three different populations

AIMS

To (i) identify the bacterial communities in the gut of oriental fruit fly (Bactrocera dorsalis) adult and (ii) determine whether the different surroundings and diets influence the bacteria composition.

METHODS AND RESULTS

Polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) fingerprinting was used to investigate bacterial diversity in the oriental fruit fly adult gut. The 16S rDNA cloned libraries from the intestinal tract of laboratory-reared (LR), laboratory sterile sugar-reared (LSSR) and field-collected (FC) populations of oriental fruit fly were compared. Phylogenetic analysis of 16S rDNA revealed that Gammaproteobacteria were dominant in the all samples (73·0-98·3%). Actinobacteria and Firmicutes were judged to be major components of a given library as they constituted 10% or more of the total clones of such library. The Flavobacteria, Deltaproteobacteria, Bacteroidetes and Alphaproteobacteria were observed in small proportions in various libraries. Further phylogenetic analyses indicated common bacterial phylotypes for all three libraries, e.g. those related to Klebsiella, Citrobacter, Enterobacter, Pectobacterium and Serratia. LIBSHUFF analysis showed that the bacterial communities of B. dorsalis from the three populations were significantly different from each other (P < 0·0085).

CONCLUSIONS

(i) The intestinal tract of B. dorsalis adult contains a diverse bacterial community, some of which are stable. (ii) Different environmental conditions and food supply could influence the diversity of the harboured bacterial communities and increase community variations.

SIGNIFICANCE AND IMPACT OF THE STUDY

Comparison of the microbial compositions and common bacterial species found in this paper may be very important for the biocontrol of B. dorsalis.

Investigation of biota associated and natural infection by sporulated bacteria in Culicidae larvae from São Paulo state, Brazil

The aim of this study was to investigate the naturally occurring bacteria from Culicidae larvae found in São Paulo state between 2006 and 2008 from the Tiete Ecological Park in the municipality of Caraguatatuba. Bacterial strains were obtained after surface sterilization of larvae followed by thermal treatment and incubation in bacteriological media under laboratory conditions. Identification was determined using cytomorphology, biochemical and physiological tests. Strains were characterized by qualitative evaluation of biological activity against Culicidae larvae, comparing protein profiles obtained by electrophoresis of crystal protoxins, electrophoresis of Lysinibacillus sphaericus isoenzymes, detection of the L(2) fraction of Hemolytic BL enterotoxin and amplification of DNA using Multiplex-PCR to detect HBL, NHE, CytK, BceT and EntFM enterotoxins. The results obtained in this study demonstrated that the endosymbiotic bacterial diversity belonging to Bacillus and related genera associated with Culicidae larvae is limited to a number of species that does not vary throughout the seasons.

Limited endosymbiont variation in Diuraphis noxia (Hemiptera: Aphididae) biotypes from the United States and South Africa

Symbiosis allows an insect access to imbalanced food sources on which other organisms cannot survive. A bacterial endosymbiont, Buchnera aphidicola, gives aphids the ability to feed on phloem depleted of certain essential amino acids by producing those required. Pseudogenes and lower plasmid copy numbers of essential amino acid genes in B. aphidicola, endosymbiont of the Russian wheat aphid, Diuraphis noxia (Kurdjumov) (Hemiptera: Aphididae), suggest that this symbiotic relationship is degenerating. The complete endosymbiont assemblages, copy numbers of plasmids (important in essential amino acid production), and sequence variation in B. aphidicola, from 10 Russian wheat aphid biotypes, were investigated. B. aphidicola was found to be monosymbiotic in the Russian wheat aphid biotypes and other Diuraphis species examined. An insert, occurring in an inverted repeat region on the leucine plasmid, was the only variation found in the approximately 10-kb B. aphidicola sequence analyzed from each Russian wheat aphid biotype. This inverted repeat was shown previously to be conserved within the family Aphididae. The insert occurred in B. aphidicola sequences isolated from four Russian wheat aphid biotypes. Copy numbers of the leucine plasmid differ between the South African and U.S. biotypes and were similar to previously reported values for biotypes from the same geographic regions. These results suggest that B. aphidicola may still contribute to Russian wheat aphid fitness when the aphid feeds on a variety of hosts.

Impact of cadmium on the bacterial communities in the gut of Metaphire posthuma

The effects of cadmium (Cd) contamination in soil onto the bacterial communities of the guts pooled from ten Metaphire posthuma were addressed during 14 days' incubation. We found that about 50% of Cd (5mg/kg, dry weight soil) in the contaminated soil was bio-accumulated into the earthworms. DNA was extracted from the guts of M. posthuma and their dwelling soil irrespective of Cd treatment for the analysis of the bacterial communities of guts in M. posthuma and in soil by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis). A distinctive cluster of bacterial communities of the guts in the earthworm with and without Cd treatment using the analysis of unweighted pair-group method using arithmetic averages (UPGMA) was observed, indicating that the bacterial community of guts could be changed by Cd. However, no differences in the bacterial communities in soil irrespective of Cd treatment were observed, which could be resulted from the bioremediation of Cd by earthworms leading to insignificant effect of Cd on bacterial communities in soil. For the sequencing of some of the dominant bands in the DGGE profile, Bradyrhizobium japonicum, Stenotrophomonas sp. D2, and Labrys, sp. CC-BB4, whose sequences display an identity of more than 97% using blast program against a known sequence in the GeneBank database and Ribosomal database, were identified. Collectively, our results showed that earthworm treatment can decrease the concentrations of Cd in soil, and Cd cause a shift in the bacterial communities in the guts of M. posthuma. The application of M. posthuma for Cd bioremediation would be desired.

An intracellular symbiont and other microbiota associated with field-collected populations of sawflies (Hymenoptera: Symphyta)

Six species of sawfly (Hymenoptera: Symphyta) from four taxonomic families (Agridae, Diprionidae, Pamphiliidae, and Tenthredinidae) were collected from locations across Canada and surveyed for their associated microbiota. Total DNA was extracted from individual insects, and polymerase chain reaction (PCR) was used to amplify the conserved 16S rRNA gene from microbiota. Denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) were undertaken to separate bacterial clones associated with the host insect. Sequencing of the PCR–DGGE and PCR–RFLP products revealed a dominance of α- and γ-Proteobacteria, with most sequences showing high similarity to bacteria previously identified from other insect species and environmental samples. Additionally, a strain of the bacterial endosymbiont Wolbachia and a Wolbachia bacteriophage were identified from the mountain ash sawfly ( Pristiphora geniculata ).

Autochthonous bacterial flora indicated by PCR-DGGE of 16S rRNA gene fragments from the alimentary tract of Costelytra zealandica (Coleoptera: Scarabaeidae)

AIMS

To locate and identify putative autochthonous bacteria within the grass grub gut that may have a role in symbiosis.

METHODS AND RESULTS

Polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) fingerprinting was used to investigate bacterial diversity in the grass grub larval gut. The microbial community profiles from five geographically distinct populations were compared and the influence of feeding was analysed. Bacterial community in the midgut was highly variable between locations and was affected by feeding. The hindgut contained a more diverse but stable bacterial community that was less affected by external conditions. Forty-seven distinct DGGE bands, representing different bacterial genotypes, could be distinguished from all samples, with 34 different bands occurring in the hindgut. The 22 most common bands were isolated and DNA was sequenced. Sequence analysis revealed that most bacteria (16/22) were affiliated to the Clostridiales with the predominant bacteria affiliated to the genus Clostridium. The remaining bacteria were aligned to the Betaproteobacteria, Deltaproteobacteria and Bacteroidetes.

CONCLUSIONS

The grass grub larva has an autochthonous microflora with predominance of Clostridium spp. in the hindgut.

SIGNIFICANCE AND IMPACT OF THE STUDY

Occurrence of an autocthonous microflora in the grass grub hindgut suggests a symbiotic relationship which could help explain the ability of larval scarabs to feed on recalcitrant organic matter.

Diversity of insect intestinal microflora

The influence of geographic location, season, age, and part of the digestive tract on bacterial diversity was evaluated on intestinal microflora of honeybees, wasps, and cockroaches using DGGE analysis. PCR-DGGE analyses with universal bacterial primers targeting 200-bp region of the 16S rDNA gene afforded the profile of complex bacterial DNA; specific primers were used to determine the profile of bifidobacteria whose concentration in digestive tract was determined by real-time PCR. Selected PCR products were identified by sequencing. The microflora of the bees exhibited little variations among the hives from distant locations. Their bifidobacterial population formed 2.8-8.4 % of total bacteria and was very homogeneous. The total gut microflora of wasps was also homogeneous, only two samples being affected by the season or the location; on the other hand, wasp bifidobacterial population was very heterogeneous. Cockroaches showed the highest variations in microflora composition, the age and diet being the ultimate factors; bifidobacteria counts also varied among tested individuals (0.1-34.1 % of total bacteria). Our results suggest that nutrition habits are the strongest factor affecting the insect microflora, giving higher variations to omnivorous species.

Application of denaturing gradient gel electrophoresis for analysing the gut microflora of Lumbricus rubellus Hoffmeister under different feeding conditions

The earthworm, Lumbricus rubellus, plays an essential role in soil ecosystems as it affects organic matter decomposition and nutrient cycling. By ingesting a mixture of organic and mineral material, a variety of bacteria and fungi are carried to the intestinal tract of the earthworm. To get a better understanding of the interactions between L. rubellus and the microorganisms ingested, this study tried to reveal if the diet affects the composition of the gut microflora of L. rubellus or if its intestinal tract hosts an indigenous, species-specific microbiota. A feeding experiment with L. rubellus was set up; individuals were collected in the field, transferred to a climate chamber and fed with food sources of different quality (dwarf shrub litter, grass litter or horse dung) for six weeks. DNA was extracted from the guts of the earthworms, as well as from the food sources and the surrounding soil, and further analysed by a molecular fingerprinting method, PCR-DGGE (Polymerase Chain Reaction -- Denaturing Gradient Gel Electrophoresis). We were able to demonstrate that the gut microbiota was strongly influenced by the food source ingested and was considerably different to that of the surrounding soil. Sequencing of dominant bands of the bacterial DGGE fingerprints revealed a strong occurrence of y-Proteobacteria in all gut samples, independent of the food source. A specific microflora in the intestinal tract of L. rubellus, robust against diet changes, could not be found.

How to get more out of molecular fingerprints: practical tools for microbial ecology

Community-level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), single-strand conformation polymorphism (SSCP), length heterogeneity-PCR (LH-PCR), terminal-restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a setting-independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness (Rr) reflecting the carrying capacity of the system, (ii) the dynamics (Dy) reflecting the specific rate of species coming to significance, and (iii) functional organization (Fo), defined through a relation between the structure of a microbial community and its functionality. These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern.

Composition of Acridid gut bacterial communities as revealed by 16S rRNA gene analysis

The gut bacterial community from four species of feral locusts and grasshoppers was determined by denaturing gradient gel electrophoresis (DGGE) analysis of bacterial 16S rRNA gene fragments. The study revealed an effect of phase polymorphism on gut bacterial diversity in brown locusts from South Africa. A single bacterial phylotype, consistent with Citrobacter sp. dominated the gut microbiota of two sympatric populations of Moroccan and Italian locusts in Spain. There was evidence for Wollbachia sp. in the meadow grasshopper caught locally in the UK. Sequence analysis of DGGE products did not reveal evidence for unculturable bacteria and homologies suggested that bacterial species were principally Gammaproteobacteria from the family Enterobacteriaceae similar to those recorded previously in laboratory reared locusts.

Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster

Drosophila melanogaster is one of the most widely used model systems in biology. However, little is known about its associated bacterial community. As a first step towards understanding these communities, we compared bacterial 16S rRNA gene sequence libraries recovered from 11 natural populations of adult D. melanogaster. Bacteria from these sequence libraries were grouped into 74 distinct taxa, spanning the phyla Proteobacteria, Bacteroidetes, and Firmicutes, which were unevenly spread across host populations. Summed across populations, the distribution of abundance of genera was closely fit by a power law. We observed differences among host population locations both in bacterial community richness and in composition. Despite this significant spatial variation, no relationship was observed between species richness and a variety of abiotic factors, such as temperature and latitude. Overall, bacterial communities associated with adult D. melanogaster hosts are diverse and differ across host populations.

Microbial communities in the larval midgut of laboratory and field populations of cotton bollworm (Helicoverpa armigera)

We compared the bacterial communities in the larval midgut of field and laboratory populations of a polyphagous pest, the cotton bollworm (Helicoverpa armigera), using denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA sequences and 16S library sequence analysis. DGGE profiles and 16S rDNA library sequence analysis indicated similar patterns of midgut microbial community structure and diversity: specific bacterial types existed in both populations, and a more diverse microbial community was observed in caterpillars obtained from the field. The laboratory population harbored a rather simple gut microflora consisting mostly of phylotypes belonging to Enterococcus (84%). For the field population, phylotypes belonging to Enterococcus (28%) and Lactococcus (11%), as well as Flavobacterium (10%), Acinetobacter (19%), and Stenotrophomonas (10%) were dominant members. These results provided the first comprehensive description of the microbial diversity of the midgut of the important pest cotton bollworm and suggested that the environment and food supply might influence the diversity of the gut bacterial community.

Molecular analysis of microbial communities identified in different developmental stages of Ixodes scapularis ticks from Westchester and Dutchess Counties, New York

Ixodes scapularis ticks play an important role in the transmission of a wide variety of pathogens between various mammalian species, including humans. Pathogens transmitted by ticks include Borrelia, Anaplasma and Babesia. Although ticks may harbour both pathogenic and non-pathogenic microflora, little is known about how the diversity of the microflora within ticks may influence the transmission of pathogens. To begin addressing this question, we examined the composition of bacterial communities present in Ixodes scapularis collected from Westchester and Dutchess Counties, New York State, at different developmental and nutritional stages. Genetic fingerprints of bacterial populations were generated by temporal temperature gradient gel electrophoresis (TTGE) separation of individual polymerase chain reaction (PCR)-amplified 16S rRNA gene fragments, followed by DNA sequence analysis for bacterial identification. The fingerprints of the TTGE bands were grouped into five clusters. The most abundant DNA sequence found in all the samples was Rickettsia, followed by Pseudomonas and Borrelia. Ralstonia, Anaplasma, Enterobacterias, Moraxella, Rhodococcus and uncultured proteobacterium were present as well. We also determined the prevalence of Anaplasma phagocytophilum and Borrelia burgdorferi by PCR and DNA sequence analysis. Statistical analyses indicated significant variations in the bacterial communities depending on tick developmental stage and degree of engorgement. We suggest that these two elements affect microbial diversity within the tick and may in turn influence pathogen transmission to humans and animals after tick bite.

Antagonistic interactions between honey bee bacterial symbionts and implications for disease

Background

Honey bees, Apis mellifera, face many parasites and pathogens and consequently rely on a diverse set of individual and group-level defenses to prevent disease. One route by which honey bees and other insects might combat disease is through the shielding effects of their microbial symbionts. Bees carry a diverse assemblage of bacteria, very few of which appear to be pathogenic. Here we explore the inhibitory effects of these resident bacteria against the primary bacterial pathogen of honey bees, Paenibacillus larvae.

Results

Here we isolate, culture, and describe by 16S rRNA and protein-coding gene sequences 61 bacterial isolates from honey bee larvae, reflecting a total of 43 distinct bacterial taxa. We culture these bacteria alongside the primary larval pathogen of honey bees, Paenibacillus larvae, and show that many of these isolates severely inhibit the growth of this pathogen. Accordingly, symbiotic bacteria including those described here are plausible natural antagonists toward this widespread pathogen.

Conclusion

The results suggest a tradeoff in social insect colonies between the maintenance of potentially beneficial bacterial symbionts and deterrence at the individual and colony level of pathogenic species. They also provide a novel mechanism for recently described social components behind disease resistance in insect colonies, and point toward a potential control strategy for an important bee disease.

Diversity and phylotype consistency of bacteria in the guts of three bee species (Apoidea) at an oilseed rape field

The gut of insects may harbour one of the largest reservoirs of a yet unexplored microbial diversity. To understand how specific insects select for their own bacterial communities, the structural diversity and variability of bacteria found in the gut of different bee species was analysed. For three successive years, adults and larvae of Apis mellifera ssp. carnica (honey bee), and Bombus terrestris (bumble bee), as well as larvae of Osmia bicornis (red mason bee) were collected at a flowering oilseed rape field. Total DNA was extracted from gut material and the bacterial diversity was analysed, independent of cultivation, by genetic profiling with single-strand conformation polymorphism (SSCP) of polymerase chain reaction (PCR)-amplified partial 16S rRNA genes. The SSCP profiles were specific for all bee species and for larvae and adults. Qualitative and quantitative differences were found in the bacterial community structure of larvae and adults of A. mellifera, but differences in B. terrestris were mainly quantitative. Sequencing of the PCR products revealed a dominance of Alpha-, Beta-, and Gammaproteobacteria, Bacteroidetes, and Firmicutes in all bee species. Single-strand conformation polymorphism profiles suggested a higher abundance and diversity of lactobacilli in adults of A. mellifera than in larvae. Further phylogenetic analyses indicated common bacterial phylotypes for all three bee species, e.g. those related to Simonsiella, Serratia, and Lactobacillus. Clades related to Delftia acidovorans, Pseudomonas aeruginosa or Lactobacillus intestinalis only contained sequences from larvae. Several of the bee-specific clusters also contained identical or highly similar sequences from bacteria detected in other A. mellifera subspecies from South Africa, suggesting the existence of cosmopolitan gut bacteria in bees.

Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of endodontic infections

The recent expanding use of cultivation-independent techniques for bacterial identification is reliant on the lack of knowledge of the conditions under which most bacteria are growing in their natural habitat and the difficulty to develop culture media that accurately reproduce these conditions. A molecular method that has been recently used in several areas to examine the bacterial diversity living in diverse environments is the denaturing gradient gel electrophoresis (DGGE). In DGGE, polymerase chain reaction (PCR)-generated DNA fragments of the same length but with different base-pair sequences can be separated. Separation is based on electrophorectic mobility of a partially melted double-strand DNA molecule in polyacrylamide gels, which is decreased when compared with that of the completely helical form of the molecule. Molecules with different sequences may have a different melting behavior and will therefore stop migrating at different positions in the gel. Application of the PCR-DGGE method in endodontic research has revealed that there are significant differences in the predominant bacterial composition between asymptomatic and symptomatic cases. This suggests that the structure of the bacterial community can play a role in the development of symptoms. In addition, new bacterial phylotypes have been disclosed in primary endodontic infections. PCR-DGGE has also confirmed that intra-radicular infections are a common finding in root-filled teeth associated with persistent periradicular lesions. The microbiota in failed cases significantly vary from teeth to teeth, with a mean number of species far higher than previously shown by culturing approaches. Application of the PCR-DGGE technique in endodontic microbiology research has the potential to shed light on several aspects of the different types of endodontic infection as well as on the effects of treatment procedures with regard to infection control.

Assessment of prey overlap between a native (Polistes humilis) and an introduced (Vespula germanica) social wasp using morphology and phylogenetic analyses of 16S rDNA

Abstract In newly invaded communities, interspecific competition is thought to play an important role in determining the success of the invader and its impact on the native community. In southern Australia, the native Polistes humilis was the predominant social wasp prior to the arrival of the exotic Vespula germanica (Hymenoptera: Vespidae). Both species forage for similar resources (water, pulp, carbohydrate and protein prey), and concerns have arisen about potential competition between them. The aim of this study was to identify the protein foods that these wasps feed on. As many prey items are masticated by these wasps to the degree that they cannot be identified using conventional means, morphological identification was complemented by sequencing fragments of the mitochondrial 16S rRNA gene. GenBank searches using blast and phylogenetic analyses were used to identify prey items to at least order level. The results were used to construct complete prey inventories for the two species. These indicate that while P. humilis is restricted to feeding on lepidopteran larvae, V. germanica collects a variety of prey of invertebrate and vertebrate origin. Calculated values of prey overlap between the two species are used to discuss the implications of V. germanica impacting on P. humilis. Results obtained are compared to those gained by solely 'conventional' methods, and the advantages of using DNA-based taxonomy in ecological studies are emphasized.

PCR-DGGE fingerprinting: novel strategies for detection of microbes in food

Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting was recently introduced into food microbiology. This paper describes the technique and reports on the state-of-the-art application of this technique to food and food-related ecosystems. Applications of PCR-DGGE in several fields of food microbiology are reviewed: the identification of microorganisms isolated from food, the evaluation of microbial diversity during food fermentation, and microbiological and commercial food quality assessment. Potentials and limitations of this culture-independent approach in food microbiology are indicated and future perspectives are discussed.