scholarly journals First Insight into Microbiome Profiles of Myrmecophilous Beetles and Their Host, Red Wood Ant Formica polyctena (Hymenoptera: Formicidae)—A Case Study

Insects ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 134 ◽  
Author(s):  
Agnieszka Kaczmarczyk-Ziemba ◽  
Mirosław Zagaja ◽  
Grzegorz K. Wagner ◽  
Ewa Pietrykowska-Tudruj ◽  
Bernard Staniec
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Species Group ◽  
Rrna Gene ◽  
Illumina Platform ◽  
Abundance Pattern ◽  
Formica Polyctena ◽  
Wide Range ◽  
Species Specific ◽  
Red Wood Ant

Formica polyctena belongs to the red wood ant species group. Its nests provide a stable, food rich, and temperature and humidity controlled environment, utilized by a wide range of species, called myrmecophiles. Here, we used the high-throughput sequencing of the 16S rRNA gene on the Illumina platform for identification of the microbiome profiles of six selected myrmecophilous beetles (Dendrophilus pygmaeus, Leptacinus formicetorum, Monotoma angusticollis, Myrmechixenus subterraneus, Ptenidium formicetorum and Thiasophila angulata) and their host F. polyctena. Analyzed bacterial communities consisted of a total of 23 phyla, among which Proteobacteria, Actinobacteria, and Firmicutes were the most abundant. Two known endosymbionts—Wolbachia and Rickettsia—were found in the analyzed microbiome profiles and Wolbachia was dominant in bacterial communities associated with F. polyctena, M. subterraneus, L. formicetorum and P. formicetorum (>90% of reads). In turn, M. angusticollis was co-infected with both Wolbachia and Rickettsia, while in the microbiome of T. angulata, the dominance of Rickettsia has been observed. The relationships among the microbiome profiles were complex, and no relative abundance pattern common to all myrmecophilous beetles tested was observed. However, some subtle, species-specific patterns have been observed for bacterial communities associated with D. pygmaeus, M. angusticollis, and T. angulata.

scholarly journals Multipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial Perspective

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Marta Turon ◽  
Maria J. Uriz ◽  
Daniel Martin
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Marine Invertebrates ◽  
Single Species ◽  
Rrna Gene ◽  
Polychaete Species ◽  
Content Type ◽  
Symbiotic Relationships ◽  
Host Sponge ◽  
Species Specific

ABSTRACTSponges establish tight associations with both micro- and macroorganisms. However, while studies on sponge microbiomes are numerous, nothing is currently known about the microbiomes of sponge-associated polychaetes and their relationships with those of their host sponges. We analyzed the bacterial communities of symbiotic polychaetes (Haplosyllisspp.) and their host sponges (Clathria reinwardti,Amphimedon paraviridis,Neofibularia hartmani, andAaptos suberitoides) to assess the influence of the sponges on the polychaete microbiomes. We identified both eukaryote partners by molecular (16S and COI genes) and morphological features, and we identified their microbial communities by high-throughput sequencing of the 16S rRNA gene (V4 region). We unravel the existence of sixHaplosyllisspecies (five likely undescribed) associated at very high densities with the study sponge species in Nha Trang Bay (central Vietnam). A single polychaete species inhabitedA. paraviridisand was different from the single species that inhabitedA. suberitoides. Conversely, two different polychaete species were found inC. reinwardtiandN. hartmani, depending on the two host locations. Regardless of the host sponge, polychaete microbiomes were species specific, which is a widespread feature in marine invertebrates. More than half of the polychaete bacteria were also found in the host sponge microbiome but at contrasting abundances. Thus, the associated polychaetes seemed to be able to select, incorporate, and enrich part of the sponge microbiome, a selection that appears to be polychaete species specific. Moreover, the bacterial diversity is similar in both eukaryotic partners, which additionally confirms the influence of food (host sponge) on the structure of the polychaete microbiome.IMPORTANCEThe symbiotic lifestyle represents a fundamental cryptic contribution to the diversity of marine ecosystems. Sponges are ideal targets to improve understanding the symbiotic relationships from evolutionary and ecological points of view, because they are the most ancient metazoans on earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn also harbor their own bacterial communities. Here, we study the microbiomes of sponge-polychaete associations and confirm that polychaetes feed on their host sponges. The study worms select and enrich part of the sponge microbiome to shape their own species-specific bacterial communities. Moreover, worm microbiome diversity runs parallel to that of its food host sponge. Considering our results on symbiotic polychaetes and previous studies on fishes and mammals, diet appears to be an important source of bacteria for animals to shape their species-specific microbiomes.

scholarly journals Termites Are Associated with External Species-Specific Bacterial Communities

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Patrik Soukup ◽  
Tomáš Větrovský ◽  
Petr Stiblik ◽  
Kateřina Votýpková ◽  
Amrita Chakraborty ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Negative Effects ◽  
Termite Species ◽  
Positive Effects ◽  
Operational Taxonomic Units ◽  
Wide Range ◽  
Species Specific ◽  
And Control

ABSTRACT All termites have established a wide range of associations with symbiotic microbes in their guts. Some termite species are also associated with microbes that grow in their nests, but the prevalence of these associations remains largely unknown. Here, we studied the bacterial communities associated with the termites and galleries of three wood-feeding termite species by using 16S rRNA gene amplicon sequencing. We found that the compositions of bacterial communities among termite bodies, termite galleries, and control wood fragments devoid of termite activities differ in a species-specific manner. Termite galleries were enriched in bacterial operational taxonomic units (OTUs) belonging to Rhizobiales and Actinobacteria, which were often shared by several termite species. The abundance of several bacterial OTUs, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus, was reduced in termite galleries. Our results demonstrate that both termite guts and termite galleries harbor unique bacterial communities. IMPORTANCE As is the case for all ecosystem engineers, termites impact their habitat by their activities, potentially affecting bacterial communities. Here, we studied three wood-feeding termite species and found that they influence the composition of the bacterial communities in their surrounding environment. Termite activities have positive effects on Rhizobiales and Actinobacteria abundance and negative effects on the abundance of several ubiquitous genera, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus. Our results demonstrate that termite galleries harbor unique bacterial communities.

scholarly journals Microbiomes of the Arctic carnivorous sponges Chondrocladia grandis and Cladorhiza oxeata suggest a specific, but differential involvement of bacterial associates

2018 ◽  
Vol 4 (2) ◽  
pp. 186-204 ◽  
Author(s):  
Joost T.P. Verhoeven ◽  
Suzanne C. Dufour
Keyword(s):  
Bacterial Communities ◽  
Gulf Of Maine ◽  
Bacterial Community Composition ◽  
Isotope Analysis ◽  
Taxonomic Diversity ◽  
The Arctic ◽  
Sponge Species ◽  
Rrna Gene ◽  
Wide Range ◽  
Species Specific

While sponges are generally known to host a wide range of microbial associates, the composition and specificity of the microbial communities in carnivorous sponges are poorly understood. We used 16S rRNA gene data to examine and compare the bacterial communities associated with distinct anatomical regions of two carnivorous sponge species, Chondrocladia grandis and Cladorhiza oxeata, sampled from Baffin Bay and the Gulf of Maine (C. grandis only). The two sponge species hosted distinct bacterial communities, with taxonomic diversity being greater in C. grandis. Some bacterial taxa (including particular oligotypes) were consistently recovered in multiple host individuals from geographically distant sites, suggesting specificity. Within C. grandis, certain bacterial taxa were enriched in particular anatomical regions, suggesting functional roles in carnivorous sponge metabolism or other biological processes. Stable isotope analysis provided no evidence for methanotrophy in the sponges examined, but Gulf of Maine C. grandis might incorporate 13C-depleted carbon via the bacteria-mediated heterotrophic degradation of other hydrocarbons. Overall, our results demonstrate that the carnivorous sponge microbiome appears host species specific and stable, even over large geographical areas. The observed differences in bacterial community composition and diversity between C. grandis and C. oxeata may reflect differences in trophic adaptability, specialization, and overall reliance on associated bacteria.

Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽  
2009 ◽  
Vol 11 (6) ◽  
pp. 847-857 ◽  
Author(s):  
Lieven Waeyenberge ◽  
Nicole Viaene ◽  
Maurice Moens
Keyword(s):  
Internal Control ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Duplex Pcr ◽  
Specific Primers ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Wide Range ◽  
Pcr Products ◽  
Species Specific

Abstract ITS1, the 5.8S rRNA gene and ITS2 of the rDNA region were sequenced from 20 different Pratylenchus species. Additionally, the same region was sequenced from seven populations of P. penetrans. After purifying, cloning and sequencing the PCR products, all sequences were aligned in order to find unique sites suitable for the design of species-specific primers for P. penetrans. Since ITS regions showed variability between and even within populations of P. penetrans, only three small DNA sequences were suitable for the construction of three potentially useful species-specific primers. New species-specific primers were paired with existing universal ITS primers and tested in all possible primer combinations. The best performing primer set, supplemented with a universal 28S rDNA primer set that served as an internal control, was tested in duplex PCR. The ideal annealing temperature, Mg2+ concentration and primer ratios were then determined for the most promising primer set. The optimised duplex PCR was subsequently tested on a wide range of different Pratylenchus spp. and 25 P. penetrans populations originating from all over the world. To test the sensitivity, the duplex PCR was conducted on DNA extracted from a single P. penetrans nematode mixed with varying amounts of nematodes belonging to another Pratylenchus species. Results showed that a reliable and sensitive P. penetrans species-specific duplex PCR was constructed.

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

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

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

scholarly journals The differences of bacterial communities in the tissues between healthy and diseased Yesso scallop (Patinopecten yessoensis)

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zichao Yu ◽  
Chao Liu ◽  
Qiang Fu ◽  
Guangxia Lu ◽  
Shuo Han ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Bacterial Communities ◽  
Prevention And Control ◽  
High Throughput Sequencing ◽  
Northern China ◽  
Adductor Muscle ◽  
Rrna Gene ◽  
Patinopecten Yessoensis ◽  
Yesso Scallop ◽  
And Control

Abstract The tissues of marine invertebrates are colonized by species-rich microbial communities. The dysbiosis of host’s microbiota is tightly associated with the invertebrate diseases. Yesso scallop (Patinopecten yessoensis), one of the most important maricultured scallops in northern China, has recently suffered massive summer mortalities, which causes huge production losses. The knowledge about the interactions between the Yesso scallop and its microbiota is important to develop the strategy for the disease prevention and control. In the present study, the bacterial communities in hemolymph, intestine, mantle and adductor muscle were compared between the healthy and diseased Yesso scallop based on the high-throughput sequencing of 16S rRNA gene. The results indicated obvious difference of the composition rather than the diversity of the bacterial communities between the healthy and diseased Yesso scallop. Vibrio, Francisella and Photobacterium were found to overgrow and dominate in the mantle, adductor muscle and intestine of the diseased scallops, respectively. The prediction of bacterial community metagenomes and the variations of KEGG pathways revealed that the proportions of the pathways related with neurodegenerative diseases and carbohydrate metabolism both increased significantly in the mantle and hemolymph of the diseased scallops. The abundance of the metabolism pathways including carbohydrate metabolism, lipid metabolism and amino acid metabolism decreased significantly in the intestine of diseased scallops. The results suggested that the changes of bacterial communities might be closely associated with the Yesso scallop’s disease, which was helpful for further investigation of the pathogenesis as well as prevention and control of the disease in Yesso scallop.

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

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

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

scholarly journals Influence of Bactrocera Dorsalis Larval Gut Bacteria on its Susceptibility to the Entomopathogenic Fungus, Metarhizium Anisopliae

2020 ◽  
Author(s):  
Joseph Gichuhi ◽  
Fathiya Khamis ◽  
Johnnie Van den Berg ◽  
Samira Mohamed ◽  
Sunday Ekesi ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Metarhizium Anisopliae ◽  
Entomopathogenic Fungus ◽  
High Throughput Sequencing ◽  
Gut Bacteria ◽  
Bactrocera Dorsalis ◽  
Rrna Gene ◽  
Standard Dosage ◽  
Germ Free ◽  
Wide Range

Abstract Symbiotic interactions between insects and bacteria have been associated with a vast variety of physiological, ecological and evolutionary consequences for the host. A wide range of bacterial communities have been found in association with the oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), an important pest of cultivated fruit in most regions of the world. We evaluated the diversity of gut bacteria in B. dorsalis specimens from several populations in Kenya and investigated the roles of individual bacterial isolates in the development of axenic B. dorsalis fly lines and their responses to the entomopathogenic fungus, Metarhizium anisopliae. We utilized a high throughput sequencing approach of the bacterial 16S rRNA gene to evaluate microbiomes, coupled with culture and mono-association for the assay. The shortest embryonic development period was recorded in flies with an intact gut microbiome while the longest period was recorded in germ-free fly lines. Similarly, larval development was shortest in flies with an intact gut microbiome. Adult B. dorsalis flies emerging from embryos inoculated with a strain of Lactococcus lactis had decreased survival when challenged with a standard dosage of M. anisopliae ICIPE69 conidia. However, there were no differences in survival between the germ-free lines and flies with an intact microbiome. These findings contribute to the selection of probiotics used in artificial diets for B. dorsalis rearing and the development of improved integrated pest management strategies based on entomopathogenic fungi.

scholarly journals Influence of Heat Events on the Composition of Airborne Bacterial Communities in Urban Ecosystems

2018 ◽  
Vol 15 (10) ◽  
pp. 2295 ◽  
Author(s):  
Zhiguo Fang ◽  
Weijun Guo ◽  
Junwen Zhang ◽  
Xiuqin Lou
Keyword(s):  
High Temperature ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Urban Ecosystems ◽  
Gene Copy ◽  
Airborne Bacteria ◽  
Rrna Gene ◽  
Before And After ◽  
Hot Weather ◽  
Heat Events

Airborne bacteria are significantly affected by meteorological and environmental conditions. However, there is little quantitative data available on the effects of these factors on airborne bacteria in urban ecosystems. In the present study, we analyzed weather-dependent changes in the composition of airborne bacterial communities using high throughput sequencing. Samples were collected before and after a period of constant hot weather at four selected sampling sites (YRBS, ZJGUSJC, TJCR, and BLQG) in Hangzhou. Our results show that the average amount of bacterial 16S rRNA gene copy numbers per m3 of air decreased significantly after constant high temperature. In addition, the number of operational taxonomic units and the Shannon–Wiener diversity indexes of the samples at all four selected sampling sites were significantly decreased after the heat event, showing notable impact on bacterial diversity. We also detected a significant increase in the abundances of spore-forming bacteria. Firmicutes increased from 3.7% to 9.9%, Bacillales increased from 2.6% to 7.6%, and Bacillaceae increased from 1.5% to 5.9%. In addition, we observed an increase in beta-Proteobacteria (18.2% to 50.3%), Rhodocyclaceae (6.9% to 29.9%), and Burkholderiaceae (8.1% to 15.2%). On the other hand, the abundance of alpha-Proteobacteria (39.6% to 9.8%), Caulobacteraceae (17.9% to 0.5%), Sphingomonadaceae (7.2% to 3.3%), and Xanthomonadaceae (3.0% to 0.5%) was significantly lower. Taken together, our data suggest that the composition of airborne bacterial communities varies greatly dependent on heat events, and that such communities include several species that are highly susceptible to high-temperature related stressors such as high air temperature, low relative humidity, and high intensity of solar radiation.

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

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

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

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