A first insight into the intestinal microbiota of snow trout (<Emphasis Type="Italic">Schizothorax zarudnyi</Emphasis>)

This study addresses the biodiversity profile of bacterial community in the intestinal lumen and mucosa of snow trout fish by applying 16S rRNA gene 454-pyrosequencing. A total of 209,106 sequences with average length 689 (±53) were filtered, denoised, trimmed, and then sorted into OTUs based on 97 % sequence similarity using the USEARCH software pipeline. Bacteria representing 10 phyla were found in the samples investigated. Fimicutes ribotypes were present in intestinal-mucosa and lumen in all fish and often dominated the libraries (average 43 and 38 %, respectively). Proteobacteria were also prevalent, but at a lower relative abundance, at 22 and 29 % in mucosa and lumen, respectively. The autochthonous microbiota was dominated by sequences belonging to the Bacilli (mean sequence abundance 24 %), in particular the Lactobacillaceae, with Lactobacillus and Pediococcous being the most abundant genera. Fewer Bacilli (mean sequence abundance 22 %) and Actinobacteria (2 %) were present in the lumen, and allochthonous communities consisted of a more even split among the bacterial classes, with increases in sequences assigned to members of the γ-Proteobacteria (16 %) and Fusobacteriia (8 %). The principal bacterial genera recorded in the lumen belonged to the lactic acid bacteria group, Cetobacterium, Clostridium and Synechococcus. Results obtained suggest that the lumen and mucosal layer of the snow trout intestine may host different microbial communities. Moreover, both regions harbour a diverse microbiome with a greater microbial diversity in the intestinal mucus compared with the luminal communities of the fish. Many of these microbes might be of high physiological relevance for the fish and may play key roles in the functioning of its gut.     

Degradation capacities of bacteria and yeasts isolated from the gut of <Emphasis Type="Italic">Dendroctonus rhizophagus</Emphasis> (Curculionidae: Scolytinae)

Bark beetles (Curculionidae: Scolytinae) feed on the xylem and phloem of their host, which are composed of structural carbohydrates and organic compounds that are not easily degraded by the insects. Some of these compounds might be hydrolyzed by digestive enzymes produced by microbes present in the gut of these insects. In this study, we evaluated the enzymatic capacity of bacteria (Acinetobacter lwoffii, Arthrobacter sp., Pseudomonas putida, Pseudomonas azotoformans, and Rahnella sp.) and yeasts (Candida piceae, Candida oregonensis, Cyberlindnera americana, Zygoascus sp., and Rhodotorula mucilaginosa) isolated from the Dendroctonus rhizophagus gut to hydrolyze cellulose, xylan, pectin, starch, lipids, and esters. All isolates, with the exception of C. piceae, showed lipolytic activity. Furthermore, P. putida, P. azotoformans, C. americana, C. piceae, and R. mucilaginosa presented amylolytic activity. Esterase activity was shown by A. lwoffii, P. azotoformans, and Rahnella sp. Cellulolytic and xylanolytic activities were present only in Arthrobacter sp. and P. azotoformans. The pectinolytic activity was not recorded in any isolate. This is the first study to provide evidence on the capacity of microbes associated with the D. rhizophagus gut to hydrolyze specific substrates, which might cover part of the nutritional requirements for the development, fitness, and survival of these insects.     

The bacterial community associated with rose-scented geranium (<Emphasis Type="Italic">Pelargonium graveolens</Emphasis>) leaves responds to anthracnose symptoms

Background

The fungus Colletotrichum is a plant pathogen that causes the anthracnose disease, resulting in huge losses in various crops including the rose-scented geranium (Pelargonium graveolens). Although the bacterial community associated with plants has an important role in the establishment of plant diseases, little is known about what happens in P. graveolens.

Aims

To increase the knowledge about the bacterial community associated with P. graveolens and its relationship with anthracnose disease symptoms.

Methods

Quantitative PCR and high-throughput sequencing were combined to determine the presence of the fungus Colletotrichum and to reveal the bacterial communities associated with different plant parts – root, stem and leaf – and in the rhizosphere and bulk soil, and also to determine the respective bacterial communities associated with P. graveolens leaves symptomatic and asymptomatic for anthracnose disease.

Results

The fungus Colletotrichum was detected in all plant parts and in the surrounding soil. Bacterial communities varied spatially in plants, and the disease symptoms also influenced the composition of the bacterial community. Abundances of operational taxonomic units (OTUs) assigned to the phylum Actinobacteria and to the genus Streptococcus were greatly increased in asymptomatic leaves.

Conclusions

The bacterial community associated to geranium leaves responds to anthracnose symptoms.

     

Variations in bacterial and fungal communities through soil depth profiles in a <Emphasis Type="Italic">Betula albosinensis</Emphasis> forest

Microbial communities in subsurface soil are specialized for their environment, which is distinct from that of the surface communities. However, little is known about the microbial communities (bacteria and fungi) that exist in the deeper soil horizons. Vertical changes in microbial alpha-diversity (Chao1 and Shannon indices) and community composition were investigated at four soil depths (0–10, 10–20, 20–40, and 40–60 cm) in a natural secondary forest of Betula albosinensis by high-throughput sequencing of the 16S and internal transcribed spacer rDNA regions. The numbers of operational taxonomic units (OTUs), and the Chao1 and Shannon indices decreased in the deeper soil layers. Each soil layer contained both mutual and specific OTUs. In the 40–60 cm soil layer, 175 and 235 specific bacterial and fungal OTUs were identified, respectively. Acidobacteria was the most dominant bacterial group in all four soil layers, but reached its maximum at 40–60 cm (62.88%). In particular, the 40–60 cm soil layer typically showed the highest abundance of the fungal genus Inocybe (47.46%). The Chao1 and Shannon indices were significantly correlated with the soil organic carbon content. Redundancy analysis indicated that the bacterial communities were closely correlated with soil organic carbon content (P = 0.001). Collectively, these results indicate that soil nutrients alter the microbial diversity and relative abundance and affect the microbial composition.     

Composition and diversity of the bacterial community in snow leopard (<Emphasis Type="Italic">Uncia uncia</Emphasis>) distal gut

Intestinal microflora influences many essential metabolic functions, and is receiving increasing attention from the scientific community. However, information on intestinal microbiota, especially for large wild carnivores, is insufficient. In the present study, the bacterial community in the feces of snow leopards (Uncia uncia) was described based on 16S rRNA gene sequence analysis. A total of 339 near-full-length 16S rRNA gene sequences representing 46 non-redundant bacterial phylotypes (operational taxonomical units, OTUs) were identified in fecal samples from four healthy snow leopards. Four different bacterial phyla were identified: Firmicutes (56.5 %), Actinobacteria (17.5 %), Bacteroidetes (13 %), and Proteobacteria (13 %). The phylum Actinobacteria was the most abundant lineage, with 40.4 % of all identified clones, but Clostridiales, with 50 % of all OTUs, was the most diverse bacterial order. The order Clostridiales was affiliated with four families: Clostridiaceae I, Lachnospiraceae, Peptostreptococcaceae, and Ruminococcaceae. Lachnospiraceae was the most diverse family with 17 OTUs identified. These findings were basically consistent with previous reports on the bacterial diversity in feces from other mammals.     

Ethnicity influences gut metabolites and microbiota of the tribes of Assam,India

Introduction

The human gut microbes and their metabolites are involved in multiple host metabolic pathways. Dysbiosis in the gut microbiota and altered metabolite profiles were reported in diseased state. In a region like Assam, where 12.4% of the populations are tribal population, evaluating the influence of ethnicity on gut microbiota and metabolites has become important to further differentiate it from the diseased state.

Objective

To study the influence of ethnicity on fecal metabolite profile and their association with the gut microbiota composition.

Methods

In this study, we determined the untargeted fecal metabolites from five ethnic groups of Assam (Tai-Aiton, Bodo, Karbi, Tea-tribe and Tai-Phake) using GC–MS and compared them among the tribes for common and unique metabolites. Metabolites of microbial origin were related with the available metagenomic data on gut bacterial profiles of the same ethnic groups and functional analysis were carried out based on HMDB.

Results

The core fecal metabolite profile of the Tea-tribe contained aniline, benzoate and acetaldehyde. PLS-DA based on the metabolites suggested that the individuals grouped based on their ethnicity. PCA plot of the data on bacterial abundance at the level of genus indicated clustering of individuals based on ethnicity. Positive correlations were observed between propionic acid and the genus Clostridium (R?=?0.43 and p?=?0.03), butyric acid and the genus Lactobacillus (R?=?0.45 and p?=?0.024), acetic acid and the genus Bacteroides (R?=?0.63 and p?=?0.001) and methane and the genus Escherichia (R?=?0.58 and p?=?0.002).

Conclusion

Results of this study indicated that ethnicity influences both gut bacterial profile and their metabolites.

     

Symbiotic bacteria associated with gut symbiotic organs and female genital accessory organs of the leaf beetle <Emphasis Type="Italic">Bromius obscurus</Emphasis> (Coleoptera: Chrysomelidae)

Leaf beetles (Coleoptera: Chrysomelidae) constitute one of the most species-rich insect families, and live exclusively on leaves or other plant parts. Early histological works described the presence of symbiotic bacteria in gut-associated symbiotic organs of some chrysomelid species, but their microbiological nature has been poorly characterized except for those associated with reed beetles of the subfamily Donaciinae. Here we investigated symbiotic bacteria of the leaf beetle Bromius obscurus (L.) belonging to the subfamily Eumolpinae. Specific bacterial 16S ribosomal RNA and gyrB gene sequences were consistently obtained from the symbiotic organs, which radially surround the foregut-midgut junction, of all adult males and females examined. In adult females, the same sequences were also obtained from a pair of genital accessory organs, which are presumably for vertical symbiont transmission. Whole mount in situ hybridization specifically detected the symbiont in the gut symbiotic organs endocellularly and also in the female genital accessory organs extracellularly. In the gut symbiotic organs, the endocellular symbiont cells were small and rosette-like or aggregated and granule-like, whereas in the female genital organs the extracellular symbiont cells were of a condensed form. Molecular phylogenetic analysis showed that the symbiont of B. obscurus constitutes a distinct lineage in the Gammaproteobacteria. Molecular evolutionary analysis has identified significantly accelerated molecular evolution and a highly adenine–thymine-biased nucleotide composition of the symbiont genes, presumably reflecting reductive evolution of the symbiont genome. These results suggest an intimate and stable host-symbiont association in B. obscurus, in which the symbiont may play some important, though hitherto unknown, biological roles in its herbivorous insect host.     

Effect of plant–soil feedbacks on the growth and competition of <Emphasis Type="Italic">Lactuca</Emphasis> species

Plant species generate specific soil communities that feedback on plant growth and competition. These feedbacks have been implicated in plant community composition and dispersion. We used Lactuca sativa and its wild progenitor Lactuca serriola to test the hypotheses that separate Lactuca species generate unique soil communities and that these soil communities differentially influence host, and neighboring, plant growth and competition. We grew each Lactuca in competition with the other, in sterile and non-sterile soils. We then examined the growth of each Lactuca species in sterile, non-sterile, and preconditioned soil. Finally, we used TRFLP techniques to explore whether the two Lactuca species generate significantly different bacterial communities in their rhizosphere soils. L. sativa proved to be the stronger competitor of the two species. However, sterilization increased the competitive effect of L. serriola background competitors. The growth experiment showed a significant effect on plant species, soil treatment, and the interaction of the two. Preconditioning soil caused reduced growth in both Lactuca species. Only L. serriola showed significantly increased growth in sterile soils. Our TRFLP analysis showed that the L. sativa soil community was significantly less diverse and that soil preconditioning had the largest impact on the community composition. These results show that Lactuca serriola’s rhizosphere communities generate a stronger negative feedback for plant growth than do the communities associated with L. sativa. Our study suggests that selection for plants that are able to grow in dense monoculture may have released Lactuca from species-specific negative soil feedbacks. This has important implications for both agriculture and the evolution of invasive plant species.     

Effects of gravel-sand mulching on soil bacterial community and metabolic capability in the semi-arid Loess Plateau,China

Gravel and sand mulching is an indigenous technology used for the crop yield for at least 300 years in the loess area of northwest China; however, little is known about the changes of soil bacterial community and metabolic capability under the mulching. In this study, we investigated the soil microbial community structure and metabolic functional diversity during mulching using Illumina MiSeq sequencing and Biolog ECO method. Totally, 9417 OTUs were classified at 97% similarity level for soil samples after 0 (control), 4, 7, and 10 years of mulching. Dendrogram result indicated that mulching affected the soil bacterial community; and the higher richness and diversity of bacterial community were detected in mulching samples. The average abundance of soil bacteria (such as Proteobacteria, Actinobacteria, Firmicutes and Nitrospirae) in mulching samples was higher than samples without mulching. Besides, some microbial communities (such as Rhodobacteraceae, Phenylobacterium, Pseudonocardia, Nonomuraea and Aeromicrobium) were only present in the mulched soil samples. However, the lower metabolic capability was observed in mulching samples based on Biolog method, which the main reason for the opposite result might be that the soil objects detected by the two methods are different. In conclusion, these results demonstrated that gravel and sand mulching affected the structure and metabolic capability of bacterial community and was one reason for crop yield.     

Stability of the microbial population in the gut of omnivorous wireworms (Coleoptera,Elateridae)

The variability of the microbial population structure of the gut of omnivorous wireworms Agriotes obscurus (L) and Selatosomus aeneus (L) was studied. The limits of intra- and interspecific and intersite variation were determined. The stability of the microbial composition of the gut allows us to reveal the list of obligate saprotrophs (with 95% probability) using only five replications. In the case of S. aeneus, the influence of starvation and diet change was studied. Starvation changed the microbial population structure, while the diet did not. The results confirm that omnivorous wireworms have a stable gut microbial population, which suggests an advanced mutualistic relationship between wireworms and their gut bacteria, possibly assisting in digestion and providing for ecological flexibility of wireworms.