Pyrosequencing analysis revealed complex endogenetic microorganism community from natural DongChong XiaCao and its microhabitat

The composition and function of bacterial communities in Bombyx mori (Lepidoptera: Bombycidae) changed dramatically with infected fungi: A new potential to culture Cordyceps cicadae

Cordyceps cicadae (Hypocreales: Cordycipitaceae) is a renowned entomopathogenic fungus used as herbal medicine in China. However, wild C. cicadae resources have been threatened by heavy harvesting. We hypothesised that Bombyx mori L. (Lepidoptera: Bombycidae) could be a new alternative to cultivate C. cicadae due to the low cost of rearing. Bacterial communities are crucial for the formation of Cordyceps and for promoting the production of metabolites. To better understand the bacterial community structure associated with Cordyceps, three Claviciptaceae fungi were used to explore the pathogenicity of the silkworms. Here, fifth-instar silkworms were infected with C. cicadae, Cordyceps cateniannulata (Hypocreales: Cordycipitaceae) and Beauveria bassiana (Hypocreales: Cordycipitaceae). Subsequently, we applied high-throughput sequencing to explore the composition of bacterial communities in silkworms. Our results showed that all three fungi were highly pathogenic to silkworms, which suggests that silkworms have the potential to cultivate Cordyceps. After fungal infection, the diversity of bacterial communities in silkworms decreased significantly, and the abundance of Staphylococcus increased in mummified larvae, which may play a role in the death process when the host suffers infection by entomopathogenic fungi. Furthermore, there were high similarities in the bacterial community composition and function in the C. cicadae and C. cateniannulata infected samples, and the phylogenetic analysis suggested that these similarities may be related to the fungal phylogenetic relationship. Our findings reveal that infection with different entomopathogenic fungi affects the composition and function of bacterial communities in silkworms and that the bacterial species associated with Cordyceps are primarily host dependent, while fungal infection affects bacterial abundance.

Filtration effect of Cordyceps chanhua mycoderm on bacteria and its transport function on nitrogen

IMPORTANCE

During the natural growth of Cordyceps chanhua, it will form a mycoderm structure specialized from hyphae. We found that the bacterial membrane of C. chanhua not only filters environmental bacteria but also absorbs and transports nitrogen elements inside and outside the body of C. chanhua. These findings are of great significance for understanding the stable mechanism of the internal microbial community maintained by C. chanhua and how C. chanhua maintains its own nutritional balance. In addition, this study also enriched our understanding of the differences in bacterial community composition and related bacterial community functions of C. chanhua at different growth stages, which is of great value for understanding the environmental adaptation mechanism, the element distribution network, and the changing process of symbiotic microbial system after Cordyceps fungi infected the host. At the same time, it can also provide a theoretical basis for some important ecological imitation cultivation technology of Cordyceps fungi.

Compositional and functional diversities of core microbial communities in wild and artificial Ophiocordyceps sinensis

Ophiocordyceps sinensis is an entomogenous fungus, and its wildlife resource is very insufficient, as it is widely traded as a natural health product. The artificial culture of O. sinensis is a remarkably effective progress in addressing the problem. Adding microorganisms may improve the process of artificial culture. To analyse the composition and function of the microbial community, high-throughput sequencing was used to explore the microbial community inhabiting wild and artificial O. sinensis and surrounding soil. Significant differences in the microbial communities across groups were revealed by the PCoA analysis. There were 51 fungal and 598 bacterial operational taxonomic units only being assigned to the fruiting bodies of wild O. sinensis (Wf) by the Venn diagram. From the LEfSe analysis, 39 fungal taxa and 75 bacterial taxa were enriched in Wf. Enzymes that were highly abundant in the core fungi were involved in physiological metabolic processes. Metabolic pathways were dominated in the core bacteria, followed by environmental information processing. The core microorganisms, with the marked differences between Wf and the other three groups, were essential for wild O. sinensis. Functional analysis verified their involvement in the growth, development, and infection of O. sinensis. These core microorganisms may be a valuable resource for the artificial culture of O. sinensis.

New insights into endophytic fungi diversity and their potential correlation with polyphyllin levels of Paris polyphylla var. yunnanensis

Endophytes confer fitness advantages to host plants. However, the ecological communities of endophytic fungi in the different tissues (rhizomes, stems, and leaves) of Paris polyphylla and the relationship of their endophytic fungi with polyphyllin levels remain unclear. In this study, the community diversity and differences of endophytic fungi in the rhizomes, stems, and leaves of P. polyphylla var. yunnanensis were investigated, and a comprehensively diverse community of endophytic fungi was represented, including 50 genera, 44 families, 30 orders, 12 classes, and 5 phyla. Distributions of endophytic fungi differed greatly across the three tissues, with six genera common to all tissues, and 11, 5, and 4 genera specific to the rhizomes, stems, and leaves, respectively. Seven genera showed a significantly positive correlation to polyphyllin contents, indicating their potential roles in polyphyllin accumulation. This study provides valuable information for further research of the ecological and biological functions of endophytic fungi of P. polyphylla.

Structure characterization of an exopolysaccharide from a Shiraia-associated bacterium and its strong eliciting activity on the fungal hypocrellin production

Hypocrellins are fungal perylenequinones (PQs) from Shiraia fruiting bodies and potential photosensitizers for cancer photodynamic therapy. Shiraia fruiting bodies harbor diverse bacterial communities dominated by Pseudomonas. The present study was to characterize the exopolysaccharide (EPS) of P. fulva SB1 which acted as an elicitor to stimulate the PQ accumulation of the host Shiraia. A bacterial EPS named EPS-1 was purified from the culture broth of P. fulva SB1, which consisted of mannose (Man) and glucose (Glc) with an average molecular weight of 9.213 × 10⁴ Da. EPS-1 had (1 → 2)-linked α-mannopyranose (Manp) backbone and side chains of α-D-Manp-(1→ and α-D-Manp-(1 → 6)-β-D-Glcp-(1 → 6)-α-D-Manp(1 → group attached to the O-6 positions of (1 → 2)-α-D-Manp. EPS-1 at 30 mg/L stimulated both intracellular and extracellular hypocrellin A (HA) by about 3-fold of the control group. The EPS-1 treatment up-regulated the expression of key genes for HA biosynthesis. The elicitation of HA biosynthesis by EPS-1 was strongly dependent on the induced reactive oxygen species (ROS) generation. The results may provide new insights on the role of bacterial EPS in bacterium-fungus interactions and effective elicitation strategy for hypocrellin production in mycelial cultures.

Characterization of Rhizosphere and Endophytic Microbial Communities Associated with Stipa purpurea and Their Correlation with Soil Environmental Factors

This study was to explore the diversity of rhizosphere and endophytic microbial communities and the correlation with soil environmental factors of Stipa purpurea on the Qinghai-Tibetan Plateau. The bacterial phylum of Proteobacteria, Firmicutes and Bacteroidota, and the fungal phylum of Ascomycota, Basidiomycota and Zygomycota were dominant in microbial communities of S. purpurea in all three sampling sites. Multiple comparison analysis showed that there were significant differences in the composition of microbial communities in the roots, leaves and rhizosphere soil. Whether it is fungi or bacteria, the OTU abundance of rhizosphere soils was higher than that of leaves and roots at the same location, while the difference among locations was not obvious. Moreover, RDA analysis showed that Zygomycota, Cercozoa, Glomeromycota, Chytridiomycota and Rozellomycota possessed strongly positive associations with altitude, dehydrogenase, alkaline phosphatase, neutral phosphatase, available kalium and available phosphate, while Ascomycota was strongly negatively associated. Changes in ammonium nitrate, alkaline phosphatase, polyphenol oxidase, total phosphorus, and altitude had a significant impact on the bacterial communities in different habitats and altitudes. Taken together, we provide evidence that S. purpurea has abundant microbial communities in the alpine grassland of the Qinghai-Tibetan Plateau, whose composition and diversity are affected by various soil environmental factors.

New insights into metabolomics profile generation in fermented tea: the relevance of bacteria and metabolites in Fuzhuan brick tea

BACKGROUND

The contribution of bacteria to fermented tea is not clear and the associated research is relatively limited. To reveal the role of microorganisms in fermented tea processing, the microbial community and metabolites of Fuzhuan brick tea (FBT), a Chinese traditional fermented tea, were revealed via high-throughput sequencing and liquid chromatography-mass spectrometry (LC-MS).

RESULTS

In FBT, bacterial communities had a higher abundance and diversity, Lactococcus and Bacillus were the main bacteria, and Eurotium was the predominant fungus. The predictive metabolic function indicated the pathways of cellular growth, environmental information, genetics and material metabolism of bacterial communities were abundant, whereas the fungal community predictive metabolic function was almost saprotroph. Using LC-MS, 1143 and 536 metabolites were defined in positive and negative ion mode, respectively. There were essential correlations between bacterial populations and metabolites, such that Bacillus was correlated significantly with 44 metabolites (P < 0.05) and Enterococcus was significantly associated with 15 metabolites (P < 0.05). Some of the main active components were significantly correlated with the bacteria, such as Enterococcus, Lactococcus and Carnobacterium.

CONCLUSION

Not only Eurotium, but also the bacteria were involved in the changes of metabolomics profile in fermented FBT. The present study assists in providing new insights into metabolomics profile generation in fermented tea. The present research lays a foundation for controlling the FBT fermentation by artificial inoculation to improve quality. © 2021 Society of Chemical Industry.

Identification and functional analysis of bacteria in sclerotia of Cordyceps militaris

Background

Cordyceps militaris is a fungus that parasitizes insects. Compounds from C. militaris are valuable in medicine and functional food. There are many kinds of bacteria in the natural sclerotia of C. militaris. However, the community structure of microorganisms in samples from different places may be different, and their corresponding ecological functions require experimental verification.

Methods

We used high-throughput sequencing technology to analyze bacterial 16S rRNA gene sequences in sclerotia of three samples of C. militaris from Liaoning Province, China. We isolated, identified and verified the function of culturable bacterial strains from the sclerotia.

Results

Pseudomonas, Pedobacter, Sphingobacterium, and Serratia were the dominant bacterial genera in the sclerotia. And function prediction showed that Pseudomonas and Pedobacter could be heterotrophic, Sphingobacterium could decompose urea, and Serratia could reduce nitrate. Two strains of bacteria isolated from the sclerotia of C. militaris, N-2 and N-26, were identified as Stenotrophomonas maltophilia and Pseudomonas baetica, respectively, based on culture and biochemical characteristics. When these isolated strains were co-cultured with C. militaris, the mycelium biomass and mycelium pellet diameter decreased, and the content of extracellular polysaccharide increased. Strain N-26 decreased the cordycepin content in C. militaris.

Conclusions

Bacteria in sclerotia have an important effect on the growth of C. militaris and the production of its metabolites.

Analysis of Internal and External Microorganism Community of Wild Cicada Flowers and Identification of the Predominant Cordyceps cicadae Fungus

The parasitoid fungus Cordyceps cicadae, whose fruiting bodies are known in China as “chan hua,” literally “cicada flower,” has been used as a traditional Chinese medicinal ingredient for centuries. However, systematic disclosure of the vital factors responsible for the formation of wild cicada flower is limited. Here, we determined the physicochemical properties of soil and simultaneously analyzed the diversities and the structures of microbial community inhabiting the coremia, sclerotia, and soil around wild cicada flowers through high-throughput sequencing. Our results indicated that cicada flower more preferentially occurred in acidic soil (pH 5.9) with abundant moisture content (MC), total nitrogen (TN), and organic matter (OM). The dominant fungal genera in soil mainly included Isaria, f__Clavariaceae_Unclassified, Umbelopsis, f__Chaetomiaceae_Unclassified, Mortierella, f__Sordariaceae_Unclassified, and Arcopilus. Among them, C. cicadae was the only fungus that was massively detected in both the coremia and sclerotia with abundance of 83.5 and 53.6%, respectively. Based on this, a C. cicadae strain named AH10-4 with excellent adenosine- and N⁶-(2-hydroxyethyl)-adenosine (HEA)-producing capability was successfully isolated. However, to the aspect of bacteria, Burkholderia–Caballeronia–Paraburkholderia, Bacillus, Acidibacter, f__Xanthobacteraceae_Unclassified, and Candidatus_Solibacter were the dominant genera in soil. Pedobacter, f__Enterobacteriaceae_Unclassified, Pandoraea, Achromobacter, Stenotrophomonas, Burkholderia–Caballeronia–Paraburkholderia, and Chitinophaga were the dominant genera in the coremia and sclerotia. Notably, Burkholderia–Caballeronia–Paraburkholderia was the shared bacteria among them with high abundance of 3.1, 11.4, and 5.2% in the sclerotia, coremia, and soil, respectively. However, the possible role of these bacteria to the occurrence of cicada flower has been unclear to our knowledge. By analyzing the correlation between physicochemical properties and microbial community of soil, we found that MC, Fe, and Zn were significantly negatively correlated with soil Isaria and that Cu was significantly negatively correlated with most dominant soil bacterial genera. But Mg was significantly positively correlated with most dominant taxa. This study provides new insight into the formation mechanisms of cicada flower and may contribute to the large-scale cultivation of cicada flowers.

Ammonium promoting methane oxidation by stimulating the Type Ia methane-oxidizing bacteria in tidal flat sediments of the Yangtze River estuary

Estuary and coastal environments have essential ecosystem functions in greenhouse gas sinks and removal of nitrogen pollution. Methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) communities play critical functions in the estuary's tidal flat sediments. Therefore, the effects of ammonium on MOB communities and methane on AOB communities need to be further explained. In this study, microcosm incubations with different contents of ammonium or methane were conducted for a relatively short (24 h) or long (28 days) period with tidal flat sediments from the Yangtze River estuary. Subsequently, the tagged highly degenerate primer PCR and DNA-based stable isotope probing method were employed to demonstrate the effects on MOB and AOB populations. The results indicated that the methane consumption was enhanced with ammonium supplements within 24 h of incubation. Supplement of 2 μmol/g d.w.s (μmol per gram dry weight soil) NH₄⁺ increased the amount of MOB and its proportion to the total bacteria (p < 0.05) for 28 days incubation. The ammonium supplement increased the proportion of Methylomonas and Methylobacter based on the 16S rRNA gene. According to the functional gene analysis, the MOB primarily engaged in methane oxidation include Methylomonas, Methylobacter, Methylomicrobium, and Methylosarcina, which were associated with Type Ia MOB. It suggested that ammonium supplement may promote methane oxidation by stimulating the Type Ia MOB in tidal flat sediments of the Yangtze River estuary. The current research helps understand the effect of ammonium on methane consumption in the estuary and coastal environments.

Endogenous bacteria inhabiting the Ophiocordyceps highlandensis during fruiting body development

Background

The genus Ophiocordyceps, which includes Ophiocordyceps sinensis, has been demonstrated to be one of the most valuable medicinal taxa. The low rate of larval infection and slow development that characterize the cultivation of this genus should be urgently addressed. To identify potential bioinoculants that stimulate the growth of Ophiocordyceps, O. highlandensis was selected as a model system, and a total of 72 samples were collected to systematically compare the microbial communities present during fruiting body development. By applying high-throughput 16S and ITS2 amplicon sequencing technology, the bacterial and fungal communities were identified in O. highlandensis and its surrounding soil, and the functional dynamics of the bacteria were explored.

Results

The results indicate that the most abundant bacteria across all the samples from O. highlandensis were Proteobacteria, Firmicutes and Bacteroidetes, while members of Ascomycota were detected among the fungi. The pathways enriched in the developmental stages were associated with carbohydrate degradation, nucleotides and pyridoxal biosynthesis, and the TCA cycle. Compared with that in the fungal community, an unexpectedly high taxonomic and functional fluctuation was discovered in the bacterial community during the maturation of O. highlandensis. Furthermore, bipartite network analysis identified four potential supercore OTUs associated with O. highlandensis growth.

Conclusions

All the findings of this study suggest unexpectedly high taxonomic and functional fluctuations in the bacterial community of O. highlandensis during its maturation. O. highlandensis may recruit different endogenous bacteria across its life cycle to enhance growth and support rapid infection. These results may facilitate Ophiocordyceps cultivation and improve the development of strategies for the identification of potential bioinoculant resources.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02227-w.

Complex microbial communities inhabiting natural Cordyceps militaris and the habitat soil and their predicted functions

Cordyceps militaris is a traditional Chinese medicinal food that is challenging to quality maintaining while mass cultivation. Many studies have found that abundant microbes inhabit Ophiocordyceps sinensis and perform important functions for their host. In this study, our objective was to reveal the microbial communities that inhabit C. militaris and analyze their potential functions. High-throughput sequencing of 16S rRNA and ITS genes was used to compare the diversity and composition of the bacterial and fungal communities associated with naturally occurring C. militaris collected from Yunnan Province, southwestern China. The diversity and richness of the microbial communities and the number of function genes of the bacteria were significantly higher in the habitat soil than in the fruiting body. The sclerotia and stromata samples shared the same microbiota and functions. The main bacterial phyla were Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria, and Ascomycota was the main fungal phylum. The growth-promoting bacteria Herbaspirillum and the plant probiotic Phyllobacterium, which may enhance C. militaris quality and facilitate its cultivation, were detected in the fruiting body samples. Genes related to metabolism were more abundant in the soil bacteria, while membrane transport genes were more abundant in the endophytic bacteria of C. militaris. Our study is the first to reveal the unexpectedly high diversity of the microbial communities and the bacterial functions inhabiting the natural C. militaris using high-throughput sequencing, and our results provide insights into mining the functions of microorganisms in the development and quality of C. militaris.

Distribution and diversity of endophytic fungi in Gentiana rigescens and cytotoxic activities

Objective

Methods

Results

Conclusion

The Diversity of Associated Microorganisms in Different Organs and Rhizospheric Soil of Arctium lappa L

Arctium lappa L. is widely used for medicinal purposes across China, and significant effort has been directed toward enhancing its quality. Association with microorganisms has been shown to influence both plant growth and metabolites, providing a possible avenue for its quality improvement. In this study, we investigated the microorganism compositions of the root, stem, leaf, fruit and rhizospheric soil of A. lappa through high-throughput Illumina sequencing of 16S rRNA genes and ITS regions. A total of 796,891 16S rRNA and 626,270 ITS reads were obtained from the samples. Analysis of the sequencing data revealed that bacterial and fungal communities were more diverse in the rhizospheric soil sample compared with other samples. Cyanobacteria, Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes phyla were found in all samples. Cyanobacteria was particularly enriched in the root, stem, leaf and fruit at 88.59%, 86.15%, 98.31% and 93.57%, respectively; Actinobacteria was the highest in rhizospheric soil, at 37.53%. Ascomycota was the most dominant fungal phylum, representing 69.17%, 58.18%, 87.93%, 90.18% and 80.21% in the root, stem, leaf, fruit, and rhizospheric soil, respectively. Several novel unclassifiable bacterial and fungal species were also detected. In total, we detected about 922 bacterial and 334 fungal species, which include a number of unclassifiable species. Additionally, the root, stem, leaf, fruit and rhizospheric soil of A. lappa were sources for screening new bioactive metabolites.

Promotion of Metabolite Synthesis in Isaria cicadae, a Dominant Species in the Cicada Flower Microbiota, by Cicada Pupae

Cicada flowers, which are edible and medicinal mushrooms, are the fruiting bodies of Isaria cicadae, a fungus that is parasitic on the larvae of cicada pupae. We hypothesize that host factors might possess stimulatory activity on metabolite synthesis in Isaria cicadae. Here, we first compared the microbial community structures of different wild cicada flowers across geographical regions, compartments, and growth stages via high-throughput sequencing. Isaria cicadae TZC-3, an isolate of the most abundant operational taxonomic unit (OTU6782) in all the fungal communities, was isolated from wild cicada flowers. Furthermore, the effects of cicada pupae on metabolite synthesis in Isaria cicadae TZC-3 were studied in submerged culture. The contents of intercellular polysaccharides, adenosine, N6-(2-hydroxyethyl)-adenosine, free amino acids, and hydrolyzed monosaccharides in the mycelia cultured with cicada pupa powder (4%) were significantly increased as compared with the contents in the control group. This indicates that a cicada pupa can act as an elicitor for metabolite synthesis in Isaria cicadae.

Composition and predictive functional analysis of bacterial communities inhabiting Chinese Cordyceps insight into conserved core microbiome

Background

Over the past few decades, most attention to Chinese Cordyceps-associated endogenous microorganism was focused on the fungal community that creates critical bioactive components. Bacterial community associated with Chinese Cordyceps has been previously described; however, most studies were only presenting direct comparisons in the Chinese Cordyceps and its microenvironments. In the current study, our objectives were to reveal the bacterial community structure composition and predict their function.

Results

We collected samples of Chinese Cordyceps from five sites located in the Qinghai-Tibet Plateau and used a high throughput sequencing method to compare Chinese Cordyceps-associated bacterial community composition and diversity quantitatively across sites. The results indicated that for the Chinese Cordyceps-associated bacterial community there is no single core microbiome, which was dominated by the both Proteobacteria and Actinobacteria. Predictive functional profiling suggested a location specific function pattern for Chinese Cordyceps and bacteria in the external mycelial cortices involved in the biosynthesis of active constituents.

Conclusions

This study is firstly used high throughput sequencing method to compare the bacterial communities inhabiting Chinese Cordyceps and its microhabitat and to reveal composition functional capabilities of the bacteria, which will accelerate the study of the functions of bacterial communities in the micro-ecological system of Chinese Cordyceps.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1472-0) contains supplementary material, which is available to authorized users.

Dynamic succession of substrate-associated bacterial composition and function during Ganoderma lucidum growth

Background

Ganoderma lucidum, a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities.

Methods

We analyzed the bacterial community dynamics in the substrate during the four typical growth stages of G. lucidum using next-generation sequencing.

Results

The physicochemical properties of the substrate (e.g. acidity, moisture, total nitrogen, total phosphorus and total potassium) changed between different growth stages. A total of 598,771 sequences from 12 samples were obtained and assigned to 22 bacterial phyla. Proteobacteria and Firmicutes were the dominant phyla. Bacterial community composition and diversity significantly differed between the elongation stage and the other three growth stages. LEfSe analysis revealed a large number of bacterial taxa (e.g. Bacteroidetes, Acidobacteria and Nitrospirae) with significantly higher abundance at the elongation stage. Functional pathway prediction uncovered significant abundance changes of a number of bacterial functional pathways between the elongation stage and other growth stages. At the elongation stage, the abundance of the environmental information processing pathway (mainly membrane transport) decreased, whereas that of the metabolism-related pathways increased.

Discussion

The changes in bacterial community composition, diversity and predicted functions were most likely related to the changes in the moisture and nutrient conditions in the substrate with the growth of G. lucidum, particularly at the elongation stage. Our findings shed light on the G. lucidum-bacteria-substrate relationships, which should facilitate the industrial cultivation of G. lucidum.