Bacterial diversity in native habitats of the medicinal fungus Ophiocordyceps sinensis on Tibetan Plateau as determined using Illumina sequencing data

Yang, Runqiang; Wang, Xiaoliang; Su, Jinhe; Li, Yang; Jiang, Si‐Ping; Gu, Feng; Yao, Yi‐Jian

doi:10.1093/femsle/fnu044

Cited by 14 publications

(14 citation statements)

References 46 publications

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“…The rank abundance curves of A, M, B, and A+M+B non-ream (S2 Fig) are similar in shape; they have steep slopes, demonstrating a low evenness of OTUs, and long tails, indicating that the majority of the sequences belong to rare organisms represented by only a few reads [46]. HW, MW, A+M+B and Random showed rank abundance curves with shallower slopes, demonstrating higher evenness.…”

Section: Resultsmentioning

confidence: 99%

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses

et al. 2017

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The current literature reveals that the intrathalline coexistence of multiple microalgal taxa in lichens is more common than previously thought, and additional complexity is supported by the coexistence of bacteria and basidiomycete yeasts in lichen thalli. This replaces the old paradigm that lichen symbiosis occurs between a fungus and a single photobiont. The lichen Ramalina farinacea has proven to be a suitable model to study the multiplicity of microalgae in lichen thalli due to the constant coexistence of Trebouxia sp. TR9 and T. jamesii in long-distance populations. To date, studies involving phycobiont diversity within entire thalli are based on Sanger sequencing, but this method seems to underestimate the diversity. Here, we aim to analyze both the microalgal diversity and its community structure in a single thallus of the lichen R. farinacea by applying a 454 pyrosequencing approach coupled with a careful ad hoc-performed protocol for lichen sample processing prior to DNA extraction. To ascertain the reliability of the pyrosequencing results and the applied bioinformatics pipeline results, the thalli were divided into three sections (apical, middle and basal zones), and a mock community sample was used. The developed methodology allowed 40448 filtered algal reads to be obtained from a single lichen thallus, which encompassed 31 OTUs representative of different microalgae genera. In addition to corroborating the coexistence of the two Trebouxia sp. TR9 and T. jamesii taxa in the same thallus, this study showed a much higher microalgal diversity associated with the lichen. Along the thallus ramifications, we also detected variations in phycobiont distribution that might correlate with different microenvironmental conditions. These results highlight R. farinacea as a suitable material for studying microalgal diversity and further strengthen the concept of lichens as multispecies microecosystems. Future analyses will be relevant to ecophysiological and evolutionary studies to understand the roles of the multiple photobionts in lichen symbioses.

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Section: Resultsmentioning

confidence: 99%

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses

et al. 2017

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“…Before DNA extraction, soil samples were treated using a 2 mm sieve to remove stone, plant roots, and tissues 16 . Total DNA was extracted from 0.25 g (wet weight) of soil sample using a PowerSoil DNA kit (MoBio Laboratories, CA, USA) following the protocol of manufacturer 28 , 41 .…”

Section: Methodsmentioning

confidence: 99%

“…Some studies have reported interactions between soil microbes and fungi. Microbial community in the native habitats of Ophiocordyceps sinensis was studied and 23 phyla were found 16 . Bacterial and archaeal community associated with different lichens were investigated, which showed that Alphaproteobacteria was dominant and bacteria may be the component of lichen symbiosis 17 .…”

Section: Introductionmentioning

confidence: 99%

Microbial communities in the native habitats of Agaricus sinodeliciosus from Xinjiang Province revealed by amplicon sequencing

Zhou

Bai

Zhao

2017

Sci Rep

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Agaricus sinodeliciosus is an edible species described from China and has been successfully cultivated. However, no studies have yet reported the influence factors implicated in the process of fructification. To better know abiotic and biotic factors, physiochemical characteristics and microbial communities were investigated in five different soil samples collected in the native habitats of specimens from northern Xinjiang, southern Xinjiang, and Zhejiang Province, respectively. There are major differences in texture and morphology among different specimens of A. sinodeliciosus from Xinjiang Province. A. sinodeliciosus from southern Xinjiang was the largest. Concentrations of DOC and TN and C/N ratio are not the main reason for the differences. Microbial communities were analyzed to find out mushroom growth promoting microbes (MGPM), which may lead to the differences. Functional microbes were picked out and can be divided into two categories. Microbes in the first category may belong to MGPM. There may be symbiotic relationships between microbes in the second category and A. sinodeliciosus. Certain analyses of microbial communities support the hypothesis that interactions between microbes and mushrooms would be implicated in morphological variation of the collected mushrooms. Redundancy analysis results indicate that high DOC/NH4 +-N ratio and NH4 +-N concentration can improve the yield of A. sinodeliciosus.

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“…In spite of we reported that there were multiple fungi and bacteria inhibiting Chinese Cordyceps and its microhabitat [10]. The publication involved in the analysis of the diversity of bacteria in the native habitat of Chinese Cordyceps was very little [16]. However, bacteria inhabiting this small ecosystem may play a role of “pioneer species” when fungus O. sinensis infecting the larva.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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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.

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Bacterial diversity in native habitats of the medicinal fungus Ophiocordyceps sinensis on Tibetan Plateau as determined using Illumina sequencing data

Cited by 14 publications

References 46 publications

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses

Microbial communities in the native habitats of Agaricus sinodeliciosus from Xinjiang Province revealed by amplicon sequencing

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

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