scholarly journals Identity, Diversity, and Molecular Phylogeny of the Endophytic Mycobiota in the Roots of Rare Wild Rice (Oryza granulate) from a Nature Reserve in Yunnan, China

2009 ◽  
Vol 76 (5) ◽  
pp. 1642-1652 ◽  
Author(s):  
Zhi-lin Yuan ◽  
Chu-long Zhang ◽  
Fu-cheng Lin ◽  
Christian P. Kubicek
Keyword(s):  
Endophytic Fungi ◽  
Wild Rice ◽  
Low Frequency ◽  
Integrated Approach ◽  
Global Scale ◽  
Fungal Species ◽  
Ecological Indices ◽  
Direct Pcr ◽  
Frequency Calculation ◽  
Culture Independent

ABSTRACT Rice (Oryza sativa L.) is, on a global scale, one of the most important food crops. Although endophytic fungi and bacteria associated with rice have been investigated, little is known about the endophytic fungi of wild rice (Oryza granulate) in China. Here we studied the root endophytic mycobiota residing in roots of O. granulate by the use of an integrated approach consisting of microscopy, cultivation, ecological indices, and direct PCR. Microscopy confirmed the ubiquitousness of dark septate endophytes (DSEs) and sclerotium-like structures in root tissues. Isolations from 204 root segments from 15 wild rice plants yielded 58 isolates, for which 31 internal transcribed spacer (ITS)-based genotypes were recorded. The best BLAST match indicated that 34.5% of all taxa encountered may represent hitherto undescribed species. Most of the fungi were isolated with a very low frequency. Calculation of ecological indices and estimation of taxon accumulation curves indicated a high diversity of fungal species. A culture-independent approach was also performed to analyze the endophytic fungal community. Three individual clone libraries were constructed. Using a threshold of 90% similarity, 35 potentially different sequences (phylotypes) were found among 186 positive clones. Phylogenetic analysis showed that frequently detected clones were classified as Basidiomycota, and 60.2% of total analyzed clones were affiliated with unknown taxa. Exophiala, Cladophialophora, Harpophora, Periconia macrospinosa, and the Ceratobasidium/Rhizoctonia complex may act as potential DSE groups. A comparison of the fungal communities characterized by the two approaches demonstrated distinctive fungal groups, and only a few taxa overlapped. Our findings indicate a complex and rich endophytic fungal consortium in wild rice roots, thus offering a potential bioresource for establishing a novel model of plant-fungal mutualistic interactions.

Wild rice controls more root endophytic fungi than cultivated rice in the F1 offsprings after the crossbreeding

2020 ◽  
Author(s):  
Lei Tian ◽  
Xiaolong Lin ◽  
Li Ji ◽  
Jingjing Chang ◽  
Xiujun Li ◽  
...  
Keyword(s):  
Endophytic Fungi ◽  
Wild Rice ◽  
Endophytic Bacteria ◽  
Bacterial Species ◽  
Fungal Species ◽  
Cultivated Rice ◽  
The Core ◽  
Wild Rice Species ◽  
Root Endophytic Fungi ◽  
Bacteria And Fungi

Abstract Background: Rice, which serves as a staple food for more than half of the world’s population, has been planted all over the world. The hybridization of wild and cultivated rice has helped rice gain resistance to variable environmental conditions. Endophytic microbiomes have been known to be transferred along with the plants. However, the endophytic bacteria or fungi for the wild and cultivated rice, and their first crossbred generation have not been illustrated until now. Results: In this study, we systematically compared the endophytic microbial community structures of Asian and African wild and cultivated rice species with their F1 offsprings. Results showed that both African and Asian wild rice controls more root endophytic fungi than cultivated rice in their first generation after crossbreeding. Furthermore, network analysis of the bacterial and fungal operational taxonomic units showed that Asian and African wild rice species can cluster and have more significant correlations than cultivated rice fungal species. The core bacterial species that connected wild rice with its F1 offsprings was Acidovorax, wherea the core bacterial species that linked cultivated rice to its F1 offsprings was Bradyrhizobium; and the core fungal species that can connect in wild rice and the F1 offsprings were Pleosporales, Myrothecium and Bullera, while the core fungal species that can connect in cultivated rice was those belonging to the Dendroclathra genus.Conclusions: This study may provide the theoretical significance of the endophytic bacteria and fungi for wild and cultivated rice along with their F1 offsprings.

scholarly journals The Diversity of Root-Associated Endophytic Fungi from Four Epiphytic Orchids in China

Diversity ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 197
Author(s):  
Tao Wang ◽  
Miao Chi ◽  
Ling Guo ◽  
Donghuan Liu ◽  
Yu Yang ◽  
...  
Keyword(s):  
Endophytic Fungi ◽  
Southern China ◽  
Culture Method ◽  
Amplicon Sequencing ◽  
Community Diversity ◽  
Mycorrhizal Symbiosis ◽  
Epiphytic Orchids ◽  
Culture Independent ◽  
Almost All

Root-associated endophytic fungi (RAF) are found asymptomatically in almost all plant groups. However, little is known about the compositions and potential functions of RAF communities associated with most Orchidaceae species. In this study, the diversity of RAF was examined in four wild epiphytic orchids, Acampe rigida, Doritis pulcherrima, Renanthera coccinea, and Robiquetia succisa, that occur in southern China. A culture-independent method involving Illumina amplicon sequencing, and an in vitro culture method, were used to identify culturable fungi. The RAF community diversity differed among the orchid roots, and some fungal taxa were clearly concentrated in a certain orchid species, with more OTUs being detected. By investigating mycorrhizal associations, the results showed that 28 (about 0.8%) of the 3527 operational taxonomic units (OTUs) could be assigned as OMF, while the OTUs of non-mycorrhizal fungal were about 99.2%. Among the OMFs, Ceratobasidiaceae OTUs were the most abundant with different richness, followed by Thelephoraceae. In addition, five Ceratobasidium sp. strains were isolated from D. pulcherrima, R. succisa, and R. coccinea roots with high separation rates. These culturable Ceratobasidium strains will provide materials for host orchid conservation and for studying the mechanisms underlying mycorrhizal symbiosis.

scholarly journals Development of a Co-Dominant Cleaved Amplified Polymorphic Sequences Assay for the Rapid Detection and Differentiation of Two Pathogenic Clarireedia spp. Associated with Dollar Spot in Turfgrass

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1489
Author(s):  
Tammy Stackhouse ◽  
Sumyya Waliullah ◽  
Alfredo D. Martinez-Espinoza ◽  
Bochra Bahri ◽  
Emran Ali
Keyword(s):  
Pcr Primers ◽  
The United States ◽  
Fungal Species ◽  
Dollar Spot ◽  
Direct Pcr ◽  
Specific Pcr ◽  
Specificity And Sensitivity ◽  
Pure Cultures ◽  
Speed Up ◽  
Cleaved Amplified Polymorphic Sequences

Dollar spot is one of the most destructive diseases in turfgrass. The causal agents belong to the genus Clarireedia, which are known for causing necrotic, sunken spots in turfgrass that coalesce into large damaged areas. In low tolerance settings like turfgrass, it is of vital importance to rapidly detect and identify the pathogens. There are a few methods available to identify the genus Clarireedia, but none of those are rapid enough and characterize down to the species level. This study produced a co-dominant cleaved amplified polymorphic sequences (CAPS) test that differentiates between C. jacksonii and C. monteithiana, the two species that cause dollar spot disease within the United States. The calmodulin gene (CaM) was targeted to generate Clarireedia spp. specific PCR primers. The CAPS assay was optimized and tested for specificity and sensitivity using DNA extracted from pure cultures of two Clarireedia spp. and other closely related fungal species. The results showed that the newly developed primer set could amplify both species and was highly sensitive as it detected DNA concentrations as low as 0.005 ng/µL. The assay was further validated using direct PCR to speed up the diagnosis process. This drastically reduces the time needed to identify the dollar spot pathogens. The resulting assay could be used throughout turfgrass settings for a rapid and precise identification method in the US.

scholarly journals Isolation and identification of phylloplane and endophytic fungi from Sapindus mukorossi

2020 ◽  
Vol 26 (2) ◽  
Author(s):  
B.D. Varpe
Keyword(s):  
Endophytic Fungi ◽  
Terrestrial Ecosystem ◽  
Fungal Species ◽  
Penicillium Expansum ◽  
Isolation And Identification ◽  
Epicoccum Nigrum ◽  
Candida Sp ◽  
Fusarium Sp ◽  
The Rich ◽  
High Level

Phylloplane biodiversity and endophytic fungi is considered one of the rich origins of novel biological activity compounds and high-level structural variation on the leaf surface. Plant leaves surface is a diverse terrestrial ecosystem, including filamentous fungi. This study aims to study the isolation and enumeration of Sapindus mukorossi phylloplane and endophytic fungal diversity. The Sapindus mukorossi isolated 14 fungal species from 9 genera of phylloplane and endophytic fungi. Cladosporium herbarum, Penicillium expansum, Fusarium oxysporum, Fusarium sp., Alternaria alternate, Collectotrichum orbiculare, Torulla herbarium, Epicoccum nigrum and Candida sp. as a phylloplane fungi. Aspergillus niger, A. flavus, Epicoccum nigrum. Penicillum digitatum, Penicillum sp. were identified as endophytic fungi.

Research Tools and Methods for the Analysis of Microbiota in Dairy Products

2018 ◽  
pp. 23-53 ◽  
Author(s):  
Sylvia Klaubauf ◽  
Frank J. J. Segers
Keyword(s):  
Dna Sequencing ◽  
Production Process ◽  
Microbial Communities ◽  
Dairy Products ◽  
Starter Cultures ◽  
Direct Pcr ◽  
Culture Independent ◽  
Profiling Techniques ◽  
Tools And Methods ◽  
Culture Dependent

Microorganisms play important roles in dairy products. They can be a source of spoilage, or they promote health or cause diseases. In dairy fermentations, microorganisms are of great importance due to their function as starter cultures and during the production process of dairy products. In order to better understand and improve the process, it is essential to identify the species that are involved and to monitor the development of microbial communities. There are several different approaches for the detection and analysis of the microbiota. The methods can be culture dependent and, for example, make use of morphological and physiological characters or DNA sequencing. Culture-independent methods include direct PCR and qPCR, but also electrophoresis-based profiling techniques as well as metagenomics. Descriptions of relevant methods are provided and their applications are discussed in this chapter.

scholarly journals Derivation of global ionospheric Sporadic E critical frequency ( f o Es) data from the amplitude variations in GPS/GNSS radio occultations

2020 ◽  
Vol 7 (7) ◽  
pp. 200320 ◽  
Author(s):  
Bingkun Yu ◽  
Christopher J. Scott ◽  
Xianghui Xue ◽  
Xinan Yue ◽  
Xiankang Dou
Keyword(s):  
Critical Frequency ◽  
Detection Threshold ◽  
Low Frequency ◽  
Satellite System ◽  
Global Scale ◽  
Satellite Mission ◽  
Frequency Detection ◽  
Sporadic E ◽  
The Uk ◽  
Global Navigation Satellite

The ionospheric sporadic E (Es) layer has a significant impact on the global positioning system (GPS)/global navigation satellite system (GNSS) signals. These influences on the GPS/GNSS signals can also be used to study the occurrence and characteristics of the Es layer on a global scale. In this paper, 5.8 million radio occultation (RO) profiles from the FORMOSAT-3/COSMIC satellite mission and ground-based observations of Es layers recorded by 25 ionospheric monitoring stations and held at the UK Solar System Data Centre at the Rutherford Appleton Laboratory and the Chinese Meridian Project were used to derive the hourly Es critical frequency ( f o Es) data. The global distribution of f o Es with a high spatial resolution shows a strong seasonal variation in f o Es with a summer maximum exceeding 4.0 MHz and a winter minimum between 2.0 and 2.5 MHz. The GPS/GNSS RO technique is an important tool that can provide global estimates of Es layers, augmenting the limited coverage and low-frequency detection threshold of ground-based instruments. Attention should be paid to small f o Es values from ionosondes near the instrumental detection limits corresponding to minimum frequencies in the range 1.28–1.60 MHz.

scholarly journals The Scaling LInear Macroweather model (SLIM): using scaling to forecast global scale macroweather from months to decades

2015 ◽  
Vol 6 (1) ◽  
pp. 489-545 ◽  
Author(s):  
S. Lovejoy ◽  
L. del Rio Amador ◽  
R. Hébert
Keyword(s):  
Stochastic Models ◽  
High Frequency ◽  
Low Frequency ◽  
Global Scale ◽  
Forecast Skill ◽  
Previous Attempt ◽  
Frequency Noise ◽  
Forecast Errors ◽  
System Memory ◽  
Two Parameter

Abstract. At scales of ≈ 10 days (the lifetime of planetary scale structures), there is a drastic transition from high frequency weather to low frequency macroweather. This scale is close to the predictability limits of deterministic atmospheric models; so that in GCM macroweather forecasts, the weather is a high frequency noise. But neither the GCM noise nor the GCM climate is fully realistic. In this paper we show how simple stochastic models can be developped that use empirical data to force the statistics and climate to be realistic so that even a two parameter model can outperform GCM's for annual global temperature forecasts. The key is to exploit the scaling of the dynamics and the enormous stochastic memories that it implies. Since macroweather intermittency is low, we propose using the simplest model based on fractional Gaussian noise (fGn): the Scaling LInear Macroweather model (SLIM). SLIM is based on a stochastic ordinary differential equations, differing from usual linear stochastic models (such as the Linear Inverse Modelling, LIM) in that it is of fractional rather than integer order. Whereas LIM implicitly assumes there is no low frequency memory, SLIM has a huge memory that can be exploited. Although the basic mathematical forecast problem for fGn has been solved, we approach the problem in an original manner notably using the method of innovations to obtain simpler results on forecast skill and on the size of the effective system memory. A key to successful forecasts of natural macroweather variability is to first remove the low frequency anthropogenic component. A previous attempt to use fGn for forecasts had poor results because this was not done. We validate our theory using hindcasts of global and Northern Hemisphere temperatures at monthly and annual resolutions. Several nondimensional measures of forecast skill – with no adjustable parameters – show excellent agreement with hindcasts and these show some skill even at decadal scales. We also compare our forecast errors with those of several GCM experiments (with and without initialization), and with other stochastic forecasts showing that even this simplest two parameter SLIM model is somewhat superior. In future, using a space–time (regionalized) generalization of SLIM we expect to be able to exploiting the system memory more extensively and obtain even more realistic forecasts.

Mycoflore des aiguilles de Pinus banksiana et Pinus resinosa. I. Champignons endophytes

1989 ◽  
Vol 67 (7) ◽  
pp. 2052-2060 ◽  
Author(s):  
D. Legault ◽  
M. Dessureault ◽  
G. Laflamme
Keyword(s):  
Endophytic Fungi ◽  
Pinus Banksiana ◽  
Pinus Resinosa ◽  
Fungal Species ◽  
Causal Agent ◽  
Strong Preference ◽  
Closed Canopy ◽  
Natural Stands ◽  
Colonization Rates

The nature and distribution of the endophytic mycoflora isolated from healthy needles of Pinus banksiana and Pinus resinosa growing in plantations or natural stands infected with Scleroderris canker were investigated. Overall colonization rates of the needles were 68 and 89% for P. banksiana and P. resinosa, respectively, and were generally higher in closed canopy stands. For a given tree, colonization rates increased with foliage age but were not influenced by twig orientation. Colonization rates by more than one fungal species were 17% for P. banksiana and 76% for P. resinosa. Two different endophytic species could be found inside the needles of P. banksiana and up to seven in P. resinosa. Brunchorstia pinea, causal agent of Scleroderris canker, was not isolated. Commonly isolated endophytic fungi show a strong preference toward their host: the endophytic mycoflora of P. banksiana needles is almost limited to Coccomyces sp. while Pragmopycnis sp. and three Leptostroma species account for most of the isolates from P. resinosa.

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