Fungal microbiome of barley grain revealed by NGS and mycological analysis

Introduction. Barley can be infected with a broad variety of fungi, which can cause considerable loss of crop yield and reduce the quality of grain. Modern vision on the geographical and ecological distribution and biodiversity of micromycetes has been established by traditional, cultivation-based methods. However, more recently, molecular methods have shifted microbiological research to a new level, making it possible to investigate hidden taxonomical biodiversity. Study objects and methods. For this study, we determined the fungal biome on the surface and inside of barley grains using the traditional mycological method and the contemporary molecular method, which employed DNA metabarcoding based on NGS (nextgeneration sequencing) of the ITS2 region. We analyzed five cultivars that were collected in two subsequent crop seasons (2014, 2015). Results and discussion. DNA metabarcoding revealed 43 operational taxonomic units, while 17 taxa of genus or species level were recovered by the traditional method. DNA metabarcoding revealed several minor species and one predominant, presumably plantpathogenic Phaeosphaeria sp., which were not detected in the agar plate-based assay. Traditionally, Fusarium fungi were identified by mycological assay. However, the resolution of DNA metabarcoding was sufficient to determine main Fusarium groups divided by ability to produce toxic secondary metabolites. The combined list of Ascomycetes consisted of 15 genera, including 14 fungi identified to species level. The list of Basidiomycota derived from DNA metabarcoding data alone included 8 genera. Conclusion. It was found that crop season predetermines the fungal community structure; mycobiota on the surface and inside of grain was significantly different.

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Identification of medicinal plant Schisandra chinensis using a potential DNA barcode ITS2

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2013.032 ◽

2013 ◽

Vol 82 (4) ◽

pp. 283-288 ◽

Cited By ~ 8

Author(s):

Xian-kuan Li ◽

Bing Wang ◽

Rong-chun Han ◽

Yan-chao Zheng ◽

Hai-bo Yin Yin ◽

...

Keyword(s):

Dna Barcode ◽

Population Level ◽

Species Level ◽

Its2 Region ◽

Schisandra Chinensis ◽

Success Rates ◽

Wild Populations ◽

Efficient Tool ◽

Different Populations ◽

Cultivated Populations

To test whether the internal transcribed spacer 2 (ITS2) region is an effective marker for using in authenticating of the Schisandra chinensis at the species and population levels, separately. And the results showed that the wild populations had higher percentage of individuals that had substitution of C→A at site 86-bp than the cultivated populations. At sites 10-bp, 37-bp, 42-bp and 235-bp, these bases of the Schisandra sphenanthera samples differed from that of S. chinensis. Two species showed higher levels of inter-specific divergence than intra-specific divergence within ITS2 sequences. However, 24 populations did not demonstrate much difference as inter-specific and intra-specific divergences were concerned. Both S. chinensis and S. sphenanthera showed monophyly at species level, yet the samples of different populations shown polyphyly at population level. ITS2 performed well when using BLAST1 method. ITS2 obtained 100% identification success rates at the species level for S. chinensis, with no ambiguous identification at the genus level for ITS2 alone. The ITS2 region could be used to identify S. chinensis and S. sphenanthera in the “Chinese Pharmacopoeia”. And it could also correctly distinguish 100% of species and 100% of genera from the 193 sequences of S. chinensis. Hence, the ITS2 is a powerful and efficient tool for species identification of S. chinensis.

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Changes in the Nutrient Composition of Barley Grain (Hordeum vulgare L.) and of Morphological Fractions of Sprouts

Scientifica ◽

10.1155/2021/9968864 ◽

2021 ◽

Vol 2021 ◽

pp. 1-7

Author(s):

Luis T. Ortiz ◽

Susana Velasco ◽

Jesús Treviño ◽

Beatriz Jiménez ◽

Almudena Rebolé

Keyword(s):

Fatty Acids ◽

Relative Concentration ◽

Barley Grain ◽

Soluble Carbohydrates ◽

Cellulose Content ◽

Hordeum Vulgare L ◽

Residual Structure ◽

Protein Amino Acids ◽

Barley Grains ◽

Green Shoot

The objectives of the current study were (1) to evaluate the effect of sprouting on protein, amino acids, fats, fatty acids, starch, total soluble carbohydrates, and ß-D-glucan content of barley grains and (2) to know the content of these nutrients in the morphological fractions of sprouts: green shoot, residual structure of sprouted grain (RSSG), residual structure of sprouted grain plus unsprouted grain (RSSG plus UG), and root fractions and to determine the proportion of each of these fractions (on fresh and dry basis) in the sprout biomass. Barley grain was sprouted in a commercial germination chamber for a period of 6 days. Raw grain was used as a control. Results showed that crude protein, ether extract, total soluble carbohydrates, and cellulose content increased, whereas starch and ß-D-glucan content decreased in sprouted when compared with the control grain. Amino acid and fatty acid profiles were also affected. Thus, aspartic acid, threonine, alanine, valine, isoleucine, lysine, and tryptophan content increased and only that of glutamic acid decreased after sprouting. Regarding fatty acids, an increase in the relative concentration of C18 : 0 and C18:3n-3 and a decrease in that of C18:1n-9 were detected. Partitioning of sprouted barley into three morphological component fractions showed that the residual structures of sprouted grains plus unsprouted grain fraction made up 82.9% and 93.6% of sprout biomass, on fresh and DM basis, respectively, and the remainder was provided by the root fraction, 10.3% and 3.2%, respectively, and by the green shoot fraction, 6.8% and 3.1%, respectively. The three morphological fractions differed in the content of the most analyzed nutrients.

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Immunological Identification of Organ Specific Proteins and Transcripts in Developing Barley Grains

Zeitschrift für Naturforschung C ◽

10.1515/znc-1993-7-814 ◽

1993 ◽

Vol 48 (7-8) ◽

pp. 609-615

Author(s):

Helge Klungland ◽

Marie Bosnes

Keyword(s):

Specific Protein ◽

Barley Grain ◽

Starchy Endosperm ◽

Sds Page ◽

Organ Specific ◽

Specific Proteins ◽

Barley Grains ◽

Immunological Identification

In vitro translated proteins from poly(A+)RNA of immature barley starchy endosperm and embryos were immunoadsorbed with antibodies raised against proteins of aleurone layers, starchy endosperm and embryos. Four starchy endosperm and eight embryo specific transcripts were detected. In addition, several mRNA s were restricted to only two of the three tissues.Comparing SDS-PAGE patterns of the in vivo protein extracts against which the antibodies were raised, four aleurone, six starchy endosperm and four embryo-specific protein bands were detectable. As for the in vitro translated proteins, several in vivo protein bands were here present in only two of the three tissues. Of eight known barley grain proteins for which antibodies were available, only three were present in developing embryos.

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Allelopathic effects of curly dock (Rumex crispus) on spring barley seed germination and early growth

Žemės ūkio mokslai ◽

10.6001/zemesukiomokslai.v24i1.3440 ◽

2017 ◽

Vol 24 (1) ◽

Author(s):

Regina Malinauskaitė

Keyword(s):

Root Elongation ◽

Spring Barley ◽

Barley Grain ◽

Barley Root ◽

Distilled Water ◽

Coleoptile Length ◽

Rumex Crispus ◽

Allelopathic Interaction ◽

Coleoptile Elongation ◽

Barley Grains

The experiment was carried out at Aleksandras Stulginskis University in 2015. The goal of the experiment was to set the allelopathic interaction and influence of Rumex crispus seeds (unsoaked and soaked for 168 hours) and ionized water on spring barley grain germination. The following experiment variants with different proportions of barley grains and R. crispus fruits were used: a) control – 30 barley grains; other variants: b) 20 barley grains and 10 R. crispus fruits, c) 15:15 and d) 10:20. During the germination in distilled water, unsoaked R. crispus fruits inhibited the barley grain germination. In alkaline ionized water, unsoaked fruits did not affect the barley grain germination, which amounted to 100%. Soaked Rumex crispus fruits stimulated the germination. The lowest germination energy (83%) and viability (92%) were determined in the case of ratio 20:10. In distilled water, unsoaked fruits increased barley root and coleoptile elongation. The longest roots (140.00 mm) and coleoptiles (108.26 mm) were in the variant 15:15. Soaked fruits increased barley root elongation, but did not have any effect on the coleoptile length. In ionized alkaline water, in the experiment variants 20:10 and 15:15, R. crispus fruits suppressed barley root and coleoptile elongation. In the case of ratio 10:20 barley formed the longest roots and coleoptiles. Soaked fruits increased barley root elongation, especially in the case of ratio 10:20, and coleoptile elongation. R. crispus fruits had no significant effect on the number of roots.

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Using pollen DNA metabarcoding to profile nectar sources of urban beekeeping in Kōtō-ku, Tokyo

10.21203/rs.3.rs-44772/v2 ◽

2020 ◽

Author(s):

Keiske Tanaka ◽

Akinobu Nozaki ◽

Hazuki Nakadai ◽

Yuh Shiwa ◽

Mariko Shimizu-Kadota

Keyword(s):

Apis Mellifera ◽

Sampling Strategy ◽

Species Level ◽

Urban Greening ◽

Operational Taxonomic Units ◽

Ecosystem Protection ◽

The Family ◽

Dna Metabarcoding ◽

The World ◽

Nectar Sources

Abstract ObjectiveApis mellifera is a species of honeybee that has been introduced around the world as an industrial beekeeping species. Recently, urban beekeeping has attracted attention as a means of ecosystem protection and urban greening. This study aimed to investigate nectar sources of urban beekeeping in Kōtō-ku, Tokyo using pollen DNA metabarcoding.ResultsWe extracted DNA from pollen collected by the honeybees of a local urban beekeeping operation. DNA metabarcoding analysis was carried out by sequencing a part of the rbcL region of the chloroplast genome. A total of 31 samples collected between mid-March, 2018 and mid-October, 2018 yielded 54 operational taxonomic units (OTUs) comprising 14 families, 32 genera, and 8 species. Whereas 5 OTUs were profiled throughout all seasons, 38 OTUs were season-specific (spring, summer, or autumn). Therefore, we were able to infer seasonal nectar sources for the beekeeping operation at the family or genus level, as well as at the species level to a lesser extent. Our pollen-sampling strategy was effective for profiling season-specific nectar sources, with the exception of a few anomalies that can be accounted for by out-of-season flowering associated with artificial gardening and/or pollen accumulation over multiple seasons.

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Effects of moisture content, loading rate, and grain orientation on fracture resistance of barley grain

Research in Agricultural Engineering ◽

10.17221/6/2009-rae ◽

2009 ◽

Vol 55 (No. 3) ◽

pp. 85-93 ◽

Cited By ~ 4

Author(s):

H. Tavakoli ◽

S.S. Mohtasebi ◽

A. Rajabipour ◽

M. Tavakoli

Keyword(s):

Moisture Content ◽

Fracture Resistance ◽

Block Design ◽

Barley Grain ◽

Deformation Curves ◽

Horizontal Orientation ◽

Proper Design ◽

Four Levels ◽

Barley Grains ◽

Agricultural Materials

Force and deformation curves of agricultural materials must be provided for the proper design of harvesting and processing machineries. In this research, the fracture resistance of barley grain was measured in terms of the grain rupture force and energy. In this study, 8 treatments were performed as a randomised complete block design with 10 replications. The barley grains were quasi-statically loaded in horizontal and vertical orientations with the moisture content at four levels: 7.34, 12.11, 16.82, and 21.58% dry basis, and loading rates at two levels: 5 and 10 mm/min. Based on the results obtained, the force required for initiating the grain rupture decreased from 161.97 to 93.94 N, and from 75.37 to 50.16 N, and the energy absorbed at the grain rupture increased from 36.42 to 74.70 mJ and from 27.34 to 62.65 mJ, for horizontal and vertical orientations, respectively, with the increase in the moisture content from 7.34 to 21.58% dry basis. This showed that seeds are more flexible in the horizontal orientation.

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Diversity of indoor fungi as revealed by DNA metabarcoding

Genome ◽

10.1139/gen-2015-0191 ◽

2017 ◽

Vol 60 (1) ◽

pp. 55-64 ◽

Cited By ~ 6

Author(s):

Helena Korpelainen ◽

Maria Pietiläinen

Keyword(s):

Air Quality ◽

Similarity Index ◽

Taxonomic Composition ◽

Its2 Region ◽

Nursery Schools ◽

Fungal Identification ◽

Dna Metabarcoding ◽

Before And After ◽

Indoor Fungi ◽

University Buildings

In the present study, we conducted DNA metabarcoding (the nuclear ITS2 region) for indoor fungal samples originating from two nursery schools with a suspected mould problem (sampling before and after renovation), from two university buildings, and from an old farmhouse. Good-quality sequences were obtained, and the results showed that DNA metabarcoding provides high resolution in fungal identification. The pooled proportions of sequences representing filamentous ascomycetes, filamentous basidiomycetes, yeasts, and other fungi equalled 62.3%, 8.0%, 28.3%, and 1.4%, respectively, and the total number of fungal genera found during the study was 585. When comparing fungal diversities and taxonomic composition between different types of buildings, no obvious pattern was detected. The average pairwise values of SørensenChao indices that were used to compare similarities for taxon composition between samples among the samples from the two university buildings, two nurseries, and farmhouse equaled 0.693, 0.736, 0.852, 0.928, and 0.981, respectively, while the mean similarity index for all samples was 0.864. We discovered that making explicit conclusions on the relationship between the indoor air quality and mycoflora is complicated by the lack of appropriate indicators for air quality and by the occurrence of wide spatial and temporal changes in diversity and compositions among samples.

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Use of Lysostaphin and Bacitracin Susceptibility for Routine Presumptive Identification of Staphylococci of Bovine Origin1

Journal of Food Protection ◽

10.4315/0362-028x-51.1.24 ◽

1988 ◽

Vol 51 (1) ◽

pp. 24-28 ◽

Cited By ~ 9

Author(s):

B. E. LANGLOIS ◽

R. J. HARMON ◽

K. AKERS

Keyword(s):

Agar Plate ◽

Rapid Identification ◽

Species Level ◽

Presumptive Identification ◽

Plate System

A simple agar plate system based on susceptibility to lysostaphin and bacitracin to differentiate between staphylococci and micrococci is described. The system also uses susceptibility to novobiocin to aid in identification to species level of staphylococci. Growth from the agar plate can be used to prepare inocula for inoculation of rapid identification systems.

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Rate of starch degradation, apparent digestibility and rate and efficiency of steer gain as influenced by barley grain volume-weight and processing method

Canadian Journal of Animal Science ◽

10.4141/cjas91-102 ◽

1991 ◽

Vol 71 (3) ◽

pp. 867-878 ◽

Cited By ~ 26

Author(s):

G. W. Mathison ◽

B. K. Kerrigan ◽

I. Vlach ◽

R. Hironaka ◽

L. P. Milligan ◽

...

Keyword(s):

Organic Matter ◽

Barley Grain ◽

Processing Method ◽

Starch Degradation ◽

Apparent Digestibility ◽

Grain Processing ◽

Volume Weight ◽

Key Words Barley ◽

Grain Volume Weight ◽

Barley Grains

The effects of barley grain volume-weight and processing method on rate of starch degradation, apparent digestibility, metabolizability and rate and efficiency of growth of steers were examined in a series of trials. The organic matter in an all-concentrate diet containing light barley grain (43 kg hL−1) was 2% less (P = 0.03) digestible than organic matter in diets containing heavier barley grains (59, 64 and 66 kg hL−1). No differences (P = 0.19) in methane production due to barley volume-weight were detected. Rates of gain (1.63–1.67 kg d−1, P = 0.90) and dry matter (DM) intakes (9.8–10.2 kg d−1, P = 0.52) of steers were not affected by including barley grains of differing volume-weights (43, 59 and 64 kg hL−1) in the diet of 90 growing-finishing steers. Steers fed the light barley had a 6% increase (P = 0.27) in DM:gain requirements in comparison with steers fed the two heavier barley grains. Steam-rolling barley in comparison with dry-rolling had no effect on either animal growth rate (1.66 versus 1.64 kg d−1, P = 0.84) or DM:gain ratio (6.15 versus 5.98, P = 0.40). Carcass characteristics were not influenced by grain type or grain processing method. Differences (P < 0.05) were detected in the rate of degradation of starch by amyloglucosidase among three barley grains. Starch in steam-rolled barley was degraded faster (P < 0.05) than starch in dry-rolled barley. Key words: Barley grain, steers, digestibility, gain, efficiency, starch degradation

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Energy and protein utilization of lucerne hay and barley grain by yearling camel calves

Animal Science ◽

10.1017/s0003356100003639 ◽

1988 ◽

Vol 47 (3) ◽

pp. 481-485 ◽

Cited By ~ 3

Author(s):

A. N. Bhattacharya ◽

S. Al-Mutairi ◽

A. Hashimi ◽

S. Economides

Keyword(s):

Barley Grain ◽

Metabolizable Energy ◽

Net Energy ◽

Feeding Value ◽

Collection Period ◽

Barley Grains ◽

Total Urine ◽

Dietary Treatments ◽

Energy Maintenance ◽

Net Energy Gain

ABSTRACTTwo trials were conducted with eight yearling camels with an average intial body weight of 300 kg, to evaluate protein and energy values of lucerne hay and barley grains. In each trial, eight animals were randomly allotted to two different dietary treatments of coarsely ground lucerne hay or lucerne hay + barley grain (50:50) in such a way that two animals in each of the two blocks received the same ration. Each trial consisted of a 10-day preliminary period followed by a 7-day collection period during which total urine and faeces collections were made, and samples were processed and composited for later analysis.All animals consumed daily an average of about 5 kg food divided in two equal meals. The apparent digestibility coefficients for organic matter, crude protein, neutral-detergent fibre and cellulose of the lucerne hay ration improved respectively from 0·615, 0·662, 0·455 and 0·555 to 0·736, 0·655, 0·547 and 0·589, as a result of incorporating 500 g/kg barley grain in place of hay in the diet. Even though there was no difference in the proportion of nitrogen retained relative to intake, the proportion of nitrogen retained relative to that absorbed was higher (P < 0·05) in the lucerne + barley group (0·769) than in the lucerne-only group (0·747). On a dry-matter basis, the feeding value in camels of digestible protein (g/kg), total digestible nutrients (g/kg), digestible energy (MJ/kg), metabolizable energy (MJ/kg), net energy maintenance (MJ/kg), net energy lactation (MJ/kg) and net energy gain (MJ/kg) were respectively 118, 552, 10·0, 8·4, 5·4, 5·0 and 2·1 for lucerne hay and 80, 800, 14·6, 12·1, 8·4, 8·8 and 5·0 for barley grain (calculated by difference).

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