scholarly journals The foliar microbiome suggests fungal and bacterial agents may be involved in the beech leaf disease pathosystem

2021 ◽  
Author(s):  
Carrie Jane Ewing ◽  
Jason Slot ◽  
Maria-Soledad Benitez Ponce ◽  
Cristina Rosa ◽  
Antonino Malacrinò ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Diversity Indices ◽  
Fagus Grandifolia ◽  
Sequence Variant ◽  
American Beech ◽  
Direct Role ◽  
Alpha And Beta Diversity ◽  
Leaf Disease ◽  
Species Analysis ◽  
Differential Abundance Analysis

Beech leaf disease (BLD) is a recently discovered disease that is causing severe damage to American beech (Fagus grandifolia) in northeastern North America. The recently described nematode Litylenchus crenatae ssp. mccannii was detected in BLD affected foliage and may be associated with the disease. However, speculation on the direct role of the nematode in infection still remains. In this study we profiled the microbial communities associated with asymptomatic, symptomatic, and naïve (control) American beech foliage by using a high throughput sequence-based metabarcoding analysis of fungi, bacteria, phytoplasmas, and nematodes. We then used both a differential abundance analysis and indicator species analysis as well as several diversity metrics to try and discover microbes associated only with symptomatic foliage. To do so we amplified the organism-specific phylogenetic informative regions of the 16S, 18S, and internal transcribed spacer (ITS1) regions using Illumina MiSeq. Our results detected the amplicon sequence variant (ASV) associated with the nematode L. crenatae ssp. mccannii, but in all symptom types. However, four ASVs associated with the bacterial genera Wolbachia, Erwinia, Paenibacillus, and Pseudomonas and one ASV associated with the fungal genus Paraphaeosphaeria were detected only in symptomatic samples. In addition, we identified significant differences based on symptom type in both the alpha and beta diversity indices for the bacterial and fungal communities. These results suggest that L. crenatae ssp. mccannii may not be fully responsible for BLD, but rather that other microbe(s), may be contributing to the syndrome, including the putative nematode endosymbiont Wolbachia sp.

scholarly journals The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 745
Author(s):  
Michelle Martin de Bustamante ◽  
Diego Gomez ◽  
Jennifer MacNicol ◽  
Ralph Hamor ◽  
Caryn Plummer
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Bacterial Microbiota ◽  
Healthy Control ◽  
Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

scholarly journals First Report of Beech Leaf Disease, Caused by Litylenchus crenatae mccannii, on American Beech (Fagus grandifolia) in Virginia

Plant Disease ◽  
2021 ◽  
Author(s):  
Mihail R. Kantor ◽  
Zafar Ahmad Handoo ◽  
Lynn Carta ◽  
Shiguang Li
Keyword(s):  
North America ◽  
Rhode Island ◽  
Morphological Characteristics ◽  
Pcr Amplification ◽  
Fagus Crenata ◽  
Fagus Grandifolia ◽  
American Beech ◽  
First Report ◽  
Leaf Disease ◽  
Foliar Nematode

Beech leaf disease (BLD) was first reported in 2012 in Lake County, Ohio on American beech trees (Fagus grandifolia Ehrh.). Since then, it spread across the Northeastern United States and has been reported from Ohio, Pennsylvania, New York, New Jersey, Connecticut, Rhode Island, Maine, West Virginia, and Ontario, Canada (Carta et al. 2020; Mara and LaMondia 2020, Reid et al. 2020). The symptoms of BLD are characterized by dark interveinal banding of leaves appearing soon after spring flush that become chlorotic and necrotic through autumn, resulting in canopy thinning in advanced stages, followed in some young trees by death. Litylenchus crenatae mccannii has similar morphological characteristics with Litylenchus crenatae (Kanzaki et al. 2019) reported on Fagus crenata from Japan. However that beech species has not shown BLD symptoms or yielded any L. crenatae mccannii in North America. There are several morphological differences between the two. The North American subspecies have shorter post-uterine sac, narrower body width in mature females, shorter tail in immature females, longer tail in mature females, and longer stylet in males when compared to the Japanese subspecies (Carta et al. 2020). BLD symptoms were found on American beech trees in Prince William Forest Park, Prince William County, Virginia in June, 2021. The affected leaves contained females, males, and juveniles with morphometrics consistent with L. crenatae mccannii (Carta et al. 2020). The crude genomic DNA from a live single Litylenchus was prepared with freeze-thaw lysis (Carta and Li, 2019). The ITS PCR were performed by using the procedures and primer set, ITS-CL-F2 and 28S-CL-R described in the previous study (Carta and Li, 2020). The visualization, the cleanup and the direct DNA sequencing of the PCR products were performed by using the procedures described in the previous studies (Carta and Li, 2018 and 2019). Sequences were submitted to GenBank as accessions MZ611855 and MZ611856. This represents the first report of BLD in Virginia. It is also approximately 300 miles south of the 2020 detection of BLD from New Cumberland, WV, and represents the southernmost detection of the disease and nematode in North America. The author(s) declare no conflict of interest. References Carta, L.K., Li, S. 2018. Improved 18S small subunit rDNA primers for problematic nematode amplification. Journal of Nematology. 50, 533-542. Carta, L.K., Li, S. 2019. PCR amplification of a long rDNA segment with one primer pair in agriculturally important nematodes. Journal of Nematology. 51, e2019-26. Carta, L.K., Li, S. 2020. Improvement of long segment ribosomal PCR amplification for the molecular taxonomic identification of Litylenchus crenatae mccannii in beech trees with beech leaf disease. Journal of Nematology. 52, e2020-016. Kanzaki, N., Ichihara, Y., Aikawa, T., Ekino, T., Masuya, H. 2019. Litylenchus crenatae n. sp. (Tylenchomorpha: Anguinidae), a leaf gall nematode parasitising Fagus crenata Blume Nematology 21 (1), 5-22. http://www.brill.com/nematology doi: 10.1163/15685411-00003190 Marra, R.E., LaMondia, J. 2020. First report of beech leaf disease, caused by the foliar nematode, Litylenchus crenatae mccannii, on American beech (Fagus grandifolia) in Connecticut. Plant Disease (early view). https://doi.org/10.1094/PDIS-02-20-0442-PDN Reed, S. E., Greifenhagen, S., Yu, Q., Hoke A., Burke D. J., Carta L. K., Handoo Z.A., Kantor, M.R., Koch, J. 2020. Foliar nematode, Litylenchus crenatae ssp. mccannii, population dynamics in leaves and buds of beech leaf disease-affected trees in Canada and the US. Forest Pathology 50 (3), e12599.

scholarly journals Study on the diversity of epiphytic bacteria on corn and alfalfa using Illumina MiSeq/NovaSeq high-throughput sequencing system

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Meixiao Wu ◽  
Yuehua Wang ◽  
Yijing Wang ◽  
Xuefei Wang ◽  
Ming Yu ◽  
...  
Keyword(s):  
High Throughput ◽  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Raw Materials ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Epiphytic Bacteria ◽  
Alpha And Beta Diversity ◽  
Paired End Sequencing

Abstract Purpose To investigate the diversity of the epiphytic bacteria on corn (Zea mays) and alfalfa (Medicago sativa) collected in Hengshui City and Xingtai City, Hebei Province, China, and explore crops suitable for natural silage. Methods The Illumina MiSeq/NovaSeq high-throughput sequencing system was used to conduct paired-end sequencing of the community DNA fragments from the surface of corn and alfalfa collected in Hengshui and Xingtai. QIIME2 and R software were used to sort and calculate the number of sequences and taxonomic units for each sample. Thereafter, the alpha and beta diversity indices at of species level were calculated, and the abundance and distribution of taxa were analyzed and compared between samples. Result At phylum level, the dominant groups were Proteobacteria (70%), Firmicutes (13%), Actinobacteria (9%), and Bacteroidetes (7%). Meanwhile, the dominant genera were Pseudomonas (8%), Acinetobacter (4%), Chryseobacterium (3%), and Hymenobacter (1%). Enterobacteriaceae (24%) were the most predominant bacteria in both the corn and alfalfa samples. Alpha diversity analysis and beta diversity indices revealed that the diversity of epiphytic microbial communities was significantly affected by plant species but not by region. The diversity and richness of the epiphytic bacterial community of alfalfa were significantly higher than those of corn. Conclusion This study contributes to the expanding knowledge on the diversity of epiphytic bacteria in corn and alfalfa silage and provides a basis for the selection of raw materials.

scholarly journals PSIX-6 Gastrointestinal microbiome of calves fed solid diets containing different levels and sources of NDF

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 418-419
Author(s):  
Gercino F Virgínio Júnior ◽  
Milaine Poczynek ◽  
Ana Paula Silva ◽  
Ariany Toledo ◽  
Amanda Cezar ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Diversity Indices ◽  
Dairy Calves ◽  
Rrna Gene ◽  
Gastrointestinal Microbiome ◽  
Fecal Microbiome ◽  
Miseq Platform ◽  
Holstein Calves ◽  
Ad Libitum ◽  
Different Levels

Abstract Different levels and sources of NDF can modify the gastrointestinal microbiome. This study evaluated 18 Holstein calves housed in not-bedded suspended individual cages and fed one of three treatments: 22NDF - conventional starter containing 22% NDF (n = 7); 31NDF - starter with 31% NDF, replacing part of the corn by soybean hull (n = 6); and 22NDF+H - conventional starter with 22% NDF plus coast-cross hay ad libitum (n = 5). All animals received 4 L of milk replacer daily (24% CP; 18.5% fat; diluted to 12.5% solids), divided into two meals, being weaned at 8th week of age. After weaning, animals were housed in tropical shelters, fed with the respective solid diet and coast-cross hay ad libitum for all treatments. To evaluate the microbiome, ruminal fluid samples were collected using a modified Geishauser oral probe at weeks 2, 4, 6, 8 and 10, two hours after the morning feeding, and fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. Ruminal microbiome had no differences in diversity for the effects of weeks, treatments or interaction of both factors (Table 1). In feces, the diversity indices and evenness were higher for 22NDF+H when compared to 22NDF, with no difference for 31NDF. All indices were significantly affected by calves age. At birth, calves had the greatest diversity and richness. Week 1 and 2 had less evenness and diversity. Bacteroidota, Firmicutes_A and Firmicutes_C were the most abundant phylum in rumen and feces. The supply of hay was only effective in modifying the fecal microbiome of dairy calves, suggesting a resilience in the ruminal microbiome.

scholarly journals Bacterial Diversity Analysis and Evaluation Proteins Hydrolysis During the Acid Whey and Fish Waste Fermentation

2021 ◽  
Vol 9 (1) ◽  
pp. 100
Author(s):  
Alba C. Mayta-Apaza ◽  
Israel García-Cano ◽  
Konrad Dabrowski ◽  
Rafael Jiménez-Flores
Keyword(s):  
Microbial Diversity ◽  
Microbial Ecology ◽  
Illumina Miseq ◽  
Human Consumption ◽  
Fish Waste ◽  
Alpha And Beta Diversity ◽  
Analysis And Evaluation ◽  
Dynamic Variations ◽  
Acid Whey ◽  
By Products

The disposal of acid whey (Aw), a by-product from fermented products, is a problem for the dairy industry. The fishery industry faces a similar dilemma, disposing of nearly 50% of fish processed for human consumption. Economically feasible and science-based alternatives are needed to overcome this problem. One possible solution is to add value to the remaining nutrients from these by-products. This study focuses on the breakdown of nutrients in controlled fermentations of Aw, fish waste (F), molasses (M), and a lactic acid bacteria (LAB) strain (Lr). The aim was to assess the dynamic variations in microbial diversity and the biochemical changes that occur during fermentation. Four treatments were compared (AwF, AwFM, AwFLr, and AwFMLr), and the fermentation lasted 14 days at 22.5 °C. Samples were taken every other day. Colorimetric tests for peptide concentrations, pH, and microbial ecology by 16S-v4 rRNA amplicon using Illumina MiSeq were conducted. The results of the microbial ecology showed elevated levels of alpha and beta diversity in the samples at day zero. By day 2 of fermentation, pH dropped, and the availability of a different set of nutrients was reflected in the microbial diversity. The fermentation started to stabilize and was driven by the Firmicutes phylum, which dominated the microbial community by day 14. Moreover, there was a significant increase (3.6 times) in peptides when comparing day 0 with day 14, making this treatment practical and feasible for protein hydrolysis. This study valorizes two nutrient-dense by-products and provides an alternative to the current handling of these materials.

scholarly journals Effect of Bovine MFGM and LF in Infant Formula on Gut Microbiome and Metabolome at Four Months of Age

2021 ◽  
Author(s):  
Maciej Chichlowski ◽  
Nicholas Bokulich ◽  
Cheryl L Harris ◽  
Jennifer L Wampler ◽  
Fei Li ◽  
...  
Keyword(s):  
Infant Formula ◽  
Beta Diversity ◽  
Milk Fat ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Term Infants ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Metabolite Profiles

Abstract Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human milk bioactive components demonstrated to support gastrointestinal (GI) and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 months of age were previously reported in healthy term infants fed a cow's milk-based infant formula with added source of bovine MFGM and bovine LF through 12 months of age. Objectives To compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at Baseline (10–14 days of age) and Day 120 (MFGM + LF: 26, Control: 33). Bacterial community profiling was performed via16S rRNA gene sequencing (Illumina MiSeq) and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using Linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/mass spectroscopy) and expressed as the fold-change between group means (Control: MFGM + LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 months. Subtle group differences in beta diversity were demonstrated at 4 months (Jaccard distance; R2 = 0.01, P = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM + LF group at 4 months. Metabolite profile differences for MFGM + LF vs Control included: lower fecal medium chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by four months of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. Trial registration:  https://clinicaltrials.gov/ct2/show/NCT02274883).

Diarimella laurentidae anam.: sp.nov. from Quebec

1998 ◽  
Vol 76 (12) ◽  
pp. 2037-2041 ◽  
Author(s):  
Vladimir Vujanovic ◽  
Marc St-Arnaud ◽  
Peterjürgen Neumann ◽  
J André Fortin
Keyword(s):  
New Species ◽  
Fagus Grandifolia ◽  
American Beech ◽  
Fungus Species ◽  
First Report ◽  
Ecological Reserve ◽  
A New Species

Diarimella laurentidae, a new species occurring on dead bark and decorticated twigs of American beech (Fagus grandifolia Ehrh.), is reported from the Muir's Wood ecological reserve, located in the centre of the Haut-Saint-Laurent region in the province of Quebec. Diarimella laurentidae is characterized by stromatic, pulvinate, black, setose fructifications composed of a basal stroma of textura angularis, a brown peripheral wall of textura porrecta, conidiomatal setae of two types, and unicellular multisetulate conidia. Its relationships with described Diarimella species is discussed. This is the first report of a species of Diarimella from North America.Key words: Diarimella laurentidae, new fungus species, coelomycete, Fagus grandifolia.

American beech and sugar maple sapling relative abundance and growth are not modified by light availability following partial and total canopy disturbances

2015 ◽  
Vol 45 (6) ◽  
pp. 632-638 ◽  
Author(s):  
Kim Bannon ◽  
Sylvain Delagrange ◽  
Nicolas Bélanger ◽  
Christian Messier
Keyword(s):  
Soil Fertility ◽  
Acer Saccharum ◽  
Sugar Maple ◽  
Light Availability ◽  
Soil Nutrient ◽  
Fagus Grandifolia ◽  
American Beech ◽  
Clear Cutting ◽  
Canopy Opening ◽  
Unmanaged Forest

Studies have reported divergent results on the effect of soil fertility and canopy opening on understory density and growth of sugar maple (AS; Acer saccharum Marsh.) and American beech (FG; Fagus grandifolia Ehrh.). The main objective of this study was to evaluate the effect of a gradient of canopy opening and soil fertility on the density and growth of AS and FG saplings in southwestern Quebec, Canada. We investigated 56 stands containing both AS and FG that were subjected to different disturbance history types (DHTs) (UF, unmanaged forest; PC, partial cut; and CC, clearcut) on various soil types. AS and FG absolute and relative sapling density varied greatly among the 56 stands; however, no significant effects of DHT, soil nutrient availability, or their interaction were found. Both species responded positively in terms of radial growth to canopy openings, with FG growth being slightly better than AS growth in PC stands compared with other canopy treatments. Contrary to our hypothesis, AS did not show significantly higher growth than FG following clear-cutting. These results do not support the idea that AS abundance and growth could be promoted by increasing the intensity of the canopy opening during harvest, at least on the generally acidic and base-poor soils that were investigated.

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