scholarly journals Microbial transfers from permanent grassland ecosystems to milk in dairy farms in the Comté cheese area

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
N. Chemidlin Prévost-Bouré ◽  
B. Karimi ◽  
S. Sadet-Bourgeteau ◽  
C. Djemiel ◽  
M. Brie ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Dairy Farms ◽  
Raw Milk ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Farming Practices ◽  
Organic Fertilization ◽  
Grassland Ecosystems ◽  
Protected Designation Of Origin

AbstractThe specificity of dairy Protected Designation of Origin (PDO) products is related to their “terroir” of production. This relationship needs better understanding for efficient and sustainable productions preserving the agroecological equilibrium of agroecosystems, especially grasslands. Specificity of PDO Comté cheese was related to the diversity of natural raw milk bacterial communities, but their sources need to be determined. It is hypothesized that raw milk indigenous microbial communities may originate from permanent grazed grasslands by the intermediate of dairy cows according to the sequence soil–phyllosphere–teat–milk. This hypothesis was evaluated on a 44 dairy farms network across PDO Comté cheese area by characterizing prokaryotic and fungal communities of these compartments by metabarcoding analysis (16S rRNA gene: V3–V4 region, 18S rRNA gene: V7–V8 region). Strong and significant links were highlighted between the four compartments through a network analysis (0.34 < r < 0.58), and were modulated by soil pH, plant diversity and elevation; but also by farming practices: organic fertilization levels, cattle intensity and cow-teat care. This causal relationship suggests that microbial diversity of agroecosystems is a key player in relating a PDO product to its “terroir”; this under the dependency of farming practices. Altogether, this makes the “terroir” even more local and needs to be considered for production sustainability.

A new semi-nested PCR protocol to amplify large 18S rRNA gene fragments for PCR-DGGE analysis of soil fungal communities

2006 ◽  
Vol 65 (1) ◽  
pp. 63-75 ◽  
Author(s):  
Miruna Oros-Sichler ◽  
Newton C.M. Gomes ◽  
Gabriele Neuber ◽  
Kornelia Smalla
Keyword(s):  
Nested Pcr ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Dgge Analysis

scholarly journals Impact of Land Use on Arbuscular Mycorrhizal Fungal Communities in Rural Canada

2013 ◽  
Vol 79 (21) ◽  
pp. 6719-6729 ◽  
Author(s):  
Mulan Dai ◽  
Luke D. Bainard ◽  
Chantal Hamel ◽  
Yantai Gan ◽  
Derek Lynch
Keyword(s):  
Land Use ◽  
Species Richness ◽  
Diversity Index ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Canadian Prairie ◽  
Highly Correlated

ABSTRACTThe influence of land use on soil bio-resources is largely unknown. We examined the communities of arbuscular mycorrhizal (AM) fungi in wheat-growing cropland, natural areas, and seminatural areas along roads. We sampled the Canadian prairie extensively (317 sites) and sampled 20 sites in the Atlantic maritime ecozone for comparison. The proportions of the different AM fungal taxa in the communities found at these sites varied with land use type and ecozones, based on pyrosequencing of 18S rRNA gene (rDNA) amplicons, but the lists of AM fungal taxa obtained from the different land use types and ecozones were very similar. In the prairie, the Glomeraceae family was the most abundant and diverse family of Glomeromycota, followed by the Claroideoglomeraceae, but in the Atlantic maritime ecozone, the Claroideoglomeraceae family was most abundant. In the prairie, species richness and Shannon's diversity index were highest in roadsides, whereas cropland had a higher degree of species richness than roadsides in the Atlantic maritime ecozone. The frequencies of occurrence of the different AM fungal taxa in croplands in the prairie and Atlantic maritime ecozones were highly correlated, but the AM fungal communities in these ecozones had different structures. We conclude that the AM fungal resources of soils are resilient to disturbance and that the richness of AM fungi under cropland management has been maintained, despite evidence of a structural shift imposed by this type of land use. Roadsides in the Canadian prairie are a good repository for the conservation of AM fungal diversity.

scholarly journals Genotype-Specific Variation in the Structure of Root Fungal Communities Is Related to Chickpea Plant Productivity

2015 ◽  
Vol 81 (7) ◽  
pp. 2368-2377 ◽  
Author(s):  
Navid Bazghaleh ◽  
Chantal Hamel ◽  
Yantai Gan ◽  
Bunyamin Tar'an ◽  
Joan Diane Knight
Keyword(s):  
Central Zone ◽  
Crop Productivity ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Canadian Prairie ◽  
Gene Markers ◽  
Content Type ◽  
Wide Range ◽  
Improvement Programs

ABSTRACTIncreasing evidence supports the existence of variations in the association of plant roots with symbiotic fungi that can improve plant growth and inhibit pathogens. However, it is unclear whether intraspecific variations in the symbiosis exist among plant cultivars and if they can be used to improve crop productivity. In this study, we determined genotype-specific variations in the association of chickpea roots with soil fungal communities and evaluated the effect of root mycota on crop productivity. A 2-year field experiment was conducted in southwestern Saskatchewan, the central zone of the chickpea growing region of the Canadian prairie. The effects of 13 cultivars of chickpea, comprising a wide range of phenotypes and genotypes, were tested on the structure of root-associated fungal communities based on internal transcribed spacer (ITS) and 18S rRNA gene markers using 454 amplicon pyrosequencing. Chickpea cultivar significantly influenced the structure of the root fungal community. The magnitude of the effect varied with the genotypes evaluated, and effects were consistent across years. For example, the roots of CDC Corrine, CDC Cory, and CDC Anna hosted the highest fungal diversity and CDC Alma and CDC Xena the lowest.Fusariumsp. was dominant in chickpea roots but was less abundant in CDC Corrine than the other cultivars. A bioassay showed that certain of these fungal taxa, includingFusariumspecies, can reduce the productivity of chickpea, whereasTrichoderma harzianumcan increase chickpea productivity. The large variation in the profile of chickpea root mycota, which included growth-promoting and -inhibiting species, supports the possibility of improving the productivity of chickpea by improving its root mycota in chickpea genetic improvement programs using traditional breeding techniques.

scholarly journals Fungal communities in sediments along a depth gradient in the Eastern Tropical Pacific

2020 ◽  
Author(s):  
Keilor Rojas-Jimenez ◽  
Hans Peter Grossart ◽  
Erik Cordes ◽  
Jorge Cortés
Keyword(s):  
Costa Rica ◽  
Marine Sediments ◽  
Sediment Cores ◽  
18S Rrna Gene ◽  
Tropical Pacific ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Eastern Tropical Pacific ◽  
Deep Waters

AbstractDeep waters represent the largest biome on Earth and the largest ecosystem of Costa Rica. Fungi play a fundamental role in global biogeochemical cycling in marine sediments, yet, they remain little explored. We studied fungal diversity and community composition in several marine sediments from 16 locations sampled along a bathymetric gradient (from a depth of 380 to 3474 m) in two transects of about 1500 km length in the Eastern Tropical Pacific (ETP) of Costa Rica. Sequence analysis of the V7-V8 region of the 18S rRNA gene obtained from sediment cores revealed the presence of 787 fungal amplicon sequence variants (ASVs). On average, we detected a richness of 75 fungal ASVs per sample. Ascomycota represented the most abundant phylum with Saccharomycetes constituting the dominant class. Three ASVs accounted for ca. 63% of all fungal sequences: the yeast Metschnikowia (49.4%), Rhizophydium (6.9%), and Cladosporium (6.7%). Although we distinguished a cluster dominated by yeasts and a second cluster dominated by filamentous fungi, we were unable to detect a strong effect of depth, temperature, salinity, dissolved oxygen, and pH on the composition of fungal communities. We highlight the need to understand further the ecological role of fungi in deep-sea ecosystems.

scholarly journals Incidence and Diversity of Potentially Highly Heat-Resistant Spores Isolated at Dairy Farms

2005 ◽  
Vol 71 (3) ◽  
pp. 1480-1494 ◽  
Author(s):  
Patsy Scheldeman ◽  
Annelies Pil ◽  
Lieve Herman ◽  
Paul De Vos ◽  
Marc Heyndrickx
Keyword(s):  
Restriction Analysis ◽  
Acid Methyl Ester ◽  
Dairy Farms ◽  
Raw Milk ◽  
Contamination Level ◽  
Rrna Gene ◽  
Selective Heating ◽  
Heat Resistant ◽  
Strain Collection ◽  
Entry Points

ABSTRACT The presence of highly heat-resistant spores of Bacillus sporothermodurans in ultrahigh-temperature or sterilized consumer milk has emerged as an important item in the dairy industry. Their presence is considered undesirable since they hamper the achievement of commercial sterility requirements. By using a selective 30-min heat treatment at 100°C, 17 Belgian dairy farms were screened to evaluate the presence, sources, and nature of potentially highly heat-resistant spores in raw milk. High numbers of these spores were detected in the filter cloth of the milking equipment and in green crop and fodder samples. About 700 strains were isolated after the selective heating, of which 635 could be screened by fatty acid methyl ester analysis. Representative strains were subjected to amplified ribosomal DNA restriction analysis, 16S rRNA gene sequencing, percent G+C content, and DNA-DNA reassociations for further identification. The strain collection showed a remarkable diversity, with representatives of seven aerobic spore-forming genera. Bacillus licheniformis and Bacillus pallidus were the most predominant species overall. Twenty-three percent of the 603 spore-forming isolates proved to belong to 18 separate novel species. These findings suggest that the selective heating revealed a pool of unknown organisms with a higher heat-resistant character. This study showed that high spore counts can occur at the dairy farm and that feed and milking equipment can act as reservoirs or entry points for potentially highly heat-resistant spores into raw milk. Lowering this spore load by good hygienic measures could probably further reduce the contamination level of raw milk, in this way minimizing the aerobic spore-forming bacteria that could lead to spoilage of milk and dairy products. Assessment and characterization of this particular flora are of great importance to allow the dairy or food industry to adequately deal with newly arising microbiological problems.

scholarly journals Nitrogen release from five organic fertilizers commonly used in greenhouse organic horticulture with contrasting effects on bacterial communities

2020 ◽  
pp. 1-16 ◽  
Author(s):  
Pierre-Paul Dion ◽  
Thomas Jeanne ◽  
Mireille Thériault ◽  
Richard Hogue ◽  
Steeve Pepin ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Mineral Soil ◽  
Organic Fertilizers ◽  
Organic N ◽  
Rrna Gene ◽  
N Availability ◽  
Organic Fertilization ◽  
Growing Medium ◽  
Organic Horticulture ◽  
The Impact

Organic fertilization in greenhouses relies on organic fertilizers with low carbon/nitrogen ratio. Nitrogen (N) availability thus depends on an efficient mineralization driven by microbial communities. However, data on the mineralization rate of such fertilizers are scarce, and their improper use can lead to either N deficiency, or N losses to the environment. Consequently, better knowledge of N availability following organic fertilization is crucial for the development of sustainable greenhouse organic horticulture. We investigated the effect of pelleted poultry manure (PM) and blood (BM), feather (FM), alfalfa (AM), and shrimp (SM) meals on N availability and bacterial communities in a peat-based organic growing medium and a mineral soil. Nitrogen and carbon (C) pools were measured periodically over a 52 wk incubation experiment. Bacterial communities were characterized by sequencing the regions V6–V8 of the 16S rRNA gene on the high-throughput Illumina MiSeq platform, 4 wk after the start of the incubation. Nitrogen mineralization plateaued for the mineral soil and the peat substrate at, respectively, 41% and 63% of applied N for PM, 56%–93% (BM), 54%–81% (FM), 34%–53% (AM), and 57%–73% (SM). Organic fertilizers supported markedly contrasted bacterial communities, closely linked to soil biochemical properties, especially mineral N, pH, and soluble C. Alfalfa meal promoted the highest Shannon diversity index in the mineral soil, whereas SM and PM increased it in the peat-based growing medium. Our results quantified the mineralization and highlighted the impact on bacterial communities of commonly used organic N fertilizers in conditions relevant to organic greenhouse horticulture.

scholarly journals Fungal communities associated with the eastern larch beetle: diversity and variation within developmental stages

2017 ◽  
Author(s):  
Audrey-Anne Durand ◽  
Jean-Philippe Buffet ◽  
Philippe Constant ◽  
Eric Déziel ◽  
Claude Guertin
Keyword(s):  
Filamentous Fungi ◽  
Bark Beetles ◽  
Developmental Stages ◽  
18S Rrna Gene ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Comprehensive Overview ◽  
Defense Compounds ◽  
Larval Stages ◽  
Dendroctonus Simplex

AbstractBacterial and fungal communities associated with bark beetles, especially some Dendroctonus species, mediate challenging aspects of the subcortical habitat for their hosts. Filamentous fungi and yeasts are important in various metabolic processes of certain bark beetles, with involvement in nutrition, protection and detoxification of plant defense compounds. The eastern larch beetle, Dendroctonus simplex, is recognized as a serious forest pest in the upper part of North America. Although D. simplex is well studied, the fungal communities and their ecological role remain to be investigated. Here, using 18S rRNA gene pyrosequencing, we provide a comprehensive overview of the yeasts and filamentous fungi associated with the eastern larch beetle and compare fungal communities between different developmental stages and microenvironments. Fungal mycobiome associated with the galleries was also investigated. Our study has unveiled an unexpected fungal diversity associated with the developmental stages. Significant differences in species richness between the developmental stages were determined. Yeasts were found to be predominant in the adult and larval stages, whereas filamentous fungi were most prevalent in the pupae. Our results indicate a possible implication of yeasts in the eastern larch beetle nutrition.

scholarly journals Identification of Bacterial and Fungal Communities in the Roots of Orchids and Surrounding Soil in Heavy Metal Contaminated Area of Mining Heaps

2020 ◽  
Vol 10 (20) ◽  
pp. 7367
Author(s):  
Miroslav Böhmer ◽  
Daniel Ozdín ◽  
Matúš Račko ◽  
Michal Lichvár ◽  
Jaroslav Budiš ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Fungal Communities ◽  
Rrna Gene ◽  
Bacterial Composition ◽  
Mining Sites ◽  
Mining Areas ◽  
Sequencing Method ◽  
The Family ◽  
Generation Sequencing ◽  
Surrounding Soil

Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas.

scholarly journals Cryptosporidiosis in Iranian Farm Workers and Their Household Members: A Hypothesis about Possible Zoonotic Transmission

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Morteza Izadi ◽  
Nematollah Jonaidi-Jafari ◽  
Amin Saburi ◽  
Hossein Eyni ◽  
Mohammad-Reza Rezaiemanesh ◽  
...  
Keyword(s):  
Significant Risk ◽  
Dairy Farms ◽  
Significant Risk Factor ◽  
18S Rrna Gene ◽  
Farm Workers ◽  
Zoonotic Transmission ◽  
Rrna Gene ◽  
Daily Work ◽  
Isfahan Province ◽  
Household Members

Objectives. The prevalence ofCryptosporidiumand the risk factors of zoonotic transmission in Najafabad, Isfahan, Iran dairy farms were examined.Methods. One fecal sample was collected from all calves less than 6 months old in eight dairy farms around Najafabad (Isfahan province, Central Iran) as well as individuals working in these farms and their household members. A two-step nested PCR protocol was used to amplify the 18S rRNA gene (830 bp).Results.Cryptosporidiumwas identified in the stool of 36 (prevalence 8.5%) of 96 farm workers and 326 household members. Furthermore, 31 (14.2%) of 218 calf samples were positive.Cryptosporidium parvumwas identified in 15 (72%) of the positive farm workers and 10 (65%) of the positive household members. Of the positive calves, 20 (64.5%) were infected withC. parvum, indicating possible zoonotic transmission in these farms. Contact with calves (P< 0.0001) was the most significant risk factor ofC. parvuminfection. A considerable negative association was observed betweenC. parvuminfection and cleaning of shoes/boots after daily work (P= 0.004), hand washing (P= 0.013), and use of piped water (P< 0.006). In the multivariate analysis with logistic regression, only contact with calves was significant.Conclusion. Zoonotic transmission ofC. parvumdue to contact with calves is predominant among farm workers and their household members of this region and appropriate health measures must be applied to control the infection and decrease of zoonotic transmission of this parasite.

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