scholarly journals Assessing the Cultivability of Bacteria and Fungi from Arable Crop Residues Using Metabarcoding Data as a Reference

Diversity ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 404
Author(s):  
Valérie Laval ◽  
Lydie Kerdraon ◽  
Matthieu Barret ◽  
Anne-Lise Liabot ◽  
Coralie Marais ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Crop Residues ◽  
A Priori ◽  
Temporal Distribution ◽  
Culture Collections ◽  
Strain Isolation ◽  
Solid Media ◽  
Culture Independent ◽  
Dependent Strain ◽  
Bacteria And Fungi

This study combined culture-dependent (strain isolation plus molecular identification) and culture-independent (metabarcoding) approaches to characterize the diversity of microbiota on wheat and oilseed rape residues. The goal was to develop a methodology to culture microorganisms with the aim of being able to establish synthetic crop residue microbial communities for further study, i.e., testing potential interactions within these communities and characterizing groups of beneficial taxa that could be used as biological control agents against plant pathogens. We generated community-based culture collections. We adapted the isolation strategy to the potential differences in the spatial and temporal distribution of diversity between bacteria and fungi. We performed (i) a high-throughput isolation from few samples with no a priori for bacteria and (ii) a low-throughput isolation from several samples with a priori—i.e., morphotype selection—for fungi. Although isolation using a single medium did not allow us to characterize the microbiome as precisely as metabarcoding, the bacterial diversity (158 ASVs, 36 genera) was relatively higher than the fungal diversity (131 ASVs, 17 genera) known to be limited by competition for growth on non-selective solid media. Isolation and metabarcoding provided consistent and complementary information: they revealed several common but also specific ASVs, leading to close microbial community profiles of the most abundant fungal and bacterial taxa in residues. Finally, by empirically comparing the different profiles, we assessed the cultivability of the most abundant fungal and bacterial taxa obtained in metabarcoding.

scholarly journals Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

2021 ◽  
Author(s):  
Valérie Laval ◽  
Lydie Kerdraon ◽  
Matthieu Barret ◽  
Anne-Lise Liabot ◽  
Coralie Marais ◽  
...  
Keyword(s):  
Molecular Identification ◽  
Crop Residues ◽  
Culture Collection ◽  
Diversity Analysis ◽  
Complementary Information ◽  
Rhizosphere Microflora ◽  
Strain Isolation ◽  
Culture Independent ◽  
Dependent Strain ◽  
Culture Dependent

AbstractThis study is the first to compare culture-dependent (strain isolation plus molecular identification) and culture-independent (whole-community metabarcode sequencing) approaches for characterizing the microbiota of crop residues. We investigated the diversity of fungal and bacterial communities in wheat and oilseed rape residues, using two different culture-dependent strategies to cover the maximum diversity for each kingdom: broad substrate sampling coupled with low-throughput isolation and diversity analysis for fungi, and reduced substrate sampling coupled with high-throughput isolation and diversity analysis for bacteria. The proportion of cultivable microorganisms was neither as low as the ‘1%’ paradigm long associated with the rhizosphere microflora, nor as high as the 50% sometimes reported for the phyllosphere microflora. It was, thus, intermediate between the values for soil and plants. This finding is consistent with residues being considered to constitute an ecotone, at the interface between soil and phyllosphere. Isolation and metabarcoding provided consistent complementary information: they revealed close community profiles, leading to the identification of several common and specific amplicon sequence variants (ASVs). The power of the culture-independent approach was thus confirmed. By contrast the culture-dependent approach was less weak than anticipated. Firstly, it provided complementary information about microbial diversity, with several ASVs not retrieved by metabarcoding being identified after isolation in the community-based culture collection. Secondly, this approach made it possible to preserve and test different taxa either individually or after the creation of synthetic communities, for deciphering the ecological functions of communities beyond merely descriptive aspects.

scholarly journals Intra-Storm Pattern Recognition through Fuzzy Clustering

Hydrology ◽  
2021 ◽  
Vol 8 (2) ◽  
pp. 57
Author(s):  
Konstantinos Vantas ◽  
Epaminondas Sidiropoulos
Keyword(s):  
Fuzzy Clustering ◽  
A Priori ◽  
Temporal Distribution ◽  
Distribution Patterns ◽  
Rainfall Data ◽  
Rainfall Runoff ◽  
Domain Specific ◽  
Runoff Modeling ◽  
National Bank ◽  
Rainfall Patterns

The identification and recognition of temporal rainfall patterns is important and useful not only for climatological studies, but mainly for supporting rainfall–runoff modeling and water resources management. Clustering techniques applied to rainfall data provide meaningful ways for producing concise and inclusive pattern classifications. In this paper, a timeseries of rainfall data coming from the Greek National Bank of Hydrological and Meteorological Information are delineated to independent rainstorms and subjected to cluster analysis, in order to identify and extract representative patterns. The computational process is a custom-developed, domain-specific algorithm that produces temporal rainfall patterns using common characteristics from the data via fuzzy clustering in which (a) every storm may belong to more than one cluster, allowing for some equivocation in the data, (b) the number of the clusters is not assumed known a priori but is determined solely from the data and, finally, (c) intra-storm and seasonal temporal distribution patterns are produced. Traditional classification methods include prior empirical knowledge, while the proposed method is fully unsupervised, not presupposing any external elements and giving results superior to the former.

Optimization of Growth Conditions of Citrus Anthracnose Agent Colletotrichum gloeosporioides Isolates in Tunisia

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Ben Hadj-Daoud H ◽  
◽  
Ben Salem I ◽  
Boughalleb-M’Hamdi N ◽  
◽  
...  
Keyword(s):  
Morphological Traits ◽  
Laboratory Experiments ◽  
Plant Pathogens ◽  
Colletotrichum Gloeosporioides ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Fruit Drop ◽  
Nutritional Conditions ◽  
Solid Media ◽  
Wide Range

Background: Colletotrichum gloeosporioides is important plant pathogens on a wide range of plant hosts such as citrus causing pre- or post-harvest infections as anthracnose, post-bloom fruit drop, tearstain and stem-end rot on fruit, or wither-tip of twigs. Method: The optimization of growth conditions of this pathogen was performed (solid media, temperature, pH and water potential under laboratory experiments). Results: Our results revealed that the maximum radial growth of C. gloeosporioides was recorded on SDA medium. All isolates were able to grow on PDA at temperatures of 15 and 30°C (over 0.7cm/day). Optimal growth radial was recorded at pH 5, 6, 7 and 8. Similar responses were obtained with both salt types, but, in general, C. gloeosporioides was more tolerant to KCl than NaCl. Conclusion: Studies of cultural, morphological traits of the pathogen are prominent to understand the response of the pathogen in different environmental and nutritional conditions.

scholarly journals High concentrations of biological aerosol particles and ice nuclei during and after rain

2013 ◽  
Vol 13 (1) ◽  
pp. 1767-1793 ◽  
Author(s):  
J. A. Huffman ◽  
C. Pöhlker ◽  
A. J. Prenni ◽  
P. J. DeMott ◽  
R. H. Mason ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Dna Analysis ◽  
Fungal Spores ◽  
Ice Nuclei ◽  
Ice Nucleators ◽  
Tightly Coupled ◽  
High Concentrations ◽  
Bacterial Aggregates ◽  
Bacteria And Fungi ◽  
Biological Aerosol Particles

Abstract. Bioaerosols are relevant for public health and may play an important role in the climate system, but their atmospheric abundance, properties and sources are not well understood. Here we show that the concentration of airborne biological particles in a forest ecosystem increases dramatically during rain and that bioparticles are closely correlated with atmospheric ice nuclei (IN). The greatest increase of bioparticles and IN occurred in the size range of 2–6 μm, which is characteristic for bacterial aggregates and fungal spores. By DNA analysis we found high diversities of airborne bacteria and fungi, including human and plant pathogens (mildew, smut and rust fungi, molds, Enterobacteraceae, Pseudomonadaceae). In addition to known bacterial and fungal IN (Pseudomonas sp., Fusarium sporotrichioides), we discovered two species of IN-active fungi that were not previously known as biological ice nucleators (Isaria farinosa and Acremonium implicatum). Our findings suggest that atmospheric bioaerosols, IN and rainfall are more tightly coupled than previously assumed.

The Long Term Spatial-temporal Distribution of Aerosol Optical Depth and Its Associated Atmospheric Circulation Over Southeast Africa.

2021 ◽  
Author(s):  
Matthews Nyasulu ◽  
Md. Mozammel Haque ◽  
Bathsheba Musonda ◽  
Cao Fang
Keyword(s):  
Human Health ◽  
Atmospheric Circulation ◽  
Atmospheric Aerosols ◽  
Crop Residues ◽  
Temporal Distribution ◽  
Western Coast ◽  
High Concentration ◽  
Anthropogenic Aerosols ◽  
Anthropogenic Aerosol

Abstract Recent studies have revealed significant impacts of increased concentration of anthropogenic aerosols in the atmosphere to both climate and human health. Southeast Africa is one of the regions where studies related to atmospheric aerosols remain scant, causing high uncertainty in predicting and understanding the impacts of these aerosols to both climate and human health. The present study therefore has investigated the long term spatial-temporal distribution of atmospheric aerosols, trends, its relationship with cloud properties and the associated atmospheric circulation over the region. High concentration of aerosol has been detected during the dry months of September to November (SON) while low during March to May (MAM) and June-July (JJA) seasons in most areas. Highest 550 was recorded in areas with low elevation such as over Lake Malawi, Zambezi valley and along the western coast of the Indian Ocean. The average of the detected concentration is however low as compared to highly polluted regions of the globe. Statistical analyses revealed insignificant change of AOD550 in most areas between 2002 and 2020 time period. The study has also revealed seasonality of aerosol distribution highly influenced by changes in atmospheric circulation. Burning of biomass during dry months such bush fires and burning of crop residues remain the major source of anthropogenic aerosol concentration over Southeast Africa hence needs to be controlled.

STUDIES ON FOOT AND ROOT ROT OF WHEAT: II. CULTURAL RELATIONSHIPS ON SOLID MEDIA OF CERTAIN MICRO-ORGANISMS IN ASSOCIATION WITH Ophiobolus graminis SACC.

1933 ◽  
Vol 8 (6) ◽  
pp. 545-552 ◽  
Author(s):  
W. C. Broadfoot
Keyword(s):  
Root Rot ◽  
Potato Dextrose Agar ◽  
Wheat Seedlings ◽  
Reliable Indication ◽  
Solid Media ◽  
Metabolic Products ◽  
Growth Reaction ◽  
Bacteria And Fungi ◽  
Micro Organisms ◽  
Pot Culture

The antagonistic and compatible growth relationships of 66 cultures of bacteria and fungi, most of which were from the soil, towards O. graminis on potato dextrose agar and Molisch's salt peptone agar, were compared with the effect of each on the virulence of this pathogene on wheat seedlings in open soil culture.Of the 21 cultures which controlled the virulence of O. graminis in the soil, only 15 of these were antagonistic on potato dextrose agar, while of the 45 cultures which gave intermediate or no control, 17 were compatible and 28 were decidedly antagonistic. From data secured indirectly, the antagonism or compatibility of the micro-organisms toward O. graminis, observed on potato dextrose agar, did not seem to depend on active alkali or acid more than on other metabolic products. The study apparently demonstrates that the growth reaction of various micro-organisms and O. graminis, associated on the two solid media used, is not a reliable indication that the same micro-organism will or will not suppress the virulence of this pathogene on wheat in soil in open pot culture.

A New Type of Antimicrobial Phenolics Produced by Plant Peroxidase and Its Possible Role in the Chemical Defense Systems against Plant Pathogens

1994 ◽  
Vol 49 (7-8) ◽  
pp. 411-414 ◽  
Author(s):  
Akio Kobayashi ◽  
Yutaka Koguchi ◽  
Hiroshi Kanzaki ◽  
Shin-ichiro Kajiyama ◽  
Kazuyoshi Kawazu
Keyword(s):  
Antimicrobial Activity ◽  
Plant Pathogens ◽  
Ethyl Acetate Extract ◽  
Spectroscopic Techniques ◽  
Antimicrobial Compounds ◽  
Horse Radish Peroxidase ◽  
Plant Peroxidase ◽  
Defense Systems ◽  
New Type ◽  
Bacteria And Fungi

Syringaldehyde readily reacted in the horse-radish peroxidase (HRPOD) system. The ethyl acetate extract of the reaction mixture showed a marked antimicrobial activity against bacteria and fungi. After repeated column chromatography three potential antimicrobial compounds were obtained from the extract. The structural elucidation of active compounds was achieved by a combination of spectroscopic techniques and chemical modification

scholarly journals A Composite Bioinoculant Based on the Combined Application of Beneficial Bacteria and Fungi

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 220 ◽  
Author(s):  
Henrietta Allaga ◽  
Bettina Bóka ◽  
Péter Poór ◽  
Viktor Dávid Nagy ◽  
Attila Szűcs ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Plant Pathogens ◽  
Azotobacter Vinelandii ◽  
Pathogenic Fungi ◽  
Screening Strategy ◽  
Plant Residues ◽  
Beneficial Bacteria ◽  
Tomato Plants ◽  
Bacteria And Fungi

A composite soil bioinoculant containing beneficial bacteria and fungi was developed for biocontrol of plant pathogens, phosphorous mobilization, stem degradation, humification, and nitrogen fixation. A Trichoderma asperellum isolate with outstanding in vitro antagonistic abilities toward a series of plant pathogenic fungi was included as a potential biocontrol component. The selected strain was also shown to promote growth and increase photosynthetic activity of tomato plants. For phosphorous mobilization and stem degradation, a Trichoderma atrobrunneum strain was selected, which produced cellulose-degrading enzymes even in the absence of stem residues, while this ability increased 10–15-fold in the presence of ground maize stem. The strain was also shown to produce large amounts of enzymes liberating organically bound phosphorous, as well as cellulase and xylanase activities in solid-state fermentation on various plant residues. A Streptomyces albus strain with excellent peroxidase-producing abilities was selected as a potential humus-producing component, while an Azotobacter vinelandii strain with the potential to provide excess nitrogen for crops was included for nitrogen fixation. The assembled soil bioinoculant had positive effect on the uptake of certain important macro- and microelements (potassium, sodium, and manganese) from the soil by field-grown tomato plants. The applied screening strategy proved to be applicable for the assembly of a composite soil bioinoculant with notable application potentials.

scholarly journals Trends in High Nature Value farmland studies: A systematic review

2017 ◽  
Vol 3 (2) ◽  
pp. 19-32 ◽  
Author(s):  
Yanina Benedetti
Keyword(s):  
Systematic Review ◽  
A Priori ◽  
Temporal Distribution ◽  
Farming Systems ◽  
Taxonomic Diversity ◽  
Subject Area ◽  
Future Research ◽  
Comprehensive Overview ◽  
Field Methods ◽  
Novel Approach

AbstractBackground. Since the High Nature Value (HNV) concept was defined in the early 1990s, several studies on HNV farmland has been increasing over the past 30 years in Europe, highlighting the interest by scientific community of HNV farming systems supporting biodiversity conservation. The aim of this study was to evaluate the trends and main gaps on HNV farmland peer-reviewed publications in order to contribute to the effectiveness of future research in this field. Methods. Searches were conducted using the databases Web of SciencesTM and Scopus in order to identify only peer-reviewed articles on HNV farmland, published prior to July 2017. The inclusion and exclusion criteria were developed a priori. Data as year, country, type of document, subject area, taxa studied and biodiversity metrics assessed were extracted and explored in order to analyse the spatial and temporal distribution of the concept, including the main topics addressed in HNV farmland literature. Results. After screening 308 original articles, 90 were selected for this review. HNV farmland studies involved several disciplines, mainly biodiversity and conservation and environmental sciences and ecology. Most peer-reviewed articles focused on HNV farming were conducted in Spain, Italy, Ireland and Portugal. The main studied taxa were plants and birds. Taxonomic diversity was the biodiversity metric more often used to assess the biodiversity status on HNV farmland areas. A positive correlation was found between HNV farmland area and HNV farmland studies conducted in respective countries. Discussion. The HNV farmland research subject is a relative novel approach, and this systematic review provides a comprehensive overview about the main topics in the HNV farmland peer-reviewed literature contributing to highlight the main gaps and provide some considerations in order to assist the performance of HNV farming systems and conservation policies, addressed to sustain high levels of biodiversity.

scholarly journals Investigation of the microbial diversity of an extremely acidic, metal-rich water body (Lake Robule, Bor, Serbia)

2014 ◽  
Vol 79 (6) ◽  
pp. 729-741 ◽  
Author(s):  
Srdjan Stankovic ◽  
Ivana Moric ◽  
Aleksandar Pavic ◽  
Branka Vasiljevic ◽  
Barrie Johnson ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Lake Water ◽  
Bacterial Species ◽  
Rflp Analysis ◽  
Solid Media ◽  
Physico Chemical ◽  
Acidiphilium Cryptum ◽  
Culture Independent ◽  
Sulfur Oxidizing ◽  
Dominant Bacteria

An investigation of the microbial diversity of the extremely acidic, metal-rich Lake Robule was carried out using culture-dependant and culture-independent (T-RFLP) methods, and the ability of indigenous bacteria from the lake water to leach copper from a mineral concentrate was tested. T-RFLP analysis revealed that the dominant bacteria in lake water samples were the obligate heterotroph Acidiphilium cryptum (~50% of total bacteria) and the iron-oxidizing autotroph Leptospirillum ferrooxidans (~40%) The iron/sulfur-oxidizing autotroph Acidithiobacillus ferrooxidans had been reported to be the most abundant bacteria in the lake in an earlier study by other authors, but it was not detected in the present study using T-RFLP. Although it was isolated on solid media and detected in enrichment (bioleaching) cultures. The presence of the two bacterial species detected by T-RFLP (L. ferrooxidans and A. cryptum) was also confirmed by cultivation on solid media. The presence and relative abundance of bacteria inhabiting Lake Robule was explained by the physiological characteristics of the bacteria and the physico-chemical characteristics of the lake water.

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