scholarly journals Foliar fungal communities strongly differ between habitat patches in a landscape mosaic

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2656 ◽  
Author(s):  
Thomas Fort ◽  
Cécile Robin ◽  
Xavier Capdevielle ◽  
Laurent Delière ◽  
Corinne Vacher
Keyword(s):  
Agricultural Practices ◽  
Growing Season ◽  
Forest Edge ◽  
Fungal Communities ◽  
Its2 Region ◽  
Ecological Communities ◽  
Landscape Mosaic ◽  
Forest Patches ◽  
Habitat Patches ◽  
Dispersal Events

BackgroundDispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over the course of the growing season, particularly along habitat edges, because of aerial dispersal of spores.MethodsWe monitored the richness and composition of foliar and airborne fungal communities over the season, along transects perpendicular to edges between vineyard and forest patches, using Illumina sequencing of the Internal Transcribed Spacer 2 (ITS2) region.ResultsIn contrast to our expectation, foliar fungal communities in vineyards and forest patches increasingly differentiate over the growing season, even along habitat edges. Moreover, the richness of foliar fungal communities in grapevine drastically decreased over the growing season, in contrast to that of forest trees. The composition of airborne communities did not differ between habitats. The composition of oak foliar fungal communities change between forest edge and centre.DiscussionThese results suggest that dispersal events between habitat patches are not major drivers of foliar fungal communities at the landscape scale. Selective pressures exerted in each habitat by the host plant, the microclimate and the agricultural practices play a greater role, and might account for the differentiation of foliar fugal communities between habitats.

scholarly journals Foliar fungal communities strongly differ between habitat patches in a landscape mosaic

2016 ◽  
Author(s):  
Thomas Fort ◽  
Cécile Robin ◽  
Xavier Capdevielle ◽  
Laurent Delière ◽  
Corinne Vacher
Keyword(s):  
Agricultural Practices ◽  
Growing Season ◽  
Forest Edge ◽  
Fungal Communities ◽  
Its2 Region ◽  
Ecological Communities ◽  
Landscape Mosaic ◽  
Forest Patches ◽  
Habitat Patches ◽  
Dispersal Events

Dispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over the course of the growing season, particularly along habitat edges, because of aerial dispersal of spores. We monitored the richness and composition of foliar and airborne fungal communities over the season, along transects perpendicular to edges between vineyard and forest patches, using Illumina sequencing of the ITS2 region. In contrast to our expectation, foliar fungal communities in vineyards and forest patches increasingly differentiate over the growing season, even along habitat edges. Moreover, the richness of foliar fungal communities in grapevine drastically decreased over the growing season, in contrast to that of forest trees. The composition of airborne communities did not differ between habitats. The composition of oak foliar fungal communities change between forest edge and centre. These results suggest that dispersal events between habitat patches are not major drivers of foliar fungal communities at the landscape scale. Selective pressures exerted in each habitat by the host plant, the microclimate and the agricultural practices play a greater role, and might account for the differentiation of foliar fugal communities between habitats.

scholarly journals Foliar fungal communities strongly differ between habitat patches in a landscape mosaic

2016 ◽  
Author(s):  
Thomas Fort ◽  
Cécile Robin ◽  
Xavier Capdevielle ◽  
Laurent Delière ◽  
Corinne Vacher
Keyword(s):  
Agricultural Practices ◽  
Growing Season ◽  
Forest Edge ◽  
Fungal Communities ◽  
Its2 Region ◽  
Ecological Communities ◽  
Landscape Mosaic ◽  
Forest Patches ◽  
Habitat Patches ◽  
Dispersal Events

Dispersal events between habitat patches in a landscape mosaic can structure ecological communities and influence the functioning of agrosystems. Here we investigated whether short-distance dispersal events between vineyard and forest patches shape foliar fungal communities. We hypothesized that these communities homogenize between habitats over the course of the growing season, particularly along habitat edges, because of aerial dispersal of spores. We monitored the richness and composition of foliar and airborne fungal communities over the season, along transects perpendicular to edges between vineyard and forest patches, using Illumina sequencing of the ITS2 region. In contrast to our expectation, foliar fungal communities in vineyards and forest patches increasingly differentiate over the growing season, even along habitat edges. Moreover, the richness of foliar fungal communities in grapevine drastically decreased over the growing season, in contrast to that of forest trees. The composition of airborne communities did not differ between habitats. The composition of oak foliar fungal communities change between forest edge and centre. These results suggest that dispersal events between habitat patches are not major drivers of foliar fungal communities at the landscape scale. Selective pressures exerted in each habitat by the host plant, the microclimate and the agricultural practices play a greater role, and might account for the differentiation of foliar fugal communities between habitats.

Dynamics of CO2 emission from chernozems under agricultural use

2017 ◽  
Vol 4 (3) ◽  
pp. 43-49
Author(s):  
M. Miroshnychenko ◽  
O. Siabruk
Keyword(s):  
Carbon Dioxide ◽  
Agricultural Practices ◽  
Growing Season ◽  
Warm Period ◽  
Direct Seeding ◽  
Soil Tillage ◽  
Plant Residues ◽  
Hydrothermal Conditions ◽  
Organic Mineral ◽  
Mineral System

Aim. The comparison of the effect of hydrothermal conditions and various agricultural practices on the emission of CO 2 from chernozems in the Left-Bank Forest-Steppe of Ukraine. Methods. The dynamics of the intensity of carbon dioxide emissions from chernozem calcic (typical chernozem – in Ukrainian classifi cation) was studied during the growing season of 2011–2012. The observations were based on two fi eld experiments with various methods of soil till- age (6–7 years from the beginning of the experiment) and fertilization systems (21–22 years from the beginning of the experiment). Particularly, plowing at 20–22 cm, disking at 10–12 cm, cultivation at 6–8 cm and direct seeding using Great Plains drill were studied among the soil tillage methods. Mineral system (N 45 P 50 K 45 ), organic system (manure 8 t/ha) and combined organic-mineral system (manure 8 t/ha + N 45 P 50 K 45 ) were studied among fertilization systems. The intensity of CO 2 fl ux was determined using the non-stationary respiratory chambers by the alkaline absorption method, with averaging of the results during the day and the frequency of once a month. Results. During the warm period, the emission of carbon dioxide from the soil changes dynamically depending on temperature and humidity. The maximum of emission coincides with the periods of warm summer showers in June-July, the minimum values are characteristic for the late autumn period. The total emission losses of carbon in chernozems over the vegetation period ranged from 480 to 910 kg/ha and varied depending on the methods of tillage ± (4.0–6.0) % and fertilization systems ± (3.8–7.1) %. The changes in the intensity of CO 2 emission from the soil under different methods of soil tillage are associated with hydrothermal regime and the depth of crop residues location. The biggest difference is observed im- mediately after tillage, but in the spring period the differences are only 12–25 %, and after drying of the top layer of soil become even less. Direct seeding technology provides the greatest emission of CO 2 from chernozem, which is fa- cilitated by better water regime and more complete mineralization of plant residues on the soil surface. Annual losses of carbon are the least under disking of soil at 10–12 cm. The changes in the intensity of CO 2 emission from the soil under different fertilization systems are associated with the involvement of the additional organic matter from plant residues and manure to the microbiological decomposition. The greatest emission was observed under the organic- mineral fertilization system, which increased the loss of carbon by 7–8 % in comparison with the mineral system in the unfavorable hydrothermal year and by 11–15 % in the more favorable year. These differences are observed mainly during the fi rst half of the growing season when there is a clear tendency to increase the intensity of soil respiration. Conclusions. The hydrothermal conditions of the warm period of the year are decisive in the formation of the CO 2 emission fl ow from chernozems. Due to the improvement of agricultural practices, emissions might be reduced but not more that by 15 % of natural factor contribution.

scholarly journals Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity

2017 ◽  
Vol 83 (17) ◽  
Author(s):  
Francesca De Filippis ◽  
Manolo Laiola ◽  
Giuseppe Blaiotta ◽  
Danilo Ercolini
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
Biological Samples ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Fungal Communities ◽  
Its2 Region ◽  
Mock Community

ABSTRACT Target-gene amplicon sequencing is the most exploited high-throughput sequencing application in microbial ecology. The targets are taxonomically relevant genes, with 16S rRNA being the gold standard for bacteria. As for fungi, the most commonly used target is the internal transcribed spacer (ITS). However, the uneven ITS length among species may promote preferential amplification and sequencing and incorrect estimation of their abundance. Therefore, the use of different targets is desirable. We evaluated the use of three different target amplicons for the characterization of fungal diversity. After an in silico primer evaluation, we compared three amplicons (the ITS1-ITS2 region [ITS1-2], 18S ribosomal small subunit RNA, and the D1/D2 domain of the 26S ribosomal large subunit RNA), using biological samples and a mock community of common fungal species. All three targets allowed for accurate identification of the species present. Nevertheless, high heterogeneity in ITS1-2 length was found, and this caused an overestimation of the abundance of species with a shorter ITS, while both 18S and 26S amplicons allowed for more reliable quantification. We demonstrated that ITS1-2 amplicon sequencing, although widely used, may lead to an incorrect evaluation of fungal communities, and efforts should be made to promote the use of different targets in sequencing-based microbial ecology studies. IMPORTANCE Amplicon-sequencing approaches for fungi may rely on different targets affecting the diversity and abundance of the fungal species. An increasing number of studies will address fungal diversity by high-throughput amplicon sequencing. The description of the communities must be accurate and reliable in order to draw useful insights and to address both ecological and biological questions. By analyzing a mock community and several biological samples, we demonstrate that using different amplicon targets may change the results of fungal microbiota analysis, and we highlight how a careful choice of the target is fundamental for a thorough description of the fungal communities.

scholarly journals Analysis of the Bacterial and Fungal Community Profiles in Bulk Soil and Rhizospheres of Three Mungbean [Vigna radiata (L.) R. Wilczek] Genotypes through PCR-DGGE

2020 ◽  
Vol 77 ◽  
pp. 1-26
Author(s):  
Anna Mae M. de los Reyes ◽  
Eureka Teresa M. Ocampo ◽  
Ma. Carmina C. Manuel ◽  
Bernadette C. Mendoza
Keyword(s):  
Plant Growth ◽  
Crop Production ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Diversity Index ◽  
Agricultural Practices ◽  
Fungal Communities ◽  
Bulk Soil ◽  
Initial Assessment ◽  
Rhizosphere Effect ◽  
Soil Microbial Diversity

Each plant species is regarded to substantially influence and thus, select for specific rhizosphere microbial populations. This is considered in the exploitation of soil microbial diversity associated with important crops, which has been of interest in modern agricultural practices for sustainable productivity. This study used PCR-DGGE (polymerase chain reaction - denaturing gradient gel electrophoresis) in order to obtain an initial assessment of the bacterial and fungal communities associated in bulk soil and rhizospheres of different mungbean genotypes under natural field conditions. Integrated use of multivariate analysis and diversity index showed plant growth stage as the primary driver of community shifts in both microbial groups while rhizosphere effect was found to be less discrete in fungal communities. On the other hand, genotype effect was not discerned but not inferred to be absent due to possible lack of manifestations of differences among genotypes based on tolerance to drought under non-stressed environment, and due to detection limits of DGGE. Sequence analysis of prominent members further revealed that Bacillus and Arthrobacter species were dominant in bacterial communities whereas members of Ascomycota and Basidiomycota were common in fungal communities of mungbean. Overall, fungal communities had higher estimated diversity and composition heterogeneity, and were more dynamic under plant growth influence, rhizosphere effect and natural environmental conditions during mungbean growth in upland field. These primary evaluations are prerequisite to understanding the interactions between plant and rhizosphere microorganisms with the intention of employing their potential use for sustainable crop production.

scholarly journals Influence of Man's Activities Level on the Toxicity of Soddy Podzolic Soil

2020 ◽  
Author(s):  
П.А. Котяк
Keyword(s):  
Podzolic Soil ◽  
Agricultural Practices ◽  
Soddy Podzolic Soil ◽  
Weather Conditions ◽  
Growing Season ◽  
Soil Toxicity ◽  
General Toxicity ◽  
The Status ◽  
Medium Toxicity ◽  
Spring Rape

Представлены результаты исследования уровня общей токсичности и микробного токсикоза дерново-подзолистой глееватой почвы при антропогенной нагрузке. Изучение токсичности почвы особенно актуально в агроценозах, где человек в значительной мере регулирует условия произрастания растений. Использование показателей токсичности при оценке агротехнических приёмов позволяет усовершенствовать существующие технологии, чтобы избежать нежелательных сопутствующих эффектов при агрогенном воздействии на агроэкосистемы. Сравнительный анализ полученных результатов показал, что почва опытного участка в начале вегетации имела класс средней и низкой токсичности (индекс токсичности фактора (ИТФ) от 0,63 до 0,82), а в конце вегетации – класс высокой и средней токсичности (ИТФ от 0,35 до 0,55). Оценка микробиологической токсичности почвы исследуемых вариантов опыта по всхожести семян тест-культуры показала в основном средний уровень микробного токсикоза: 69,75% – на индуцированных образцах, 60,97% – на контрольных образцах. Урожайность зелёной массы ярового рапса находилась на невысоком уровне, что могло быть связано с неблагоприятными погодными условиями вегетационного периода и варьировала в пределах от 76 до 218 ц/га. Проведённые исследования по установлению влияния антропогенной нагрузки на токсический статус дерново-подзолистой почвы в условиях Ярославской области показали, что лучшими характеристиками обладают варианты: система отвальной обработки почвы, фон «Органо-минеральный субстрат + NPK» как с внесением гербицида, так и без его применения при возделывании ярового рапса. В этих условиях снижается общая токсичность почвы, статус микробного токсикоза не меняется, что позволяет сохранять почвенное плодородие, иметь оптимальное фитосанитарное состояние и получать качественный урожай выращиваемых культур. The results of the research of general toxicity level and microbial toxicosis of soddy podzolic gleyic soil at man-caused load are presented. The study of soil toxicity is especially important in agrocenoses, where a person largely regulates the conditions of plant growth. The use of toxicity indicators in assessing agricultural practices allows improving existing technologies in order to avoid undesirable concomitant effects during agrogenic effects on agroecosystems. A comparative analysis of the obtained results showed that the soil of the test area at the beginning of the growing season had a medium and low toxicity class (factor toxicity index (FTI) from 0.63 to 0.82) and at the end of the growing season it had a high and medium toxicity class (FTI from 0.35 to 0.55). Assessment of the microbiological toxicity of the soil of test variants under investigation by seed germination of the test-crop showed mainly the average level of microbial toxicosis: 69.75% on the induced samples, 60.97% on the control samples. The yield of green mass of spring rape was at a low level, which could be associated with unfavorable weather conditions of the growing season and varied from 76 to 218 hkg / ha. Researches conducted to establish influence of man's activities on the toxic status of soddy podzolic soil in the conditions of the Yaroslavl region showed that the best characteristics are options: a system of moldboard tillage, background "Organic-mineral substrate + NPK" both with the herbicide application and without its use in the cultivation of spring rape. Under these conditions the general toxicity of the soil decreases, the status of microbial toxicosis does not change which allows maintaining soil fertility, having an optimal phytosanitary condition and obtaining a quality yield of crops grown.

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