scholarly journals The Diverse Assemblage of Fungal Endophytes from Orchids in Madagascar Linked to Abiotic Factors and Seasonality

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 96 ◽  
Author(s):  
Kazutomo Yokoya ◽  
Lawrence W. Zettler ◽  
Jake Bell ◽  
Jonathan P. Kendon ◽  
Alison S. Jacob ◽  
...  
Keyword(s):  
Seed Germination ◽  
Mycorrhizal Fungi ◽  
Large Scale ◽  
Abiotic Factors ◽  
Preliminary Investigation ◽  
Fungal Endophytes ◽  
Life Forms ◽  
Small Subset ◽  
Orchid Seed ◽  
Conservation Projects

The inselbergs of the Central Highlands of Madagascar are one of many ‘micro-hotspots’ of biodiversity on the island, particularly for Orchidaceae. In this region are several genera that have a large number of endemic species that are in serious decline or edging towards extinction. Studies relating to diversity of orchids and their fungal partners (both mycorrhizal and non-mycorrhizal root associates) deserve more attention, as climate change and human induced decline in resilience of species in the wild is at an all-time high. Identification of mycorrhizal fungi (MF) via conventional seed baited-protocorms has limitations for large scale studies and its application for time-bound conservation projects. The paper describes the value of understanding fungal diversity in the roots of orchids at different stages of maturity. The first part of the study was a preliminary investigation mainly to identify culturable Rhizoctonia endophytes, and the second part looked at all life forms of available taxa together with associated soil characteristics. We isolated and identified 19 putative MF from 18 of the 50 taxa spread over an area of 250 sq. km, covering three life forms, growth phases of the orchid taxa, and habitat types. In the rest of the taxa, we were unable to detect any putative MF, but had varying numbers of non-mycorrhizal endophytes. We also found that diversity of putative MF was higher in plants from soils with the lowest P levels recorded. Putative mycorrhizal OTUs were predominantly from the Tulasnella lineage, followed by Ceratobasidium and Serendipita. Within a small subset of samples, a difference in colonised endophytes depending on the collection season was observed. In vitro germination studies using 10 OTUs of mycorrhizal fungi in 14 orchid species showed mostly generalist associations. When orchid seed and fungal sources were studied irrespective of habitat, life form, and distance from each other (orchid seed and fungal source), compatibility for symbiotic seed germination was observed in most cases. Issues with the identification of compatible MF and symbiotic system of seed germination are discussed.

scholarly journals Low-specific Symbiotic Germination of Dendrobium Huoshanense in Vitro, an Endangered Epiphytic Orchid Endemic From South China

2021 ◽  
Author(s):  
Yan-Jing Tang ◽  
Jun Dai ◽  
Yang Li ◽  
Dong-Yu Zhou ◽  
Yong-Mei Xing ◽  
...  
Keyword(s):  
Seed Germination ◽  
Mycorrhizal Fungi ◽  
Blue Staining ◽  
Fungal Strains ◽  
Epiphytic Orchid ◽  
Symbiotic Germination ◽  
Orchid Seed ◽  
Dendrobium Huoshanense ◽  
Initial Seed

Abstract Background: Dendrobium huoshanense is an endangered epiphytic orchid and is endemic to Anhui province of China with a narrow distribution. In nature, orchid seed germination depends on specific mycorrhizal fungi and it is generally assumed that there is a high specific symbiotic germination in narrow distribution orchid. To evaluate the mycorrhizal compatibility and germination-promoting activity of mycorrhizal fungi of D. huoshanense in vitro, we isolated and identified cultured mycorrhizal fungi from the roots of D. huoshanense and D. officinale. A total of 20 mycorrhizal fungal strains (D. huoshanense (n = 6), D. officinale (n = 12), D. nobile (n = 1), D. moniliforme (n = 1)) were used to test the germination-promoting activity of D. huoshanense. Results: In symbiotic germination tests, the mycorrhizal fungi displayed different efficiency in stimulating D. huoshanense seed germination, nine strains stimulated seed development to an advanced seedling stage, while the rest promoted only initial seed germination to stage 2 or stage 3, and the most effective in promoting rapid seed germination was strain 12825(seb) isolated from D. moniliforme, besides, the second most effective fungus was strain WX-7(seb) isolated from D. officinale, both of them belong to Sebacina isolated from non-D. huoshanense. In this study, all twenty fungal strains formed pelotons inside seeds of D. huoshanense based on the trypan blue staining results. Conclusions: Despite its narrow specific habitat preference, D. huoshanense was found to be a mycorrhizal generalist during symbiotic seed germination in vitro. The study is the first to demonstrate the different abilities of orchid mycorrhizal fungi to promote seed germination, protocorm formation and seedling development of D. huoshanense in vitro, providing important microbiological resources for its conservation and reintroduction in nature.

Adsorption Isotherm Predictions for Multiple Molecules in MOFs Using the Same Deep Learning Model

2019 ◽  
Author(s):  
Ryther Anderson ◽  
Achay Biong ◽  
Diego Gómez-Gualdrón
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Molecular Simulation ◽  
Large Scale ◽  
Learning Model ◽  
Operating Conditions ◽  
Small Subset ◽  
Screening Methods ◽  
Large Set ◽  
Metal Organic

<div>Tailoring the structure and chemistry of metal-organic frameworks (MOFs) enables the manipulation of their adsorption properties to suit specific energy and environmental applications. As there are millions of possible MOFs (with tens of thousands already synthesized), molecular simulation, such as grand canonical Monte Carlo (GCMC), has frequently been used to rapidly evaluate the adsorption performance of a large set of MOFs. This allows subsequent experiments to focus only on a small subset of the most promising MOFs. In many instances, however, even molecular simulation becomes prohibitively time consuming, underscoring the need for alternative screening methods, such as machine learning, to precede molecular simulation efforts. In this study, as a proof of concept, we trained a neural network as the first example of a machine learning model capable of predicting full adsorption isotherms of different molecules not included in the training of the model. To achieve this, we trained our neural network only on alchemical species, represented only by their geometry and force field parameters, and used this neural network to predict the loadings of real adsorbates. We focused on predicting room temperature adsorption of small (one- and two-atom) molecules relevant to chemical separations. Namely, argon, krypton, xenon, methane, ethane, and nitrogen. However, we also observed surprisingly promising predictions for more complex molecules, whose properties are outside the range spanned by the alchemical adsorbates. Prediction accuracies suitable for large-scale screening were achieved using simple MOF (e.g. geometric properties and chemical moieties), and adsorbate (e.g. forcefield parameters and geometry) descriptors. Our results illustrate a new philosophy of training that opens the path towards development of machine learning models that can predict the adsorption loading of any new adsorbate at any new operating conditions in any new MOF.</div>

Large-scale mapping of the catenas vegetation in Subarctic tundra

1995 ◽  
pp. 3-21
Author(s):  
S. S. Kholod
Keyword(s):  
Spatial Distribution ◽  
Vegetation Cover ◽  
Large Scale ◽  
Block Diagram ◽  
Abiotic Factors ◽  
Ecological Factors ◽  
Spatial Arrangement ◽  
Geological Time ◽  
Ecological Barriers ◽  
Functional Zones

One of the most difficult tasks in large-scale vegetation mapping is the clarification of mechanisms of the internal integration of vegetation cover territorial units. Traditional way of searching such mechanisms is the study of ecological factors controlling the space heterogeneity of vegetation cover. In essence, this is autecological analysis of vegetation. We propose another way of searching the mechanisms of territorial integration of vegetation. It is connected with intracoenotic interrelation, in particular, with the changing role of edificator synusium in a community along the altitudinal gradient. This way of searching is illustrated in the model-plot in subarctic tundra of Central Chukotka. Our further suggestion concerns the way of depicting these mechanisms on large-scale vegetation map. As a model object we chose the catena, that is the landscape formation including all geomorphjc positions of a slope, joint by the process of moving the material down the slope. The process of peneplanation of a mountain system for a long geological time favours to the levelling the lower (accumulative) parts of slopes. The colonization of these parts of the slope by the vegetation variants, corresponding to the lowest part of catena is the result of peneplanation. Vegetation of this part of catena makes a certain biogeocoenotic work which is the levelling of the small infralandscape limits and of the boundaries in vegetation cover. This process we name as the continualization on catena. In this process the variants of vegetation in the lower part of catena are being broken into separate synusiums. This is the process of decumbation of layers described by V. B. Sochava. Up to the slope the edificator power of the shrub synusiums sharply decreases. Moss and herb synusium have "to seek" the habitats similar to those under the shrub canopy. The competition between the synusium arises resulting in arrangement of a certain spatial assemblage of vegetation cover elements. In such assemblage the position of each element is determined by both biotic (interrelation with other coenotic elements) and abiotic (presence of appropriate habitats) factors. Taking into account the biogeocoenotic character of the process of continualization on catena we name such spatial assemblage an exolutionary-biogeocoenotic series. The space within each evolutionary-biogeocoenotic series is divided by ecological barriers into some functional zones. In each of the such zones the struggle between synusiums has its individual expression and direction. In the start zone of catena (extensive pediment) the interrelations of synusiums and layers control the mutual spatial arrangement of these elements at the largest extent. Here, as a rule, there predominate edificator synusiums of low and dwarfshrubs. In the first order limit zone (the bend of pediment to the above part of the slope) one-species herb and moss synusiums, oftenly substituting each other in similar habitats, get prevalence. In the zone of active colonization of slope (denudation slope) the coenotic factor has the least role in the spatial distribution of the vegetation cover elements. In particular, phytocoenotic interactions take place only within separate microcoenoses of herbs, mosses and lichens. In the zone of the attenuation of continualization process (the upper most parts of slope, crests) phytocoenotic interactions are almost absent and the spatial distribution of vegetation cover elements depends exclusively on the abiotic factors. The principal scheme of the distribution of vegetation cover elements and the disposition of functional zones on catena are shown on block-diagram (fig. 1).

scholarly journals Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Amrita Srivathsan ◽  
Emily Hartop ◽  
Jayanthi Puniamoorthy ◽  
Wan Ting Lee ◽  
Sujatha Narayanan Kutty ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Low Cost ◽  
Small Body ◽  
Small Subset ◽  
Similar Species ◽  
Large Species ◽  
Morphological Examination ◽  
Species Discovery ◽  
Short Period

Abstract Background More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such “molecular operational taxonomic units” (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries. Results We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8 weeks. We discovered > 650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; > 99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genus Megaselia. We demonstrate for one Megaselia species how the molecular data can guide the description of a new species (Megaselia sepsioides sp. nov.). Conclusions We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.

scholarly journals Joint regression and learning from pairwise rankings for personalized image aesthetic assessment

2021 ◽  
Author(s):  
Jin Zhou ◽  
Qing Zhang ◽  
Jian-Hao Fan ◽  
Wei Sun ◽  
Wei-Shi Zheng
Keyword(s):  
Large Scale ◽  
Assessment Model ◽  
Generic Model ◽  
Small Subset ◽  
Deep Convolutional Neural Networks ◽  
Personal Taste ◽  
Hinge Loss ◽  
Novel Approach ◽  
Large Scale Dataset ◽  
Image Pairs

AbstractRecent image aesthetic assessment methods have achieved remarkable progress due to the emergence of deep convolutional neural networks (CNNs). However, these methods focus primarily on predicting generally perceived preference of an image, making them usually have limited practicability, since each user may have completely different preferences for the same image. To address this problem, this paper presents a novel approach for predicting personalized image aesthetics that fit an individual user’s personal taste. We achieve this in a coarse to fine manner, by joint regression and learning from pairwise rankings. Specifically, we first collect a small subset of personal images from a user and invite him/her to rank the preference of some randomly sampled image pairs. We then search for the K-nearest neighbors of the personal images within a large-scale dataset labeled with average human aesthetic scores, and use these images as well as the associated scores to train a generic aesthetic assessment model by CNN-based regression. Next, we fine-tune the generic model to accommodate the personal preference by training over the rankings with a pairwise hinge loss. Experiments demonstrate that our method can effectively learn personalized image aesthetic preferences, clearly outperforming state-of-the-art methods. Moreover, we show that the learned personalized image aesthetic benefits a wide variety of applications.

scholarly journals Repeated surveying over 6 years reveals that fine-scale habitat variables are key to tropical mountain ant assemblage composition and functional diversity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mulalo M. Muluvhahothe ◽  
Grant S. Joseph ◽  
Colleen L. Seymour ◽  
Thinandavha C. Munyai ◽  
Stefan H. Foord
Keyword(s):  
Climate Change ◽  
Species Composition ◽  
High Altitude ◽  
Functional Diversity ◽  
Large Scale ◽  
Climate Models ◽  
Spatial Scales ◽  
Abiotic Factors ◽  
Composition Analysis ◽  
Fine Scale

AbstractHigh-altitude-adapted ectotherms can escape competition from dominant species by tolerating low temperatures at cooler elevations, but climate change is eroding such advantages. Studies evaluating broad-scale impacts of global change for high-altitude organisms often overlook the mitigating role of biotic factors. Yet, at fine spatial-scales, vegetation-associated microclimates provide refuges from climatic extremes. Using one of the largest standardised data sets collected to date, we tested how ant species composition and functional diversity (i.e., the range and value of species traits found within assemblages) respond to large-scale abiotic factors (altitude, aspect), and fine-scale factors (vegetation, soil structure) along an elevational gradient in tropical Africa. Altitude emerged as the principal factor explaining species composition. Analysis of nestedness and turnover components of beta diversity indicated that ant assemblages are specific to each elevation, so species are not filtered out but replaced with new species as elevation increases. Similarity of assemblages over time (assessed using beta decay) did not change significantly at low and mid elevations but declined at the highest elevations. Assemblages also differed between northern and southern mountain aspects, although at highest elevations, composition was restricted to a set of species found on both aspects. Functional diversity was not explained by large scale variables like elevation, but by factors associated with elevation that operate at fine scales (i.e., temperature and habitat structure). Our findings highlight the significance of fine-scale variables in predicting organisms’ responses to changing temperature, offering management possibilities that might dilute climate change impacts, and caution when predicting assemblage responses using climate models, alone.

scholarly journals Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 234 ◽  
Author(s):  
Eric A. Griffin ◽  
Joshua G. Harrison ◽  
Melissa K. McCormick ◽  
Karin T. Burghardt ◽  
John D. Parker
Keyword(s):  
Phylogenetic Diversity ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Tree Diversity ◽  
Trophic Levels ◽  
Community Diversity ◽  
And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

scholarly journals Effect of Environmental Factors on the Germination and Emergence of Drunken Horse Grass (Achnatherum inebrians)

Weed Science ◽  
2020 ◽  
pp. 1-29
Author(s):  
Yonghuan Yue ◽  
Guili Jin ◽  
Weihua Lu ◽  
Ke Gong ◽  
Wanqiang Han ◽  
...  
Keyword(s):  
Seed Germination ◽  
Environmental Factors ◽  
Abiotic Factors ◽  
Seedling Emergence ◽  
Management Strategies ◽  
Germination Percentage ◽  
Western China ◽  
Burial Depth ◽  
Achnatherum Inebrians ◽  
Water Ph

Abstract Drunken horse grass [Achnatherum inebrians (Hance) Keng] is a perennial poisonous weed in western China. A comprehensive understanding of the ecological response of A. inebrians germination to environmental factors would facilitate the formulation of better management strategies for this weed. Experiments were conducted under laboratory conditions to assess the effects of various abiotic factors, including temperature, light, water, pH and burial depth, on the seed germination and seedling emergence of A. inebrians. The seeds germinated at constant temperatures of 15, 20, 25, 30, 35°C and in alternating-temperature regimes of 15/5, 20/10, 25/15, 30/20, 35/25, 40/30°C, and the seed germination percentages under constant and alternating temperatures ranged from 51% to 94% and 15% to 93%, respectively. Maximum germination occurred at a constant temperature of 25°C, and germination was prevented at 45/35°C. Light did not appear to affect seed germination. The germination percentage of seeds was more than 75% in the pH range of 5 to 10, with the highest germination percentage at pH 6. The seeds germinated at osmotic potentials of 0 MPa to -1.0 MPa, but decreasing osmotic potential inhibited germination, with no germination at -1.2MPa. After 21 d of low osmotic stress, the seeds that did not germinate after rehydration had not lost their vitality. The seedling emergence percentage was highest (90%) when seeds were buried at 1 cm but declined with increasing burial depth and no emergence at 9 cm. Deep tillage may be effective in limiting the seed germination and emergence of this species. The results of this study provide useful information on the conditions necessary for A. inebrians germination and provide a theoretical basis for science-based prediction, prevention and control of this species.

scholarly journals Spatial variation and mechanisms of leaf water content in grassland plants at the biome scale: evidence from three comparative transects

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ruomeng Wang ◽  
Nianpeng He ◽  
Shenggong Li ◽  
Li Xu ◽  
Mingxu Li
Keyword(s):  
Spatial Variation ◽  
Water Content ◽  
Large Scale ◽  
Life Forms ◽  
Important Variable ◽  
Leaf Water ◽  
Leaf Water Content ◽  
Desert Grassland ◽  
Large Spatial Scale ◽  
Grassland Plants

AbstractLeaf water content (LWC) has important physiological and ecological significance for plant growth. However, it is still unclear how LWC varies over large spatial scale and with plant adaptation strategies. Here, we measured the LWC of 1365 grassland plants, along three comparative precipitation transects from meadow to desert on the Mongolia Plateau (MP), Loess Plateau, and Tibetan Plateau, respectively, to explore its spatial variation and the underlying mechanisms that determine this variation. The LWC data were normally distributed with an average value of 0.66 g g−1. LWC was not significantly different among the three plateaus, but it differed significantly among different plant life forms. Spatially, LWC in the three plateaus all decreased and then increased from meadow to desert grassland along a precipitation gradient. Unexpectedly, climate and genetic evolution only explained a small proportion of the spatial variation of LWC in all plateaus, and LWC was only weakly correlated with precipitation in the water-limited MP. Overall, the lasso variation in LWC with precipitation in all plateaus represented an underlying trade-off between structural investment and water income in plants, for better survival in various environments. In brief, plants should invest less to thrive in a humid environment (meadow), increase more investment to keep a relatively stable LWC in a drying environment, and have high investment to hold higher LWC in a dry environment (desert). Combined, these results indicate that LWC should be an important variable in future studies of large-scale trait variations.

A Re-Examination of Research on the Language of Black Children: The Need for a New Framework

1982 ◽  
Vol 164 (2) ◽  
pp. 157-172 ◽  
Author(s):  
Ida J. Stockman ◽  
Fay Boyd Vaughn-Cooke
Keyword(s):  
Working Class ◽  
Large Scale ◽  
Black Children ◽  
Cross Sectional Study ◽  
Linguistic Knowledge ◽  
Small Subset ◽  
Review Of The Literature ◽  
Sectional Study ◽  
Cross Sectional ◽  
New Framework

A review of the literature on the language of working-class Black children revealed that only a small subset of this research has focused on the acquisition and development of linguistic knowledge. Consequently major gaps exist in what is known about the linguistic abilities of these children. In an attempt to narrow these gaps, a team of researchers has initiated a large scale longitudinal and cross-sectional study of the acquisition of language by working-class Black children at the Center for Applied Linguistics in Washington, D. C. This paper will present a detailed description of the Center study. It will also critically evaluate existing research on the linguistic abilities of working-class Black children and its impact on language acquisition studies focusing on this population. The evaluation reveals that a new framework for analyzing the language of working-class Black children should be selected. The theory and methodology of the new framework are described.

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