scholarly journals Determining Diversity of Freshwater Fungi on Decaying Leaves: Comparison of Traditional and Molecular Approaches

2003 ◽  
Vol 69 (5) ◽  
pp. 2548-2554 ◽  
Author(s):  
Liliya G. Nikolcheva ◽  
Amanda M. Cockshutt ◽  
Felix Bärlocher
Keyword(s):  
Species Richness ◽  
Fungal Biomass ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rflp Analysis ◽  
Fungal Species ◽  
Aquatic Hyphomycetes ◽  
Molecular Techniques ◽  
Red Maple ◽  
Molecular Approaches ◽  
Community Evenness

ABSTRACT Traditional microscope-based estimates of species richness of aquatic hyphomycetes depend upon the ability of the species in the community to sporulate. Molecular techniques which detect DNA from all stages of the life cycle could potentially circumvent the problems associated with traditional methods. Leaf disks from red maple, alder, linden, beech, and oak as well as birch wood sticks were submerged in a stream in southeastern Canada for 7, 14, and 28 days. Fungal biomass, estimated by the amount of ergosterol present, increased with time on all substrates. Alder, linden, and maple leaves were colonized earlier and accumulated the highest fungal biomass. Counts and identifications of released conidia suggested that fungal species richness increased, while community evenness decreased, with time (up to 11 species on day 28). Conidia of Articulospora tetracladia dominated. Modifications of two molecular methods—denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis—suggested that both species richness and community evenness decreased with time. The dominant ribotype matched that of A. tetracladia. Species richness estimates based on DGGE were consistently higher than those based on T-RFLP analysis and exceeded those based on spore identification on days 7 and 14. Since traditional and molecular techniques assess different aspects of the fungal organism, both are essential for a balanced view of fungal succession on leaves decaying in streams.

Fungal richness does not buffer the effects of streams salinization on litter decomposition

2021 ◽  
Vol 57 ◽  
pp. 5
Author(s):  
Janine Pereira da Silva ◽  
Aingeru Martínez ◽  
Ana Lúcia Gonçalves ◽  
Felix Bärlocher ◽  
Cristina Canhoto
Keyword(s):  
Mass Loss ◽  
Litter Decomposition ◽  
Fungal Biomass ◽  
Fungal Species ◽  
Aquatic Hyphomycetes ◽  
Negative Effects ◽  
Stream Functioning ◽  
Induced Changes ◽  
Sporulation Rate ◽  
The Impact

Freshwater salinization is a world-wide phenomenon threatening stream communities and ecosystem functioning. In these systems, litter decomposition is a main ecosystem-level process where fungi (aquatic hyphomycetes) play a central role linking basal resource and higher levels of food-web. The current study evaluated the impact of aquatic hyphomycete richness on leaf litter decomposition when subjected to salinization. In a microcosm study, we analysed leaf mass loss, fungal biomass, respiration and sporulation rate by fungal assemblages at three levels of species richness (1, 4, 8 species) and three levels of salinity (0, 8, 16 g NaCl L‑1). Mass loss and sporulation rate were depressed at 8 and 16 g NaCl L‑1, while fungal biomass and respiration were only negatively affected at 16 g L‑1. A richness effect was only observed on sporulation rates, with the maximum values found in assemblages of 4 species. In all cases, the negative effects of high levels of salinization on the four tested variables superimposed the potential buffer capacity of fungal richness. The study suggests functional redundancy among the fungal species even at elevated salt stress conditions which may guarantee stream functioning at extreme levels of salinity. Nonetheless, it also points to the possible importance of salt induced changes on fungal diversity and identity in salinized streams able to induce bottom-up effects in the food webs.

scholarly journals Effects of Artificial Defoliation of Pines on the Structure and Physiology of the Soil Fungal Community of a Mixed Pine-Spruce Forest

2005 ◽  
Vol 71 (4) ◽  
pp. 1996-2000 ◽  
Author(s):  
Ken Cullings ◽  
Christopher Raleigh ◽  
Michael H. New ◽  
Joan Henson
Keyword(s):  
Species Richness ◽  
Filamentous Fungus ◽  
Fungal Community ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microbial Communities ◽  
Soil Fungus ◽  
Fungal Species ◽  
Ectomycorrhizal Fungus ◽  
Spruce Forest ◽  
Soil Fungal Community

ABSTRACT Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P < 0.001); the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P < 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.

scholarly journals A Brief History of Endophyte Detection Techniques in Grasses

2019 ◽  
Vol 8 (3) ◽  
pp. 66
Author(s):  
Rana Zaheer Ahmad ◽  
Fuad Ameen ◽  
Rida Khalid ◽  
Mousa A. Alghuthaymi ◽  
Reem Alsalmi ◽  
...  
Keyword(s):  
Molecular Phylogenetics ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Economic Value ◽  
Molecular Techniques ◽  
Morphological Identification ◽  
Detection Techniques ◽  
Molecular Approaches ◽  
Gradient Gel Electrophoresis ◽  
History Of ◽  
Traditional Approaches

Endophytes are the plant mutualists that live asymptomatically inside plant tissue and are found in nearly whole plant kingdom. Endophytic fungi receive shelter and nutrition from host plants and in return provide great advantages to the host. Grasses are a useful forage species and are of great agricultural and socio-economic value. The presence of endophytes in these grasses provide protection, persistence and improved yield against herbivores, insects, pathogens, drought and several other biotic and abiotic stresses. This review summarizes traditional and modern molecular techniques to identify endophytes from turf and forage grasses. Traditional approaches include direct observation, staining, laser micro dissection and pressure catapulting and cultivation-dependent methods that provide a morphological identification of endophytic mycobiota in grass tissues. Earlier studies on endophytes using these methods resulted in several technical implications which molecular approaches are able to solve now-a-days. Molecular approaches include DNA extraction, PCR based DNA Fingerprinting techniques, Denaturing Gradient Gel Electrophoresis, Sanger sequencing, Pyrosequencing, Immunoblot assay, Biosensors, DNA Barcoding and Molecular Phylogenetics etc. A comparison of these detection techniques will facilitate other researchers as well to develop new ways for the detection of endophytes that will contribute to the improvement of grassland in future.

scholarly journals Initial Colonization, Nutrient Supply, and Fungal Activity on Leaves Decaying in Streams

2000 ◽  
Vol 66 (3) ◽  
pp. 1114-1119 ◽  
Author(s):  
K. R. Sridhar ◽  
Felix Bärlocher
Keyword(s):  
Fungal Biomass ◽  
Principal Component ◽  
Fungal Species ◽  
Aquatic Hyphomycetes ◽  
Spore Production ◽  
Second Phase ◽  
Inorganic N ◽  
Order Stream ◽  
Low Levels ◽  
Leaf Disks

ABSTRACT Aquatic hyphomycetes dominate leaf decomposition in streams, and their biomass is an important component in the diet of leaf-eating invertebrates. After 2 weeks of exposure in a first-order stream, maple leaf disks had low levels of fungal biomass and species diversity. Spore production by aquatic hyphomycetes also was low. Subsets of these disks were left in the stream for another 3 weeks or incubated in defined mineral solutions with one of three levels of nitrate and phosphate. Stream disks lost mass, increased ergosterol levels and spore production, and were colonized by additional fungal species. External N and P significantly stimulated mass loss, ergosterol accumulation, and spore production of laboratory disks. On disks incubated without added N and P, ergosterol levels declined while conidium production continued, suggesting conversion of existing hyphal biomass to propagules. In all other treatments, approximately equal amounts of newly synthesized biomass were invested in hyphae and conidia. Net yield (fungal biomass per leaf mass lost) varied between 1% (in the laboratory, without added N or P) and 31% (decay in stream). In most treatments, the three aquatic hyphomycete species that dominated spore production during the first 2 weeks in the stream also produced the largest numbers of conidia in the following 3 weeks. Principal-component analysis suggested two divergent trends from the initial fungal community established after 2 weeks in the stream. One culminated in the community of the second phase of stream exposure, and the other culminated in the laboratory treatment with the highest levels of N and P. The results suggest that fungal production in streams, and, by extension, production of invertebrates and higher tropic levels, is stimulated by inorganic N and P.

scholarly journals Design and Operation of Empirical Manganese-Removing Bioreactors and Integration into a Composite Modular System for Remediating and Recovering Metals from Acidic Mine Waters

2021 ◽  
Vol 11 (9) ◽  
pp. 4287
Author(s):  
Ana Laura Santos ◽  
D. Barrie Johnson
Keyword(s):  
Mine Water ◽  
Rflp Analysis ◽  
Packed Bed ◽  
Fungal Species ◽  
Molecular Techniques ◽  
Modular System ◽  
Mine Waters ◽  
Leptothrix Discophora ◽  
Initial Processing

Packed bed bioreactors were used to remove soluble manganese from a synthetic mine water as the final stage of an integrated bioremediation process. The synthetic mine water had undergone initial processing using a sulfidogenic bioreactor (pH 4.0–5.5) which removed all transition metals present in elevated concentrations (Cu, Ni, Zn and Co) apart from manganese. The aerobic bioreactors were packed with pebbles collected from a freshwater stream that were coated with black-colored, Mn(IV)-containing biofilms, and their capacity to remove soluble Mn (II) from the synthetic mine water was tested at varying hydraulic retention times (11–45 h) and influent liquor pH values (5.0 or 6.5). Over 99% of manganese was removed from the partly processed mine water when operated at pH 6.5 and a HRT of 45 h. Molecular techniques (clone libraries and T-RFLP analysis) were used to characterize the biofilms and identified two heterotrophic Mn-oxidizing microorganisms: the bacterium Leptothrix discophora and what appears to be a novel fungal species. The latter was isolated and characterized in vitro.

BACTERIAL PROFILES OF KARVACHAR HOT SPRING IDENTIFIED BY COMBINATION OF DIFFERENT MOLECULAR APPROACHES

2020 ◽  
Vol 54 (2 (252)) ◽  
pp. 147-153
Author(s):  
H.H. Panosyan
Keyword(s):  
Clone Library ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Hot Spring ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Composition ◽  
Metagenome Analysis ◽  
Molecular Approaches ◽  
Gradient Gel Electrophoresis

Molecular techniques, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA genes clone library construction and metagenomic analysis, were used to describe the bacterial composition of the Karvachar geothermal spring. It was shown the predominance of bacteria belonging to the phyla Proteobacteria, Bacteroidetes, Firmicutes and Cyanobacteria in the studied spring. Representatives of phylum Firmicutes were not detected in the clone library, while DGGE profiling and metagenome analysis confirmed the presence of Firmicutes as one of the major components in the bacterial community.

scholarly journals Molecular Epidemiology of Tuberculosis: Current Insights

2006 ◽  
Vol 19 (4) ◽  
pp. 658-685 ◽  
Author(s):  
Barun Mathema ◽  
Natalia E. Kurepina ◽  
Pablo J. Bifani ◽  
Barry N. Kreiswirth
Keyword(s):  
Vaccine Development ◽  
Epidemiologic Studies ◽  
Molecular Techniques ◽  
Tb Control ◽  
Molecular Approaches ◽  
Accuracy And Precision ◽  
Outbreak Investigations ◽  
Short And Long Term ◽  
Exogenous Reinfection

SUMMARY Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB.

scholarly journals Diversity of methanogens in ruminants in Queensland

2008 ◽  
Vol 48 (7) ◽  
pp. 722 ◽  
Author(s):  
D. Ouwerkerk ◽  
A. F. Turner ◽  
A. V. Klieve
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Rumen Fluid ◽  
Bos Indicus ◽  
Methane Emissions ◽  
Molecular Techniques ◽  
Feed Conversion ◽  
Methanogen Community ◽  
Gradient Gel Electrophoresis ◽  
Reduce Emissions ◽  
Cattle And Sheep

Methane emissions from ruminant livestock represent a loss of carbon during feed conversion, which has implications for both animal productivity and the environment because this gas is considered to be one of the more potent forms of greenhouses gases contributing to global warming. Many strategies to reduce emissions are targeting the methanogens that inhabit the rumen, but such an approach can only be successful if it targets all the major groups of ruminant methanogens. Therefore, a thorough knowledge of the diversity of these microbes in different breeds of cattle and sheep, as well as in response to different diets, is required. A study was undertaken using the molecular techniques denaturing gradient gel electrophoresis, DNA cloning and DNA sequence analysis to define the extent of diversity among methanogens in ruminants, particularly Bos indicus cross cattle, on differing forages in Queensland. It was found that the diversity of methanogens in forage-fed cattle in Queensland was greater than in grain-fed cattle but there was little variability in methanogen community composition between cattle fed different forages. The species that dominate the rumen microbial communities of B. indicus cross cattle are from the genus Methanobrevibacter, although rumen-fluid inoculated digestors fed Leucaena leucocephala leaf were populated with Methanosphaera-like strains, with the Methanobrevibacter-like strains displaced. If ruminant methane emissions are to be reduced, then antimethanogen bioactives that target both broad groups of ruminant methanogens are most likely to be needed, and as a part of an integrated suite of approaches that redirect rumen fermentation towards other more useful end products.

scholarly journals Seasonal Diversity of Arbuscular Mycorrhizal Fungi in Mangroves of Goa, India

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
James D’Souza ◽  
Bernard Felinov Rodrigues
Keyword(s):  
Species Richness ◽  
Mycorrhizal Fungi ◽  
Monsoon Season ◽  
Arbuscular Mycorrhizal ◽  
Fungal Spore ◽  
Fungal Species ◽  
Spore Density ◽  
Species Variation ◽  
Fungal Community Composition ◽  
Mangrove Plant

Seasonal dynamics of arbuscular mycorrhizal (AM) fungal community composition in three common mangrove plant species, namely, Acanthus ilicifolius, Excoecaria agallocha, and Rhizophora mucronata, from two sites in Goa, India, were investigated. In all three species variation in AM fungal spore density was observed. Maximum spore density and AM species richness were recorded in the premonsoon season, while minimum spore density and richness were observed during monsoon season at both sites. A total of 11 AM fungal species representing five genera were recorded. Acaulospora laevis was recorded in all seasons at both sites. Multivariate analysis revealed that season and host coaffected AM spore density and species richness with the former having greater influence than the latter.

Taxonomy and phylogeny of calcareous sponges (Porifera: Calcarea: Calcinea) from Brazilian mid-shelf and oceanic islands

Zootaxa ◽  
2017 ◽  
Vol 4311 (3) ◽  
pp. 301 ◽  
Author(s):  
FERNANDA AZEVEDO ◽  
ANDRÉ PADUA ◽  
FERNANDO MORAES ◽  
ANDRÉ ROSSI ◽  
GUILHERME MURICY ◽  
...  
Keyword(s):  
Species Richness ◽  
Morphological Characters ◽  
Oceanic Islands ◽  
Biological Communities ◽  
Calcareous Sponges ◽  
Molecular Approaches ◽  
Strategic Value ◽  
Molecular Tree ◽  
Trindade Island ◽  
Fernando De Noronha

Despite the enormous economic, scientific and strategic value of the Brazilian oceanic and mid-shelf islands (BOMIs), the biological communities of these islands are still poorly known. An example is their fauna of calcareous sponges (Porifera: Calcarea), with only six species described up to date. In the present study, we analysed the Calcinean sponges from the mid-shelf Abrolhos Archipelago and four of the five Brazilian oceanic islands (São Pedro e São Paulo Archipelago, Fernando de Noronha Archipelago, Rocas Atoll, and Trindade Island), using both morphological and molecular approaches for taxonomy. Fourteen species were found, of which 12 are new to science: Arturia trindadensis sp. nov., Borojevia tenuispinata sp. nov., B. trispinata sp. nov., Clathrina insularis sp. nov., C. lutea sp. nov., C. mutabilis sp. nov., C. zelinhae sp. nov., Ernstia citrea sp. nov., E. multispiculata sp. nov., E. rocasensis sp. nov., E. sanctipauli sp. nov., and E. solaris sp. nov. These results raised in 63% the species richness of calcareous sponges from the BOMIs. Clathrina aurea and Leucetta floridana were recollected and the former had its geographical distribution expanded. The molecular tree obtained confirmed the morphological identifications and allowed a discussion about the evolution of morphological characters, and the usefulness of some of those characters in the taxonomy of Calcinea. 

Sign in / Sign up

Export Citation Format

Share Document