Matching Items (11)

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Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

Description

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

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Created

Date Created
  • 2016-06-02

Manipulating the banana rhizosphere microbiome for biological control of Panama disease

Description

Panama disease caused by Fusarium oxysporum f. sp. cubense infection on banana is devastating banana plantations worldwide. Biological control has been proposed to suppress Panama disease, though the stability and

Panama disease caused by Fusarium oxysporum f. sp. cubense infection on banana is devastating banana plantations worldwide. Biological control has been proposed to suppress Panama disease, though the stability and survival of bio-control microorganisms in field setting is largely unknown. In order to develop a bio-control strategy for this disease, 16S rRNA gene sequencing was used to assess the microbial community of a disease-suppressive soil. Bacillus was identified as the dominant bacterial group in the suppressive soil. For this reason, B. amyloliquefaciens NJN-6 isolated from the suppressive soil was selected as a potential bio-control agent. A bioorganic fertilizer (BIO), formulated by combining this isolate with compost, was applied in nursery pots to assess the bio-control of Panama disease. Results showed that BIO significantly decreased disease incidence by 68.5%, resulting in a doubled yield. Moreover, bacterial community structure was significantly correlated to disease incidence and yield and Bacillus colonization was negatively correlated with pathogen abundance and disease incidence, but positively correlated to yield. In total, the application of BIO altered the rhizo-bacterial community by establishing beneficial strains that dominated the microbial community and decreased pathogen colonization in the banana rhizosphere, which plays an important role in the management of Panama disease.

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Created

Date Created
  • 2015-08-05

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Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils

Description

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling

Increasing temperatures have been shown to impact soil biogeochemical processes, although the corresponding changes to the underlying microbial functional communities are not well understood. Alterations in the nitrogen (N) cycling functional component are particularly important as N availability can affect microbial decomposition rates of soil organic matter and influence plant productivity. To assess changes in the microbial component responsible for these changes, the composition of the N-fixing (nifH), and denitrifying (nirS, nirK, nosZ) soil microbial communities was assessed by targeted pyrosequencing of functional genes involved in N cycling in two major biomes where the experimental effect of climate warming is under investigation, a tallgrass prairie in Oklahoma (OK) and the active layer above permafrost in Alaska (AK). Raw reads were processed for quality, translated with frameshift correction, and a total of 313,842 amino acid sequences were clustered and linked to a nearest neighbor using reference datasets. The number of OTUs recovered ranged from 231 (NifH) to 862 (NirK). The N functional microbial communities of the prairie, which had experienced a decade of experimental warming were the most affected with changes in the richness and/or overall structure of NifH, NirS, NirK and NosZ. In contrast, the AK permafrost communities, which had experienced only 1 year of warming, showed decreased richness and a structural change only with the nirK-harboring bacterial community. A highly divergent nirK-harboring bacterial community was identified in the permafrost soils, suggesting much novelty, while other N functional communities exhibited similar relatedness to the reference databases, regardless of site. Prairie and permafrost soils also harbored highly divergent communities due mostly to differing major populations.

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Agent

Created

Date Created
  • 2015-07-21

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NifH-Harboring Bacterial Community Composition across an Alaskan Permafrost Thaw Gradient

Description

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N[subscript 2]-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples

Since nitrogen (N) is often limiting in permafrost soils, we investigated the N[subscript 2]-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes with those most closely related to group I nifH-harboring Alpha- and Beta-Proteobacteria in higher abundance above water table depth while those related to group III nifH-harboring Delta Proteobacteria more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N[subscript 2]-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.

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Agent

Created

Date Created
  • 2016-11-24

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Immunological Responses to the White-Nose Syndrome Pathogen and their Potential Use as Control

Description

White-nose syndrome (WNS) is a fungal infection devastating bat populations throughout eastern North America. WNS is caused by a fungus, Pseudogymnoascus destructans (Pd), that invades the skin of hibernating bats.

White-nose syndrome (WNS) is a fungal infection devastating bat populations throughout eastern North America. WNS is caused by a fungus, Pseudogymnoascus destructans (Pd), that invades the skin of hibernating bats. While there are a number of treatments being researched, there is currently no effective treatment for WNS that is deployed in the field, except a few being tested on a limited scale. Bats have lowered immune function and response during hibernation, which may increase susceptibility to infection during the winter months. Antimicrobial peptides (AMPs) are a crucial component of the innate immune system and serve as barriers against infection. AMPs are constitutively expressed on skin and facilitate wound healing, stimulate other immune responses, and may also stay active on bat skin during hibernation. AMPs are expressed by all tissues, have direct killing abilities against microbes, and are a potential treatment for bats infected with Pd. In this investigation, the fungicidal activity of several readily available commercial AMPs were compared, and killing assay protocols previously investigated by Frasier and Lake were replicated to establish a control trial for use in future killing assays. Another aim of this investigation was to synthesize a bat-derived AMP for use in the killing assay. Sequences of bat-derived AMPs have been identified in bat skin samples obtained from a large geographic sampling of susceptible and resistant species. Contact was made with GenScript Inc., the company from which commercially available AMPs were purchased, to determine the characteristics of peptide sequences needed to synthesize an AMP for lab use. Based on recommendations from GenScript Inc., peptide sequences need to have a hydrophobicity of less than 50% and a sequence length of less than 50 amino acids. These criteria serve as a potential barrier because none of the known bat-derived sequences analyzed satisfy both of these requirements. The final aim of this study was to generate a conceptual model of the immune response molecules activated when bats are exposed to a fungal pathogen such as Pd. Overall, this work investigated sources of variability between trials of the killing assay, analyzed known bat-derived peptide sequences, and generated a conceptual model that will serve as a guideline for identification of immune response molecules on the skin of bats in future proteomics work.

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Agent

Created

Date Created
  • 2019-05

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A Review of the Current Understanding on Immune Cell Sensitivity to Variation in Energy Availability

Description

This study takes a broad look into the existing research on the relationship between two physiological topics, nutrition and immunity in vertebrates, specifically the mammalian and avian branches. This was

This study takes a broad look into the existing research on the relationship between two physiological topics, nutrition and immunity in vertebrates, specifically the mammalian and avian branches. This was achieved by critiquing available studies on different types of immune cells, and how variable energy availability, as well as specific pathogens, impact cell function. Notably, most studies examined individuals with compromised immune systems, which reveals an existing knowledge gap in the linkages between nutrition and immunity in healthy organisms. Links between immunity and nutrition were identified across the studies, with the three main energy molecules, carbohydrates, lipids, and proteins, implicated in functional roles as immune modulators. Stimulatory and inhibitory effects occur dependent on elevated and depleted nutrient levels, and multiple cell types are sensitive to changes in nutrient availability. Further studies should be conducted on healthy individuals of model species, as well as wildlife and other non-model species to identify and describe the effects of host nutritional status on the spread of pathogens and the implications at the population level for humans, domestic animals, and wildlife.

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Agent

Created

Date Created
  • 2017-12

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Evaluating the viability of a DNA-based chip targeted for C. trachomatis, N. gonorrhoeae, and other pathogens of interest

Description

Sexually transmitted diseases like gonorrhea and chlamydia, standardly treated with antibiotics, produce over 1.2 million cases annually in the emergency department (Jenkins et al., 2013). To determine a need for

Sexually transmitted diseases like gonorrhea and chlamydia, standardly treated with antibiotics, produce over 1.2 million cases annually in the emergency department (Jenkins et al., 2013). To determine a need for antibiotics, hospital labs utilize bacterial cultures to isolate and identify possible pathogens. Unfortunately, this technique can take up to 72 hours, leading to several physicians presumptively treating patients based solely on history and physical presentation. With vague standards for diagnosis and a high percentage of asymptomatic carriers, several patients undergo two scenarios; over- or under-treatment. These two scenarios can lead to consequences like unnecessary exposure to antibiotics and development of secondary conditions (for example: pelvic inflammatory disease, infertility, etc.). This presents a need for a laboratory technique that can provide reliable results in an efficient matter. The viability of DNA-based chip targeted for C. trachomatis, N. gonorrhoeae, and other pathogens of interest were evaluated. The DNA-based chip presented several advantages as it can be easily integrated as a routine test given the process is already well-known, is customizable and able to target multiple pathogens within a single test and has the potential to return results within a few hours as opposed to days. As such, implementation of a DNA-based chip as a diagnostic tool is a timely and potentially impactful investigation.

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Agent

Created

Date Created
  • 2016-12

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Investigating Antimicrobial Controls for Bat White-Nose Syndrome

Description

Across large areas of eastern and midwestern North America, a severe reduction in multiple populations of bat species has been observed as the result of the emerging fungal disease, white-nose

Across large areas of eastern and midwestern North America, a severe reduction in multiple populations of bat species has been observed as the result of the emerging fungal disease, white-nose syndrome (WNS). WNS is caused by a psychrophilic (i.e. cold loving) fungus, Pseudogymnoascus destructans (Pd), that invades the skin of bats during hibernation. Recent studies have shown that during hibernation, bats have decreased immune system activity which would suggest increased susceptibility to infection. Antimicrobial peptides (AMPs) are an important component of the innate immune system and are expressed constitutively within all tissues that serve as barriers against infection. Killing pathogens at the level of the skin could prevent the need for more complex immune responses likely inhibited during hibernation, and therefore AMPs could be critical in combating infection by Pd and reducing population loss of susceptible bat species. In this investigation, the fungicidal activity of commercially available AMPs derived from the skin of multiple taxa, including amphibians, catfish, and humans were compared in order to study immunity at the level of the skin. Additionally, our aim was to create optimal methods for a low-cost antimicrobial-assay protocol that would provide quantitative results. We found that killing abilities at various concentrations of dermaseptin S-1 against Ca ATCC 10231 were consistent with literature values, while our values for magainin 2 and parasin 1 were far from the values previously recorded by other studies. It is possible that some differences can be accounted for by the difference in antimicrobial assay procedures, but our findings suggest potential differences to the well-known killing abilities of certain peptides nonetheless. Overall, the protocol established for the antimicrobial assays using serial dilutions and Sabouraud Dextrose plates was successful.

Contributors

Agent

Created

Date Created
  • 2018-05

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Investigating Antimicrobial Controls for Bat White-Nose Syndrome

Description

Across large areas of eastern and midwestern North America, a severe reduction in multiple populations of bat species has been observed as the result of the emerging fungal disease, white-nose

Across large areas of eastern and midwestern North America, a severe reduction in multiple populations of bat species has been observed as the result of the emerging fungal disease, white-nose syndrome (WNS). WNS is caused by a psychrophilic (i.e. cold loving) fungus, Pseudogymnoascus destructans (Pd), that invades the skin of bats during hibernation. Recent studies have shown that during hibernation, bats have decreased immune system activity which would suggest increased susceptibility to infection. Antimicrobial peptides (AMPs) are an important component of the innate immune system and are expressed constitutively within all tissues that serve as barriers against infection. Killing pathogens at the level of the skin could prevent the need for more complex immune responses likely inhibited during hibernation, and therefore AMPs could be critical in combating infection by Pd and reducing population loss of susceptible bat species. In this investigation, the fungicidal activity of commercially available AMPs derived from the skin of multiple taxa, including amphibians, catfish, and humans were compared in order to study immunity at the level of the skin. Additionally, our aim was to create optimal methods for a low-cost antimicrobial-assay protocol that would provide quantitative results. We found that killing abilities at various concentrations of dermaseptin S-1 against Ca ATCC 10231 were consistent with literature values, while our values for magainin 2 and parasin 1 were far from the values previously recorded by other studies. It is possible that some differences can be accounted for by the difference in antimicrobial assay procedures, but our findings suggest potential differences to the well-known killing abilities of certain peptides nonetheless. Overall, the protocol established for the antimicrobial assays using serial dilutions and Sabouraud Dextrose plates was successful.

Contributors

Agent

Created

Date Created
  • 2018-05

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The Influence of the Gut Microbiome on Human Health

Description

Bacteria are often regarded s pathogens, with deleterious impacts on the human body. However, it is known that the presence of trillions of bacteria on and in the human body

Bacteria are often regarded s pathogens, with deleterious impacts on the human body. However, it is known that the presence of trillions of bacteria on and in the human body impart beneficial effects on human health. Like a fingerprint, each individual’s microbiome is unique. The composition of bacteria in one person’s gut is different from the gut bacteria in another individual. Together, the human gut microbiome is a complex mix of organisms that is commonly referred to as “the second brain.� Its role in the human body goes beyond digestion and immune system function. The health of the microbiome factors into risk for illnesses as diverse as depression, obesity, bowel disorders and autism (Perlmutter et al., 2015). In context of the myriad of bacteria that live on and within the human body, the composition of bacteria in the gut may have the most significant impact on an individual’s well-being. This “superorganism� co-evolved with its host in order to provide essential and mutually beneficial functions (Ragonnaud et al., 2021).

Affecting millions of Americans, depression is one of the leading causes of the Global Burden of Disease (GBD), followed by anxiety (Gibson-Smith et al., 2018). Communication that occurs between the human brain and the gut microbiome has been found to be a major contributor towards mental health. The human gut microbiome is comprised of many microbes that can communicate with the brain through the gut-brain axis. However, factors such as stress and diets can interfere with this process, especially after increasing the permeability of the intestine (Khoshbin et al., 2020). Perturbation of the gut-brain axis has been implicated across a wide scale of neurodegenerative disorders, with respect to psychopathology (Bonaz et al., 2018). The environment of the gut, along with which species reside there, can help determine the link between gut function and disease. Therefore, it may be possible to prevent the degradation of an individual’s immune function and well-being through alteration of the gut microbiome. (abstract)

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Agent

Created

Date Created
  • 2021-05