Biology subjects

Choudhury, R. A.

Publications and source records attributed to Choudhury, R. A..

11 recordsLinked to original sources

bioRxiv2025

Growth inhibition in co-cultivation of Cyclocybe aegerita and Hericium erinaceus mushrooms

Mushroom production relies heavily on compost and other substrates to grow and maintain fungal cultures. Large scale production of mushrooms can be achieved in specialized trays and grow rooms, however small-scale production of specialty mushrooms like lions mane (Hericium erinaceus) and pioppino mushrooms (Cyclocybe aegerita) relies on inoculation of small blocks of mushroom substrate in polypropylene bags, leaving spent mushroom substrate after production. Co-cultivation of mushrooms has been explored for the generation of novel secondary metabolites, however there is relatively little information about the effects of co-cultivation on yield. Our objective was to co-cultivate H. erinaceus and C. aegerita in the same bag and compare the overall colonization and yield with single inoculation bags. Overall, there was slower colonization and a significant reduction in the weight of harvested mushrooms from the mixed inoculation bag compared to the single inoculation bags, as well as a higher risk of contamination. We continue to explore new ways to improve the economic and environmental sustainability of mushroom production.

ecology↗

bioRxiv2024

Red harvester ants (Pogonomyrmex barbatus) do not distinguish between sorghum head mold symptomatic and asymptomatic seeds

Red harvester ants, Pogonomyrmex barbatus (Smith) (Hymenoptera: Formicidae), common in the Lower Rio Grande Valley of Texas, are known to gather seeds from areas around their nests and store the seeds inside their nests for later consumption. As these ants often nest in and near agricultural fields, some of these seeds may be from crops and may also be infected with fungal plant pathogens. These pathogens can degrade seed coats and may cause the seeds to rot within the ant nests, decreasing storage time and potentially spreading the pathogen to other stored seeds. We studied how head mold, a common sorghum disease, changed ant preferences for sorghum seeds. Using seed depots, we evaluated foraging preferences for sorghum seeds with and without head mold and then monitored how many seeds of each type were collected by the colonies after 1, 2, 4, and 24 hours. We found that red harvester ants did not have any significant preference for infected or uninfected seeds, taking both equally over time. Given this non-preference, ants were assumed to be storing infected seeds next to uninfected seeds within their colonies. However, the risk that stored pathogen-infected seeds poses as a source of future seed infection to seeds within the nest and plants in the surrounding field needs to be further examined.

ecology↗

bioRxiv2024

Advancing source tracking: systematic review and source-specific genome database curation of fecally shed prokaryotes

Approaches for shotgun metagenomic sequencing are being adapted to many environmental monitoring tasks but remain poorly suited for source attribution within fecal source tracking (FST) studies due to a lack of knowledge regarding the source specificity of fecally shed microbial populations. To address this gap, we performed a systematic literature review and curated a large collection of genomes (n=26,018) representing fecally shed prokaryotic species across broad and narrow source categories commonly implicated in FST studies of recreational waters (i.e., cats, dogs, cows, seagulls, chickens, pigs, birds, ruminants, human feces, and wastewater). These data include genome sequences recovered from metagenomic and isolation-based studies which we examined extensively with comparative genomic approaches to characterize trends across source categories and produce a finalized genome database for each source category which is available online (n=12,730). We find that across these sources, the total number of genomes recovered varies substantially: from none in seagulls to 9,085 in pigs. According to available data, on average 81% of the genomes representing species-level populations occur only within a single source. Using fecal slurries to test the performance of each source database, we report read capture rates that vary with fecal source alpha diversity and database size. Lastly, while extensive work has been performed on the rumen system of cows and other ruminants, we note the scarcity of genomic characterization of prokaryotes in the feces of these animals. We expect this resource to be useful to FST-related objectives, One Health research, and sanitation efforts globally. Table of Contents Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/598882v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@daeadcorg.highwire.dtl.DTLVardef@713d09org.highwire.dtl.DTLVardef@5e538borg.highwire.dtl.DTLVardef@bed833_HPS_FORMAT_FIGEXP M_FIG C_FIG SynopsisWe curate nine prokaryotic genomic databases for fecal source-tracking, summarize their source-specificity, and show their usefulness by bioinformatically testing mock impaired surface water samples.

bioinformatics↗

bioRxiv2024

Red harvester ant nests impact soil compaction but not temperature in peri-urban habitats of the Lower Rio Grande Valley

Ants are vital ecosystem engineers that can influence soil properties, subsequent soil processes, and associated biota via underground nest construction. Harvester ants consume seeds and are often found in arid areas, frequently altering soil chemistry and bulk density of the soils in and around their nest sites. Many species of harvester ants also intentionally remove vegetation around nest openings, creating cones or discs of bare soil that may further alter soil temperatures. However, much of the work investigating the impacts of harvester ants on soil properties has occurred in shrubland and grassland settings rather than suburban environments. We aimed to determine if Pogonomyrmex barbatus (Smith) (Hymenoptera: Formicidae) nests in a suburban habitat in the Lower Rio Grande Valley in Texas similarly altered soil properties. First, we measured active nest disc size to determine changes and colony persistence. Then we assessed soil compaction and surface temperature along a gradient centered on the disc. We found that disc size did not increase throughout the two-year observation period and that nests with smaller discs were less likely to persist between years. While we did not observe any changes in surface temperature across the gradient, we found a significant increase in soil compaction with greater distance from the center of the disc. These data indicate that increased nest size increases the extent of soil impacted. The impacts of nests reducing soil compaction, particularly within a suburban landscape with precipitation run-off issues and a highly disturbed plant community should be addressed in future studies.

ecology↗

bioRxiv2022

Red harvester ant (Order: Hymenoptera) preference for cover crop seeds in South Texas

Harvester ants are known to selectively forage seeds, potentially impacting nearby plant community composition. In agricultural areas, harvester ants may be viewed as pests by foraging on crop seeds or as beneficials by preferentially removing weed seeds. However, little work has been done on harvester ant preferences for cover crop seeds. Local observations suggest that ants may take cover crop seeds, but no studies have evaluated ant agricultural impacts or seed preferences in the Lower Rio Grande Valley (LRGV). We examined red harvester ant (Pogonomyrmex barbatus Smith) preferences for commonly used cover crop seeds in the LRGV (vetch, oat, fescue, sunn hemp, and radish with wheatgrass as a control) and a commonly used bacterial seed inoculation treatment meant to increase root nodulation. We tested seed sets using choice tests housed in seed depots located within the foraging range of ant colonies with no prior exposure to the selected seeds. Of the evaluated cover crop seeds, wheatgrass and oat were the first to be removed entirely from the depot, with vetch remaining after 24 h. When we inoculated the two most preferred seeds to determine if there was a preference for non-inoculated seeds, we found no difference between inoculated and non-inoculated seeds. There were also significant changes in activity over time for both trials. These data indicate that harvester ant foraging preferences and activity can inform grower management recommendations regarding the risks of using certain cover crops and months sowing should be conducted in fields with known harvester ant presence.

ecology↗

bioRxiv2021

Rhizobial adhesives enhance nodule formation in sunn hemp

Inoculation of legume seed with rhizobacteria before planting is an efficient and convenient way of introducing effective rhizobacteria to soil vicinity of legume root and ensuring nitrogen fixation in cover cropped field. However, there are still challenges in identifying the proper seed coating technique to ensure microbial survival in adverse environmental conditions and maintaining the symbiotic relation with plants. The objectives of this study are firstly, to analyze the effectiveness of different sticking agents aiding inoculation of Bradyrhizobium japonicum L. in sunn hemp seeds to enhance root nodule formation. Secondly, to observe nodulation pattern over time as affected by the treatment and lastly to check if there is significant difference between main root and lateral root nodulation pattern due to the treatments. Two similar field studies were conducted in fall 2019 and summer 2020 using four sticking agents: water, peanut oil, 10% jaggery solution, and 40% gum arabic solution. The fall study showed no significant differences among total nodules across treatments, but percentage of active nodules was highest in the oil treatment and lowest in the water treatment. In the summer study, significantly higher total nodules were seen in the jaggery treatment and the lowest was in water treatment again, however, there were no differences in percentage of total active nodules across treatments. Interestingly, the trend across weeks showed gum arabic treatment exhibiting higher main root nodulation and jaggery treatment exhibiting higher lateral root nodulation. Overall, water as an adhesive was less effective in aiding nodulation compared to other treatments. Peanut oil and jaggery showed better performance as adhesives aiding active nodulation and could be more effective than gum arabic or water.

plant biology↗

bioRxiv2020

Spinach growers value host resistance and synthetic fungicides in the fight against downy mildew

California spinach growers struggle to manage spinach downy mildew disease. The disease is especially difficult in the organic crop, which currently relies on resistant varieties to maintain disease-free crop. Alternative control measures are available, but it is not clear how growers perceive the efficacy of these methods. It is also not clear who growers contact to find out information on spinach downy mildew disease management. In this study, we conducted an online survey of people involved in spinach production, asking about their beliefs in the efficacy of different control methods and who they contact frequently to discuss spinach downy mildew control. We found that respondents were most positive about the efficacy of resistant varieties and synthetic pesticides, with much lower perceived efficacy for the practices of disking diseased fields, roguing diseased plants, and organic pesticides. Growers most frequently contacted pest control advisors (PCAs) about management strategies for spinach downy mildew. These results suggest that respondents are most confident about the efficacy of resistant varieties and synthetic pesticides and may be hesitant to adopt new control strategies like organic pesticides. The results also suggest that future extension efforts can be focused on PCAs to reach the most stakeholders with up to date research on downy mildew control.

scientific communication and education↗

bioRxiv2020

Imidacloprid Movement into Fungal Conidia is Lethal to Mycophagous Beetles

O_LIApplications of systemic pesticides can have unexpected direct and indirect effects on nontarget organisms, producing ecosystem-level impacts. C_LIO_LIWe investigated whether a systemic insecticide (imidacloprid) could be absorbed by a plant pathogenic fungus infecting treated plants and whether the absorbed levels were high enough to have detrimental effects on the survival of a mycophagous beetle. Beetle larvae fed on these fungi were used to assess the survival effects of powdery mildew and imidacloprid in a factorial design. Fungal conidia were collected from treated and untreated plants and were tested for the presence and concentration of imidacloprid. C_LIO_LISurvival of beetles fed powdery mildew from imidacloprid-treated leaves was significantly lower than that of beetles from all other treatments. C_LIO_LIImidacloprid accumulated in fungal conidia and hyphae was detected at levels considered lethal to other insects, including coccinellid beetles. C_LIO_LIWater-soluble systemic insecticides may disrupt mycophagous insects as well as other nontarget organisms, with significant implications for biodiversity and ecosystem function. C_LI

ecology↗

bioRxiv2019

Host density dependence and environmental factors affecting laurel wilt invasion

Host size, density and distribution, in addition to climate, can affect the likelihood a pathogen will invade and saturate landscapes. Laurel wilt, caused by the vector-borne forest pathogen Raffaelea lauricola, has devastated populations of native Lauraceae in the Southeastern US, and continues to spread. We surveyed 87 plots in six coastal islands in South Carolina, Georgia and North Florida, and one inland site (Archbold Biological Station) in South Florida for laurel wilt-affected and non-affected individual plants belonging to the genus Persea. The coastal island sites were surveyed once in 2008 or 2009, and the inland site was surveyed eight times from 2011 to 2013. Disease incidence per plot ranged from 0% to 96%, with mean disease incidence 45% across all sites. Disease incidence was positively correlated with trunk diameter and density of hosts with trunk diameter > 5 cm, but negatively with the degree of clustering, which was highest for small trees. A recursive partitioning model indicated that higher disease incidence was associated with moderate temperatures, wider trunk diameter, lower relative humidity, and lower wind speeds. Disease progress over time at Archbold followed a Gompertz curve, plateauing at 3% in two years. The dispersal kernel for disease incidence from a focus followed a negative exponential distribution. The number of plots with diseased trees at Archbold was similar for redbay (P. borbonia) and swampbay (P. palustris), but was lower for silkbay (P. humilis). Understanding how host density, size, and diversity interact with environmental effects will help guide future risk prediction efforts.

plant biology↗

bioRxiv2018

Modeling Uncertainty in Grapevine Powdery Mildew Epidemiology Using Fuzzy Logic

Powdery mildew is the most important disease of grapevines worldwide. Despite the potential for rapid spread by the causal pathogen, grape powdery mildew has been effectively managed using fungicide applications applied based on a calendar schedule or modeled disease risk index. Various epidemiological models for predicting disease development or risk have helped to improve disease management. The Gubler-Thomas (GT) risk index is a popular disease risk model used by many growers in the western U.S. We modified the GT risk index using fuzzy logic to address both biological and mechanical uncertainty in the pathosystem. The spraying schedule suggested by the fuzzy-modified GT risk index was tested in eight site-years. Overall, the fuzzy-modified risk index maintained comparable levels of disease control as both the original model and a calendar based treatment, and had significantly less disease than the untreated control. The fungicide use efficiency of the fuzzy-modified GT risk index suggests that the updated risk index was significantly more efficient with fungicide applications than both the calendar and original GT risk index.

epidemiology↗

bioRxiv2017

Temperature and Light Effects on Germination of Peronospora effusa Sporangia

Spinach downy mildew, caused by the biotrophic oomycete Peronospora effusa, is an economically important disease that is found in all spinach growing regions of the US. To effectively predict disease risk we need to understand the response of P. effusa to different environmental conditions. We conducted several germination assays, exposing P. effusa sporangia to different temperature and lighting conditions. Between 5 and 25{degrees}C under constant darkness, germination of P. effusa sporangia on water agar declined. These results were qualitatively different from a previous study of P. effusa germination that found a bimodal response curve, with increased germination at lower and higher temperatures. Time course studies revealed that sporangia consistently germinated within the first twelve hours of plating, regardless of incubation temperature. Sporangia exposed to blue light had significantly reduced germination when compared with those exposed to red, yellow, or no light. Light intensity and color significantly impacted germination, although the effect of color varied by light intensity.

plant biology↗