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Twenty percent (20%) of annual deaths worldwide are attributed to microbial pathogens. Pathogenic illnesses pose major threats to the overall health and safety of humans. These illnesses can result in death, prolonged hospital stays, and increased hospital expenses. The goal of this research is to study the evolution and ecology of microorganisms and surveillance of human pathogens in local the ponds. Surveillance of pathogens can inform the local and global efforts for monitoring and supporting public health measures to fight diseases. Surveillance is the essential tool to inform policies, prevent infections and control responses. Samples were collected from four ponds in Jackson, TN: Lane College, Muse Park, Fairgrounds and Campbell Street Park. DNA was isolated from the water samples using ethanol precipitation followed by the ZymoBIOMICS DNA Miniprep kit. Samples were prepared for the whole genome sequencing by PCR using the Rapid Barcoding and the 16S PCR Barcoding kits from Nanopore to amplify the DNA samples. The metagenomic DNA was sequenced with the Nanopore M1KC MinION sequencer. The reads were then analyzed by the Epi2Me, What's in my pot (WIMP) or 16S Fastq workflows. All four of the ponds are known to have pathogenic in them. The Lane College Pond has Clostridium and Pseudomonas. The Fairgrounds Pond has Bacillus and Legionella. The Campbell Street Pond has Clostridium, Bacillus, Leptospira and Pseudomonas. The Muse Park Pond has Leptospira, Legionella, and Clostridium. Further studies can be done with this project to examine the concept of how pathogens affect microbiomes in an aquatic environment. This work is supported by a grant from the National Science Foundation EES 2011938.
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Abstract 2127 Using Metagenomics to Explore Biodiversity in Local Ponds
The microbiome is a group of microorganisms living in a particular environment. Microorganisms living in ponds play an important role in the health and balance of these ecosystems. This study aimed to understand how microorganisms vary in different local ponds using metagenomics. Water samples were collected from local ponds around Jackson, Tennessee, to be examined for the presence of microorganisms. DNA was extracted using a standard ethanol precipitation protocol followed by clean-up with a ZymoBIOMICS genomic DNA mini kit. The whole genome DNA was then amplified using the Nanopore Polymerase Chain Reaction (PCR) Barcoding kit due to low DNA yield and to allow multiplexing during DNA sequencing. This process involves fragmentation of the genomic DNA and addition of a linker oligonucleotide using an engineered transposase followed by amplification of the DNA with specific primers containing a unique barcode. All amplified genomic DNA samples were cleaned using MagBeads, prepped for the Genomic libraries, and ran on the Nanopore MinION Mk1c DNA sequencer. DNA reads were analyzed using the Epi2Me What's in My Pot workflow to identify specific microorganisms using standard sequence alignment to NCBI reference sequences. Initial findings showed that the microorganisms differed significantly from pond-to-pond. Each pond had its own unique mix of microorganisms, and some ponds had more diverse microorganisms than others. Various types of bacteria, archaea, and fungi were found, but their abundance and distribution varied across ponds. Environmental factors that were documented to influence diversity of microorganisms were also studied. These factors, including acidity of the water and oxygen levels, seemed to affect the types of microorganisms present. Some connections between specific microorganisms and these environmental factors suggests that they work together in the pond ecosystem. Understanding these differences can contribute to effective management and conservation of local ponds. Further research on how the microorganisms change over time, as well as studying other environmental factors and how the microorganisms function in the ponds. This information can help monitor water quality, protect the environment, and manage ponds more effectively. This work is supported by an HBCU-UP Implementation Project grant from the National Science Foundation EES 2011938.
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- Award ID(s):
- 2011938
- PAR ID:
- 10505272
- Publisher / Repository:
- Journal of Biological Chemistry
- Date Published:
- Journal Name:
- Journal of Biological Chemistry
- Volume:
- 300
- Issue:
- S
- ISSN:
- 0021-9258
- Page Range / eLocation ID:
- 106652
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Lane College is a small, liberal arts, Historically Black College in Jackson, TN. The Division of Natural and Physical Sciences provides undergraduate research experiences for students majoring in biology, chemistry, computer science, mathematics, or physics. To increase inclusivity, all students within one of the five majors are encouraged to apply, regardless of GPA, classification, or previous research experience. This eight-week program features a bi-weekly professional development session and a symposium at the end of the program where students present their research findings. During the summer of 2023, seven biology students completed a metagenomics research study with the goal to explore the biodiversity of different local freshwater aquatic environments. The students collected water samples from four local ponds with metadata such as pH, temperature, dissolved oxygen, and GPS coordinates. Initial observations of aquatic life using microscopy and dichotomous keys were made. The DNA was extracted from the samples using ethanol precipitation followed by clean-up with the ZymoBIOMICS DNA Miniprep kit. DNA was amplified using the Nanopore Rapid PCR barcoding kit or the 16S PCR barcoding kit and sequenced with the Nanopore MinION Mk1C. DNA sequences were initially analyzed using the Nanopore Minnow and Epi2Me What's in My Pot Workflows. Each student explored the subsequent data to answer specific research questions about the biodiversity in each environment, such as the impact of pH, dissolved oxygen, whether the pond was static or free flowing, or the presence of different pathogenic or toxic microbes. Overall, they found that while there was some overlap, aquatic organisms varied in the ponds depending on whether the pond was static or free flowing, pH, dissolved oxygen, and location. Some of the students continued these research projects during the fall 2023 semester in the Biology Undergraduate Research course where they refined their research questions and analyzed the data using additional bioinformatics tools available on Galaxy.more » « less
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Abstract Urbanization can influence local richness (alpha diversity) and community composition (beta diversity) in numerous ways. For instance, reduced connectivity and land cover change may lead to the loss of native specialist taxa, decreasing alpha diversity. Alternatively, if urbanization facilitates nonnative species introductions and generalist taxa, alpha diversity may remain unchanged or increase, while beta diversity could decline due to the homogenization of community structure. Wetlands and ponds provide critical ecosystem services and support diverse communities, making them important systems in which to understand the consequences of urbanization. To determine how urban development shapes pond community structure, we surveyed 68 ponds around Madison, Wisconsin, USA, which were classified as urban, greenspace, or rural based on surrounding land use. We evaluated how landscape and local pond factors were correlated with the alpha diversity of aquatic plants, macroinvertebrates, and aquatic vertebrates. We also analyzed whether surrounding land use was associated with changes in community composition and the presence of specific taxa. We found a 23% decrease in mean richness (alpha diversity) from rural to urban pond sites and a 15% decrease from rural to greenspace pond sites. Among landscape factors, adjacent developed land, mowed lawn cover, and greater distances to other waterbodies were negatively correlated with observed pond richness. Among pond level factors, habitat complexity was associated with increased richness, while nonnative fishes were associated with decreased richness. Beta diversity was relatively high for all ponds due to turnover in composition between sites. Urban ponds supported more nonnative species, lacked a subset of native species found in rural ponds, and had slightly higher beta diversity than greenspace and rural ponds. Our results suggest that integrating ponds into connected greenspaces, maintaining riparian vegetation, preventing nonnative fish introductions, and promoting habitat complexity may mitigate the negative effects of urbanization on aquatic richness. While ponds are small in size and rarely incorporated into urban conservation planning, the high beta diversity of distinct pond communities emphasizes their importance for supporting urban biodiversity.more » « less
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1016/j.jbc.2024.106652
