1. The extraction of microorganisms in the Great South Bay
Sydney Altbacker, Joseph Conti, Dylan Pané
Claire Birone
Babylon Junior Senior High School
Abstract
Microorganisms are organisms that range in size from one to five micrometers in diameter. In the Great South Bay microorganisms are one of the lowest member in the aquatic food chain. Through the testing of the water in the Great South Bay, this project showed the microorganisms present off of the Gilgo Beach bayside docks, off of a bulkhead on the Carll’s River, and determined the genus and species of the organisms as best as possible through genetic sequencing. The microorganisms were extracted using a micropipette under a microscope. The DNA was extracted from the organism. Before the samples were sent to CSH, PCR was conducted to replicate the CO1 gene. The samples were then sequenced and compared to known sequences in DNA subway as well as GenBank.
Figure 1: Gel Image indicating banding results. Green results were sequenced and had strong banding patterns.
Method:
The water samples were collected from two separate locations in the Great South Bay and were stored in a freezer at Babylon Junior Senior High School. The first and second locations is water surrounding a wooden bulkhead off of houses on the Carll’s river. The third collection site is on the bay side of Gilgo beach, also water off of a bulkhead that has lawns and sandy areas. After the water was collected, the microorganisms were extracted using a micropipette under a microscope. Multiples of the same organisms of the same species as identified by a taxonomic key were put in the same test tubes.
Once the organisms were extracted they were lysed using a lysis buffer. The DNA was extracted from the organism and PCR was conducted on the COI and rbcL genes. The amplification was conducted to get the desired amount of gene segments for electrophoresis. Gel electrophoresis is necessary in the barcoding process because it indicates whether or not the PCR process was successful in replicating the genes of interest. The data then was formatted into phylogenetic trees and this shows the relationship of the microorganisms collected to known species .
Introduction
Microorganisms, ranging from one to five micrometers in size, feed on inorganic plant nutrients called nitrates and phosphates. When released into the environments in large amounts, nitrates and phosphates can greatly affect the habitat of many organisms and microorganisms. Rapid algae growth can also become dense causing sunlight to not reach organisms that need it, hence killing those organisms.
Algae is a type of microorganism found in the Great South Bay. When algae grows uncontrollably it is called a Harmful Algal Bloom, which can disrupt the local ecosystem. These HABs have the capability to kill a vast amount of marine life by blocking sunlight and creating excessive amounts of dissolved oxygen. The amount of eelgrass beds across various locations in the bay have declined because the HAB’s blockage of sunlight, as well as many fish and shellfish. Since then, high nitrate levels are still recorded and if anything, have raised and caused more algal and plant growth in the bay. The dissolved oxygen then makes harmful environments for microorganisms such as bioindicators.
Figure 5:
Sample PBT-019 is a rod shaped animal microorganism. The organism was sequenced but no strong banding matches were found.
Figure 2:Tree showing the relationship of possible genus species matches to sequenced DNA of plant samples. Xerosicyos decaryi was made the outgroup due to high banding mismatches.
Figure 6: Sample PBT- 001 a box shaped microorganism under 100x Microscope. The organism was sequenced but no strong banding matches were found.
Figure 4: Map indicating the locations around the Great South Bay where samples were collected.
Figure 3:Tree showing the relationship of possible genus species matches to sequenced DNA of animal samples. Homo sapiens were made the out group, matches were due to human error.