환경 DNA: 생태학에서의 장점과 한계

E-DNA 또는 환경 DNA는 환경 내 생물의 유전 물질로, 특히 생태학에서 서식지의 생물 종을 모니터링하는 데 사용됩니다.

### 생태학에서의 환경 DNA(eDNA): 애플리케이션, 워크플로, 장점 및 한계
* "**eDNA는 환경에서 발견되는 생물의 유전 물질**로, 특히 생태학 분야에서 그 중요성이 점점 커지고 있습니다."
* 🔍 E-DNA는 **"관심 있는 서식지의 종을 모니터링"**하는 데 사용됩니다. 이는 기존 모니터링 방법에 추가적인 정보를 제공합니다.
* 🌊 수중 환경의 맥락에서 물고기와 같은 유기체는 **"배설물이나 피부 세포를 통해 끊임없이 유전 물질을 잃어버리는데, 여기에는 eDNA가 포함되어 있다"**고 합니다.
* 🔄 eDNA 메타바코딩 워크플로에는 **"물 샘플을 수집하고, DNA를 추출하고, 범용 프라이머를 사용하여 특정 유전자 마커를 PCR을 통해 증폭하고, 앰플리콘을 시퀀싱"**하는 과정이 포함됩니다.
* 📚 보존된 유전자 영역이 종의 고유 식별자 역할을 하기 때문에 **"종은 다양한 동물의 염기서열이 포함된 참조 데이터베이스를 사용하여 분류됩니다."**
* ✅ E-DNA는 **희귀종을 감지**할 수 있으며 약 **2주 동안 환경에 존재**합니다.
* ❌ 그러나 보편적이면서도 특정 프라이머를 설계해야 하는 어려움과 풍부함이나 **바이오매스를 정량화하기 어렵다는 점** 등 eDNA에는 한계가 있습니다.
* 🤔 "데이터베이스에 참조 서열이 부족하거나 **한 종의 표적 서열이 다른 종과 동일**한 경우 종 식별이 어려울 수 있습니다."

e-dna is short for environmental DNA, and as the name already indicates, e-dna is genetic material of organisms found in the environment. Multiple applications of eDNA are of increasing importance, especially in the field of ecology. E-dna is used to monitor species in a habitat of interest. To explain what e-dna is, an aquatic environment is taken as an example. Organisms living in it, like this fish, constantly lose genetic material, which is found in excrements or shed skin cells, and those contain DNA. This form of DNA from organisms found in the environment is referred to as e-dna. But what is eDNA used for? To determine which species are living in an environment like the sea, one would have to either catch those individuals to identify and count them, or one would have to identify them with other monitoring systems. Especially in a complex ecosystem such as the ocean, fishing can be considered invasive and laborious, and video surveillance systems may be extremely expensive. Besides those more classical monitoring methods, eDNA provides an additional layer of information.

some advantages since e-dna is present in the environment for about two weeks. It is possible to detect rare species, which might not have been caught in nets or fishing boats. How can such information be gained from eDNA? In the first step, the water sample is collected. From this sample, the DNA is extracted. The water sample contains eDNA from different organisms. However, at this moment, the species of origin of those DNA fragments are not known. In case one wants to determine the species composition in an environment, the next step usually involves metabarcoding. For simplicity, this example does not show the entire genome but a short sequence. A specific genetic marker needs to be amplified from the extracted DNA using PCR. To make sure that all animals can later be detected, the eDNA of all animals has to be amplified. A critical step is to select universal primers that bind to all animal DNA. Target genes for the primer design have to be highly conserved. A sequence with an extremely high degree of similarity among different species is often found in mitochondrial genes. Those primers bind

to the same sequence of animal edna. The primers have additional overhangs, which are used for the library preparation and the sequencing step later. But the details about this will not be covered in this video. Check out the indicated video here for more information about that. In brief, DNA fragments of various organisms are amplified in high quantity. And after millions of amplicons have been generated with PCR, those reads can be sequenced with an Illumina instrument at ease. After some data processing, including different bioinformatics steps such as the removal of primers and unwanted reads, the species can be classified using a database with reference sequences. At this step, it is very important to have a reference database of good quality. That is, it contains sequences from a large spectrum of animals. Those genome databases help to distinguish which species are present in the environment from which the eDNA was collected from. In those conserved gene regions, only single nucleotides may differ between the species. And each are like a fingerprint that allows species identification. Even though eDNA is a great tool for

ecologists. There are, of course, limitations. One is that the primers used to amplify eDNA material need to be universal and bind to DNA from all target animals, but they need to be specific enough to exclude animals from outside the target group. If for one organism the primer binding sequence is different, the primer may not bind anymore, and the DNA of the respective species will not be amplified. This species will not be detected in the study, even if the organism was present in the environment. Further, it is hard to draw conclusions about the abundance or biomass of animals. Much eDNA from one species could indicate that this species is abundant, but it could also have various other explanations. One might be that a dead individual of a rare species may release elevated levels of eDNA. Quantification of eDNA data is still questionable at this moment, also especially for rare or even undiscovered species. Another limitation is that the databases do not have good reference sequences of those species. Species identification might also be difficult if the target sequence of one

species is so conserved that it is identical to that of another. In this case, two species cannot be distinguished. If you could take something home today and know what edna is, please like this video. Also, feel free to subscribe to this channel and check out this video here. Thanks for watching.

Biomonitoring using eDNA (environmental DNA)

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E-DNA 또는 환경 DNA는 환경 속 생물체의 유전 물질로, 생태학에서 그 중요성이 점점 커지고 있습니다.

다양한 서식지의 생물종을 모니터링하는 데 사용되며, 희귀종을 발견하고 침습적인 방법을 피할 수 있는 이점을 제공합니다.

E-DNA는 물 샘플에서 수집한 다음 특정 유전자 마커와 범용 프라이머를 사용하여 존재하는 종을 결정하는 메타바코딩이라는 과정을 거칩니다.

동물 eDNA 시퀀싱에는 DNA 단편을 증폭하고 Illumina 기기로 시퀀싱한 다음 참조 데이터베이스를 사용하여 종을 분류하는 과정이 포함됩니다.

다양한 동물 서열이 포함된 고품질 참조 데이터베이스는 환경에 존재하는 종을 정확하게 식별하는 데 매우 중요합니다.

이 기술은 종을 구별하기 위해 뉴클레오티드 차이가 최소화된 보존된 유전자 영역에 의존합니다.

생태학 연구에서 eDNA 분석의 한계

eDNA 프라이머는 보편적이면서도 특이적이어야 하기 때문에 모든 대상 동물의 DNA를 증폭하는 것이 어렵습니다.

높은 수치는 희귀종의 죽은 개체와 같은 다양한 요인으로 인해 발생할 수 있기 때문에 eDNA를 통해 동물의 풍부함에 대한 결론을 도출하는 것은 어렵습니다.

특히 희귀종이나 미발견 종의 경우, 데이터베이스에 참조 서열이 부족하기 때문에 eDNA 데이터의 정량화 및 종 식별은 여전히 의문입니다.

일부 종은 너무 비슷해서 서로 구별할 수 없을 정도입니다.

이러한 현상은 종 식별 및 분류에 대한 의문을 제기합니다.

이 주제에 대한 더 많은 콘텐츠를 보려면 채널을 구독하세요.