User:Fengyuli2002/Microbial dark matter

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= Microbial dark matter = Microbial dark matter comprises the vast majority of microbial organisms (usually bacteria and archaea) that microbiologists are unable to culture in the laboratory, due to lack of knowledge or ability to supply the required growth conditions. Microbial dark matter is unrelated to the dark matter of physics and cosmology, but is so-called for the difficulty in effectively studying it as a result of its inability to be cultured by current methods. It is difficult to estimate its relative magnitude, but the accepted gross estimate is that as little as one percent of microbial species in a given ecological niche are culturable. Despite difficulties, microbial dark matter displays its importance in the ecosystem and potential for biotechnological applications.

In recent years, more effort has been directed towards deciphering microbial dark matter by means of recovering genome DNA sequences from environmental samples via culture independent methods such as single cell genomics and metagenomics. These studies have enabled insights into the evolutionary history and the metabolism of the sequenced genomes, providing valuable knowledge required for the cultivation of microbial dark matter lineages.

Research methods on microbial dark matter
The exploration of microbial dark matter primarily employs culture-independent methods. These techniques have revolutionized our ability to study unculturable microorganisms directly from environmental samples. Examples of these techniques including single cell genomics and metagenomics.

Single cell genomics
Single-cell genomics involves isolating and sequencing the genome from a single microbial cell. This method allows researchers to study the genetic material of individual cells without the need for culturing. It has been particularly useful in identifying and analyzing microorganisms that are part of microbial dark matter, since it significantly eliminates the problem of cell-to-cell variability.

Metagenomics
Metagenomics involves sequencing the collective genetic material from an environmental sample. This approach provides a broader view of the microbial diversity within an ecosystem and helps in identifying genetic signatures of unculturable microbes. Through metagenomics, scientists can reconstruct partial or complete genomes of microbial dark matter species.

Ecological and technological significance
Microbial dark matter plays a fundamental role in ecological systems and offers promising avenues for biotechnological innovation. This vast, largely unexplored microbial sector helps maintaining ecological balance and advancing biotechnologies.

Ecological Roles
Microbial dark matter organisms are pivotal in nutrient cycling, such as nitrogen fixation, carbon sequestration, and decomposition, which are essential for ecosystem functionality and resilience. These microbial processes are critical for soil fertility, plant growth, and climate regulation. For example, uncultured archaeal groups have been identified as major players in global nitrogen cycles, suggesting that microbial dark matter contributes significantly to processes that were previously attributed only to known microbial taxa.

Furthermore, microbial dark matter is involved in biodegradation and detoxification processes, which are crucial in natural and anthropogenic polluted environments. These microbes help in breaking down pollutants and recycling essential elements, thus mitigating environmental damage and supporting ecosystem restoration

Biotechnological Applications
In pharmaceuticals, microbial dark matter has been a source of novel bioactive compounds, including antibiotics and anticancer agents, which are derived from their unique genetic resources. These compounds often possess unique structures and modes of action that can be pivotal in developing new treatments for diseases.

The potential of microbial dark matter in biofuel production is also notable. Certain uncultured microbes have shown capabilities in producing bioethanol and biodiesel from various organic materials, presenting a sustainable alternative to fossil fuels. This application is particularly promising in the context of global efforts to reduce carbon emissions and promote renewable energy sources.

In agriculture, enzymes from microbial dark matter can enhance crop resilience and yield by improving nutrient uptake and providing resistance against pathogens and environmental stresses. These applications are just beginning to be explored but offer potential to improve agricultural practices, making them more sustainable and efficient.

Current challenges
Research on microbial dark matter faces several challenges that has hindered progress in this field.

Current sequencing and analytical technologies may not capture the full diversity of microbial dark matter. Incomplete or contaminated DNA samples can lead to gaps in genomic reconstructions and misinterpretations of functional capabilities.

The exploration of microbial dark matter often involves invasive sampling from sensitive or pristine environments. There are ethical considerations regarding the impact of such research on these ecosystems and the broader implications of exploiting microbial resources.