The discovery that life can exist and even flourish in environments devoid of sunlight has long been a topic of fascination for scientists. A recent study published in Science Advances by Chinese researchers has shed new light on this phenomenon, revealing how microbes in deep subsurface areas derive energy from chemical reactions driven by crustal faulting. This groundbreaking research challenges the conventional wisdom that “all life depends on sunlight” and offers critical insights into the existence of life deep below Earth’s surface.

Led by Professors Hongping He and Jianxi Zhu from the Guangzhou Institute of Geochemistry, a team of researchers simulated crustal faulting activities to understand how free radicals produced during rock fracturing can decompose water, generating hydrogen and oxidants like hydrogen peroxide. These substances create a distinct redox gradient within fracture systems, which can further react with iron in groundwater and rocks – oxidizing ferrous iron (Fe²⁺) to ferric iron (Fe³⁺) or reducing ferric iron (Fe³⁺) to ferrous iron (Fe²⁺), depending on local redox conditions.

In microbe-rich fractures, the researchers found that hydrogen production driven by earthquake-related faulting was up to 100,000 times greater than that from other known pathways, such as serpentinization and radiolysis. This process effectively drives iron’s redox cycle, influencing geochemical processes of elements like carbon, nitrogen, and sulfur – sustaining microbial metabolism in the deep biosphere.

This study has far-reaching implications for our understanding of life on Earth and beyond. Professors He and Zhu note that fracture systems on other Earth-like planets could potentially provide habitable conditions for extraterrestrial life, offering a new avenue for the search for life beyond Earth. The research was financially supported by various sources, including the National Science Fund for Distinguished Young Scholars and the Strategic Priority Research Program of CAS.

In conclusion, this groundbreaking study has challenged our understanding of life’s dependence on sunlight and revealed a previously unknown source of energy for microbes in deep subsurface areas. As we continue to explore the mysteries of the deep biosphere, we may uncover even more secrets that will rewrite the textbooks on life on Earth and beyond.

The field of genetic engineering has taken a significant leap forward with the development of two new genome editing technologies by a team of Chinese researchers led by Prof. Gao Caixia from the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences. These innovations, collectively known as Programmable Chromosome Engineering (PCE) systems, have been published in the prestigious journal Cell.

The PCE system is an upgrade to the well-known Cre-Lox technology, which has long been used for precise chromosomal manipulation. However, this older method had three major limitations that hindered its broader application: low recombination efficiency, reversible recombination activity, and the need for a scar (a small DNA fragment) at the editing site.

The research team tackled each of these challenges by developing novel methods to advance the state of this technology. Firstly, they created a high-throughput platform for rapid recombination site modification and proposed an asymmetric Lox site design that reduces reversible recombination activity by over 10-fold.

Secondly, they utilized their recently developed AiCE model – a protein-directed evolution system integrating general inverse folding models with structural and evolutionary constraints – to develop AiCErec. This approach enabled precise optimization of Cre’s multimerization interface, resulting in an engineered variant with a recombination efficiency 3.5 times that of the wild-type Cre.

Lastly, they designed and refined a scarless editing strategy for recombinases by harnessing the high editing efficiency of prime editors to develop Re-pegRNA, a method that uses specifically designed pegRNAs to perform re-prime editing on residual Lox sites, precisely replacing them with the original genomic sequence.

The integration of these three innovations led to the creation of two programmable platforms, PCE and RePCE. These platforms allow flexible programming of insertion positions and orientations for different Lox sites, enabling precise, scarless manipulation of DNA fragments ranging from kilobase to megabase scale in both plant and animal cells.

Key achievements include targeted integration of large DNA fragments up to 18.8 kb, complete replacement of 5-kb DNA sequences, chromosomal inversions spanning 12 Mb, chromosomal deletions of 4 Mb, and whole-chromosome translocations. As a proof of concept, the researchers used this technology to create herbicide-resistant rice germplasm with a 315-kb precise inversion.

This groundbreaking work not only overcomes the historical limitations of the Cre-Lox system but also opens new avenues for precise genome engineering in various organisms, demonstrating its transformative potential for genetic engineering and crop improvement.

Plant immunity is a complex system that helps plants defend against bacterial threats. Scientists at the University of California, Davis, have used artificial intelligence to upgrade this system, enabling plants to recognize a wider range of bacterial dangers. This breakthrough could lead to new ways to protect crops like tomatoes and potatoes from devastating diseases.

Plants have an immune system, just like animals, which includes immune receptors that help detect bacteria and defend against them. One of these receptors, called FLS2, helps plants recognize flagellin – a protein in the tiny tails bacteria use to swim. However, bacteria are constantly evolving to avoid detection, making it challenging for plants to keep up.

To help plants stay ahead, researchers used natural variation coupled with artificial intelligence, specifically AlphaFold, to predict the 3D shape of proteins and reengineer FLS2. By comparing receptors that recognize more bacteria with those that focus on specific types, they identified which amino acids to change.

The team was able to “resurrect a defeated receptor” – one where the pathogen had won – and enable the plant to resist infection in a targeted and precise way. This opens the door to developing broad-spectrum disease resistance in crops using predictive design.

One of the researchers’ targets is Ralstonia solanacearum, a major crop threat that causes bacterial wilt and can infect over 200 plant species, including staple crops like tomato and potato. Looking ahead, the team is developing machine learning tools to predict which immune receptors are worth editing in the future and narrowing down the number of amino acids that need to be changed.

This approach could be used to boost the perception capability of other immune receptors using a similar strategy, potentially leading to new ways to protect crops from devastating diseases. The research was supported by the National Institutes of Health and the United States Department of Agriculture’s National Institute for Food and Agriculture.