DNA sequencing and AI help craft largest database of marine microbes

A recent study has compiled the most detailed database of marine microbe information ever, helping researchers better understand the variety of life in the oceans. This database not only includes information on the microbes themselves but also provides details about their biological functions, geographical locations, and habitat types.

The new catalog helps in "understanding the ocean’s full diversity, containing more than 317 million gene groups from marine organisms around the world,” said lead author Elisa Laiolo of the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia, in a statement. Researchers made the catalog focusing on marine microbes as they greatly impact human lives through their influence on the ocean’s health and the Earth’s climate.

The resource is freely available through the KAUST Metagenomic Analysis Platform (KMAP). The details of the team's were published in the journal Comprehensive list Scientists mapping marine biodiversity face challenges due to the limited feasibility of studying most marine organisms in a lab. DNA sequencing technologies have been crucial in overcoming this, enabling direct identification of organisms from ocean samples, as noted by the research team.

Identifying organisms in an ocean sample is achievable by analyzing their genetic material, as each species possesses a distinct set of genes. According to the team, two key technological advancements have enabled this on a large scale. Firstly, the significant acceleration in the speed and reduction in the cost of DNA sequencing technologies have enabled researchers to sequence the genetic material in thousands of ocean samples.

Secondly, the emergence of substantial computational power and (AI) technologies has made it feasible to analyze millions of sequences. Utilizing KMAP, the team examined extracted from 2,102 ocean samples collected at various depths and locations globally. This advanced computing infrastructure successfully pinpointed 317.5 million gene groups, with over half of them categorized based on organism type and gene function.

Researchers claim that the integration of this data with details about sample locations and habitat types has yielded an unparalleled catalog, offering insights into the distribution and activities of microbes in different marine environments. Valuable insights The catalog has unveiled variations in microbial activity between the water column and ocean floor, along with a notable presence of fungi in the 'twilight' mesopelagic zone.

These revelations and others are poised to assist scientists in understanding the role of microbes residing in diverse habitats, their impact on ecosystems, their contributions to ocean health, and their influence on climate dynamics. Furthermore, researchers claim that the catalog establishes a foundational reference for monitoring the repercussions of human induced factors such as pollution and global warming on marine life.

It also provides a vast repository of genetic material that researchers can explore for novel genes applicable to drug development, energy, and agriculture, according to the team. The team says that KMAP Ocean Gene Catalog 1.0 represents the inaugural phase in creating a comprehensive atlas of the global ocean genome.

The team now aims to systematically document every gene present in each marine species worldwide, encompassing a broad spectrum from bacteria and fungi to plants and animals. “Our analysis highlights the need to continue sampling the oceans, focusing on under studied areas, such as the deep sea and the ocean floor.

Also, since the ocean is forever changing – both due to human activity and to natural processes – the catalog will need continual updating,” said Laiolo in a . The global ocean genome (the pool of genes in marine organisms and the functional information they encode) is a major, untapped resource for science and society with a growing range of biotechnology applications in sectors such as biomedicine, energy, and food.

Shotgun sequencing and metagenomics can now be used to catalog the diversity of ocean microbial life and to explore its functional potential, but has been limited by sample coverage, access to suitable sequencing platforms, and computational capacity. Here we provide a novel synthesis of the global ocean genome based on analysis of 2,102 sampled ocean metagenomes, with gene assembly and annotation via the KAUST Metagenome Analysis Platform (KMAP) Global Ocean Gene Catalog 1.0 containing ~317.5 million gene clusters.

Taxonomically, we report the distribution of marine genes across the tree of life and different ocean basins and depth zone biomes. Functionally, we map its relationship to protein families and biogeochemical processes, including the major microbial metabolic pathways that process three elements that play fundamental roles in biogeochemical cycles and are relevant to climate change.

These data extend our understanding of the complex, dynamic nature of the ocean microbiome and its metabolic capabilities. Further research is of critical global importance both to unlock the potential of the ocean genome and to understand and predict the effects of human induced changes, including pollution and climate change.

Further hypothesis driven research should target under sampled deep sea and benthic microbial communities using enhanced metagenomic methods, to better understand marine ecosystem functioning. Investment in the necessary computational capacity is essential, as are suitable intellectual property frameworks..