Monitoring the environment with artificial intelligence

December 13, 2018

Microorganisms perform key functions in ecosystems and their diversity reflects the health of their environment. However, they are still largely under-exploited in current biomonitoring programs because they are difficult to identify. Researchers from the University of Geneva (UNIGE), Switzerland, have recently developed an approach combining two cutting edge technologies to fill this gap. They use genomic tools to sequence the DNA of microorganisms in samples, and then exploit this considerable amount of data with artificial intelligence. They build predictive models capable of establishing a diagnosis of the health of ecosystems on a large scale and identify species that perform important functions. This new approach, published in the journal Trends in Microbiology, will significantly increase the observation capacity of large ecosystems and reduce the time of analysis for very efficient routine biomonitoring programs.

Monitoring the health status of ecosystems is of crucial importance in a context of sustainable development and increasing human pressure on the environment. Different species of micro-organisms sensitive to changes in their surroundings are used as bio-indicators for monitoring environmental quality. However, their morphological identification requires a lot of time and expertise. "A year ago, we were able to establish a water quality index based solely on the DNA sequences of unicellular algae present in the samples, without needing to visually identify each species", explains Jan Pawlowski, Professor at the Department of Genetics and Evolution of the UNIGE Faculty of Science.

Use DNA sequences without having to identify them

Genomic tools make it possible to quickly and very accurately describe the biological communities inhabiting an environment. However, a large proportion of the data cannot be used to conduct environmental health diagnoses because many DNA sequences are not referenced in existing databases. The species that possess these sequences are therefore unknown, as well as their ecological role. "In order to exploit all environmental genomics data, namely all the biodiversity of the samples, we used a machine learning algorithm", notes Tristan Cordier, a member of the Geneva group and first author of the study.

The biologists used samples of different known ecological quality status, ranging from good to bad, from which they sequenced the DNA. The combination of this information allowed them to build a reference system with the data from each sample. "A predictive model was then developed with this algorithm, based on our training data. These include data from reference diagnoses and data from the sequencing of unknown species", says Jan Pawlowski. This model is refined and validated over time by including new reference samples to the existing training dataset.

Discover new bio-indicators

The combination of these two cutting edge technologies makes it possible to obtain ecological values for DNA sequences without having to identify them. Species of microorganisms, already described or not, performing important functions can be discovered through this approach, as well as new bio-indicators. "Our research shares some similarities with the research on the human microbiome. Both aim to unravel microbial communities and identify biomarkers that can be used as powerful diagnostic tools to detect environmental pollution or human disease", concludes Tristan Cordier.

Université de Genève

Related DNA Articles from Brightsurf:

A new twist on DNA origami
A team* of scientists from ASU and Shanghai Jiao Tong University (SJTU) led by Hao Yan, ASU's Milton Glick Professor in the School of Molecular Sciences, and director of the ASU Biodesign Institute's Center for Molecular Design and Biomimetics, has just announced the creation of a new type of meta-DNA structures that will open up the fields of optoelectronics (including information storage and encryption) as well as synthetic biology.

Solving a DNA mystery
''A watched pot never boils,'' as the saying goes, but that was not the case for UC Santa Barbara researchers watching a ''pot'' of liquids formed from DNA.

Junk DNA might be really, really useful for biocomputing
When you don't understand how things work, it's not unusual to think of them as just plain old junk.

Designing DNA from scratch: Engineering the functions of micrometer-sized DNA droplets
Scientists at Tokyo Institute of Technology (Tokyo Tech) have constructed ''DNA droplets'' comprising designed DNA nanostructures.

Does DNA in the water tell us how many fish are there?
Researchers have developed a new non-invasive method to count individual fish by measuring the concentration of environmental DNA in the water, which could be applied for quantitative monitoring of aquatic ecosystems.

Zigzag DNA
How the cell organizes DNA into tightly packed chromosomes. Nature publication by Delft University of Technology and EMBL Heidelberg.

Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.

DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.

A new spin on DNA
For decades, researchers have chased ways to study biological machines.

From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.

Read More: DNA News and DNA Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to