Exploring what lies beneath

The recently held KAUST Global Ocean Genome workshop brought together internationally recognized scientists from KAUST and abroad to discuss and assess the progress of the global ocean genome. Photo by Andrea Bachofen-Echt.

By David Murphy, KAUST News

The recently held KAUST Global Ocean Genome workshop brought together internationally recognized scientists from both KAUST and abroad to discuss and assess the progress of the global ocean genome.

The four-day workshop held between October 29 and November 1 focused on updating the current inventory of genes in the microbial communities of the global ocean. Through diverse keynote lectures and presentations, workshop attendees assessed the progress made toward providing an adequate representation of the microbial communities, and their associated gene pools and environments in the global ocean.

Attendees also explored the functional capacities of the global ocean microbiome as represented by the global ocean genome and examined the global distribution and sequence variability of key functional genes. The workshop saw attendees attempt to further new analytical approaches to mine the global ocean genome for genes of industrial interest.

Enhancing existing collaborations

Alongside the University researchers and students present, the workshop featured international researchers from Canada, Denmark, France, Germany, Japan, Spain and Switzerland. In the opening address of the workshop, Pierre Magistretti, distinguished professor of bioscience and dean of the University's Biological and Environmental Science Division, welcomed the overseas attendees and highlighted the research ethos of KAUST.

"For those of you who have come to KAUST for the first time, I think KAUST will leave you with an impressive impression," Magistretti said. "I hope this workshop will enhance existing collaborations between KAUST, the University's Red Sea Research Center (RSRC) and research institutions around the world."

Carlos Duarte, director of the RSRC and the Tarek Ahmed Juffali Research Chair in Red Sea Ecology, addresses KAUST Global Ocean Genome workshop attendees. Photo by Andrea Bachofen-Echt.

In his opening remarks, Carlos Duarte, director of the RSRC and the Tarek Ahmed Juffali Research Chair in Red Sea Ecology, outlined how the University is committed to genome and microbiome research.

"At KAUST, we use brute force and intelligent, big-data systems to explore the wealth of knowledge in the ocean metagenome data. We are focusing on microbiome research, and we want KAUST to become a repository of global metagenome data," Duarte emphasized.

Chris Bowler from the Institute of Biology, Ecole Normale Supérieure (ENS), and chair for the first session of the workshop, felt that worldwide research in global genomes is only expanding with no sign of plateau in the near future.

Pablo Sánchez Fernández, a postdoctoral fellow in bioinformatics from the Institut de Ciències del Mar (ICM) -The Spanish National Research Council (CSIC), discussed mesopelagic gene and microbial species enrichment across the global tropical and subtropical ocean. Throughout his talk he drew attention to the largest biome on Earth—the "dark ocean."

'15 million unique genes'

Takashi Gojobori, KAUST distinguished professor of bioscience and associate director of the University's Computational Bioscience Research Center, gave a keynote lecture entitled "Comparative marine metagenomics in the global ocean project." In his address, Gojobri discussed research findings from field experiments in the Sea of Japan and the Red Sea.

"The sea around Japan shows clear examples of seasonal changes, and what we think from our studies is that the Red Sea can be a close model of the global warming effect," Gojobori said. "In Japan, we have developed automatic seawater sampling instruments, and I feel that widespread, automatic genomic sampling can be achieved in the coming years."

Carlos Duarte, director of the RSRC and the Tarek Ahmed Juffali Research Chair in Red Sea Ecology, speaks to KAUST Global Ocean Genome workshop attendees. Photo by Andrea Bachofen-Echt.

"There has been a growing sequencing effort since 2007, and we are getting a better picture of the global ocean genome. However, the role of increased sequencing depth in building the ocean microbial gene catalog has not yet been examined," Duarte acknowledged.

Duarte noted that a total inventory of genes can never be reached. "As a rule of thumb, about 15 million unique genes are discovered for every tera base pair sequenced in microbial communities. There are millions of microbial ocean genomes to be discovered," he said.

Naiara Rodriguez from AZTI Tecnalia, a Spanish nonprofit technology center focused on marine and foodstuff research, covered the challenges of high-throughput sequencing of the global ocean eukaryotic plankton. Rodriguez felt that there cannot be one monitoring technique that works for all ocean genome research. She also highlighted how researchers can run into issues especially when carrying out genetic sampling.

Addressing taxonomy difficulties

Bowler delivered a keynote on the "Exploration of Tara Oceans metatranscriptomics data." In his presentation, he focused on how approximately one-third of marine eukaryotic plankton cannot be assigned to any known taxonomic group and the challenge this poses.

"The marine eukaryote reference genome catalog is 115 million unique genes and still climbing. A huge amount of discovery remains within this catalog—we're in the dark in terms of taxonomy and what sequence these genes are in," Bowler noted.

Chris Bowler from the Institute of Biology, Ecole Normale Supérieure (ENS), deliveres his keynote on the “Exploration of Tara Oceans metatranscriptomics data.” Photo by Andrea Bachofen-Echt.

"In our studies, we've seen some interesting differences between metagenomics and metatranscriptomics data. Expression profiles of iron-responsive genes at a global scale are congruent with modeled iron concentrations. By integrating global data with a localized response, we provide a framework for understanding the resilience of plankton ecosystems in a changing environment," he added.

David Kamanda Ngugi, a research scientist based in the University's RSRC, focused his talk on the widespread distribution of salvage pathways in oceanic microbes: implications for autotrophs. Ngugi emphasized how all cell growth in the world's oceans are limited without nucleotides. Throughout his address, he identified that nucleotides are a ubiquitous constituent of life and that there is a healthy abundance of genes in the global ocean.

Looking at virus samples

Day two of the workshop opened with a keynote address from Professor Chris SuttleDepartment of Earth, Ocean and Atmospheric SciencesUniversity of British Columbia. In his keynote entitled "Vignettes of virus variation in the oceans," Suttle described his research on viruses and their role in the environment. He spoke on sequencing, RNA viruses and on recent fieldwork.

"Our team has been collecting virus communities for the past three years and there is a lot of diversity out there—if we could sequence that diversity that would be great. In our samples, we found 125 distinct evolutionary groups. We've found that there is a great diversity of RNA viruses," Suttle said.

"We are looking at virus samples in the Red Sea that could have been there for three million years—from the last time the Red Sea drained and dried out. We're looking at a really interesting area with viruses that are unknown," he added.

Professor Chris Suttle, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, opens day two of the Global Ocean Genome conference with his keynote address. Photo by Andrea Bachofen-Echt.

"We really need to get deeper sequencing to try and find out what is out there. We really need to get a reference genome—without reference genomes, we're in trouble. One of the challenges of metagenomics is trying to figure out what to do when you don't have a reference genome," Suttle noted.

Following on from Suttle, Duarte spoke on behalf of Elena Lara from the Istituto di Scienze Marine, Venice, Italy, who could not attend the workshop. Her presentation "Ecogenomics of deep-sea viral communities" outlined the largest but least explored in the Earth's biosphere—the "deep ocean."

"The 'deep ocean' contains 70 percent of the ocean's microbial cells and 60 percent of its heterotrophic activity," Duarte said

"There are ubiquitous viral populations in the bathypelagic layer—the 'bathypelagic virosphere' hosts much more viral diversity than previously believed. Viruses in the deep, dark ocean are fundamental players for the Earth's and the ocean's functioning," he added.

The unanswered question

Marli Vlok, a Ph.D. student in The Suttle Lab based in the Department of Botany, University of British Columbia, speaks about underestimated entities in the marine environment during the KAUST Global Ocean Genome workshop. Photo by Andrea Bachofen-Echt.

Marli Vlok, a Ph.D. student in The Suttle Lab based in the Department of Botany, University of British Columbia, spoke about underestimated entities in the marine environment. Vlok described how RNA virus genomes exhibit biogeographical patterns that are affected by many factors.

"There are so many RNA viruses that remain unknown—the question is, are we missing half the viruses in the ocean? Marine RNA virus assemblages have unprecedented diversity. In our study, we found viruses and sequences that affect a whole range of animals, bacteria and plants," Vlok said.

Kasper Uper Kjeldsen from Aarhus University, Denmark, discussed microbial community assembly and evolution in subsea floor sediment during the Global Ocean Genome workshop. Photo by Andrea Bachofen-Echt.

In his keynote lecture, Kasper Uper Kjeldsen from Aarhus University, Denmark, covered microbial community assembly and evolution in subsea floor sediment, specifically in Aarhus Bay in his native Denmark. Kjeldsen and his team's research are focused on trying to understand how microbial communities evolve as they get buried and the substrates supporting their growth, depleted in the seabed.

"A lot of genetic diversity can be found in Aarhus Bay, and when you look at sediments, it is highly zonated. In our study, we found that a core group of species exist across all sediment levels—we've found very low levels of diversity with subsurface sediment populations," Kjeldsen said.

"We can estimate the turnover time for carbon in cells. The efficacy of natural selection does not change with sediment depth," he added.

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