Editorial: Metagenomics in Limnology and Oceanography

Abstract

The publication of this special issue, “Linking metagenomics to aquatic microbial ecology,” in Limnology and Oceanography, is long overdue. But perhaps it could not have appeared in L&O any earlier. The term “metagenomics” was invented in the late 1990s to describe the retrieval of genetic information from microorganisms without preselection by PCR, which gets only the targeted gene, or by isolating and culturing the organisms in the lab, which gets only a few microbes. Before metagenomics, microbial ecologists were well on their way to identifying microorganisms by using approaches that focused on the genes for ribosomal RNA. But with few exceptions, the rRNA gene data did not say much about what the organisms do—their role in ecological and biogeochemical processes. Metagenomic data tell us about their potential roles, and the other “omic” approaches (metatranscriptomics, metaproteomics, and so on) get closer to their ongoing activity. Metagenomics and its relatives took over microbial ecology after 2000, as documented by Pep Gasol's analysis of publications in the field since 1980 (Microbial Ecology of the Oceans, third edition 2018). Pep found that metagenomics started to have an impact, as measured by citation numbers, at least 10 years ago. Until this special issue, the metagenomic wave has left L&O largely untouched. According to the Web of Science, out of the nearly 10,000 papers published in the journal since its beginning, only seven report metagenomic results. An additional two papers have metatranscriptomic data, while no L&O paper has metaproteomic or other omic data from organisms. By contrast, since its start in 2007, the ISME Journal has published 432 metagenomic papers. All seven of the L&O metagenomic papers appeared after 2009, which so happens is when I published a primer about metagenomics and other omics in the L&O Bulletin at the invitation of then editor, John Dolan. (In case you are wondering, the L&O Bulletin article is why Deputy Editor-in-Chief Maggie Xenopoulos thought of me for this piece.) My article did not exactly launch an avalanche of papers on the topic. While this special issue appears late in metagenomic history, arguably it is appearing in L&O at just about the right time. The field has evolved to the point where it can now more forcefully explore questions of interest to L&O readers, as discussed in the issue's introduction by Grossart et al. Where once even extracting DNA was challenging, metagenomic methods now can be used by many L&O readers, not just the specialists who developed the methods. These methods have also gotten cheaper. In particular, sequencing costs have declined dramatically while sequencing power has exploded beyond belief. Because of the huge decrease in costs, microbial ecologists can analyze more samples and explore ecological and biogeochemical questions that were not feasible until recently. Metagenomic-wielding investigators can now take more time points or sample more locations; replication is no longer a foreign word. In this regard, a metagenomic paper is starting to look more like a typical L&O paper. Finally, after being dominated by work in the oceans for many years, metagenomics is catching up to the range of aquatic habitats covered by L&O. Reflecting the recent growth in freshwater omics, this special issue has more freshwater papers than marine ones (16 vs. 6). I suppose purely oceanographic methods have appeared in L&O, but it seems appropriate that this freshwater-dominated special issue is coming out in a journal published by a society that started in 1936 as the Limnological Society of America. I hope this special issue will encourage more omic papers in L&O. The journal needs these papers if it is to see the latest advances in microbial ecology and microbial biogeochemistry. It would be an exaggeration to say that metagenomics needs L&O. But publication of more omic papers in L&O would signal a maturation of the field, that it is focusing less on methodology and more on understanding microbial communities and processes. Of course, metagenomics has already contributed many new insights into the ecology and biogeochemistry of microbes. This special issue shows how it can do even more.