Background: Biological trace elements are used in small amounts but are required for all living organisms. They are key components of many proteins and enzymes involved in important biological processes. Many trace element-dependent proteins have been characterized in various microbes, but very little is known about their occurrence, functions, and interactions in microbial communities in marine environments, especially in depth-related marine ecosystems.
Results: In this study, by analyzing metagenomic data from different geographic locations and water depths in the oceans around the world, we identified the distribution of genes encoding trace element-dependent proteins (for copper, molybdenum, tungsten, cobalt, nickel, and selenium) in a variety of marine samples from the upper ocean to the deep sea, which demonstrates vertical patterns of trace element utilization in marine microbes. More than 63,000 metalloprotein and selenoprotein genes belonging to nearly 100 families were predicted, constituting the largest environmental metalloprotein and selenoprotein gene dataset reported so far. Further examination of the interactions among trace elements revealed significant correlations between some of them (especially molybdenum or tungsten and selenium) and more active elemental crosstalk in the epipelagic zone of the ocean. Comparison of the patterns of trace element utilization across samples suggested that additional unknown factors might play a more important role in shaping trace element utilization in marine microbes living in certain locations. Finally, analysis of the relationship between water depth and metalloprotein/selenoprotein families revealed that the evolution of approximately half of the metalloprotein and selenoprotein families in marine microbial world could be influenced by ocean depth at either the global or the local level.
Conclusions: Our findings provide new insights into the utilization and functions of trace elements in marine microbes along a vertical gradient across the ocean.