Search for: All records

One of the biggest barriers to conducting ocean science around the globe is limited access to computational tools and resources, including software, computing infrastructure, and data. Open tools, such as open-source software, open data, and online computing resources, offer promising solutions toward more equitable access to scientific resources. Here, we discuss the enabling power of these tools in under-resourced and non-English speaking regions, based on experience gained in the organization of three independent programs in West African, Latin American, and Indian Ocean nations. These programs have embraced the “hackweek” learning model that bridges the gap between data science and domain applications. Hackweeks function as knowledge exchange forums and foster meaningful international and regional connections among scientists. Lessons learned across the three case studies include the importance of using open computational and data resources, tailoring programs to regional and cultural differences, and the benefits and challenges of using cloud-based infrastructure. Sharing capacity in marine open data science through the regional hackweek approach can expand the participation of more diverse scientific communities and help incorporate different perspectives and broader solutions to threats to marine ecosystems and communities. 

ABSTRACT While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi , Nitrospirae , Euryarchaeota , and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments. IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.