A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters

Alexander Crits-Christoph; Spencer Diamond; Basem Al-Shayeb; Luis Valentin-Alvarado; Jillian F Banfield

doi:10.1038/s43705-022-00140-5

A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters

ISME Commun. 2022 Aug 13;2(1):70. doi: 10.1038/s43705-022-00140-5.

Authors

Alexander Crits-Christoph¹, Spencer Diamond², Basem Al-Shayeb¹, Luis Valentin-Alvarado¹, Jillian F Banfield^{3

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Affiliations

¹ Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
² Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
³ Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
⁴ Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
⁵ Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jbanfield@berkeley.edu.
⁶ Chan Zuckerberg Biohub, San Francisco, CA, USA. jbanfield@berkeley.edu.

Abstract

Bacteria of the phylum Acidobacteria are one of the most abundant groups across soil ecosystems, yet they are represented by comparatively few sequenced genomes, leaving gaps in our understanding of their metabolic diversity. Recently, genomes of Acidobacteria species with unusually large repertoires of biosynthetic gene clusters (BGCs) were reconstructed from grassland soil metagenomes, but the degree to which species with this trait are widespread is still unknown. To investigate this, we assembled 46 metagenome-assembled genomes recovered from permanently saturated organic-rich soils of a vernal (spring) pool ecosystem in Northern California. We obtained high and medium-quality draft genomes for three novel species from Candidatus Angelobacter (a proposed subdivision 1 Acidobacterial genus), a genus that is genomically enriched in genes for specialized metabolite biosynthesis. Acidobacteria were particularly abundant in the vernal pool sediments, and a Ca. Angelobacter species was the most abundant bacterial species detected in some samples. We identified numerous diverse biosynthetic gene clusters in these genomes, and also in five additional genomes from other publicly available soil metagenomes for other related Ca. Angelobacter species. Metabolic analysis indicates that Ca. Angelobacter likely are aerobes that ferment organic carbon, with potential to contribute to carbon compound turnover in soils. Using metatranscriptomics, we identified in situ metabolic activity and expression of specialized metabolic traits for two species from this genus. In conclusion, we expand genomic sampling of the uncultivated Ca. Angelobacter, and show that they represent common and sometimes highly abundant members of dry and saturated soil communities, with a high degree of capacity for synthesis of diverse specialized metabolites.