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ABSTRACT Desert kangaroo rats (Dipodomys deserti) construct burrows that can create micro-niches favorable to increased microbial activity. The aim of this study was to characterize the bacterial communities found in kangaroo rat burrows, in proximal desert surface sand, and in samples from kangaroo rats. We collected samples from burrow ceilings of actively inhabited burrows, from burrows that were no longer in use, and from the proximal surface sand in the Sonoran Desert, Yuma, AZ. Following DNA extraction from samples, 16S rRNA gene sequencing was performed, and functional predictions were made and assessed for each characterized bacterial community. Active burrow samples exhibited greater alpha diversity but similar beta diversity when compared to surface sand (P< 0.05), with no significant differences observed between abandoned and active burrows. Bacterial genera and genes related to nitrogen fixation, nitrification, and urea hydrolysis were found in significantly higher abundance in active burrows compared to the surface sand (P< 0.05). The core microbiome of active burrow samples was different from surface sand, including higher abundances ofAcidimicrobialesandAcidobacteriasubdivision Gp7. Active burrow samples included 30 unique genera. Kangaroo rat anal swabs shared 12, cheek pouches shared 6 unique genera with burrows. These findings suggest that kangaroo rats can shape the microbial composition of their burrow environment through the introduction of food material and waste, facilitating increased species richness and bacterial diversity.IMPORTANCEAnimals can alter soil parameters, including microbial composition through burrowing activities, excretion, and dietary composition. Desert kangaroo rats (Dipodomys deserti) construct burrows within loose desert sand that have microclimatic conditions different from the surrounding desert climate. In this study, we explored the effect of disturbance from kangaroo rat activities on the bacterial composition of sand. We compared the bacterial community compositions of kangaroo rat (D. deserti) samples, their burrows, and the proximal surface sand. The results showed that burrow sand shows higher richness and diversity of bacterial community with higher abundances of bacterial genera and genes associated with nitrogen fixation, nitrification, and urea hydrolysis compared to the surface sand. These findings suggest that kangaroo rats affect the microbial composition of their burrow environment through the introduction of food material and waste.
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Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression
Abstract Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species’ divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species’ pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.
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- Award ID(s):
- 2019589
- PAR ID:
- 10400108
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- The ISME Journal
- Volume:
- 17
- Issue:
- 6
- ISSN:
- 1751-7362
- Format(s):
- Medium: X Size: p. 813-822
- Size(s):
- p. 813-822
- Sponsoring Org:
- National Science Foundation
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