Abstract
Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages displayed the highest gamma-diversity. Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta- diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.
Highlights
Bacteria are the most diverse organisms on the planet [1]
Sample processing, sequencing, and core amplicon data analysis were performed by the Earth Microbiome Project, and all amplicon sequence data and metadata have been made public through the data portal
Because salinity influences bacterial community composition [18], we further tested whether taxon richness varied between non-saline and saline habitats
Summary
Bacteria are the most diverse organisms on the planet [1]. Bacterial richness and composition influences ecosystem functioning, whether in host-associated communities, soils, or oceans [2,3,4,5,6,7]. We have yet to answer a number of basic questions about bacterial diversity, including “Which habitats contain the highest diversity of bacteria?” More broadly, evaluating geographic patterns in biodiversity across habitats and spatial scales can illuminate the processes influencing and consequences of biodiversity [8,9,10,11,12]. While many studies document spatial patterns of bacterial diversity, most are restricted to a particular geographic region or habitat, such as soil, sediment, or water [13,14,15]. The Earth Microbiome Project (EMP) comprises 27,751 samples from 97 studies from a wide range of habitats and geographic regions that are processed in the exact same way [16].
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