Title: Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

Abstract

ABSTRACT Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within the dominant leaf litter bacterium, Curtobacterium , which comprises 7.8% of the bacterial community at a grassland site undergoing global change manipulations. We use cultured bacterial isolates to interpret metagenomic data, collected in situ over 2 years, together with lab-based physiological assays to determine the extent of trait variation within this abundant OTU. The response of Curtobacterium to seasonal variability and the global change manipulations, specifically an increase in relative abundance under decreased water availability, appeared to be conserved across six Curtobacterium lineages identified at this site. Genomic and physiological analyses in the lab revealed that degradation of abundant polymeric carbohydrates within leaf litter, cellulose and xylan, is nearly universal across the genus, which may contribute to its high abundance in grassland leaf litter. However, the degree of carbohydrate utilization and temperature preference for this degradation varied greatly among clades. Overall, we find that traits within Curtobacterium are conserved at different phylogenetic depths. Wemore » speculate that similar to bacteria in marine systems, diverse microbes within this taxon may be structured in distinct ecotypes that are key to understanding Curtobacterium abundance and distribution in the environment. IMPORTANCE Despite the plummeting costs of sequencing, characterizing the fine-scale genetic diversity of a microbial community—and interpreting its functional importance—remains a challenge. Indeed, most studies, particularly studies of soil, assess community composition at a broad genetic level by classifying diversity into taxa (OTUs) defined by 16S rRNA sequence similarity. However, these classifications potentially obscure variation in traits that result in fine-scale ecological differentiation among closely related strains. Here, we investigated “microdiversity” in a highly diverse and poorly characterized soil system (leaf litter in a southern Californian grassland). We focused on the most abundant bacterium, Curtobacterium , which by standard methods is grouped into only one OTU. We find that the degree of carbohydrate usage and temperature preference vary within the OTU, whereas its responses to changes in precipitation are relatively uniform. These results suggest that microdiversity may be key to understanding how soil bacterial diversity is linked to ecosystem functioning.« less

Authors:

Chase, Alexander B. ^[1]; Karaoz, Ulas  ^[2];

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Brodie, Eoin L. ^[2]; Gomez-Lunar, Zulema ^[3]; Martiny, Adam C. ^[4]; Martiny, Jennifer B. H. ^[1]; Zhou, ed., Jizhong; Hawkes, Christine; Buckley, Daniel

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+ Show Author Affiliations

1. Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
2. Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
3. Department of Earth System Science, University of California, Irvine, California, USA
4. Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA, Department of Earth System Science, University of California, Irvine, California, USA

Publication Date:

Fri Dec 29 00:00:00 EST 2017

Research Org.:

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:

1437767

Alternate Identifier(s):

OSTI ID: 1432219

Grant/Contract Number:  

SC-SC0016410; PS02-09ER09-25; AC02-05CH11231; SC0016410

Resource Type:

Published Article

Journal Name:

mBio

Additional Journal Information:

Journal Name: mBio Journal Volume: 8 Journal Issue: 6; Journal ID: ISSN 2161-2129

Publisher:

American Society for Microbiology

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; Actinobacteria; Curtobacterium; Microbacteriaceae; drought; ecotypes; glycoside hydrolases; nitrogen addition