Contribute to Temporal Changes in Microbial Diversity Conditionally Rare Taxa Disproportionately 2014

Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial “rare biosphere” to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community membership, represented a broad diversity of bacterial and archaeal lineages, and explained large amounts of temporal community dissimilarity (i.e., up to 97% of Bray-Curtis dissimilarity). Most of the CRT were detected at multiple time points, though we also identified “one-hit wonder” CRT that were observed at only one time point. Using a case study from a temperate lake, we gained additional insights into the ecology of CRT by comparing routine community time series to large disturbance events. Our results reveal that many rare taxa contribute a greater amount to microbial community dynamics than is apparent from their low proportional abundances. This observation was true across a wide range of ecosystems, indicating that these rare taxa are essential for understanding community changes over time. IMPORTANCE Microbial communities and their processes are the foundations of ecosystems. The ecological roles of rare microorganisms are largely unknown, but it is thought that they contribute to community stability by acting as a reservoir that can rapidly respond to environmental changes. We investigated the occurrence of typically rare taxa that very occasionally become more prominent in their communities (“conditionally rare”). We quantified conditionally rare taxa in time series from a wide variety of ecosystems and discovered that not only were conditionally rare taxa present in all of the examples, but they also contributed disproportionately to temporal changes in diversity when they were most abundant. This result indicates an important and general role for rare microbial taxa within their communities. Received 27 May 2014 Accepted 16 June 2014 Published 15 July 2014 Citation Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA. 2014. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio 5(4):e01371-14. doi:10.1128/mBio.01371-14. Editor Nicole Dubilier, Max Planck Institute for Marine Microbiology Copyright © 2014 Shade et al. This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Address correspondence to Jack A. Gilbert, gilbertjack@anl.gov. Microbial communities predominate Earth’s diverse ecosystems, contributing immense biomass and underpinning integral biogeochemical processes. They sustain the bases of food webs, provide key natural products that support human health and energy needs, and recycle carbon and nutrients that would otherwise stagnate. Despite the central role of microbial communities in biological systems, we are just beginning to understand the intricate interactions between their members and how these interactions contribute to ecosystem functions. Of particular interest is the role of rare microorganisms within a community, which make up the majority of the observed membership at any given time (1–5) (see Fig. S1 in the supplemental material). Determining whether these taxa remain rare or periodically bloom to abundance will change our understanding of each organism’s role in microbially mediated ecosystem functions and, importantly, in the stability of ecosystems in general. Rare microbial community members encompass an immense diversity (the “rare biosphere”) (6–9). Still, the ecological roles of the vast majority of rare microorganisms remain unclear. Some rare microorganisms are likely on their way to local extinction (8) or are transient taxa that are “passing through” an environment (10–13). Some rare taxa may even be active, providing important functions that are disproportionate to their abundance or growth rate (14–16), and others may be dormant or inactive, awaiting favorable environmental conditions to grow (17, 18). An increase in the abundance of rare microorganisms that “wait” for favorable environmental conditions could be attributed to growth from low abundance, to awakening from dormancy, or to differential surRESEARCH ARTICLE July/August 2014 Volume 5 Issue 4 e01371-14 ® mbio.asm.org 1 m b.asm .rg on A uust 5, 2014 P ubished by m b.asm .rg D ow nladed fom vival (i.e., escape from predation). Though there are a variety of ecological explanations for rare-to-prevalent dynamics, we still lack general empirical documentation of the phenomenon among microbial communities, and so their general incidence remains uncertain. Because rare microbial taxa are difficult to observe, even less is known about their dynamics than is known about their ecological roles. A key unknown is how often rare taxa become abundant and hence play a potentially greater role in the ecology of a given system. However, there are a small but growing number of studies that have documented the dynamics of rare microbial taxa and provide some insights. For example, in the Arctic Ocean, rare microorganisms exhibited biogeography, indicating that some rare taxa, like more abundant taxa, have distributions based on their ecological requirements (19). In a sulfide-rich artesian spring, rare taxa exhibited patchiness over 1 mm (20), which also suggests that rare taxa can have clear distributions at fine spatial scales. Additionally, some coastal sand communities have rare members that do not often become abundant, suggesting that these members have a minimal influence on biogeochemical processes (21). Conversely, in other coastal sand communities, rare microbial taxa were shown to be as sensitive as prevalent taxa to environmental changes caused by an off-shore oil spill (22). The discrepancy between the latter two studies highlights our modest knowledge of the potential contributions of rare taxa and especially calls into question whether such conclusions are transferable to other ecosystems. Therefore, to understand the general importance of rare microbial taxa, their contributions to the larger community and their dynamics, we must systematically interrogate microbial communities from a variety of ecosystems by using consistent methods. The availability of inexpensive, high-throughput sequencing technologies has led to an increased number of temporal studies of microbial communities (23). One of these studies identified a microbial taxon that bloomed to abundance from an apparently persistently rare state (24, 25). The dynamic of rarity to prevalence has also been observed in two other studies of marine bacterioplankton (14, 26). Here, we asked how the pattern of microbial rarity to prevalence is manifested in communities inhabiting very different ecosystems. We refer to microbial taxa that are typically in low abundance in one locality but occasionally become prevalent over time as “conditionally rare.” Our objective was to understand the incidence of conditionally rare taxa (CRT) and their contribution to changes in microbial communities through time. We introduce a simple method for identifying CRT from temporal studies of diverse microbial communities and apply this method to a suite of time series data sets generated by using 454 pyrosequencing or Illumina sequencing of 16S rRNA gene fragments. Each data set contained a large percentage of very rare taxa, as typical for microbial communities (see Fig. S1 in the supplemental material). These data sets were previously analyzed by using a closed-reference operational taxonomic unit (OTU)-picking protocol (27) for direct comparison of their temporal patterns (see Table S1 in the supplemental material) (28). Because this OTU-picking protocol discards reads that do not match reference sequences at a minimum of 97% identity, it minimizes the rare OTUs arising from sequencing or PCR errors. The closed-reference protocol also avoids the “OTU splitting” that may occur when OTUs are defined by using a de novo protocol. We show that within many ecosystems, CRT contributed to temporal patterns of microbial diversity disproportionately to their relative abundances, suggesting an important role for CRT in structuring microbial communities over time. We also explicitly examine the influences of sampling frequency, study duration, and sequencing depth on the detection of CRT.