High Resolution Time Series Reveals Cohesive but Short-Lived Communities in Coastal Plankton

ARTICLE DOI: 10.1038/s41467-017-02571-4 OPEN High resolution time series reveals cohesive but short-lived communities in coastal plankton Antonio M. Martin-Platero1,6, Brian Cleary2,3, Kathryn Kauffman 1, Sarah P. Preheim1,7, Dennis J. McGillicuddy, Jr4, Eric J. Alm1,2,5 & Martin F. Polz1 Because microbial plankton in the ocean comprise diverse bacteria, algae, and protists that are subject to environmental forcing on multiple spatial and temporal scales, a fundamental 1234567890():,; open question is to what extent these organisms form ecologically cohesive communities. Here we show that although all taxa undergo large, near daily fluctuations in abundance, microbial plankton are organized into clearly defined communities whose turnover is rapid and sharp. We analyze a time series of 93 consecutive days of coastal plankton using a technique that allows inference of communities as modular units of interacting taxa by determining positive and negative correlations at different temporal frequencies. This approach shows both coordinated population expansions that demarcate community boundaries and high frequency of positive and negative associations among populations within communities. Our analysis thus highlights that the environmental variability of the coastal ocean is mirrored in sharp transitions of defined but ephemeral communities of organisms. 1 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. 2 Broad Institute, Cambridge, MA 02139, USA. 3 Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. 4 Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA. 5 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. 6Present address: Department of Microbiology, University of Granada, Granada 18071, Spain. 7Present address: Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, MD 21218, USA. Antonio M. Martin- Platero and Brian Cleary contributed equally to this work. Correspondence and requests for materials should be addressed to E.J.A. (email: [email protected]) or to M.F.P. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:266 | DOI: 10.1038/s41467-017-02571-4 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-017-02571-4 ecause microbes in the surface waters of the ocean have key Because we use fixed-point (Eulerian) sampling, as has been Broles in global carbon and nutrient cycling, they have been standard in ocean time-series studies, our data integrate temporal under intense scrutiny, revealing an increasingly complete and spatial components of variability associated with the con- picture of their global taxonomic composition and functional tinuous movement of water masses via tidal cycles and ocean – repertoires (e.g., refs.1 3). What remains poorly understood, currents. To assess organismal diversity, we carried out Illumina- however, are spatio-temporal dynamics of the vast majority of based tag-sequencing of bacterial 16S and eukaryotic 18S rRNA taxa, which include diverse representatives from all domains of genes followed by identification of OTUs (Methods). To max- life, pursuing different ecological strategies. These include bac- imize ecological resolution of OTUs, we used distribution-based teria forming complex biofilms on different types of organic clustering (dbc), which does not assume a fixed sequence simi- particles or existing as free-living, single cells, and photosynthetic, larity cut-off to define OTUs but instead identifies the sequence filter-feeding, and predatory eukaryotic plankton. For these similarity at which clusters display cohesive behavior across organisms, ocean water represents a nutrient poor but highly samples17. This approach usually yields clusters comprising very heterogeneous ecological landscape on different spatial and closely related sequences and resulted in a total of 49,637 bacterial temporal scales with physical and chemical gradients ranging and eukaryotic OTUs, of which 9660 reoccurred on more than – from micrometers to kilometers4 6. For example, direct compe- 10 days. These recurrent OTUs were used to test the extent to titive or cooperative interactions may lead to rapid micro-scale which plankton are naturally organized into clusters of taxa with successions on suspended organic particles7, whereas large-scale correlated dynamics as expected for communities of interacting algal blooms may trigger growth of bacteria that degrade specific organisms. algal exudates8. Owing to the apparent difference in scales of such Initial analysis of the time series indicated relatively stable interactions, it remains unknown whether communities with dynamics across higher taxonomic ranks (phylum to family), but clearly defined boundaries in time and space can be identified very rapid, near daily fluctuations among both bacterial and across the entire plankton, or whether taxonomic turnover is eukaryotic OTUs (Fig. 1). Although a similar pattern was noted in more gradual and continuous, affecting limited groups of a shorter daily time series of coastal plankton on the US West organisms at a time. Coast16, our longer time series revealed another pervasive pattern: Analyses of time series of microbial plankton have to date been although many individual OTUs tended to persist at low relative equivocal towards the question of organization into cohesive abundance across the entire time series, they frequently showed communities. Although longer but sparsely sampled time series limited periods of expansion, during which they rose to higher have provided evidence for seasonal recurrence and successions relative abundance (on average, across the period of the of some microbial taxa (e.g., refs.9,10), such patterns have so far expansion), before returning to a low level. Such patterns have proven weak across the entire plankton and have provided no previously been described as seed bank dynamics18,19 and Fig. 2 – indication of sharp transitions11 13. In fact, more densely sam- shows a typical example of such variation of a eukaryotic pled but short time series have revealed brief and intense fluc- primary-producer (diatom) and bacterial heterotrophic (Flavo- tuations in relative abundance of operational taxonomic units bacteria) OTU, which both fluctuated at low levels during most of – (OTUs)14 16, which are the most highly resolved taxonomic units the time series but displayed higher amplitude of fluctuation in ribosomal RNA-based diversity studies. However, because during a limited period. These dynamics are consistent with current time series have either been longer but sparsely sampled ecological forcing acting at multiple temporal scales, wherein or densely sampled but short, their resolution is limited over time baseline carrying capacity for an OTU gradually increases at scales relevant for both detecting microbial growth and transi- larger temporal and spatial scales but biological interactions tions in ecological conditions so that associated community might induce shorter term fluctuations due to cooperation, – change had been difficult to constrain. We therefore reasoned succession, competition, and predation20 23. We therefore that to assess the extent of organization into communities over hypothesized that communities of interacting organisms should time, an extended high-resolution time series of bacterial and show coordinated expansions of OTUs over longer periods along eukaryotic plankton was necessary that could capture both rapid with more rapid fluctuations driven by direct positive or negative changes due to organismic interactions as well as longer range biotic interactions, together with environmental forcing. dynamics due to transitions in overall ecological conditions. Here we sample and analyze coastal bacterial and eukaryal plankton over 93 consecutive days and show that although Identifying microbial communities amidst high OTU varia- individual taxa fluctuate on near daily time scales, the amplitude tion. To allow for detection of such coordinated longer expan- of these fluctuations is characteristically greater during limited sions coupled to shorter term biotic and environmental time periods, indicating preferential growth. To determine whe- interactions, we developed a novel clustering method based on ther such temporally limited expansions are coordinated across wavelet analysis (WaveClust). As in previous applications to multiple taxa as expected from cohesively behaving communities, ecological time series22,24, wavelet analysis allowed us to we use wavelet-based analysis to establish correlations over dif- decompose each OTU time series into lower and higher fre- ferent time spans. This analysis shows that highly cohesive quency components, while maintaining both temporal resolution communities can be identified that are differentiated by envir- and phase information. This enables identification of temporally onmental and organismal features and that turnover rapidly on coordinated periods of low-frequency expansion in addition to the order of a few days. dynamics either due to positive or negative interactions at higher frequency where interactions here denote correlated dynamics. Given the information in each decomposed time series, we were Results specifically interested in defining pairwise interactions between Contrasting plankton dynamics at different taxonomic reso- OTUs

Load more