Adaptive Radiation by Waves of Gene Transfer Leads to Fine-Scale Resource Partitioning in Marine Microbes

ARTICLE Received 25 Feb 2016 | Accepted 9 Aug 2016 | Published 22 Sep 2016 DOI: 10.1038/ncomms12860 OPEN Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes Jan-Hendrik Hehemann1,w,*, Philip Arevalo2,*, Manoshi S. Datta3,*, Xiaoqian Yu4, Christopher H. Corzett1, Andreas Henschel1,w, Sarah P. Preheim1,w, Sonia Timberlake5,w, Eric J. Alm1,5,6 & Martin F. Polz1 Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Pathway architecture is predictive of function and ecology, under- scoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes. 1 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. 2 Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. 3 Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. 4 Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. 5 Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA. 6 Broad Institute, Cambridge, Massachusetts 02139, USA. w Present addresses: MARUM Center for Marine Environmental Sciences, University of Bremen Max Planck Institute for Marine Microbiology, Celsiusstrae 1, 28359 Bremen, Germany (J.-H.H.); Department of Electrical Engineering and Computer Science/Institute Center Smart Infrastructure (iSmart), Masdar Institute, 54224 Abu Dhabi, United Arab Emirates (A.H.); Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA (S.P.P.); AbVitro, Inc. 27 Drydock Ave, Boston, Massachusetts, USA (S.T.). * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to M.F.P. (email: [email protected]). NATURE COMMUNICATIONS | 7:12860 | DOI: 10.1038/ncomms12860 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms12860 daptive radiations are thought to have played an algal glycan alginate as having undergone extensive evolutionary important role in the diversification of life. They manifest changes across the majority of populations (Fig. 1a,b; Supple- Aas rapid ecological differentiation of a single clade of mentary Fig. 1). These include both population-specific presence organisms in response to ecological opportunity thought to arise and absence of the pathway, as well as major differences in its primarily from resource availability following extinctions or architecture. For example, several populations contain a canonical colonization of new habitats1,2. A prime example are Darwin’s pathway consisting of four polysaccharide lyase (PL) families14, finches, which quickly diverged from a single ancestor into while others lack up to three of the four lyase families (Fig. 1b). several, locally adapted species on the Galapagos Islands due to These four families perform different molecular functions in the evolvability of beak shape, which allowed rapid adaptation to alginate pathway: alginate lyases (Aly) PL6 and PL7 initiate the novel resources. In recent years, laboratory evolution and extracellular lysis of the polymer, and members of two mesocosm studies using microbes have provided experimental oligoalginate lyase (Oal) families PL15 and PL17 complete support for ecological opportunity triggering adaptive degradation into monomers15–18. The latter two gene families radiations3–6. However, for microbes in the wild, adaptive are the keystone carbohydrate active enzymes19 of the core radiations, both ancient and recent, have remained difficult to pathway, since they generate sugar monomers that can be further document. First, the details of ancient diversifications are nearly catabolized, and their absence abolishes pathway functionality. impossible to reconstruct, since past ecological opportunities are These initial observations suggested the possibility of a fine- often unknowable, and horizontal gene transfer (HGT) can erode grained analysis of the evolutionary history and potential adaptive phylogenetic signal. Furthermore, it is even questionable whether significance of the alginate pathway differentiation. adaptive radiations might be possible in contemporary environments, considering that the long co-evolutionary history of microbes and their resources has led to high niche filling6.Asa Pathways have assembled primarily horizontally. Cursory consequence, we do not know genetic mechanisms and ecological inspection of the alginate pathway across our Vibrionaceae opportunities that could give rise to adaptive radiations in populations appears consistent with an ancient, single HGT since complex natural environments. a core set of alginate degradation genes is present in a majority of Here we ask whether a group of very closely related but the clade including the deeply branching Aliivibrio (Fig. 1a; ecologically differentially associated bacterial populations show Supplementary Figs 1 and 2). However, detailed phylogenetic the characteristics of an adaptive radiation, including rapid reconstruction (Methods) that includes an additional 395 diversification of a single clade into multiple, ecologically high-quality genomes obtained from Genbank for reference differentiated clades, associated with traits adaptive towards (Supplementary Fig. 3) reveals an unexpectedly complex history environmental opportunities1. These populations were originally (Fig. 1d,e). In most cases, multiple copies of each alginate lyase identified as genotypic clusters in protein-coding marker genes family represent independently evolving subfamilies that did not with differential distribution among size fractions within the arise by duplication within the Vibrionaceae (see Methods for same water samples indicating association with different resource statistical support for definition of subfamiles). In fact, there is types such as dissolved or particulate organic matter and zoo- or little vertical descent and the majority of clades with alginate phytoplankton7–10. Subsequent work has established that these degradation pathways acquired both Oal and Aly genes hor- clusters also act as gene flow11, social12 and behavioural13 units izontally (Fig. 1d,e). Across all our populations, transfer of Oal suggesting that they possess many attributes commonly genes was so common that every population exchanged at least associated with sexual species. However, because our sampling one gene copy with at least one other population (Fig. 1d). Even scheme considers only bacteria co-existing in small-scale among the seven closely related populations of the crown group microhabitats, we designate them as populations to which we we estimate three independent initial acquisitions of Oal assign species names if a previously described type strain falls subfamilies from a variety of sources followed by lateral spread within the genotypic cluster identified as a distinct population. among populations and acquisitions of new subfamilies Our test case is a clade of very closely related Vibrionaceae (Fig. 1a,d). Moreover, Alys and Oals are distributed across isolates, which we previously hypothesized to comprise at least multiple regions on chromosome 1, chromosome 2 and a putative seven recently speciated populations based on their genetic and extrachromosomal element in one Vibrio breoganii (FF50) and environmental structure. We show that this clade rapidly one Vibrio sp. F13 (9CS106) isolate with nearly closed genomes. diversified into population-specific ecophysiological types specia- These regions are significantly enriched in genes annotated as lized for the degradation of different physical manifestations mobile elements, transposases and integrases (hypergeometric (chain length, solubility and concentration) of the same algal test, P ¼ 0.0019). Some of these regions also display significantly glycan. This specialization is manifest as unique pathway decreased GC content consistent with the recent introduction of configurations that arose by extensive horizontal gene transfer foreign DNA (Supplementary Table 1). Hence multiple lines of and are highly predictive of metabolic performance. We first evidence reject the seemingly ancient acquisition and subsequent reconstruct the evolution of the different pathway types and vertical modification of the core pathway and instead suggest characterize their physiological properties. We then show that multiple recent acquisitions and transfers. environmental associations are consistent with the physiological The core pathway of Oals was extended in a surprisingly rapid predictions and propose a model of glycan degradation involving and complex sequence of events by independent acquisitions and the evolution of interacting populations.

Load more