Microbiomes Reduce Their Host's Sensitivity to Interspecific Interactions

Abstract

Bacteria associated with eukaryotic hosts can affect host fitness and trophic interactions between eukaryotes, but the extent to which bacteria influence the eukaryotic species interactions within trophic levels that modulate biodiversity and species coexistence is mostly unknown. Here, we used phytoplankton, which are a classic model for evaluating interactions between species, grown with and without associated bacteria to test whether the bacteria alter the strength and type of species interactions within a trophic level. We demonstrate that host-associated bacteria alter host growth rates and carrying capacity. This did not change the type but frequently changed the strength of host interspecific interactions by facilitating host growth in the presence of an established species. These findings indicate that microbiomes can regulate their host species' interspecific interactions. As between-species interaction strength impacts their ability to coexist, our findings show that microbiomes have the potential to modulate eukaryotic species diversity and community composition.IMPORTANCE Description of the Earth's microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

Keywords: biodiversity; eukaryotic species interactions; microbiome; species coexistence.

FIG 1

(A) Micrographs depicting the presence and absence of phytoplankton-associated bacteria prior to and after using our axenification protocol on Chlorella sorokiniana. Samples were stained with DAPI (4′,6-diamidino-2-phenylindole) and viewed at a ×100 magnification with an oil immersion lens on a Zeiss AxioImager M2 epifluorescence microscope. Bacteria and phytoplankton were visualized under a DAPI filter (bandpass, 450- to 490-nm excitation; long pass, 515-nm emission). See micrographs of the other phytoplankton species in Fig. S1 in the supplemental material. (B) Gel electrophoresis analysis of xenic and axenic phytoplankton cultures, with 16S rRNA gene amplification on the top and 18S rRNA gene amplification on the bottom. Lanes: 1, 1-kb ladder; 2 and 3, axenic and xenic Scenedesmus acuminatus, respectively; 4 and 5, axenic and xenic Coelastrum microporum, respectively; 6 and 7, axenic and xenic Monoraphidium minutum, respectively; 8 and 9, axenic and xenic Oocystis polymorpha, respectively; 10 and 11, axenic and xenic Chlorella sorokiniana, respectively; 12 and 13, axenic and xenic Selenastrum capricornutum, respectively. Negative template controls (lane 14) and a positive template control of extracted DNA from quagga mussel (Dreissena bugensis) and its associated bacteria (lane 15) were also included.

FIG 2

Host-associated bacterial communities alter the strength but not the type of ecological interactions between hosts. Ecological interactions between phytoplankton species ranged from competitive interactions (decreased growth rate relative to that of monoculture) to facilitative interactions (increased growth rate compared to that of monoculture). From left to right, growth rates are for Coelastrum microporum (C.m.), Selenastrum capricornutum (S.c.), Monoraphidium minutum (M.m.), and Scenedesmus acuminatus (S.a.). Phytoplankton-associated bacterial communities frequently altered the rate of exponential growth of their phytoplankton host during the first 26 h postinoculation both in monocultures and when introduced at a low density into (i.e., invading) an established phytoplankton culture (biculture) via linear regression. In addition to this model incorporating all species combinations, asterisks indicate for which species combinations the axenic status significantly affected the growth rate, as determined using two-sample t tests on subsets of the data. A red asterisk indicates a P value of <0.05, and a black asterisk indicates a P value of <0.10.

FIG 3

Host-associated bacterial communities reduce their host’s sensitivity to interspecific interactions. Using a layout that is parallel to that used in Fig. 2, we showed that host-associated bacteria had either no effect on interactions between their hosts or a facilitative effect on the growth of the host when rare by decreasing the rare phytoplankton host’s sensitivity to interspecific interactions. The y axis shows the difference between each host’s sensitivity to interaction in the xenic versus axenic treatment, where sensitivity (S_i) is equal to (μ_i,alone − μ_i,invading)/μ_i,alone. The axenic status significantly affected the S_i values according to our linear model, which was run on all four panels of data using the original S_i values of xenic and axenic cultures rather than the subtracted values. In addition to this model incorporating all species combinations, asterisks indicate for which species combinations the axenic status significantly (P < 0.05) affected sensitivity to the established species, as determined using one-sample t tests on subsets of the data.