Dataset Information

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters.

ABSTRACT: Numerous ecological processes, such as bacteriophage infection and phytoplankton-bacterial interactions, often occur via strain-specific mechanisms. Therefore, studying the causes of microbial dynamics should benefit from highly resolving taxonomic characterizations. We sampled daily to weekly over 5 months following a phytoplankton bloom off Southern California and examined the extent of microdiversity, that is, significant variation within 99% sequence similarity clusters, operational taxonomic units (OTUs), of bacteria, archaea, phytoplankton chloroplasts (all via 16S or intergenic spacer (ITS) sequences) and T4-like-myoviruses (via g23 major capsid protein gene sequence). The extent of microdiversity varied between genes (ITS most, g23 least) and only temporally common taxa were highly microdiverse. Overall, 60% of taxa exhibited microdiversity; 59% of these had subtypes that changed significantly as a proportion of the parent taxon, indicating ecologically distinct taxa. Pairwise correlations between prokaryotes and myoviruses or phytoplankton (for example, highly microdiverse Chrysochromulina sp.) improved when using single-base variants. Correlations between myoviruses and SAR11 increased in number (172 vs 9, Spearman>0.65) and became stronger (0.61 vs 0.58, t-test: P<0.001) when using SAR11 ITS single-base variants vs OTUs. Whole-community correlation between SAR11 and myoviruses was much improved when using ITS single-base variants vs OTUs, with Mantel rho=0.49 vs 0.27; these results are consistent with strain-specific interactions. Mantel correlations suggested >1??m (attached/large) prokaryotes are a major myovirus source. Consideration of microdiversity improved observation of apparent host and virus networks, and provided insights into the ecological and evolutionary factors influencing the success of lineages, with important implications to ecosystem resilience and microbial function.

SUBMITTER: Needham DM

PROVIDER: S-EPMC5520149 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters.

Needham David M DM Sachdeva Rohan R Fuhrman Jed A JA

The ISME journal 20170411 7

Numerous ecological processes, such as bacteriophage infection and phytoplankton-bacterial interactions, often occur via strain-specific mechanisms. Therefore, studying the causes of microbial dynamics should benefit from highly resolving taxonomic characterizations. We sampled daily to weekly over 5 months following a phytoplankton bloom off Southern California and examined the extent of microdiversity, that is, significant variation within 99% sequence similarity clusters, operational taxonomi ...[more]

PMID: 28398348

Similar Datasets

Project description:Rising atmospheric CO 2 and ocean acidification are fundamentally altering conditions for life of all marine organisms, including phytoplankton. Differences in CO 2 related physiology between major phytoplankton taxa lead to differences in their ability to take up and utilize CO 2. These differences may cause predictable shifts in the composition of marine phytoplankton communities in response to rising atmospheric CO 2. We report an experiment in which seven species of marine phytoplankton, belonging to four major taxonomic groups (cyanobacteria, chlorophytes, diatoms, and coccolithophores), were grown at both ambient (500 μatm) and future (1,000 μatm) CO 2 levels. These phytoplankton were grown as individual species, as cultures of pairs of species and as a community assemblage of all seven species in two culture regimes (high-nitrogen batch cultures and lower-nitrogen semicontinuous cultures, although not under nitrogen limitation). All phytoplankton species tested in this study increased their growth rates under elevated CO 2 independent of the culture regime. We also find that, despite species-specific variation in growth response to high CO 2, the identity of major taxonomic groups provides a good prediction of changes in population growth and competitive ability under high CO 2. The CO 2-induced growth response is a good predictor of CO 2-induced changes in competition (R2 > .93) and community composition (R2 > .73). This study suggests that it may be possible to infer how marine phytoplankton communities respond to rising CO 2 levels from the knowledge of the physiology of major taxonomic groups, but that these predictions may require further characterization of these traits across a diversity of growth conditions. These findings must be validated in the context of limitation by other nutrients. Also, in natural communities of phytoplankton, numerous other factors that may all respond to changes in CO2, including nitrogen fixation, grazing, and variation in the limiting resource will likely complicate this prediction.

Project description:Disentangling the role of competition in regulating the distribution of sympatric species can be difficult because species can have different habitat preferences or time use that introduce non-random patterns that are not related to interspecific interactions. We adopted a multi-step approach to systematically incorporate habitat preferences while investigating the co-occurrence of two presumed competitors, morphologically similar, and closely related ground-dwelling birds: the brown tinamou (Crypturellus obsoletus) and the tataupa tinamou (C. tataupa). First, we used single-species occupancy models to identify the main landscape characteristics affecting site occupancy, while accounting for detection probability. We then used these factors to control for the effect of habitat while investigating species co-occurrence. In addition, we investigated species present-time partitioning by measuring the degree of overlap in their activity time. Both species were strictly diurnal and their activity time highly overlapped (i.e., the species are not present-time partitioning). The distribution of the two species varied across the landscape, and they seemed to occupy opposite portions of the study area, but co-occurrence models and species interaction factors suggested that the tinamous have independent occupancy and detection. In addition, co-occurrence models that accounted for habitat performed better than models without habitat covariates. The observed co-occurrence pattern is more likely related to habitat preferences, wherein species segregated by elevation. These results provide evidence that habitat characteristics can play a bigger role than interspecific interactions in regulating co-existence of some species. Therefore, exploring habitat preferences while analyzing co-occurrence patterns is essential, in addition to being a feasible approach to achieve more accurate estimation of parameters reflecting species interactions. Occupancy models can be a valuable tool in such modeling.

Dataset Information

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters.

Publications

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets