Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats

Abstract

The bacterial phylum Verrucomicrobia was formally described two decades ago and originally believed to be a minor member of many ecosystems; however, it is now recognized as ubiquitous and abundant in both soil and aquatic systems. Nevertheless, knowledge of the drivers of its relative abundance and within-phylum habitat preferences remains sparse, especially in lake systems. Here, we documented the distribution of Verrucomicrobia in 12 inland lakes in Southeastern Michigan, a Laurentian Great Lake (Lake Michigan), and a freshwater estuary, which span a gradient in lake sizes, depths, residence times, and trophic states. A wide range of physical and geochemical parameters was covered by sampling seasonally from the surface and bottom of each lake, and by separating samples into particle-associated and free-living fractions. On average, Verrucomicrobia was the 4th most abundant phylum (range 1.7-41.7%). Fraction, season, station, and depth explained up to 70% of the variance in Verrucomicrobia community composition and preference for these habitats was phylogenetically conserved at the class-level. When relative abundance was linearly modeled against environmental data, Verrucomicrobia and non-Verrucomicrobia bacterial community composition correlated to similar quantitative environmental parameters, although there were lake system-dependent differences and > 55% of the variance remained unexplained. A majority of the phylum exhibited preference for the particle-associated fraction and two classes (Opitutae and Verrucomicrobiae) were identified to be more abundant during the spring season. This study highlights the high relative abundance of Verrucomicrobia in north temperate lake systems and expands insights into drivers of within-phylum habitat preferences of the Verrucomicrobia.

Fig 1. Maps of sampling site locations.

(A) Inland lakes (yellow), (B) Lake Michigan (red), and (C) Muskegon Lake (orange), with (D) the locations displayed together. Map created using the U.S. Geological Survey, National Geospatial Program, National Map Viewer.

Fig 2. Verrucomicrobia relative abundance box-and-whisker plot and inverse Simpson.

Verrucomicrobia relative abundance is illustrated in samples categorized by lake type and (A) sampling depth, (B) season, or (C) fraction. Inverse Simpson averaged from 100 trials is illustrated in samples categorized by lake type and (D) sampling depth, (E) season, or (F) fraction. Red asterisks indicate significance between all samples in the panel. Red plus signs indicate significance of one subset of samples within the panel.

Fig 3. Principal coordinates analysis (PCoA) ordinations (first two principal coordinates are displayed) based on Bray-Curtis dissimilarity.

PCoAs visualizing the compositional differences of (A-C) the verrucomicrobial and (D-F) the whole bacterial community in Laurentian, estuary, and inland lake samples, respectively. Data points are colored by season, shaped by depth, and filled in by fraction. Axis labels include the % variation captured by the respective dimension of the ordination.

Fig 4. Verrucomicrobia phylogenetic tree and OTU habitat preferences.

Only OTUs with a significant preference in at least one habitat were displayed. Habitats were categorized based on depth (surface, bottom, sediment), lake type (Laurentian, estuary, inland), fraction (particle, free), and season (spring, summer, fall). The tree is colored by verrucomicrobial class.