Changes in Microbiome Activity and Sporadic Viral Infection Help Explain Observed Variability in Microcosm Studies

Abstract

The environmental conditions experienced by microbial communities are rarely fully simulated in the laboratory. Researchers use experimental containers (“bottles”), where natural samples can be manipulated and evaluated. However, container-based methods are subject to “bottle effects”: changes that occur when enclosing the plankton community that are often times unexplained by standard measures like pigment and nutrient concentrations. We noted variability in a short-term, nutrient amendment experiment during a 2019 Lake Erie, Microcystis spp. bloom. We observed changes in heterotrophic bacteria activity (transcription) on a time-frame consistent with a response to experimental changes in nutrient availability, demonstrating how the often overlooked microbiome of cyanobacterial blooms can be altered. Samples processed at the time of collection (T0) contained abundant transcripts from Bacteroidetes, which reduced in abundance during incubation in all bottles, including controls. Significant biological variability in the expression of Microcystis-infecting phage was observed between replicates, with phosphate-amended treatments showing a 10-fold variation. The expression patterns of Microcystis-infecting phage were significantly correlated with ∼35% of Microcystis-specific functional genes and ∼45% of the cellular-metabolites measured across the entire microbial community, suggesting phage activity not only influenced Microcystis dynamics, but the biochemistry of the microbiome. Our observations demonstrate how natural heterogeneity among replicates can be harnessed to provide further insight on virus and host ecology.

A tale of two blooms: do ecological paradigms for algal bloom success and succession require revisiting?

“…Blooms dominate the western basin nearly every summer incurring consequences for ecosystem and human health while capturing the attention of the popular press ( Fig. 1 ) ( Ames et al, 2019 ; Bridgeman et al, 2013 ; Pound et al, 2022 ; Rinta-Kanto et al, 2009a ; Steffen et al, 2017 ). While Microcystis spp.…”

Sulfolipid substitution ratios of Microcystis aeruginosa and planktonic communities as an indicator of phosphorus limitation in Lake Erie

“…The moderating effect of N amendments on the substitution ratio was possibly due to N‐induced shifts in heterotrophic community composition. N‐amended bottles tended to experience a larger increase in transcription by heterotrophic bacteria compared to control than seen in cyanobacteria (Pound et al 2022). This could have had the effect of reducing the SQDG : PG ratio.…”

“…Physicochemical properties of the lake water column were measured using an EXO2 multiparameter sonde (YSI, Inc.) at time of water collection. Homogenized water was aliquoted into twenty‐one 1.2‐liter polycarbonate bottles and subjected to four nutrient addition treatments: 1 μ M P as KH 2 PO 4 : K 2 HPO 4 (Wilhelm et al 2003; Belisle et al 2016), and 180 μ M‐N as either KNO 3 , NH 4 Cl, or urea (Pound et al 2022). P additions were conducted in triplicate.…”

Manipulation of the seagrass‐associated microbiome reduces disease severity

“…Statistical analyses of microbiome data were conducted separately for each year because different primer sets were used. Microbiome data from field surveys and lab experiments were also analysed separately because microbial communities change in lab experiments (Pound et al, 2022), and this change was more pronounced in 2018 when the experimental design included the low salinity rinse.…”