The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities

Gundersen, Madeleine S.; Morelan, Ian Arthur; Andersen, Tom; Bakke, Ingrid; Vadstein, Ôlav

doi:10.1101/2021.07.18.452870

Cited by 3 publications

(6 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S3). Our findings thereby contrast results from a continuous culture study in which periodical disturbance induced a shift towards a more deterministic assembly of microbial communities (28). However, another continuous culture experiment suggested that high species diversities in the starting communities increase the contribution of stochastic events during community assembly (29).…”

Section: Figure 2 Community Structures A) Overview Pcoa Biplot Includ...contrasting

confidence: 99%

The Cost of Adaptability: Resource Availability Constrains Functional Stability Under Pulsed Disturbances

Rain‐Franco

Peter

Moraes

et al. 2022

Preprint

View full text Add to dashboard Cite

Global change exposes ecosystems to changes in the frequency, magnitude and concomitancy of disturbances, which impact the composition and functioning. Here we experimentally evaluate effects of salinity disturbances and eutrophication on bacterial communities from coastal ecosystems. The resistance, resilience and functional stability of these communities is critically important for water quality, productivity and consequently ecosystem services, such as fishery yields. Yet, little is known about the underlying traits. Microbial functional stability can be maintained via resistance and resilience, which are reflected in genomic traits such as genome size and codon usage bias and may be linked to metabolic costs. To study the impact of pulsed disturbances on community assembly and functioning in dependence of metabolic costs, we performed a 41-days pulse disturbance experiment crossed with two levels of resource availability. Our setup triggered stochastic community re-assembly processes in all treatments. In contrast, we observed consistent and resource availability dependent patterns of superordinate community structural patterns and functioning, such as genomic trait distributions, species diversity, and functional resistance in response to disturbances. Genomic traits reflected the selection for taxa possessing resistant- and resilience-related traits, particularly under high nutrient availability. Our findings thereby mark an important step towards unraveling the compositional and genomic underpinnings of functional resistance in microbial communities after exposure to consecutive pulse disturbances. Our work demonstrates how resource availability alleviates metabolic constraints on resistance and resilience. This has important consequences for predicting water quality and ecosystem productivity of environments exposed to global change.

show abstract

Section: Figure 2 Community Structures A) Overview Pcoa Biplot Includ...contrasting

confidence: 99%

The Cost of Adaptability: Resource Availability Constrains Functional Stability Under Pulsed Disturbances

Rain‐Franco

Peter

Moraes

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…For each sample, the bacterial density was quantified using flow cytometry (BC Accuri C6) 12 . In brief, the bacterial communities were diluted in 0.1x TE buffer, mixed with 2x SYBR Green II RNA gel stain (ThermoFisher Scientific) and incubated in the dark at room temperature for 15 minutes.…”

Section: Quantification Of Bacterial Densitymentioning

confidence: 99%

“…The selection-switch dataset 12 was acquired directly from the author, in which the innoculum samples were discarded. The OTU reference sequences were aligned with SINA version 1.6.1 44 using the SILVA Release 138 NR 99 SSU dataset 45 .…”

Section: Alignment and Phylogentic Treementioning

confidence: 99%

“…The bacterial communities were sampled and characterised through 16S ribosomal DNA (rDNA) sequencing [13][14][15] at 18 time-points over a 50 day period. In contrast to many other microbiome experiments, in this experiment the authors determined bacterial density by flow cytometry 12 , even though these data were not mentioned in the article. As sequencing on its own only provides relative abundances of microbes in each, knowing bacterial densities allowed us to estimate absolute abundances.…”

Section: Introductionmentioning

confidence: 99%

“…To study interactions in rand K-selected communities, we analysed a 2x2 factorial crossover microcosm experiment that tested varying feeding regime and resource availability (high/low). 12 Briefly, half of the microcosms were pulse-fed resources which promotes the growth of r-strategists, whereas the other half received a steady, continuous supply of nutrients promoting K-strategists. We hereafter refer to these selection regimes as rand K-selection.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Robust bacterial co-occurence community structures are independent of r- and K-selection history

Pettersen

Gundersen

Almaas

2021

Preprint

Self Cite

View full text Add to dashboard Cite

Selection for bacteria which are K-strategists instead of r-strategists has been shown to improve fish health and survival in aquaculture. We considered an experiment where microcosms were inoculated with natural seawater and the selection regime was switched from K-selection (by continuous feeding) to r-selection (by pulse feeding) and vice versa. We found the networks of significant co-occurrences to contain clusters of taxonomically related bacteria having positive associations. Comparing this with the time dynamics, we found that the clusters most likely were results of similar niche preferences of the involved bacteria. In particular, the distinction between r- or K-strategists was evident. Each selection regime seemed to give rise to a specific pattern, to which the community converges regardless of its prehistory. Furthermore, the results proved robust to parameter choices in the analysis, such as the filtering threshold, level of random noise, replacing absolute abundances with relative abundances, and the choice of similarity measure. Even though our data and approaches cannot directly predict ecological interactions, our approach provides insights on how the selection regime affects the composition and workings of the microbial community, providing a basis for aquaculture experiments targeted at eliminating opportunistic fish pathogens.

show abstract

An exploration of the impact of phylogenetic tree structure on NTI and βNTI estimates of community assembly

Gundersen,

Vadstein

2023

Preprint

Self Cite

View full text Add to dashboard Cite

The nearest taxon index (NTI) and beta nearest taxon index (βNTI) are popular analytical tools for assessing the community assembly processes in a variety of ecosystems. However, the fundamental dependence of these models on the underlying phylogenetic tree is often overlooked and can potentially lead to erroneous conclusions. In this paper, we investigated how outlier sequences in the phylogenetic tree and reduction of the metacommunity richness affect estimates of the assembly processes. We estimated assembly in two datasets investigating fish-microbiota interactions. We found that outlier sequences can drastically change the interpretation of assembly processes. NTI consistently increased after outlier sequences were removed, which changed the ecological interpretation for 82.8% of the communities in one of the datasets. Similarly, βNTI was strongly affected by outliers in the phylogenetic tree, changing the ecological interpretation for 44.7% (Dataset 1) and 6.3% (Dataset 2) of the community comparisons. Lower metacommunity richness generally resulted in decreased NTI and increased βNTI, but the effect sizes were small and generally did not result in a change in ecological interpretation. This exploratory work highlights the need to assess the phylogenetic tree for spurious outlier sequences prior to null model analysis.

show abstract

The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities

Cited by 3 publications

References 56 publications

The Cost of Adaptability: Resource Availability Constrains Functional Stability Under Pulsed Disturbances

The Cost of Adaptability: Resource Availability Constrains Functional Stability Under Pulsed Disturbances

Robust bacterial co-occurence community structures are independent of r- and K-selection history

An exploration of the impact of phylogenetic tree structure on NTI and βNTI estimates of community assembly

Contact Info

Product

Resources

About