Lake microbial communities are resilient after a whole-ecosystem disturbance

Shade, Ashley; Read, Jordan S.; Youngblut, Nicholas D.; Fierer, Noah; Knight, Rob; Kratz, Timothy K.; Lottig, Noah R.; Roden, Eric E.; Stanley, Emily H.; Stombaugh, Jesse; Whitaker, Rachel J.; Wu, Chin H.; McMahon, Katherine D.

doi:10.1038/ismej.2012.56

Cited by 207 publications

(209 citation statements)

References 57 publications

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“…The experimental results with lake epilimnion microbial communities (26,(48)(49)(50)(51) also support scenario A. Generally, lake mixing increases nutrient input to the nutrient limited epilimnion (50), which should stimulate microbial diversity.…”

Section: Consistency Between Experimental Results and Theoretical Presupporting

confidence: 69%

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Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

Zhou

Deng

Zhang

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

695

555

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Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.community assembly | disturbances | metagenomics | GeoChip | remediation

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Section: Consistency Between Experimental Results and Theoretical Presupporting

confidence: 69%

“…Several studies have also examined the resilience of lake microbial communities after disturbances (26,(48)(49)(50)(51). The experimental results with lake epilimnion microbial communities (26,(48)(49)(50)(51) also support scenario A.…”

Section: Consistency Between Experimental Results and Theoretical Prementioning

confidence: 63%

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

Zhou

Deng

Zhang

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

695

555

View full text Add to dashboard Cite

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“…However, previous experiments on P. parvum invasion processes showed that communities in large (1,570-L) enclosures and small (2-L) microcosms presented no significant differences in plankton dynamics for longer periods than those encompassed by our experiment (30). Furthermore, the difference between days was probably also caused by medium-term responses of the community to initial environmental changes because stabilization of communities in response to disturbances is a continuous process that can extend for longer periods than those covered by our incubation period (33).…”

Section: Discussionmentioning

confidence: 61%

Dynamics of an experimental microbial invasion

Acosta

Zamor

Najar

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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The ecological dynamics underlying species invasions have been a major focus of research in macroorganisms for the last five decades. However, we still know little about the processes behind invasion by unicellular organisms. To expand our knowledge of microbial invasions, we studied the roles of propagule pressure, nutrient supply, and biotic resistance in the invasion success of a freshwater invasive alga, Prymnesium parvum, using microcosms containing natural freshwater microbial assemblages. Microcosms were subjected to a factorial design with two levels of nutrient-induced diversity and three levels of propagule pressure, and incubated for 7 d, during which P. parvum densities and microbial community composition were tracked. Successful invasion occurred in microcosms receiving high propagule pressure whereas nutrients or community diversity played no role in invasion success. Invaded communities experienced distinctive changes in composition compared with communities where the invasion was unsuccessful. Successfully invaded microbial communities had an increased abundance of fungi and ciliates, and decreased abundances of diatoms and cercozoans. Many of these changes mirrored the microbial community changes detected during a natural P. parvum bloom in the source system. This role of propagule pressure is particularly relevant for P. parvum in the reservoirdominated southern United States because this species can form large, sustained blooms that can generate intense propagule pressures for downstream sites. Human impact and global climate change are currently causing widespread environmental changes in most southern US freshwater systems that may facilitate P. parvum establishment and, when coupled with strong propagule pressure, could put many more systems at risk for invasion. microbial ecology | diversity | invasion resistance | propagule pressure | Prymnesium

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“…Microbial diversity is not resilient to all types of disturbance In this study, it is demonstrated that (1) the operational parameter SRT can selectively enrich for organisms based on life-history strategy (that is, selection of r-K-strategists); (2) in contrast to studies that show resilience of microbial diversity to pulsedisturbances (Shade et al, 2012), microbial communities in activated sludge did not fully recover to their original state after the press disturbance and (3) the recovery of microbial composition is not a prerequisite for the recovery of general ecosystem functions. Concordantly, our results support the functional redundancy hypothesis for microbial ecosystems (Allison and Martiny, 2008) and indicate that after a major disturbance, new microbial communities reassemble to perform the same ecosystem functions.…”

Section: Discussionmentioning

confidence: 80%

Disturbance and temporal partitioning of the activated sludge metacommunity

et al. 2014

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The resilience of microbial communities to press disturbances and whether ecosystem function is governed by microbial composition or by the environment have not been empirically tested. To address these issues, a whole-ecosystem manipulation was performed in a full-scale activated sludge wastewater treatment plant. The parameter solids retention time (SRT) was used to manipulate microbial composition, which started at 30 days, then decreased to 12 and 3 days, before operation was restored to starting conditions (30-day SRT). Activated sludge samples were collected throughout the 313-day time series in parallel with bioreactor performance ('ecosystem function'). Bacterial small subunit (SSU) rRNA genes were surveyed from sludge samples resulting in a sequence library of 4417 000 SSU rRNA genes. A shift in community composition was observed for 12-and 3-day SRTs. The composition was altered such that r-strategists were enriched in the system during the 3-day SRT, whereas K-strategists were only present at SRTsX12 days. This shift corresponded to loss of ecosystem functions (nitrification, denitrification and biological phosphorus removal) for SRTsp12 days. Upon return to a 30-day SRT, complete recovery of the bioreactor performance was observed after 54 days despite an incomplete recovery of bacterial diversity. In addition, a different, yet phylogenetically related, community with fewer of its original rare members displaced the pre-disturbance community. Our results support the hypothesis that microbial ecosystems harbor functionally redundant phylotypes with regard to general ecosystem functions (carbon oxidation, nitrification, denitrification and phosphorus accumulation). However, the impacts of decreased rare phylotype membership on ecosystem stability and micropollutant removal remain unknown.

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Lake microbial communities are resilient after a whole-ecosystem disturbance

Cited by 207 publications

References 57 publications

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

Dynamics of an experimental microbial invasion

Disturbance and temporal partitioning of the activated sludge metacommunity

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