Fundamentals of Microbial Community Resistance and Resilience

Shade, Ashley; Peter, Hannes; Allison, Steven D.; Baho, Didier L.; Berga, Mercè; Bürgmann, Helmut; Huber, David H.; Langenheder, Silke; Lennon, Jay T.; Martiny, Jennifer B. H.; Matulich, Kristin L.; Schmidt, Thomas M.; Handelsman, Jo

doi:10.3389/fmicb.2012.00417

Cited by 1,168 publications

(1,119 citation statements)

References 178 publications

(228 reference statements)

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“…Previously identified shifts in microbial communities in response to DWH oil, both in the water column and sediments, indicated significant susceptibility of these communities; susceptibility defined as the degree to which community composition changes in response to disturbance (Shade et al, 2012). These observations are in accordance with the majority of ecological studies addressing the effect of disturbances such as carbon inputs on microbial communities, which have found evidence of susceptibility (reviewed by Allison and Martiny, 2008).…”

Section: Introductionsupporting

confidence: 75%

“…This indicates that the microbial community faced largely a press (long-term) disturbance given the time scale of microbial generation cycles and migration processes (Shade et al, 2012). Press disturbances often result in community shifts driven by the response traits of individual populations to the disturbance, presumably sensitivity to toxic compounds and hydrocarbon degradation capabilities in the case of oil contamination.…”

Section: Discussionmentioning

confidence: 99%

“…Although some previous studies applied ecological theory to describe the response and recovery of community dynamics to disturbance (cf. Prosser et al, 2007;Shade et al, 2012), the relationship of disturbance and specialization remains largely unexplored in microbial communities. Disturbed communities are typically observed to encompass reduced taxonomic and/or phylogenetic diversity compared with undisturbed controls, but whether this pattern translates to reduced functional diversity or increased specialization remains largely unknown.…”

Section: Introductionmentioning

confidence: 99%

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Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

et al. 2015

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Although petroleum hydrocarbons discharged from the Deepwater Horizon (DWH) blowout were shown to have a pronounced impact on indigenous microbial communities in the Gulf of Mexico, effects on nearshore or coastal ecosystems remain understudied. This study investigated the successional patterns of functional and taxonomic diversity for over 1 year after the DWH oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques. Gamma- and Alphaproteobacteria were enriched in oiled sediments, in corroboration of previous studies. In contrast to previous studies, we observed an increase in the functional diversity of the community in response to oil contamination and a functional transition from generalist populations within 4 months after oil came ashore to specialists a year later, when oil was undetectable. At the latter time point, a typical beach community had reestablished that showed little to no evidence of oil hydrocarbon degradation potential, was enriched in archaeal taxa known to be sensitive to xenobiotics, but differed significantly from the community before the oil spill. Further, a clear succession pattern was observed, where early responders to oil contamination, likely degrading aliphatic hydrocarbons, were replaced after 3 months by populations capable of aromatic hydrocarbon decomposition. Collectively, our results advance the understanding of how natural benthic microbial communities respond to crude oil perturbation, supporting the specialization-disturbance hypothesis; that is, the expectation that disturbance favors generalists, while providing (microbial) indicator species and genes for the chemical evolution of oil hydrocarbons during degradation and weathering.

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Section: Introductionsupporting

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

et al. 2015

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“…In contrast, it is generally believed that extreme disturbances such as drought often decrease compositional stochasticity by acting as selection factors (13), eliminating a large portion of the regional species pool. In addition, perturbations can also be classified as pulses or presses, depending on their duration (26). Whereas pulse perturbations are relatively discrete and short term, press perturbations are continuous and of long duration.…”

Section: Significancementioning

confidence: 99%

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

Zhou

Deng

Zhang

et al. 2014

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

628

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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“…The full-scale CWW treatment system, an ongoing three-phase fluidized bed biological coking wastewater treatment system in Shaoguan, Guangdong Province of China, was run with south and north two paralleled units [1][2][3][4]. These two paralleled systems have been operating for more than years at daily capacity of approximately 1680 m 3 ± 80 m 3 .…”

Section: Mini Reviewmentioning

confidence: 99%

The Resilience of Microbial Community Involved in Coking Wastewater Treatment System

Zhu¹,

Wu²,

Zhou³

et al. 2017

Next Generat Sequenc & Applic

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Biological treatment processes are the most important step for removing various nutrient matters due to their high removal efficiency and low operational cost. The activated sludge technology was used extensively in coking wastewater biological treatment processes where a complex prokaryotic microbial consortium played an important role in the processes of oxygen-depleting organics, toxics and nutrients removal and preventing discharge of pathogens. Thus, a thorough knowledge of the ecology of the coking wastewater activated sludge communities is required to improve system operation and stability. Therefore, there is necessary to reveal the resilience of microbial community involved in coking wastewater treatment system. Keywords: Biological treatment processes; Nutrient matters; Wastewater; Pathogens; Microbial community Mini ReviewIn this report, we investigated a full-scale coking wastewater treatment system with two paralleled units to see the resilience of microbial community. The full-scale CWW treatment system, an ongoing three-phase fluidized bed biological coking wastewater treatment system in Shaoguan, Guangdong Province of China, was run with south and north two paralleled units [1][2][3][4]. These two paralleled systems have been operating for more than years at daily capacity of approximately 1680 m 3 ± 80 m 3 . The total hydraulic retention time (HRT) was 46 h. These two paralleled systems were able to maintain a stable process performance during operation and also the final effluent meet the national stringent effluent standards. The coking wastewater activated sludge of anaerobic process was collected from the corresponding bioreactor of two paralleled systems in March 2016. Illumina MiSeq high throughput sequencing technology was performed to reveal the relative abundance and diversity of microbiology in these two parallel systems. Since coking wastewater is usually regarded as an extreme environment with high toxicity and refractoriness, the microorganisms involved should be quite different from those in domestic wastewater [5]. But the microbial community which is responsible for the cooking wastewater treatment process is still significantly different?The composition of the PCR products of V4 region of 16S rRNA genes was determined by MiSeq Sequencing. After MiSeq Sequencing. The raw data were processed and analyzed following the pipelines of Mothur and QIIME Raw data were denoised using the Mothur implementation of PyroNoise algorithm. Chimeric sequences were identified and removed using UCHIME with de novo method. Quality sequences were assigned to samples according to their unique 8-bp barcodes. Operational taxonomic units (OTUs, defined at the 97% sequence similarity level) were picked using average neighbor method after the Needleman alignment and a single-linkage precluster procedure. Taxonomy classification was identified using RDP Classifier at the 80% confidence threshold by default. Alpha-(number of OTUs, Chao 1, and Simpson and Shannon indices) diversity were statistically ...

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Fundamentals of Microbial Community Resistance and Resilience

Cited by 1,168 publications

References 178 publications

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

The Resilience of Microbial Community Involved in Coking Wastewater Treatment System

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