Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

Smith, Heidi J.; Zelaya, Anna J.; León, Kara B. De; Chakraborty, Romy; Elias, Dwayne A.; Hazen, Terry C.; Arkin, Adam P.; Cunningham, A. B.; Fields, Matthew W.

doi:10.1093/femsec/fiy191

Cited by 53 publications

(34 citation statements)

References 193 publications

(248 reference statements)

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“…According to previous studies (Lovley and Chapelle 1995; Smith et al . 2018), the shallow subsurface could have a high degree of hydrological connectedness with the surface compared to the deep subsurface, because there was an interface between the saturated and vadose zone as the result of fluctuation of water table. The fluctuating water table may introduce vadose zone microbes into the saturated zone (Lin et al .…”

Section: Discussionmentioning

confidence: 99%

Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone–aquifer sediments

Zhong

Chen

et al. 2020

J Appl Microbiol

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Aims This study attempted to demonstrate the vertical shift in bacterial, archaeal and fungal communities along the vadose zone–aquifer sediments and their respective responses to environmental factors. Methods and Results We collected samples from the vadose zone and three aquifer sediments along a 42·5 m bore of a typical agricultural land. The results showed that the bacterial community shifted greatly with depth. The classes of Actinobacteria (19·5%) and NC10 (11·0%) were abundant in the vadose zone while Alphaproteobacteria (22·3%) and Gammaproteobacteria (20·1%) were enriched in the aquifer. Archaeal and fungal communities were relatively more homogeneous with no significant trend as a function of depth. Process analyses further indicated that selection dominated in the bacterial community, whereas stochastic processes governed archaeal and fungal communities. Moreover environment–bacteria interaction analysis showed that metal(loid)s, especially alkali metal, had a closer correlation with the bacterial community than physicochemical variables. Conclusions Depth strongly affected bacterial rather than archaeal and fungal communities. Metal(loid)s prevailed over physicochemical variables in shaping the bacterial community in the vadose zone–aquifer continuum. Significance and Impact of the Study Our study provides a new perspective on the structure of microbial communities from the vadose zone to the deep aquifers.

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Section: Discussionmentioning

confidence: 99%

Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone–aquifer sediments

Zhong

Chen

et al. 2020

J Appl Microbiol

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“…2017; Smith et al . 2018). In this case, differences in community composition would not necessarily correlate with spatial distance even if dispersal was limited between local communities.…”

Section: Discussionmentioning

confidence: 99%

Selection imposed by local environmental conditions drives differences in microbial community composition across geographically distinct groundwater aquifers

Fillinger

Hug

Griebler

2019

FEMS Microbiology Ecology

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Several studies have analyzed biogeographic distribution patterns of microbial communities across broad spatial scales. However, it is often unclear to what extent differences in community composition across different regions are caused by dispersal limitation or selection, and if selection is caused by local environmental conditions alone or additional broad-scale region-specific factors. This is especially true for groundwater environments, which have been understudied in this context relative to other non-subsurface habitats. Here, we analyzed microbial community composition based on exact 16S rRNA amplicon sequence variants (ASVs) from four geographically separated aquifers located in different regions along a latitudinal transect of ∼700 km across Germany. Using a combination of variation partitioning and ecological null models revealed that differences in microbial community composition were mainly the product of selection imposed by local environmental conditions and to a smaller but still significant extent dispersal limitation and drift across regions. Only ∼23% of the total variation in microbial community composition remained unexplained, possibly due to underestimated effects of dispersal limitation among local communities within regions and temporal drift. No evidence was found for selection due to region-specific factors independent of local environmental conditions.

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“…There are numerous challenges and barriers associated with in situ studies ( Griebler and Lueders, 2009 ; Rocha et al, 2016 ; Smith et al, 2018 ; Zelaya et al, 2019 ). These include the difficulty to sample at sufficient spatio-temporal resolution and the fact that when working in the natural environment external variables/forces cannot be controlled or separated out, which often results in confounding variables.…”

Section: Approach To Applying the Framework For Integrated Conceptuamentioning

confidence: 99%

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

et al. 2021

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Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.

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Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

Cited by 53 publications

References 193 publications

Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone–aquifer sediments

Vertical distribution of microbial communities and their response to metal(loid)s along the vadose zone–aquifer sediments

Selection imposed by local environmental conditions drives differences in microbial community composition across geographically distinct groundwater aquifers

Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

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