Effects of Current Velocity on the Nascent Architecture of Stream Microbial Biofilms

Battin, Tom J.; Kaplan, Louis; Newbold, J. Denis; Cheng, Xianhao; Hansen, Claude M. E.

doi:10.1128/aem.69.9.5443-5452.2003

Cited by 255 publications

(219 citation statements)

References 58 publications

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“…On the other hand, respiratory carbon dioxide from these heterotrophs can be assimilated by the phototrophs. This interaction produces benthic biofilms with 'self-sufficient' carbon cycling that is less dependent on external carbon sources if inorganic nutrients and light (as the energy source) are provided 39,70 .Owing to the priming effect, complementary interactions between phototrophs and 13 heterotrophs may also promote the metabolism of the recalcitrant DOM that is often delivered from terrestrial sources into streams. The priming effect enables exudates from phototrophs to provide energy and nutrients (such as nitrate and phosphate) to the biofilm that may otherwise be limiting to microbial growth 71 .…”

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confidence: 99%

The ecology and biogeochemistry of stream biofilms

et al. 2016

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The perception that most microorganisms live as complex communities that are attached to surfaces has profoundly changed microbiology over the past decades. Most, if not all, bacteria can form biofilms, which are communities of cells embedded in a porous extracellular matrix.Dental plaque, the microorganisms on catheters and implants that cause persistent infections and the fouling of ship hulls and pipework are all examples of biofilms with important implications for public health and industrial processes. Most contemporary biofilm research rests on the discovery made more than 35 years ago by Maurice Lock, Gill Geesey and Bill Costerton: bacteria attached to surfaces dominate microbial life in streams [1][2][3] . These microbiologists pioneered research into stream biofilms, also termed periphyton or epilithon, and described them as complex aggregates of bacteria, algae, protozoa, fungi and meiobenthos. The early study of stream biofilms also highlighted the relevance of interactions between microbial phototrophs and heterotrophs for energy fluxes and the role of the biofilm matrix as the site of extracellular enzyme activity and adsorption of dissolved organic matter (DOM) 3,4 .Since these early days, the study of the ecology and biogeochemistry of stream biofilms has slowly developed in the wake of thriving research on bacterial biofilms -often comprising 3 only a single strain, of interest to medical microbiology, rather than the polymicrobial communities found in stream biofilms -and on the microbial ecology of marine and lake planktonic communities 5 . Unlike bacterial biofilms grown in the laboratory, biofilms in streams are continuously exposed to a diverse inoculum that includes bacteria, archaea, algae, fungi, protozoa and even metazoa. These diverse biological 'building blocks', when combined with the dynamic flow of streamwater, generate biofilms with inherently complex and varying physical structures that have implications for microbial functioning and ecosystem processes 6 . In streams, biofilms are key sites of enzymatic activity 7 , including organic matter cycling, ecosystem respiration and primary production and, as such, form the basis of the food web.Why should we study the ecology and biogeochemistry of stream biofilms? Streams sculpt the continental surface, forming dense and conspicuous channel networks that can be thought of as ecological arteries that perfuse the landscape. Streams are connected to their catchments through various surface and subsurface flow paths and notably through the hyporheic zone in the streambed at the interface between groundwater and streamwater 8 . Microbial cells, solutes and particles enter streams through these flow paths and, en route to downstream ecosystems and ultimately to the oceans, they may interact with the biofilms that colonize the large surface area provided by the streambed as a 'microbial skin' (BOX 1). As a result, the streambed and its biofilm microbiome contribute to biogeochemical fluxes 8 . Indeed, stream biofilms are now recognized as su...

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confidence: 99%

The ecology and biogeochemistry of stream biofilms

et al. 2016

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“…In recent years, the simultaneous use of multiple color stains has been increasingly adopted to characterize various EPS components in biofilms (Neu et al 2002;Battin et al 2003;Chen et al 2006;Adav et al 2010). Accordingly, more and more fluorochromes (typically purchased from Sigma, Molecular Probe, and Life Technologies) have been tested and selected to probe in-situ the corresponding content distribution of EPS.…”

Section: Multiple Fluorescence Staining and Clsmmentioning

confidence: 99%

“…Nevertheless, CLSM can provide an accurate representation of EPS in young biofilms, assessing the qualitative and quantitative changes in the early stages of development. As a result, for dense or thicker biofilms, which have been embedded and physically sectioned, embedding may be done using nanoplast, epon, paraffin, or a socalled tissue freezing medium, and subsequent sectioning may be carried out using a normal microtome or a cryotome (Battin et al 2003;Savidge and Pothoulakis 2004). Furthermore, obtaining higher-resolution images of thick biofilm samples by two-photon LSM instead of conventional single-photon laser microscopy has proven possible if appropriate excitation wavelengths and fluorochromes are used .…”

Section: Multiple Fluorescence Staining and Clsmmentioning

confidence: 99%

Detection Techniques for Extracellular Polymeric Substances in Biofilms: A Review

Pan

Zhu

Chen

et al. 2016

BioRes

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Extracellular polymeric substances (EPS) are one of the main components of biofilm, prompting biofilm to form a cohesive three-dimensional framework. Numerous methods are available to help characterize the properties and the structural, chemical and physical organizations of EPS during the biofilm formation process. This review highlights key techniques from different disciplines that have been successfully applied in-situ and non-destructively to describe the complex composition and distribution of EPS in biofilm, especially microscopic, spectroscopic, and the combination of multi-disciplinary methods that can provide new insights into the complex structure/function correlations in biofilms. Among them, confocal laser scanning microscopy (CLSM) is emphasized, and its principles, applications, advantages, and limitations are summarized. Multidisciplinary techniques have been developed and recommended to study EPS during the biofilm formation process, providing more in-depth insights into the composition and spatial distributions of EPS, so as to improve our understanding of the role EPS plays in biofilms ultimately.

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“…Emergent properties have 217 been used to refer to a variety of phenomena in ecology, however here we use 218 emergent properties as it has been defined by Salt (1979) 24 : "An emergent property 219 of an ecological unit is one which is wholly unpredictable from observation of the 220 components of that unit", which is consistent with its contemporary use in microbial 221 ecology. 25 For example, the potential importance of emergent properties to influence 222 ecosystem processes has been demonstrated in a series of experimental flow-223 through flumes that mimicked development and metabolism of stream biofilms 26 . 224 .…”

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confidence: 99%

“…http://dx.doi.org/10.1101/065128 doi: bioRxiv preprint first posted online Jul. 21, 2016; Transient storage (i.e., an increase in residence time of the water and its solutes 225 near the biofilm relative to the flow around it) increased as the microbial biofilm 226 density increased 26 . Microbial biofilm formation is an EP 27 that affects the important 227 ecosystem process of hydrological transient storage 26 .…”

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Understanding How Microbiomes Influence The Systems They Inhabit: Moving From A Correlative To A Causal Research Framework

Hall

Bernhardt

Bier

et al. 2016

Preprint

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Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits) from and those properties that are currently unable to be predicted from constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

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Effects of Current Velocity on the Nascent Architecture of Stream Microbial Biofilms

Cited by 255 publications

References 58 publications

The ecology and biogeochemistry of stream biofilms

The ecology and biogeochemistry of stream biofilms

Detection Techniques for Extracellular Polymeric Substances in Biofilms: A Review

Understanding How Microbiomes Influence The Systems They Inhabit: Moving From A Correlative To A Causal Research Framework

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