scholarly journals Synthetic periphyton as a model community to examine species dynamics in complex microbial consortia

2021 ◽  
Author(s):  
Olga Lamprecht ◽  
Bettina Wagner ◽  
Nicolas Derlon ◽  
Ahmed Tlili
Keyword(s):  
Species Interactions ◽  
Rational Design ◽  
Abiotic Factors ◽  
Single Species ◽  
Microbial Consortia ◽  
Specific Response ◽  
Functional Responses ◽  
Microbial Composition ◽  
Community Function ◽  
Species Dynamics

Phototrophic biofilms, also known as periphyton, drive crucial ecosystem processes and are subject to alterations due to a multitude of biotic and abiotic factors. In this context, understanding species dynamics in periphyton is a fundamental, yet challenging, requirement to accurately predict outcomes on functions and properties of complex communities. To address this challenge, we developed a workflow applying rational design based on existing knowledge on natural periphyton, to successfully obtain a stable, diverse and highly reproducible synthetic periphyton. We show that by using our synthetic community, with a known microbial composition, we are able to monitor dynamics of single species during periphyton development and their specific response to stressors such as increased temperature and herbicides. Importantly, we clearly demonstrate that these responses are mainly driven by species interactions and how they link to changes of community function and structure. Our synthetic periphyton is a powerful tool to perform mechanistic studies on periphyton structural and functional responses, as well as on species propagation, to any biotic and abiotic stressors and their combinations.

scholarly journals One versus Many: Polymicrobial Communities and the Cystic Fibrosis Airway

mBio ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Fabrice Jean-Pierre ◽  
Arsh Vyas ◽  
Thomas H. Hampton ◽  
Michael A. Henson ◽  
George A. O’Toole
Keyword(s):  
Cystic Fibrosis ◽  
Species Interactions ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Community Function ◽  
Cystic Fibrosis Airway ◽  
Airway Infections ◽  
Culture Independent ◽  
Polymicrobial Communities

ABSTRACT Culture-independent studies have revealed that chronic lung infections in persons with cystic fibrosis (pwCF) are rarely limited to one microbial species. Interactions among bacterial members of these polymicrobial communities in the airways of pwCF have been reported to modulate clinically relevant phenotypes. Furthermore, it is clear that a single polymicrobial community in the context of CF airway infections cannot explain the diversity of clinical outcomes. While large 16S rRNA gene-based studies have allowed us to gain insight into the microbial composition and predicted functional capacities of communities found in the CF lung, here we argue that in silico approaches can help build clinically relevant in vitro models of polymicrobial communities that can in turn be used to experimentally test and validate computationally generated hypotheses. Furthermore, we posit that combining computational and experimental approaches will enhance our understanding of mechanisms that drive microbial community function and identify new therapeutics to target polymicrobial infections.

scholarly journals High-order interactions dominate the functional landscape of microbial consortia

2018 ◽  
Author(s):  
Alicia Sanchez-Gorostiaga ◽  
Djordje Bajić ◽  
Melisa L. Osborne ◽  
Juan F. Poyatos ◽  
Alvaro Sanchez
Keyword(s):  
Species Interactions ◽  
Species Traits ◽  
High Order ◽  
Microbial Consortia ◽  
Order Effects ◽  
High Performing ◽  
Community Function ◽  
Functional Interactions ◽  
Complex Interactions ◽  
And Function

AbstractUnderstanding the link between community composition and function is a major challenge in microbial ecology, with implications for the management of natural microbiomes and the design of synthetic consortia. For this purpose, it is critical to understand the extent to which community functions and properties can be predicted from species traits and what role is played by complex interactions. Inspired by the study of complex genetic interactions and fitness landscapes, here we have examined how the amylolytic function of combinatorial assemblages of seven starch-degrading soil bacteria depends on the functional contributions from each species and their interactions. Filtering our experimental results through the theory of enzyme kinetics, we show that high-order functional interactions dominate the amylolytic rate of our consortia, even though this function is biochemically simple, redundantly distributed in the community, and additive in the absence of inter-species interactions. As the community grows in size, the contribution of high-order functional interactions grows too, making the community function increasingly unpredictable. We can explain the prevalence of high order effects and their sign from the redundancy of ecological interactions in the network, in particular from redundant facilitation towards a high-performing community member. Our results suggest that even simple functions can be dominated by complex interactions, posing challenges for the predictability and bottom-up engineering of ecosystem function in complex multi-species communities.

scholarly journals Evaluating Coexistence of Fish Species with Coastal Cutthroat Trout in Low Order Streams of Western Oregon and Washington, USA

Fishes ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 4
Author(s):  
Kyle D. Martens ◽  
Jason Dunham
Keyword(s):  
Pacific Northwest ◽  
Species Interactions ◽  
Coho Salmon ◽  
Cutthroat Trout ◽  
Single Species ◽  
The Pacific ◽  
Small Streams ◽  
Coastal Cutthroat Trout ◽  
Multiple Species ◽  
Low Order

When multiple species of fish coexist there are a host of potential ways through which they may interact, yet there is often a strong focus on studies of single species without considering these interactions. For example, many studies of forestry–stream interactions in the Pacific Northwest have focused solely on the most prevalent species: Coastal cutthroat trout. To examine the potential for interactions of other fishes with coastal cutthroat trout, we conducted an analysis of 281 sites in low order streams located on Washington’s Olympic Peninsula and along the central Oregon coast. Coastal cutthroat trout and juvenile coho salmon were the most commonly found salmonid species within these streams and exhibited positive associations with each other for both presence and density. Steelhead were negatively associated with the presence of coastal cutthroat trout as well as with coho salmon and sculpins (Cottidae). Coastal cutthroat trout most frequently shared streams with juvenile coho salmon. For densities of these co-occurring species, associations between these two species were relatively weak compared to the strong influences of physical stream conditions (size and gradient), suggesting that physical conditions may have more of an influence on density than species interactions. Collectively, our analysis, along with a review of findings from prior field and laboratory studies, suggests that the net effect of interactions between coastal cutthroat trout and coho salmon do not appear to inhibit their presence or densities in small streams along the Pacific Northwest.

scholarly journals Sustainable exploitation of temperate fish stocks

2009 ◽  
Vol 6 (1) ◽  
pp. 124-127 ◽  
Author(s):  
Henrik Sparholt ◽  
Robin M. Cook
Keyword(s):  
Species Interactions ◽  
Fishery Management ◽  
Regional Scale ◽  
Single Species ◽  
Fishing Effort ◽  
Theoretical Concept ◽  
Maximum Sustainable Yield ◽  
Production Model ◽  
The Status ◽  
Long Time

The theory of maximum sustainable yield (MSY) underpins many fishery management regimes and is applied principally as a single species concept. Using a simple dynamic biomass production model we show that MSY can be identified from a long time series of multi-stock data at a regional scale in the presence of species interactions and environmental change. It suggests that MSY is robust and calculable in a multispecies environment, offering a realistic reference point for fishery management. Furthermore, the demonstration of the existence of MSY shows that it is more than a purely theoretical concept. There has been an improvement in the status of stocks in the Northeast Atlantic, but our analysis suggests further reductions in fishing effort would improve long-term yields.

scholarly journals Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Daniela Rosado ◽  
Raquel Xavier ◽  
Jo Cable ◽  
Ricardo Severino ◽  
Pedro Tarroso ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Diversity ◽  
Water Temperature ◽  
Abiotic Factors ◽  
Seasonal Effect ◽  
Microbial Composition ◽  
Surrounding Water ◽  
European Seabass ◽  
And Function ◽  
The Impact

AbstractFish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

scholarly journals Dynamics of Microbial Indicators in Waste Water

2017 ◽  
Vol 74 (2) ◽  
pp. 116
Author(s):  
Vlad STOIAN ◽  
Roxana VIDICAN ◽  
Ioan ROTAR ◽  
Florin PĂCURAR
Keyword(s):  
Abiotic Factors ◽  
Specific Response ◽  
Filamentous Bacteria ◽  
Qualitative And Quantitative ◽  
External Pressures ◽  
Quantitative Changes ◽  
Water Ecosystems ◽  
Microbial Groups ◽  
Foam Production

Water ecosystems are constantly under the pressure of a high number of biotic and abiotic factors, and their action leads to the occurrence of fluctuations in species and populations. The specific response of organisms to external pressures leads to the reorganization of ecosystems, with qualitative and quantitative changes. The aim is to identify the microbial groups with the highest potential in the waste waters. Data were collected during 2015-16 in Bistrita. Identifying the bioindicators quality of microorganisms and their importance in ecosystems was done by comparing them with international databases. The use of microorganisms as bioindicators involves knowing the requirements for one or more environmental variables. The concept refers to the ability of microorganisms to accumulate pollutants. Flagellates are tolerant to acidity and react quickly and with sensitivity to environmental stress by inhibiting their movement. The multiplication of flagellates and filamentous bacteria is manifested through water disturbance and foam production.

Population growth and density dependence

2019 ◽  
pp. 63-80
Author(s):  
Gary G. Mittelbach ◽  
Brian J. McGill
Keyword(s):  
Population Growth ◽  
Density Dependence ◽  
Growth Model ◽  
Species Interactions ◽  
Single Species ◽  
Positive Density ◽  
Allee Effects ◽  
Species Population ◽  
Exponential Growth Model ◽  
Single Species Population

This chapter reviews the basic mathematics of population growth as described by the exponential growth model and the logistic growth model. These simple models of population growth provide a foundation for the development of more complex models of species interactions covered in later chapters on predation, competition, and mutualism. The second half of the chapter examines the important topic of density-dependence and its role in population regulation. The preponderance of evidence for negative density-dependence in nature is reviewed, along with examples of positive density dependence (Allee effects). The study of density dependence in single-species populations leads naturally to the concept of community-level regulation, the idea that species richness or the total abundance of individuals in a community may be regulated just like abundance in a single-species population. The chapter concludes with a look at the evidence for community regulation in nature and a discussion of its importance.

Answers.

2020 ◽  
pp. 179-214
Author(s):  
Paul A. Rees
Keyword(s):  
Community Ecology ◽  
Population Ecology ◽  
Species Interactions ◽  
Abiotic Factors ◽  
Multiple Choice ◽  
Ecological Genetics ◽  
Major Topic ◽  
Production Ecology ◽  
Material Cycles ◽  
Ecological Methods

Abstract A multiple choice question has a stem (the 'question'), a key (the 'answer') and a number of distracters (wrong answers intended to distract the student from the key). This part of the book contains the key to each question along with a brief explanation of why this is correct and, in some cases, what the distracters mean. The questions are grouped into 10 major topic areas: (1) The history and foundations of ecology, (2) Abiotic factors and environmental monitoring, (3) Taxonomy and biodiversity, (4) Energy flow and production ecology, (5) Nutrient and material cycles, (6) Ecophysiology, (7) Population ecology, (8) Community ecology and species interactions, (9) Ecological genetics and evolution, (10) Ecological methods and statistics.

scholarly journals Labour sharing promotes coexistence in atrazine degrading bacterial communities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Loren Billet ◽  
Marion Devers ◽  
Nadine Rouard ◽  
Fabrice Martin-Laurent ◽  
Aymé Spor
Keyword(s):  
Bacterial Communities ◽  
Gene Loss ◽  
Bacterial Species ◽  
Single Species ◽  
Microbial Consortia ◽  
The Public ◽  
Herbicide Atrazine ◽  
Set Up ◽  
Multiple Species ◽  
Isolated Species

AbstractMicrobial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.

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