scholarly journals Solutions in microbiome engineering: prioritizing barriers to organism establishment

2021 ◽  
Author(s):  
Michaeline B. N. Albright ◽  
Stilianos Louca ◽  
Daniel E. Winkler ◽  
Kelli L. Feeser ◽  
Sarah-Jane Haig ◽  
...  
Keyword(s):  
Microbial Community ◽  
Ecosystem Function ◽  
Restoration Ecology ◽  
Propagule Pressure ◽  
Environmental Filtering ◽  
Biotic Interactions ◽  
Invasion Biology ◽  
Engineering Research

AbstractMicrobiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

scholarly journals Biotic Interactions Are More Important than Propagule Pressure in Microbial Community Invasions

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Michaeline B. N. Albright ◽  
Sanna Sevanto ◽  
La Verne Gallegos-Graves ◽  
John Dunbar
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Ecosystem Functioning ◽  
Propagule Pressure ◽  
Microbial Community Composition ◽  
Biotic Interactions ◽  
Relative Importance ◽  
Production Traits ◽  
Microbial Composition ◽  
The Impact

ABSTRACT Microbial probiotics are intended to improve functions in diverse ecosystems, yet probiotics often fail to establish in a preexisting microbiome. This is a species invasion problem. The relative importance of the two major factors controlling establishment in this context—propagule pressure (inoculation dose and frequency) and biotic interactions (composition of introduced and resident communities)—is unknown. We tested the effect of these factors in driving microbial composition and functioning following 12 microbial community invasions (e.g., introductions of many microbial invaders) in microcosms. Ecosystem functioning over a 30-day postinvasion period was assessed by measuring activity (respiration) and environment modification (dissolved organic carbon abundance). To test the dependence on environmental context, experiments were performed in two resource environments. In both environments, biotic interactions were more important than propagule pressure in driving microbial composition and community function, but the magnitude of effect varied by environment. Successful invaders comprised approximately 8% of the total number of operational taxonomic units (OTUs). Bacteria were better invaders than fungi, with average relative abundances of 7.4% ± 6.8% and 1.5% ± 1.4% of OTUs, respectively. Common bacterial invaders were associated with stress response traits. The most resilient bacterial and fungal families, in other words, those least impacted by invasions, were linked to antimicrobial resistance or production traits. Illuminating the principles that determine community composition and functioning following microbial invasions is key to efficient community engineering. IMPORTANCE With increasing frequency, humans are introducing new microbes into preexisting microbiomes to alter functioning. Example applications include modification of microflora in human guts for better health and those of soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved with a better understanding of microbial invasions. We conducted a microbial community invasion experiment to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).

scholarly journals Principles for engineering microbial composition and ecosystem functioning

2019 ◽  
Author(s):  
Michaeline B.N. Albright ◽  
Sanna Sevanto ◽  
La Verne Gallegos-Graves ◽  
John Dunbar
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Ecosystem Functioning ◽  
Functional Outcomes ◽  
Propagule Pressure ◽  
Biotic Interactions ◽  
Plant Litter ◽  
Relative Importance ◽  
Microbial Composition ◽  
The Impact

AbstractMicrobial probiotics are designed to improve functions in diverse ecosystems, yet probiotics often fail to have the desired beneficial effects. The introduction of probiotics to an environment with a preexisting microbiome is analogous to an invasion event, but is rarely considered in this light. Here, we tested the relative importance of propagule pressure (inoculation dose and frequency) compared to biotic interactions (composition of introduced and resident communities) in driving microbial composition and functional outcomes following microbial community invasions in experimental microcosms. Ecosystem functioning was assessed through measurements of CO2 production and DOC (dissolved organic carbon) accumulation, an activity and an environmental modification metric, respectively. Further, to test the dependence of propagule pressures versus biotic interactions was dependent on environmental context, experiments were performed on two different substrates, R2A agar and plant litter. In both environments, we found that biotic interactions were more important than propagule pressure in driving microbial composition. Moreover, bacteria were more successful invaders than fungi. While successful invasion is a first step, ultimately the success of microbial invasions in microbiome engineering applications is measured by the impact on ecosystem functioning. As with shaping the microbiome composition, biotic interactions were key to functional outcomes, but the magnitude of the functional impact varied by environment. Identifying general principles that determine the community composition and functioning following microbial invasions is key to efficient community engineering.SignificanceWith increasing frequency humans are introducing new microbes into pre-existing microbiomes to alter functioning. Examples include, modification of microflora in human guts for better health, and soil for food security and/or climate management. Probiotic applications are often approached as trial-and-error endeavors and have mixed outcomes. We propose that increased success in microbiome engineering may be achieved by better understanding of microbial invasions. We conducted a microbial community invasion experiment, to test the relative importance of propagule pressure and biotic interactions in driving microbial community composition and ecosystem functioning in microcosms. We found that biotic interactions were more important than propagule pressure in determining the impact of microbial invasions. Furthermore, the principles for community engineering vary among organismal groups (bacteria versus fungi).

Linking Microbial Community Dynamics in BIOX® Leaching Tanks to Process Conditions: Integrating Lab and Commercial Experience

2017 ◽  
Vol 262 ◽  
pp. 38-42 ◽  
Author(s):  
Mariette Smart ◽  
Robert J. Huddy ◽  
Catherine J. Edward ◽  
Charl Fourie ◽  
Trust Shumba ◽  
...  
Keyword(s):  
South Africa ◽  
Community Structure ◽  
Microbial Community ◽  
Research University ◽  
Community Dynamics ◽  
Operating Conditions ◽  
Process Conditions ◽  
Significant Shift ◽  
Engineering Research ◽  
Microbial Community Dynamics

In the commercial BIOX® process, an acidophilic mixed bacterial and archaeal community dominated by iron and sulphur oxidising microorganisms is used to facilitate the recovery of precious metals from refractory gold-bearing sulphidic mineral concentrates. Characterisation of the microbial communities associated with commercial BIOX® reactors from four continents revealed a significant shift in the microbial community structure compared to that of the seed culture, maintained at SGS (South Africa). This has motivated more detailed study of the microbial community dynamics in the process. Microbial speciation of a subset of the BIOX® reactors at Fairview mines (Barberton, South Africa) and two laboratory maintained reactors housed at Centre for Bioprocess Engineering Research, University of Cape Town, has been performed tri-annually for three years by quantitative real-time polymerase chain reaction. The laboratory BIOX® culture maintained on Fairview concentrate was dominated by the desired iron oxidiser, Leptospirillum ferriphilum, and sulphur oxidiser, Acidithiobacillus caldus, when operated under standard BIOX® conditions. Shifts in the microbial community as a result of altered operating conditions were transient and did not result in a loss of the microbial diversity of the BIOX® culture. The community structure of the Fairview mines BIOX® reactor tanks showed archaeal dominance of these communities by organisms such as the iron oxidiser Ferroplasma acidiphilum and a Thermoplasma sp. for the period monitored. Shifts in the microbial community were observed across the monitoring period and mapped to changes in performance of the commercial process plant. Understanding the effect of changes in the plant operating conditions on the BIOX® community structure may assist in providing conditions that support the desired microbial consortium for optimal biooxidation to maximize gold recovery.

scholarly journals Towards a function-first framework to make soil microbial ecology predictive

2021 ◽  
Author(s):  
Johannes Rousk ◽  
Lettice Hicks
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Functional Response ◽  
Community Composition ◽  
Ecosystem Function ◽  
Bacterial Growth ◽  
Response Curve ◽  
Ecosystem Functions ◽  
Soil Microbial

<p>Soil microbial communities perform vital ecosystem functions, such as the decomposition of organic matter to provide plant nutrition. However, despite the functional importance of soil microorganisms, attribution of ecosystem function to particular constituents of the microbial community has been impeded by a lack of information linking microbial function to community composition and structure. Here, we propose a function-first framework to predict how microbial communities influence ecosystem functions.</p><p>We first view the microbial community associated with a specific function as a whole, and describe the dependence of microbial functions on environmental factors (e.g. the intrinsic temperature dependence of bacterial growth rates). This step defines the aggregate functional response curve of the community. Second, the contribution of the whole community to ecosystem function can be predicted, by combining the functional response curve with current environmental conditions. Functional response curves can then be linked with taxonomic data in order to identify sets of “biomarker” taxa that signal how microbial communities regulate ecosystem functions. Ultimately, such indicator taxa may be used as a diagnostic tool, enabling predictions of ecosystem function from community composition.</p><p>In this presentation, we provide three examples to illustrate the proposed framework, whereby the dependence of bacterial growth on environmental factors, including temperature, pH and salinity, is defined as the functional response curve used to interlink soil bacterial community structure and function. Applying this framework will make it possible to predict ecosystem functions directly from microbial community composition.</p>

scholarly journals The Coupled Influence of Thermal Physiology and Biotic Interactions on the Distribution and Density of Ant Species along an Elevational Gradient

Diversity ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 456
Author(s):  
Lacy D. Chick ◽  
Jean-Philippe Lessard ◽  
Robert R. Dunn ◽  
Nathan J. Sanders
Keyword(s):  
Observational Data ◽  
Species Interactions ◽  
Phylogenetic Signal ◽  
Environmental Filtering ◽  
Null Model ◽  
Biotic Interactions ◽  
Elevational Gradient ◽  
High Elevation ◽  
Elevational Range ◽  
Stressful Environments

A fundamental tenet of biogeography is that abiotic and biotic factors interact to shape the distributions of species and the organization of communities, with interactions being more important in benign environments, and environmental filtering more important in stressful environments. This pattern is often inferred using large databases or phylogenetic signal, but physiological mechanisms underlying such patterns are rarely examined. We focused on 18 ant species at 29 sites along an extensive elevational gradient, coupling experimental data on critical thermal limits, null model analyses, and observational data of density and abundance to elucidate factors governing species’ elevational range limits. Thermal tolerance data showed that environmental conditions were likely to be more important in colder, more stressful environments, where physiology was the most important constraint on the distribution and density of ant species. Conversely, the evidence for species interactions was strongest in warmer, more benign conditions, as indicated by our observational data and null model analyses. Our results provide a strong test that biotic interactions drive the distributions and density of species in warm climates, but that environmental filtering predominates at colder, high-elevation sites. Such a pattern suggests that the responses of species to climate change are likely to be context-dependent and more specifically, geographically-dependent.

scholarly journals Strength in Numbers: Combining Multi-Source Remotely Sensed Data to Model Plant Invasions in Coastal Dune Ecosystems

2019 ◽  
Vol 11 (3) ◽  
pp. 275 ◽  
Author(s):  
Marco Malavasi ◽  
Vojtěch Barták ◽  
Tommaso Jucker ◽  
Alicia Teresa Rosario Acosta ◽  
Maria Laura Carranza ◽  
...  
Keyword(s):  
Linear Models ◽  
Propagule Pressure ◽  
Central Italy ◽  
Three Dimensional ◽  
Biotic Interactions ◽  
Coastal Dunes ◽  
Plant Invasions ◽  
Remotely Sensed Data ◽  
Relative Contribution ◽  
Optical Imagery

A common feature of most theories of invasion ecology is that the extent and intensity of invasions is driven by a combination of drivers, which can be grouped into three main factors: propagule pressure (P), abiotic drivers (A) and biotic interactions (B). However, teasing apart the relative contribution of P, A and B on Invasive Alien Species (IAS) distributions is typically hampered by a lack of data. We focused on Mediterranean coastal dunes as a model system to test the ability of a combination of multi-source Remote Sensing (RS) data to characterize the distribution of five IAS. Using generalized linear models, we explored and ranked correlates of P, A and B derived from high-resolution optical imagery and three-dimensional (3D) topographic models obtained from LiDAR, along two coastal systems in Central Italy (Lazio and Molise Regions). Predictors from all three factors contributed significantly to explaining the presence of IAS, but their relative importance varied among the two Regions, supporting previous studies suggesting that invasion is a context-dependent process. The use of RS data allowed us to characterize the distribution of IAS across broad, regional scales and to identify coastal sectors that are most likely to be invaded in the future.

scholarly journals Climatic effects on turnover of lowland forest bird communities across a precipitation gradient

2018 ◽  
Author(s):  
Juan Pablo Gomez ◽  
José Miguel Ponciano ◽  
Scott K. Robinson
Keyword(s):  
Community Composition ◽  
Species Abundance ◽  
Environmental Filtering ◽  
Bird Species ◽  
Biotic Interactions ◽  
Dry Forest ◽  
Precipitation Gradient ◽  
Climatic Effects ◽  
Lowland Forest ◽  
Abundance And Distribution

AbstractOne of the main goals of community ecology is to understand the influence of the abiotic environment on the abundance and distribution of species. It has been hypothesized that dry forests are harsher environments than wet forests, which leads to the prediction that environmental filtering should be a more important determinant of patterns of species abundance and composition than in wet forest, where biotic interactions or random assembly should be more important. We attempt to understand the influence of rainfall on the abundance and distribution of bird species along a steep precipitation gradient in an inter-Andean valley in Colombia. We gathered data on species distributions, abundance, morphological traits and phylogenetic relationships to determine the influence of rainfall on the taxonomic, functional and phylogenetic turnover of species along the Magdalena Valley. We demonstrate that there is a strong turnover of community composition at the limit of the dry forest. The taxonomic turnover is steeper than the phylogenetic turnover, suggesting that replacement of closely related species accounts for a disproportionate number of changes along the gradient. We found evidence for environmental filtering in dry forest as species tend to be more tolerant of higher temperature ranges, stronger rainfall seasonality and lower minimum rainfall. On the other hand, wet forest species tend to compete actively for nest space but not for the resources associated with the axes we measured. Our results suggest that rainfall is a strong determinant of community composition when comparing localities above and below the 2400 mm rainfall isocline.

scholarly journals The Ecology and Evolution of Alien Plants

2018 ◽  
Vol 49 (1) ◽  
pp. 25-47 ◽  
Author(s):  
Mark van Kleunen ◽  
Oliver Bossdorf ◽  
Wayne Dawson
Keyword(s):  
Propagule Pressure ◽  
Rapid Evolution ◽  
Biotic Interactions ◽  
Functional Trait ◽  
Alien Plants ◽  
Great Promise ◽  
Habitat Specificity ◽  
Alien Plant ◽  
Open Questions ◽  
Underlying Mechanisms

We review the state of the art of alien plant research with emphasis on conceptual advances and knowledge gains on general patterns and drivers, biotic interactions, and evolution. Major advances include the identification of different invasion stages and invasiveness dimensions (geographic range, habitat specificity, local abundance) and the identification of appropriate comparators while accounting for propagule pressure and year of introduction. Developments in phylogenetic and functional trait research bear great promise for better understanding of the underlying mechanisms. Global patterns are emerging with propagule pressure, disturbance, increased resource availability, and climate matching as major invasion drivers, but species characteristics also play a role. Biotic interactions with resident communities shape invasion outcomes, with major roles for species diversity, enemies, novel weapons, and mutualists. Mounting evidence has been found for rapid evolution of invasive aliens and evolutionary responses of natives, but a mechanistic understanding requires tighter integration of molecular and phenotypic approaches. We hope the open questions identified in this review will stimulate further research on the ecology and evolution of alien plants.

scholarly journals Environmental Filtering Influences Functional Community Assembly of Epibenthic Communities

2021 ◽  
Vol 8 ◽  
Author(s):  
Lauren Sutton ◽  
Franz J. Mueter ◽  
Bodil A. Bluhm ◽  
Katrin Iken
Keyword(s):  
Community Assembly ◽  
Chukchi Sea ◽  
Environmental Filtering ◽  
Biotic Interactions ◽  
Beaufort Sea ◽  
Functional Trait ◽  
Functional Community ◽  
Trait Convergence ◽  
High Trait ◽  
Epibenthic Communities

Community assembly theory states that species assemble non-randomly as a result of dispersal limitation, biotic interactions, and environmental filtering. Strong environmental filtering likely leads to local assemblages that are similar in their functional trait composition (high trait convergence) while functional trait composition will be less similar (high trait divergence) under weaker environmental filters. We used two Arctic shelves as case studies to examine the relationship between functional community assembly and environmental filtering using the geographically close but functionally and environmentally dissimilar epibenthic communities on the Chukchi and Beaufort Sea shelves. Environmental drivers were compared to functional trait composition and to trait convergence within each shelf. Functional composition in the Chukchi Sea was more strongly correlated with environmental gradients compared to the Beaufort Sea, as shown by a combination of RLQ and fourth corner analyses and community-weighted mean redundancy analyses. In the Chukchi Sea, epibenthic functional composition, particularly body size, reproductive strategy, and several behavioral traits (i.e., feeding habit, living habit, movement), was most strongly related to gradients in percent mud and temperature while body size and larval development were most strongly related to a depth gradient in the Beaufort Sea. The stronger environmental filter in the Chukchi Sea also supported the hypothesized relationship with higher trait convergence, although this relationship was only evident at one end of the observed environmental gradient. Strong environmental filtering generally provides a challenge for biota and can be a barrier for invading species, a growing concern for the Chukchi Sea shelf communities under warming conditions. Weaker environmental filtering, such as on the Beaufort Sea shelf, generally leads to communities that are more structured by biotic interactions, and possibly representing partitioning of resources among species from intermediate disturbance levels. We provide evidence that environmental filtering can structure functional community composition, providing a baseline of how community function could be affected by stressors such as changes in environmental conditions or increased anthropogenic disturbance.

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