scholarly journals Rare Microbial Taxa Emerge When Communities Collide: Freshwater and Marine Microbiome Responses to Experimental Seawater Intrusion

2019 ◽  
Author(s):  
Jennifer D. Rocca ◽  
Marie Simonin ◽  
Justin P. Wright ◽  
Alex Washburne ◽  
Emily Bernhardt
Keyword(s):  
Community Assembly ◽  
Environmental Filtering ◽  
Biotic Interactions ◽  
Structure And Function ◽  
Reciprocal Transplant ◽  
Critical Component ◽  
Central Question ◽  
Marine Communities ◽  
Rare Biosphere ◽  
And Function

AbstractWhole microbial communities regularly merge with one another, often in tandem with their environments, in a process called community coalescence. Such events allow us to address a central question in ecology – what processes shape community assembly. We used a reciprocal transplant and mixing experiment to directly and independently unravel the effects of environmental filtering and biotic interactions on microbiome success when freshwater and marine communities coalesce. The brackish treatment and community mixing resulted in strong convergence of microbiome structure and function toward the marine. Brackish exposure imposed a 96% taxa loss from freshwater and 66% loss from marine microbiomes, which was somewhat counterbalanced by the emergence of tolerant rare taxa. Community mixing further resulted in 29% and 49% loss from biotic interactions between freshwater and marine microbiomes, offset somewhat by mutualistically-assisted rare microbial taxa. Our study emphasizes the importance of the rare biosphere as a critical component of community resilience.

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.

scholarly journals Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria

2020 ◽  
Author(s):  
Samir Giri ◽  
Leonardo Oña ◽  
Silvio Waschina ◽  
Shraddha Shitut ◽  
Ghada Yousif ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Bacterial Species ◽  
Exchange Interactions ◽  
Structure And Function ◽  
Phylogenetic Distance ◽  
And Function ◽  
Microbial Community Assembly ◽  
Feeding Interactions

AbstractThe exchange of metabolites among different bacterial genotypes is key for determining the structure and function of microbial communities. However, the factors that govern the establishment of these cross-feeding interactions remain poorly understood. While kin selection theory predicts that individuals should direct benefits preferentially to close relatives, the potential benefits resulting from a metabolic exchange may be larger for more distantly related species. Here we distinguish between these two possibilities by performing pairwise cocultivation experiments between auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients were able to grow in the vast majority of pairs tested (78%), suggesting that metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient as well as the dissimilarity of their metabolic networks was positively associated with the growth of auxotrophic recipients. Finally, this result was corroborated in an in-silico analysis of a co-growth of species from a gut microbial community. Together, these findings suggest metabolic cross-feeding interactions are more likely to establish between strains that are metabolically more dissimilar. Thus, our work identifies a new rule of microbial community assembly, which can help predict, understand, and manipulate natural and synthetic microbial systems.SignificanceMetabolic cross-feeding is critical for determining the structure and function of natural microbial communities. However, the rules that determine the establishment of these interactions remain poorly understood. Here we systematically analyze the propensity of different bacterial species to engage in unidirectional cross-feeding interactions. Our results reveal that synergistic growth was prevalent in the vast majority of cases analyzed. Moreover, both phylogenetic and metabolic dissimilarity between donors and recipients favored a successful establishment of metabolite exchange interactions. This work identifies a new rule of microbial community assembly that can help predict, understand, and manipulate microbial communities for diverse applications.

Community Ecology of Stream Fishes: Concepts, Approaches, and Techniques

2010 ◽  
Keyword(s):  
Community Ecology ◽  
Fish Assemblages ◽  
Abiotic Factors ◽  
Biotic Interactions ◽  
Theoretical Models ◽  
Field Studies ◽  
Structure And Function ◽  
Activity Levels ◽  
Ecological Communities ◽  
And Function

<em>Abstract</em>.—Ecological communities are structured by a combination of stochastic and deterministic processes, the latter including both abiotic factors and biotic interactions such as predation. Many studies, mostly in relatively stable ecosystems such as lakes, have demonstrated top-down effects on community structure and function. Communities or species in dynamic nonequilibrium ecosystems such as streams may also respond strongly to predation pressure. In this chapter, we review experimental research on effects of predation on fish assemblages in lotic systems, focusing on developments in the decades since Matthews and Heins (1987). Direct experimental evidence indicates that predators strongly affect lotic fish assemblages via direct and indirect pathways of lethal and nonlethal interactions. Across studies, predators consistently reduced prey density, caused changes in prey habitat use, and decreased prey activity levels. Predators may also affect aspects of prey life history and reproduction in streams, and the presence of multiple predator species may result in prey risk enhancement. Our review identified five areas needing additional research that may lead to further advances in stream fish community ecology: (1) linking predation experiments with theoretical models of fish assemblage structure and function, (2) quantifying functional traits of predators and prey, (3) manipulating whole assemblages and testing multispecies interactions, (4) understanding the role of predation in human-modified ecosystems, and (5) application of analytical approaches that facilitate integration among these areas of research as well as with observational field studies.

scholarly journals Functional volumes, niche packing and species richness: biogeographic legacies in the Congo Basin

2020 ◽  
Vol 7 (3) ◽  
pp. 191582 ◽  
Author(s):  
Frederik Van de Perre ◽  
Michael R. Willig ◽  
Steven J. Presley ◽  
Itoka Jean-Claude Mukinzi ◽  
Mbalitini Sylvestre Gambalemoke ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Assembly ◽  
Species Coexistence ◽  
Environmental Filtering ◽  
Biotic Interactions ◽  
Congo Basin ◽  
Climatic Fluctuations ◽  
Fundamental Goal ◽  
Vicariance Event ◽  
Lowland Forests

Understanding the determinants of species coexistence in complex and species-rich communities is a fundamental goal of ecology. Patterns of species coexistence depend on how biotic interactions and environmental filtering act over ecological and evolutionary time scales. Climatic fluctuations in lowland rainforests of the Congo Basin led to the number of vertebrate species being significantly lower in central compared with northern ecoregions of the Basin. We used null models to assess whether climatic variations affected the community assembly of shrews. A consistent limit to functional similarity of species was not related to species richness. Rather, species richness is constrained by environmental factors, and these constraints are stronger in the central lowland forests of the Congo Basin. By constraining species geographic distributions, historical effects of rainforest refugia arising from climatic fluctuations may affect contemporary species composition of local shrew communities. The Congo River represents a vicariance event that led to allopatric speciation of shrews and continues to represent a barrier to dispersal. Ultimately, the historical effects of this barrier have led to differences in the functional volume of shrew communities in northern and central ecoregions. We suggest that the analyses of community assembly can be used to identify Holocene refugia in the Congo Basin.

scholarly journals Interspecies bacterial competition regulates community assembly in the C. elegans intestine

2021 ◽  
Author(s):  
Anthony Ortiz ◽  
Nicole M. Vega ◽  
Christoph Ratzke ◽  
Jeff Gore
Keyword(s):  
Community Assembly ◽  
Bacterial Communities ◽  
Mapk Pathway ◽  
Dominant Role ◽  
Bacterial Species ◽  
Environmental Filtering ◽  
Community Diversity ◽  
Interspecies Interactions ◽  
C Elegans ◽  
And Function

AbstractFrom insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. To further our understanding of how intestinal bacterial communities assemble and function, we study the C. elegans microbiota with a bottom-up approach by feeding this nematode with bacterial monocultures as well as mixtures of two to eight bacterial species. We find that bacteria colonizing well in monoculture do not always do well in co-cultures due to interspecies bacterial interactions. Moreover, as community diversity increases, the ability to colonize the worm gut in monoculture becomes less important than interspecies interactions for determining community assembly. To explore the role of host–microbe adaptation, we compare bacteria isolated from C. elegans intestines and non-native isolates, and we find that the success of colonization is determined more by a species’ taxonomy than by the isolation source. Lastly, by comparing the assembled microbiotas in two C. elegans mutants, we find that innate immunity via the p38 MAPK pathway decreases bacterial abundances yet has little influence on microbiota composition. These results highlight that bacterial interspecies interactions, more so than host–microbe adaptation or gut environmental filtering, play a dominant role in the assembly of the C. elegans microbiota.

scholarly journals Understanding Community Assembly Based on Functional Traits, Ontogenetic Stages, Habitat Types and Spatial Scales in a Subtropical Forest

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1055 ◽  
Author(s):  
Yanpeng Li ◽  
Yue Bin ◽  
Han Xu ◽  
Yunlong Ni ◽  
Ruyun Zhang ◽  
...  
Keyword(s):  
Leaf Area ◽  
Functional Traits ◽  
Community Assembly ◽  
Spatial Scales ◽  
Environmental Filtering ◽  
Biotic Interactions ◽  
Habitat Types ◽  
Ontogenetic Stages ◽  
Dispersion Patterns ◽  
Natural Communities

Community assembly in natural communities is commonly explained by stochastic and niche-based processes such as environmental filtering and biotic interactions. Many studies have inferred the importance of these processes using a trait-based approach, however, there are still unknowns around what factors affect the importance of different assembly processes in natural communities. In this study, the trait dispersion patterns of 134 species were examined across different functional traits, habitat types, ontogenetic stages and spatial scales from a 20-ha Dinghushan Forest Dynamic Plot in China. The results showed that (1) functional traits related to productivity such as specific leaf area and leaf area mainly showed functional clustering, indicating these two functional traits were more affected by environmental filtering. However, trait dispersion patterns depended on more than the ecological significances of functional traits. For example, trait dispersions of leaf dry matter content, leaf thickness and maximum height did not show consistent patterns across habitat types and ontogenetic stages, suggesting more complex mechanisms may operate on these traits; (2) the trait dispersion varied with the habitat types and ontogenetic stages. Specifically, we found that habitat types only affected the strength of trait dispersions for all the five traits, but ontogenetic stages influenced both the strength and direction of trait dispersions, which depended on the traits selected; (3) the relative importance of soil, topography and space to trait dispersion varied with ontogenetic stages. Topography and space were more important for trait dispersion of saplings but soil was more important for trait dispersion of adults; (4) biotic interactions dominated community assembly at smaller spatial scales but environmental filtering dominated community assembly at larger spatial scales. Overall, the results highlight the importance of functional traits, habitat types, ontogenetic stages and spatial scales to community assembly in natural communities.

The microbial rare biosphere: current concepts, methods and ecological principles

2020 ◽  
Author(s):  
Francisco Pascoal ◽  
Rodrigo Costa ◽  
Catarina Magalhães
Keyword(s):  
Community Assembly ◽  
Historical Perspective ◽  
Conceptual Models ◽  
Current Knowledge ◽  
Rare Biosphere ◽  
Ecological Principles ◽  
Integrative View ◽  
Domains Of Life ◽  
And Function ◽  
Microbial Community Assembly

Abstract Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions, and metabolic activity which make-up this communal pool, usually referred to as the ‘rare biosphere’, across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy, and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition, and function.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

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