scholarly journals Unification of Environmental Metabolomics with Metacommunity Ecology

2020 ◽  
Author(s):  
Robert E. Danczak ◽  
Rosalie K. Chu ◽  
Sarah J. Fansler ◽  
Amy E. Goldman ◽  
Emily B. Graham ◽  
...  
Keyword(s):  
Null Model ◽  
Analytical Techniques ◽  
Functional Trait ◽  
Ecological Communities ◽  
Metacommunity Ecology ◽  
Β Diversity ◽  
Environmental Metabolomics ◽  
Α Diversity ◽  
Underlying Mechanisms ◽  
Mass Spectrometric Techniques

AbstractEnvironmental metabolomics, enabled by high-resolution mass spectrometric techniques, have demonstrated the biogeochemical importance of the metabolites which comprise natural organic matter (NOM). However, significant gaps exist in our understanding of the spatiotemporal organization of NOM composition. We suggest that the underlying mechanisms governing NOM can be revealed by applying tools and concepts from metacommunity ecology to environmental metabolomics. After illustrating the similarities between metabolomes and ecological communities, we call this conceptual synthesis ‘meta-metabolome ecology’ and demonstrate its potential utility using a freshwater mass spectrometry dataset. Specifically, we developed three relational metabolite dendrograms using combinations of molecular properties (i.e., aromaticity index, double-bond equivalents, etc.) and putative biochemical transformations. Using these dendrograms, which are similar to phylogenetic or functional trait trees in ecological communities, we illustrate potential analytical techniques by investigating relationally-informed α-diversity and β-diversity metrics (e.g., MPD, MNTD, UniFrac), and null model analyses (e.g., NRI, NTI, and βNTI). Furthermore, we demonstrate that this synthesis allows ecological communities (e.g., microbes) and the metabolites they produce and consume using the same framework. We propose that applying this framework to a broad range of ecosystems will reveal generalizable principles that can advance our predictive capabilities regarding NOM dynamics.

A quantitative null model of additive diversity partitioning: examining the response of beta diversity to extinction

Paleobiology ◽  
2007 ◽  
Vol 33 (1) ◽  
pp. 116-124 ◽  
Author(s):  
Karen M. Layou
Keyword(s):  
Null Model ◽  
Sampling Strategy ◽  
Diversity Partitioning ◽  
Opposite Pattern ◽  
Β Diversity ◽  
Α Diversity ◽  
Before And After ◽  
Four Levels ◽  
Total Diversity ◽  
Selective Extinction

Paleobiological diversity is often expressed as α (within-sample), β (among-sample), and γ (total) diversities. However, when studying the effects of extinction on diversity patterns, only variations in α and γ diversities are typically addressed. A null model that examines changes in β diversity as a function of percent extinction is presented here.The model examines diversity in the context of a hierarchical sampling strategy that allows for the additive partitioning of γ diversity into mean α and β diversities at varying scales. Here, the sampling hierarchy has four levels: samples, beds, facies, and region; thus, there are four levels of α diversity (α1, α2, α3, α4) and three levels of β diversity (β1, β2, and β3). Taxa are randomly assigned to samples within the hierarchy according to probability of occurrence, and initial mean α and β values are calculated. A regional extinction is imposed, and the hierarchy is resampled from the remaining extant taxa. Post-extinction mean α and β values are then calculated.Both non-selective and selective extinctions with respect to taxon abundance yield decreases in α, β, and γ diversities. Non-selective extinction with respect to taxon abundance shows little effect on diversity partitioning except at the highest extinction magnitudes (above 75% extinction), where the contribution of α1 to total γ increases at the expense of β3, with β1 and β2 varying little with increasing extinction magnitude. The pre-extinction contribution of α1 to total diversity increases with increased probabilities of taxon occurrence and the number of shared taxa between facies. Both β1 and β2 contribute equally to total diversity at low occurrence probabilities, but β2 is negligible at high probabilities, because individual samples preserve all the taxonomic variation present within a facies. Selective extinction with respect to rare taxa indicates a constant increase in α1 and constant decrease in β3 with increasing extinction magnitudes, whereas selective extinction with respect to abundant taxa yields the opposite pattern of an initial decrease in α1 and increase in β3. Both β1 and β2 remain constant with increasing extinction for both cases of selectivity. By comparing diversity partitioning before and after an extinction event, it may be possible to determine whether the extinction was selective with respect to taxon abundances, and if so, whether that selectivity was against rare or abundant taxa.Field data were collected across a Late Ordovician regional extinction in the Nashville Dome of Tennessee, with sampling hierarchy similar to that of the model. These data agree with the abundant-selective model, showing declines in α, β, and γ diversities, and a decrease in α1 and increase in β3, which suggests this extinction may have targeted abundant taxa.

scholarly journals Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties

2020 ◽  
Author(s):  
Robert E. Danczak ◽  
Amy E. Goldman ◽  
Rosalie K. Chu ◽  
Jason G. Toyoda ◽  
Vanessa A. Garayburu-Caruso ◽  
...  
Keyword(s):  
Environmental Filtering ◽  
Molecular Properties ◽  
Freshwater Ecosystem ◽  
Ecological Communities ◽  
Ecological Concept ◽  
Metacommunity Ecology ◽  
Novel Approach ◽  
Underlying Mechanisms ◽  
Insight Into ◽  
Dom Composition

AbstractStream and river systems transport and process substantial amounts of dissolved organic matter (DOM) from terrestrial and aquatic sources to the ocean, with global biogeochemical implications. However, the underlying mechanisms affecting the spatiotemporal organization of DOM composition are under-investigated. To understand the principles governing DOM composition, we leverage the recently proposed synthesis of metacommunity ecology and metabolomics, termed ‘meta-metabolome ecology.’ Applying this novel approach to a freshwater ecosystem, we demonstrated that despite similar molecular properties across metabolomes, metabolite identity significantly diverged due to environmental filtering. We refer to this phenomenon as ‘thermodynamic redundancy,’ which is analogous to the ecological concept of functional redundancy. We suggest that under thermodynamic redundancy, divergent metabolomes can support equivalent biogeochemical function just as divergent ecological communities can support equivalent ecosystem function. As these analyses are performed in additional ecosystems, potentially generalizable principles, like thermodynamic redundancy, can be revealed and provide insight into DOM dynamics.

scholarly journals Microbiome assembly predictably shapes diversity across a range of disturbance frequencies

2021 ◽  
Author(s):  
Ezequiel Santillan ◽  
Stefan Wuertz
Keyword(s):  
Temporal Dynamics ◽  
Ecological Communities ◽  
Β Diversity ◽  
Α Diversity ◽  
Deterministic Processes ◽  
Specialized Function ◽  
Successional Stages ◽  
And Function ◽  
Microbiome Assembly

Diversity is frequently linked to the functional stability of ecological communities. However, its association with assembly mechanisms remains largely unknown, particularly under fluctuating disturbances. Here, we subjected complex bacterial communities in bioreactor microcosms to different frequencies of organic loading shocks, tracking temporal dynamics in their assembly, structure and function. Null modelling revealed a stronger role of stochasticity at intermediate disturbance frequencies, preceding the formation of a peak in α-diversity. Communities at extreme ends of the disturbance range had the lowest α-diversity and highest within-treatment similarity in terms of β-diversity, with stronger deterministic assembly. Stochasticity prevailed during the initial successional stages, coinciding with better specialized function (nitrogen removal). In contrast, general functions (carbon removal and microbial aggregate settleability) benefited from stronger deterministic processes. We showed that changes in assembly processes predictably precede changes in diversity under a gradient of disturbance frequencies, advancing our understanding of the mechanisms behind disturbance-diversity-function relationships.

scholarly journals Microbes and macro-invertebrates show parallel β-diversity but contrasting α-diversity patterns in a marine natural experiment

2019 ◽  
Vol 286 (1912) ◽  
pp. 20190999 ◽  
Author(s):  
Giovanni Rapacciuolo ◽  
J. Michael Beman ◽  
Lauren M. Schiebelhut ◽  
Michael N. Dawson
Keyword(s):  
Natural Experiment ◽  
Similar Degree ◽  
Ecological Communities ◽  
Diversity Patterns ◽  
Β Diversity ◽  
Α Diversity ◽  
Marine Lakes ◽  
Regional Species Pool ◽  
Marine Realm ◽  
Spatio Temporal

Documenting ecological patterns across spatially, temporally and taxonomically diverse ecological communities is necessary for a general understanding of the processes shaping biodiversity. A major gap in our understanding remains the comparison of diversity patterns across a broad spectrum of evolutionarily and functionally diverse organisms, particularly in the marine realm. Here, we aim to narrow this gap by comparing the diversity patterns of free-living microbes and macro-invertebrates across a natural experiment provided by the marine lakes of Palau: geographically discrete and environmentally heterogeneous bodies of seawater with comparable geological and climatic history, and a similar regional species pool. We find contrasting patterns of α-diversity but remarkably similar patterns of β-diversity between microbial and macro-invertebrate communities among lakes. Pairwise dissimilarities in community composition among lakes are positively correlated between microbes and macro-invertebrates, and influenced to a similar degree by marked gradients in oxygen concentration and salinity. Our findings indicate that a shared spatio-temporal and environmental context may result in parallel patterns of β-diversity in microbes and macro-invertebrates, in spite of key trait differences between these organisms. This raises the possibility that parallel processes also influence transitions among regional biota across the tree of life, at least in the marine realm.

Characterization of Gut Microbiota Composition in Hemodialysis Patients With Normal Weight Obesity

2020 ◽  
Vol 105 (6) ◽  
pp. 2006-2014 ◽  
Author(s):  
Ting-Yun Lin ◽  
Ping-Hsun Wu ◽  
Yi-Ting Lin ◽  
Szu-Chun Hung
Keyword(s):  
Gut Microbiota ◽  
Hemodialysis Patients ◽  
Normal Weight ◽  
Normal Body Mass Index ◽  
Fat Percentage ◽  
Β Diversity ◽  
Α Diversity ◽  
Increased Risk ◽  
Normal Weight Obesity ◽  
Underlying Mechanisms

Abstract Background Normal weight obesity (NWO), defined by a normal body mass index (BMI) but increased body fat percentage (BF%), is associated with an increased risk of cardiovascular disease and mortality. NWO is characterized by inflammation and muscle wasting in chronic kidney disease (CKD), but the underlying mechanisms remain largely unknown. Gut microbiota has been implicated in the regulation of host metabolism and may play important roles in the development of NWO in CKD. Methods In this case-control study, we examined the gut microbial diversity and taxonomy in 96 hemodialysis patients with normal weight (BMI < 25 kg/m2 and BF% ≤ 25% for men or ≤ 35% for women; n = 32), NWO (BMI < 25 kg/m2 and BF% > 25% for men or > 35% for women; n = 32), and overweight/obesity (BMI ≥ 25 kg/m2; n = 32), matched for age, gender, and diabetes. BF% was measured using bioimpedance spectroscopy device. Gut microbiota was determined by 16S rRNA sequencing. Results We found that α-diversity was significantly different among the 3 adiposity phenotypes, with NWO being the least diverse. α-diversity was positively correlated with BMI, subjective global assessment score, and physical activity, but negatively correlated with interleukin-6 and tumor necrosis factor-α. Patients with or without NWO were distinguished with respect to principal coordinate analysis of β-diversity. Notably, the relative abundance of butyrate-producing bacteria, such as Faecalibacterium prausnitzii and Coprococcus, was markedly reduced in patients with NWO. Conclusion Our findings support associations between gut dysbiosis and a proinflammatory and catabolic state in hemodialysis patients with NWO.

scholarly journals Is Phylogeny More Useful than Functional Traits for Assessing Diversity Patterns Under Community Assembly Processes?

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1159 ◽  
Author(s):  
Jinshi Xu ◽  
Han Dang ◽  
Mao Wang ◽  
Yongfu Chai ◽  
Yaoxin Guo ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Functional Traits ◽  
Community Assembly ◽  
Phylogenetic Diversity ◽  
Environmental Changes ◽  
Taxonomic Diversity ◽  
Elevational Gradient ◽  
Functional Trait ◽  
Β Diversity ◽  
Α Diversity

Phylogenetic and functional diversities and their relationship are important for understanding community assembly, which relates to forest sustainability. Thus, both diversities have been used in ecological studies evaluating community responses to environmental changes. However, it is unclear whether these diversity measures can uncover the actual community assembly processes. Herein, we examined their utility to assess such assembly processes by analyzing similarities in phylogenetic, functional, and taxonomic α- and β-diversities along an elevational gradient. Additionally, we examined the relationships among environment, phylogeny, and functional traits within the community. Based on our results, we evaluated whether phylogenetic or functional diversity could better reveal the actual community assembly processes. We found that taxonomic, phylogenetic, and functional α-diversities were correlated with one another. Although the functional α-diversity showed a linear correlation with the elevational gradient, taxonomic and phylogenetic α-diversities showed unimodal patterns. Both phylogenetic and functional β-diversities correlated with taxonomic β-diversity, but there was no significant relationship between the former. Overall, our results evidenced that phylogenetic diversity and taxonomic diversity showed similar patterns, whereas functional diversity showed a relatively independent pattern, which may be due to limitations in the functional trait dimensions used in the present study. Although it is difficult to unravel whether the environment shapes phylogeny or functional traits within a community, phylogenetic diversity is a good proxy for assessing the assembly processes, whereas functional diversity may improve knowledge on the community by maximizing information about the functional trait dimensions.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Robert Lavallée ◽  
Claude Guertin
Keyword(s):  
Population Density ◽  
Gut Microbiome ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Economic Damage ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Local Conditions ◽  
Β Diversity ◽  
Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

scholarly journals Arthropod community structure in pastures of an island archipelago (Azores): looking for local–regional species richness patterns at fine-scales

2004 ◽  
Vol 94 (2) ◽  
pp. 111-121 ◽  
Author(s):  
P.A.V. Borges ◽  
V.K. Brown
Keyword(s):  
Species Richness ◽  
Regional Scale ◽  
Local Scale ◽  
Local Species Richness ◽  
Β Diversity ◽  
Arthropod Species ◽  
Α Diversity ◽  
Local Species ◽  
Richness Patterns

AbstractThe arthropod species richness of pastures in three Azorean islands was used to examine the relationship between local and regional species richness over two years. Two groups of arthropods, spiders and sucking insects, representing two functionally different but common groups of pasture invertebrates were investigated. The local–regional species richness relationship was assessed over relatively fine scales: quadrats (= local scale) and within pastures (= regional scale). Mean plot species richness was used as a measure of local species richness (= α diversity) and regional species richness was estimated at the pasture level (= γ diversity) with the ‘first-order-Jackknife’ estimator. Three related issues were addressed: (i) the role of estimated regional species richness and variables operating at the local scale (vegetation structure and diversity) in determining local species richness; (ii) quantification of the relative contributions of α and β diversity to regional diversity using additive partitioning; and (iii) the occurrence of consistent patterns in different years by analysing independently between-year data. Species assemblages of spiders were saturated at the local scale (similar local species richness and increasing β-diversity in richer regions) and were more dependent on vegetational structure than regional species richness. Sucking insect herbivores, by contrast, exhibited a linear relationship between local and regional species richness, consistent with the proportional sampling model. The patterns were consistent between years. These results imply that for spiders local processes are important, with assemblages in a particular patch being constrained by habitat structure. In contrast, for sucking insects, local processes may be insignificant in structuring communities.

scholarly journals Skin Microbiome in Patients with Hand Eczema and Healthy Controls: A Three-week Prospective Study

2021 ◽  
Author(s):  
Line Brok Nørreslet ◽  
Berit Lilje ◽  
Anna Cäcilia Ingham ◽  
Sofie Marie Edslev ◽  
Maja-Lisa Clausen ◽  
...  
Keyword(s):  
Prospective Study ◽  
Disease Severity ◽  
Amplicon Sequencing ◽  
Hand Eczema ◽  
Skin Microbiome ◽  
Healthy Controls ◽  
16S Rrna Amplicon Sequencing ◽  
Chronic Hand Eczema ◽  
Α Diversity ◽  
Underlying Mechanisms

The pathogenesis of chronic hand eczema remains unclear. Insights into the skin microbiome in hand eczema and its potential relevance to disease severity may help to elucidate the underlying mechanisms of hand eczema. The aim of this study was to characterize the microbiome in patients with hand eczema and healthy controls. A 5-visit prospective study was conducted over a period of 3 weeks. At each visit, bacterial swabs were taken from the hands of patients with hand eczema and controls. The microbiome was examined using DNA extraction and 16S rRNA amplicon sequencing (V3–V4 regions). Fifty patients with hand eczema and 50 controls were included (follow-up rate=100%). The baseline bacterial α-diversity was reduced on the hands of patients with hand eczema compared with controls (effect size=–0.31; 95% confidence interval (95% CI) –0.50; –0.11; p = 0.003). The dysbiosis on the patients’ hands was stable over the study period, was associated with disease severity, and was characterized by reduced bacterial diversity and different bacterial community compositions.

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