scholarly journals A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

mBio ◽  
2016 ◽  
Vol 7 (2) ◽  
Author(s):  
Cheryl P. Andam ◽  
James R. Doroghazi ◽  
Ashley N. Campbell ◽  
Peter J. Kelly ◽  
Mallory J. Choudoir ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Genetic Drift ◽  
Range Expansion ◽  
Beta Diversity ◽  
Phylogenetic Diversity ◽  
Dispersal Limitation ◽  
Ecological Processes ◽  
Diversity Gradient ◽  
Regional Diversification ◽  
Insight Into

ABSTRACT We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and both beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Hence, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift. IMPORTANCE Biogeographic patterns provide insight into the evolutionary and ecological processes that govern biodiversity. However, the evolutionary and ecological processes that govern terrestrial microbial diversity remain poorly characterized. We evaluated the biogeography of the genus Streptomyces to show that the diversity of terrestrial bacteria is governed by many of the same processes that govern the diversity of many plant and animal species. While bacteria of the genus Streptomyces are a preeminent source of antibiotics, their evolutionary history, biogeography, and biodiversity remain poorly characterized. The observations we describe provide insight into the drivers of Streptomyces biodiversity and the processes that underlie microbial diversification in terrestrial habitats.

scholarly journals Local-scale determinants of arboreal spider beta diversity in a temperate forest: roles of tree architecture, spatial distance, and dispersal capacity

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5596 ◽  
Author(s):  
Qiongdao Zhang ◽  
Dong He ◽  
Hua Wu ◽  
Wei Shi ◽  
Cong Chen
Keyword(s):  
Beta Diversity ◽  
Environmental Gradient ◽  
Dispersal Limitation ◽  
Local Scale ◽  
Tree Architecture ◽  
Habitat Specialization ◽  
Spatial Distance ◽  
Species Variation ◽  
Dispersal Capacity ◽  
Canopy Volume

Spiders are a functionally important taxon in forest ecosystems, but the determinants of arboreal spider beta diversity are poorly understood at the local scale. We examined spider assemblages in 324 European beech (Fagus sylvatica) trees of varying sizes across three forest stands in Würzburg (Germany) to disentangle the roles of tree architecture, spatial distance, and dispersal capacity on spider turnover across individual trees. A large proportion of tree pairs (66%) showed higher compositional dissimilarity in spider assemblages than expected by chance, suggesting prominent roles of habitat specialization and/or dispersal limitation. Trees with higher dissimilarity in DBH and canopy volume, and to a lesser extent in foliage cover, supported more dissimilar spider assemblages, suggesting that tree architecture comprised a relevant environmental gradient of sorting spider species. Variation partitioning revealed that 28.4% of the variation in beta diversity was jointly explained by tree architecture, spatial distance (measured by principal coordinates of neighbor matrices) and dispersal capacity (quantified by ballooning propensity). Among these, dispersal capacity accounted for a comparable proportion as spatial distance did (6.8% vs. 5.9%). Beta diversity did not significantly differ between high- and low-vagility groups, but beta diversity in species with high vagility was more strongly determined by spatially structured environmental variation. Altogether, both niche specialization, along the environmental gradient defined by tree architecture, and dispersal limitation are responsible for structuring arboreal spider assemblages. High dispersal capacity of spiders appears to reinforce the role of niche-related processes.

scholarly journals Prospective evaluation of the fecal microbiome in dogs with large-cell lymphoma receiving chop chemotherapy

2021 ◽  
Author(s):  
◽  
Jason Couto
Keyword(s):  
Microbial Diversity ◽  
Beta Diversity ◽  
Large Cell ◽  
Amplicon Sequencing ◽  
Healthy Controls ◽  
Chop Chemotherapy ◽  
Fecal Samples ◽  
Fecal Microbiome ◽  
Alpha And Beta Diversity ◽  
Healthy Dogs

The fecal microbiome composition has been associated with reduced efficacy of cancer therapy and adverse side effects in humans, and chemotherapy has been shown to alter the gut microbiome. The relationship between microbiota and chemotherapy efficacy and tolerability has not been investigated in dogs. We aimed to evaluate changes in fecal microbial diversity during a cycle of CHOP chemotherapy in dogs with lymphoma and whether these changes correlated with adverse events or treatment response. Eighteen dogs with lymphoma were prospectively enrolled, and stool samples were acquired weekly for 6 weeks during CHOP. Fecal samples was analyzed via 16S rRNA amplicon sequencing as previously described. Treatment-associated differences in richness, alpha and beta diversity were determined through comparison to data from healthy controls (n = 26) using factorial ANOVA and PERMANOVA. Dogs with lymphoma had decreased fecal microbial diversity when compared with healthy controls at baseline and throughout treatment (p= 0.0002, 0.0003, 0.0001). Alpha and beta diversity did not significantly change in dogs throughout a cycle of CHOP chemotherapy (p = 0.520 and 0.995). Samples pre-treated with antibiotics were significantly less diverse (alpha and beta diversity) than untreated samples (p = 0.002, 0.0001 respectively). Dogs with lymphoma and fecal samples under the presence of antibiotics had higher levels of Escherchia species in their feces compared to normal dogs. The fecal microbiome of healthy dogs and dogs with lymphoma receiving CHOP is relatively stable over time, but dogs with lymphoma have reduced microbial diversity compared to healthy dogs before and during treatment. An increase in Proteobacteria abundance during treatment may be related to chemotherapy and/or antibiotic use.

scholarly journals Different processes shape prokaryotic and picoeukaryotic assemblages in the sunlit ocean microbiome

2018 ◽  
Author(s):  
Ramiro Logares ◽  
Ina M. Deutschmann ◽  
Caterina. R. Giner ◽  
Anders K. Krabberød ◽  
Thomas S. B. Schmidt ◽  
...  
Keyword(s):  
Ecosystem Function ◽  
Sequence Data ◽  
Scale Effects ◽  
Dispersal Limitation ◽  
Global Scale ◽  
Global Ocean ◽  
Ecosystem Functions ◽  
Ecological Processes ◽  
Surface Ocean

ABSTRACTThe smallest members of the sunlit-ocean microbiome (prokaryotes and picoeukaryotes) participate in a plethora of ecosystem functions with planetary-scale effects. Understanding the processes determining the spatial turnover of this assemblage can help us better comprehend the links between microbiome species composition and ecosystem function. Ecological theory predicts thatselection,dispersalanddriftare main drivers of species distributions, yet, the relative quantitative importance of these ecological processes in structuring the surface-ocean microbiome is barely known. Here we quantified the role of selection, dispersal and drift in structuring surface-ocean prokaryotic and picoeukaryotic assemblages by using community DNA-sequence data collected during the global Malaspina expedition. We found that dispersal limitation was the dominant process structuring picoeukaryotic communities, while a balanced combination of dispersal limitation, selection and drift shaped prokaryotic counterparts. Subsequently, we determined the agents exerting abiotic selection as well as the spatial patterns emerging from the action of different ecological processes. We found that selection exerted via temperature had a strong influence on the structure of prokaryotic communities, particularly on species co-occurrences, a pattern not observed among communities of picoeukaryotes. Other measured abiotic variables had limited selective effects on microbiome structure. Picoeukaryotes presented a higher differentiation between neighbouring communities and a higher distance-decay when compared to prokaryotes, agreeing with their higher dispersal limitation. Finally, drift seemed to have a limited role in structuring the sunlit-ocean microbiome. The different predominance of ecological processes acting on particular subsets of the ocean microbiome suggests uneven responses to environmental change.SIGNIFICANCE STATEMENTThe global ocean contains one of the largest microbiomes on Earth and changes on its structure can impact the functioning of the biosphere. Yet, we are far from understanding the mechanisms that structure the global ocean microbiome, that is, the relative importance of environmentalselection,dispersaland random events (drift). We evaluated the role of these processes at the global scale, based on data derived from a circumglobal expedition and found that these ecological processes act differently on prokaryotes and picoeukaryotes, two of the main components of the ocean microbiome. Our work represents a significant contribution to understand the assembly of marine microbial communities, providing also insights on the links between ecological mechanisms, microbiome structure and ecosystem function.

scholarly journals Phylogenetic relationships among the clownfish-hosting sea anemones

2019 ◽  
Author(s):  
Benjamin M. Titus ◽  
Charlotte Benedict ◽  
Robert Laroche ◽  
Luciana C. Gusmão ◽  
Vanessa Van Deusen ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Taxonomic Revision ◽  
Sea Anemone ◽  
Coral Triangle ◽  
Sea Anemones ◽  
Ecological Processes ◽  
Holistic Understanding ◽  
The Family ◽  
Genus 2 ◽  
Insight Into

AbstractThe clownfish-sea anemone symbiosis has been a model system for understanding fundamental evolutionary and ecological processes. However, our evolutionary understanding of this symbiosis comes entirely from studies of clownfishes. A holistic understanding of a model mutualism requires systematic, biogeographic, and phylogenetic insight into both partners. Here, we conduct the largest phylogenetic analysis of sea anemones (Order Actiniaria) to date, with a focus on expanding the biogeographic and taxonomic sampling of the 10 nominal clownfish-hosting species. Using a combination of mtDNA and nuDNA loci we test 1) the monophyly of each clownfish-hosting family and genus, 2) the current anemone taxonomy that suggests symbioses with clownfishes evolved multiple times within Actiniaria, and 3) whether, like the clownfishes, there is evidence that host anemones have a Coral Triangle biogeographic origin. Our phylogenetic reconstruction demonstrates widespread poly-and para-phyly at the family and genus level, particularly within the family Stichodactylidae and genus Sticodactyla, and suggests that symbioses with clownfishes evolved minimally three times within sea anemones. We further recover evidence for a Tethyan biogeographic origin for some clades. Our data provide the first evidence that clownfish and some sea anemone hosts have different biogeographic origins, and that there may be cryptic species of host anemones. Finally, our findings reflect the need for a major taxonomic revision of the clownfish-hosting sea anemones.

Taxonomic Dependency of Beta Diversity for Bacteria, Archaea and Fungi in a Semi-Arid Lake

2021 ◽  
Author(s):  
Haijun Yuan ◽  
Weizhen Zhang ◽  
Huaqun Yin ◽  
Runyu Zhang ◽  
Jianjun Wang
Keyword(s):  
Water Depth ◽  
Beta Diversity ◽  
Species Turnover ◽  
Environmental Drivers ◽  
Ecological Processes ◽  
Environmental Selection ◽  
Community Variation ◽  
Taxonomic Groups ◽  
Semi Arid ◽  
Total Beta

Abstract Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of Proteobacteria, Chloroflexi, Euryarchaeota and Rozellomycota increased towards deep water, while Acidobacteria, Parvarchaeota and Chytridiomycota decreased. For bacteria and archaea, there were significant (P < 0.05) decreasing water-depth patterns for LCBD and LCBDRepl (i.e., species replacement), while increasing patterns for total beta diversity and turnover, implying that total beta diversity and LCBD were dominated by species turnover or LCBDRepl. Further, bacteria showed a strong correlation with archaea regarding LCBD, total beta diversity and turnover. Such parallel patterns among bacteria and archaea were underpinned by similar ecological processes like environmental selection. Total beta diversity and turnover were largely affected by sediment total nitrogen, while LCBD and LCBDRepl were mainly constrained by water NO2−-N and NO3−-N. For fungal community variation, no significant patterns were observed, which may be due to different drivers like water nitrogen or phosphorus. Taken together, our findings provide compelling evidences for disentangling the underlying mechanisms of community variation in multiple aquatic microbial taxonomic groups.

scholarly journals Rapid climate change results in long-lasting spatial homogenization of phylogenetic diversity

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Bianca Saladin ◽  
Loïc Pellissier ◽  
Catherine H. Graham ◽  
Michael P. Nobis ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
Climate Change ◽  
Spatial Variability ◽  
Phylogenetic Diversity ◽  
Climate Changes ◽  
Northern Europe ◽  
Seed Plants ◽  
Climate Oscillations ◽  
The Past ◽  
Rapid Climate Change ◽  
Insight Into

Abstract Scientific understanding of biodiversity dynamics, resulting from past climate oscillations and projections of future changes in biodiversity, has advanced over the past decade. Little is known about how these responses, past or future, are spatially connected. Analyzing the spatial variability in biodiversity provides insight into how climate change affects the accumulation of diversity across space. Here, we evaluate the spatial variation of phylogenetic diversity of European seed plants among neighboring sites and assess the effects of past rapid climate changes during the Quaternary on these patterns. Our work shows a marked homogenization in phylogenetic diversity across Central and Northern Europe linked to high climate change velocity and large distances to refugia. Our results suggest that the future projected loss in evolutionary heritage may be even more dramatic, as homogenization in response to rapid climate change has occurred among sites across large landscapes, leaving a legacy that has lasted for millennia.

scholarly journals Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research

Diversity ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 288
Author(s):  
Nuria Macías-Hernández ◽  
Marc Domènech ◽  
Pedro Cardoso ◽  
Brent C. Emerson ◽  
Paulo Alexandre Vieira Borges ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Dna Barcode ◽  
Phylogenetic Reconstruction ◽  
Local Communities ◽  
Background Information ◽  
Ecological Processes ◽  
Phylogenetic Structure ◽  
Topological Constraint ◽  
Ecosystem Research

Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies.

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