scholarly journals Ecotype Simulation 2: An improved algorithm for efficiently demarcating microbial species from large sequence datasets

2020 ◽  
Author(s):  
Jason M. Wood ◽  
Eric D. Becraft ◽  
Daniel Krizanc ◽  
Frederick M. Cohan ◽  
David M. Ward
Keyword(s):  
Evolutionary Dynamics ◽  
Microbial Mats ◽  
Hot Springs ◽  
Sequence Data ◽  
Ecological Theory ◽  
Single Species ◽  
Population Based ◽  
Natural Microbial Community ◽  
High Throughput Dna Sequencing ◽  
Fundamental Units

AbstractBackgroundMicrobial systematists have used molecular cutoffs to classify the vast diversity present within a natural microbial community without invoking ecological theory. The use of ecological theory is needed to identify whether or not demarcated groups are the ecologically distinct, fundamental units (ecotypes), necessary for understanding the system. Ecotype Simulation, a Monte-Carlo approach to modeling the evolutionary dynamics of a microbial population based on the Stable Ecotype Model of microbial speciation, has proven useful for finding these fundamental units. For instance, predicted ecotypes of Synechococcus forming microbial mats in Yellowstone National Park hot springs, which were previously considered to be a single species based on phenotype, have been shown to be ecologically distinct, with specialization to different temperature and light levels. Unfortunately, development of high-throughput DNA sequencing methods has outpaced the ability of the program to analyze all of the sequence data produced.ResultsWe developed an improved version of the program called Ecotype Simulation 2, which can rapidly analyze alignments of very large sequence datasets. For instance, while the older version takes days to analyze 200 sequences, the new version can analyze 1.92 × 105 sequences in about six hours. The faster simulation identified similar ecotypes as found with the slower version, but from larger amounts of sequence data.ConclusionsBased on ecological theory, Ecotype Simulation 2 provides a much-needed approach that will help guide microbial ecologists and systematists to the natural, fundamental units of bacterial diversity.

scholarly journals Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

2006 ◽  
Vol 361 (1475) ◽  
pp. 1985-1996 ◽  
Author(s):  
Frederick M Cohan
Keyword(s):  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Molecular Approaches ◽  
Bacterial Speciation ◽  
Bacterial Systematics ◽  
History Of ◽  
Operational Criteria ◽  
Fundamental Units ◽  
Ecological Differences

To completely understand the ecology of a bacterial community, we need to identify its ecologically distinct populations (ecotypes). The greatest promise for enumerating a community's constituent ecotypes is held by molecular approaches that identify bacterial ecotypes as DNA sequence clusters. These approaches succeed when ecotypes correspond with sequence clusters, but some models of bacterial speciation predict a one-to-many and others a many-to-one relationship between ecotypes and sequence clusters. A further challenge is that sequence-based phylogenies often contain a hierarchy of clusters and subclusters within clusters, and there is no widely accepted theory to guide systematists and ecologists to the size of cluster most likely to correspond to ecotypes. While present systematics attempts to use universal thresholds of sequence divergence to help demarcate species, the recently developed ‘community phylogeny’ approach assumes no universal thresholds, but demarcates ecotypes based on the analysis of a lineage's evolutionary dynamics. Theory-based approaches like this one can give a conceptual framework as well as operational criteria for hypothesizing the identity and membership of ecotypes from sequence data; ecology-based approaches can then confirm that the putative ecotypes are actually ecologically distinct. Bacterial ecotypes that are demonstrated to have a history of coexistence as ecologically distinct lineages (based on sequence analysis) and as a prognosis of future coexistence (based on ecological differences), are the fundamental units of bacterial ecology and evolution, and should be recognized by bacterial systematics.

scholarly journals Sex-specific associations of ceramides with cardiopulmonary fitness in the general population

2021 ◽  
Vol 28 (Supplement_1) ◽  
Author(s):  
J Zatloukal ◽  
MRP Markus ◽  
R Ewert ◽  
S Glaeser ◽  
N Friedrich ◽  
...  
Keyword(s):  
Risk Factor ◽  
Cardiopulmonary Exercise Testing ◽  
Positive Association ◽  
Single Species ◽  
Population Based ◽  
Linear Regression Models ◽  
Maximal Power ◽  
Cardiopulmonary Fitness ◽  
Beneficial Effects ◽  
Long Chain

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): German Federal Ministry of Education & Research (BMBF) Introduction According to the WHO 17.9 million people die because of cardiovascular diseases (CVD) each year, being the 3rd leading cause of death worldwide. Low cardiorespiratory fitness (CRF) is an important risk factor for CVD. Recent research showed that long-chain unsaturated ceramides are associated with higher risk of cardiovascular events, thus identifying ceramides as a potential novel and independent risk factor. However, not all ceramides are equal. We previously showed beneficial effects of very-long-chain ceramides (i.e. C24:0 and C24:0/C16:0 ratio) with higher concentrations being inversely associated with all-cause mortality and CVD events. Purpose We would like to investigate, if ceramides mediated their effects on developing CVD by affecting CRF. Therefore, we explored the association of three specific ceramides (C16:0, C22:0 and C24:0) and their ratios with different parameters of CRF. Methods We used data of the population-based Study of Health in Pomerania (SHIP-1) from North Germany (N: 1,247/men: 583, median age: 50.8 years/women: 664, median age: 50.2 years). Ceramides and CRF were assessed by LC/MS assay and symptom-limited cardiopulmonary exercise testing, respectively. VO2peak, VO2@AT, Wmax and respective indexing per kg body weight were used as outcomes. We used sex-stratified, multiple adjusted linear regression models. Participants with asthma, chronic lung disease, LVEF < 40% and cancer were excluded. Results In men, a 1-unit higher C24:0/C16:0 ratio was associated with higher VO2peak/kg (0.199 ml/min/kg [95% CI: 0.032, 0.365], P = 0.019), Wmax (1.368 W [0.033, 2.404], P = 0.010) and Wmax/kg (0.018 W/kg [0.007, 0.029], P = 0.002). In addition, a 1 µg/ml higher C24:0 concentration was related to greater Wmax/kg (0.054 W/kg [0.009, 0.099], P = 0.018). In women, a 1-unit greater C24:0/C16:0 ratio was associated with greater VO2peak (8.603 ml/min [0.019, 17.013], P = 0.045), VO2peak/kg (0.186 ml/min/kg [0.054, 0.319], P = 0.006), VO2@AT/kg (0.136 ml/min/kg [0.040, 0.231], P = 0.005) as well as higher Wmax/kg (0.015 W/kg [0.004, 0.026], P = 0.007). Furthermore, a 1 µg/ml higher C16:0 concentration was related to lower Wmax (-55.447 W [-101.775, -9.119], P = 0.019) and Wmax/kg (-0.736 W/kg [-1.341, -0.130], P = 0.017). Conclusions We report sex-specific associations between ceramides and CRF. In women, C24:0/C16:0 ratio was associated with more CRF parameters than in men. Furthermore, the single species C16:0 was significantly associated with lower maximal power in women only, whereas in men the single species C24:0 was significantly associated with higher maximal power. The positive association of the C24:0/C16:0 ratio with maximal CRF capacity is in agreement with previous findings of beneficial effects on the risk for CVD events and mortality. Future studies should explore the reason for different sex-specific ceramide profiles and whether ceramides are causally mediating their effects on CVD through CRF.

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

scholarly journals In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexusaggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat

2021 ◽  
Vol 9 (3) ◽  
pp. 652
Author(s):  
Shigeru Kawai ◽  
Joval N. Martinez ◽  
Mads Lichtenberg ◽  
Erik Trampe ◽  
Michael Kühl ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Environmental Conditions ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Photosynthetic Bacterium ◽  
Early Morning ◽  
Metabolic Flexibility

Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.

Relationships and revised status of Nagathrips (Thysanoptera: Phlaeothripinae) 

Zootaxa ◽  
2017 ◽  
Vol 4231 (4) ◽  
pp. 577
Author(s):  
R. VARATHARAJAN ◽  
TH. JOHNSON ◽  
SINGH TARUNKUMAR
Keyword(s):  
Sequence Data ◽  
Mitochondrial Gene ◽  
Antennal Segment ◽  
Single Species ◽  
Original Description ◽  
Partial Sequence

The generic name Nagathrips was erected as a sub-genus of Mesothrips for the single species, crenulatus Varatharajan and Singh (2000). Subsequent studies revealed character states that were not included in the original description. These are: prosternal basantra absent; antennal segment III with one slender sense cone, segment IV with three similar sense cones; fore wings parallel-sided with no median constriction. These character states are not found in any species of Mesothrips, a genus of the Tribe Haplothripini (Mound & Minaei 2007), but are typical of members of the Liothrips-lineage (Dang et al. 2014). To confirm such a relationship partial sequence data of the mitochondrial gene (CO1) was obtained and compared with that of Gynaikothrips species. 

scholarly journals Worldwide tracing of mutations and the evolutionary dynamics of SARS-CoV-2

2020 ◽  
Author(s):  
Zhong-Yin Zhou ◽  
Hang Liu ◽  
Yue-Dong Zhang ◽  
Yin-Qiao Wu ◽  
Min-Sheng Peng ◽  
...  
Keyword(s):  
Substitution Rate ◽  
Evolutionary Dynamics ◽  
Vaccine Development ◽  
Sequence Data ◽  
Immune Recognition ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Theoretical Support ◽  
Recurrent Mutations

AbstractUnderstanding the mutational and evolutionary dynamics of SARS-CoV-2 is essential for treating COVID-19 and the development of a vaccine. Here, we analyzed publicly available 15,818 assembled SARS-CoV-2 genome sequences, along with 2,350 raw sequence datasets sampled worldwide. We investigated the distribution of inter-host single nucleotide polymorphisms (inter-host SNPs) and intra-host single nucleotide variations (iSNVs). Mutations have been observed at 35.6% (10,649/29,903) of the bases in the genome. The substitution rate in some protein coding regions is higher than the average in SARS-CoV-2 viruses, and the high substitution rate in some regions might be driven to escape immune recognition by diversifying selection. Both recurrent mutations and human-to-human transmission are mechanisms that generate fitness advantageous mutations. Furthermore, the frequency of three mutations (S protein, F400L; ORF3a protein, T164I; and ORF1a protein, Q6383H) has gradual increased over time on lineages, which provides new clues for the early detection of fitness advantageous mutations. Our study provides theoretical support for vaccine development and the optimization of treatment for COVID-19. We call researchers to submit raw sequence data to public databases.

scholarly journals Changes in Quinone Profiles of Hot Spring Microbial Mats with a Thermal Gradient

1999 ◽  
Vol 65 (1) ◽  
pp. 198-205 ◽  
Author(s):  
Akira Hiraishi ◽  
Taichi Umezawa ◽  
Hiroyuki Yamamoto ◽  
Kenji Kato ◽  
Yonosuke Maki
Keyword(s):  
Thermal Gradient ◽  
Microbial Mats ◽  
Hot Springs ◽  
Hot Spring ◽  
Thermal Gradients ◽  
Cyanobacterial Mats ◽  
Dissimilarity Index ◽  
Quinone Profile ◽  
Bacterial Mats ◽  
Different Temperatures

ABSTRACT The respiratory and photosynthetic quinones of microbial mats which occurred in Japanese sulfide-containing neutral-pH hot springs at different temperatures were analyzed by spectrochromatography and mass spectrometry. All of the microbial mats that developed at high temperatures (temperatures above 68°C) were so-called sulfur-turf bacterial mats and produced methionaquinones (MTKs) as the major quinones. A 78°C hot spring sediment had a similar quinone profile.Chloroflexus-mixed mats occurred at temperatures of 61 to 65°C and contained menaquinone 10 (MK-10) as the major component together with significant amounts of either MTKs or plastoquinone 9 (PQ-9). The sunlight-exposed biomats growing at temperatures of 45 to 56°C were all cyanobacterial mats, in which the photosynthetic quinones (PQ-9 and phylloquinone) predominated and MK-10 was the next most abundant component in most cases. Ubiquinones (UQs) were not found or were detected in only small amounts in the biomats growing at temperatures of 50°C and above, whereas the majority of the quinones of a purple photosynthetic mat growing at 34°C were UQs. A numerical analysis of the quinone profiles was performed by using the following three parameters: dissimilarity index (D), microbial divergence index (MDq ), and bioenergetic divergence index (BDq ). A D matrix tree analysis showed that the hot spring mats consisting of the sulfur-turf bacteria, Chloroflexus spp., cyanobacteria, and purple phototrophic bacteria formed distinct clusters. Analyses ofMDq and BDq values indicated that the microbial diversity of hot spring mats decreased as the temperature of the environment increased. The changes in quinone profiles and physiological types of microbial mats in hot springs with thermal gradients are discussed from evolutionary viewpoints.

Adaptive Diversification Due to Resource Competition in Asexual Models

2011 ◽  
Author(s):  
Michael Doebeli
Keyword(s):  
Resource Selection ◽  
Evolutionary Dynamics ◽  
Resource Competition ◽  
Single Species ◽  
Character Displacement ◽  
Adaptive Diversification ◽  
Ecological Character ◽  
Ecological Character Displacement ◽  
Phenotypic Diversification ◽  
Established Species

This chapter focuses on evolutionary branching in niche position due to frequency-dependent competition. When the majority phenotype of a population is competing for one type of resource, selection may favor minority phenotypes that consume different types of resources, which could result in phenotypic differentiation and divergence. The idea of divergence due to competition is also the basis for the well-known concept of ecological character displacement, although here the focus is not so much on the origin of diversity arising in a single species, but rather on the evolutionary dynamics of existing diversity between different and already established species. Ecological character displacement embodies the possibility that competition between species can drive divergence in characters determining resource use. However, there are alternative evolutionary scenarios for phenotypic diversification. In the context of resource competition, one such alternative is that individuals diversify their diet by evolving a wider niche.

scholarly journals Short-Term Stable Isotope Probing of Proteins Reveals Taxa Incorporating Inorganic Carbon in a Hot Spring Microbial Mat

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Laurey Steinke ◽  
Gordon W. Slysz ◽  
Mary S. Lipton ◽  
Christian Klatt ◽  
James J. Moran ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Inorganic Carbon ◽  
Microbial Mats ◽  
Carbon Fixation ◽  
Hot Springs ◽  
Hot Spring ◽  
Stable Isotope Probing ◽  
Short Term ◽  
Low Light ◽  
Assembly Sequences

ABSTRACT The upper green layer of the chlorophototrophic microbial mats associated with the alkaline siliceous hot springs of Yellowstone National Park consists of oxygenic cyanobacteria (Synechococcus spp.), anoxygenic Roseiflexus spp., and several other anoxygenic chlorophototrophs. Synechococcus spp. are believed to be the main fixers of inorganic carbon (Ci), but some evidence suggests that Roseiflexus spp. also contribute to inorganic carbon fixation during low-light, anoxic morning periods. Contributions of other phototrophic taxa have not been investigated. In order to follow the pathway of Ci incorporation into different taxa, mat samples were incubated with [13C]bicarbonate for 3 h during the early-morning, low-light anoxic period. Extracted proteins were treated with trypsin and analyzed by mass spectrometry, leading to peptide identifications and peptide isotopic profile signatures containing evidence of 13C label incorporation. A total of 25,483 peptides, corresponding to 7,221 proteins, were identified from spectral features and associated with mat taxa by comparison to metagenomic assembly sequences. A total of 1,417 peptides, derived from 720 proteins, were detectably labeled with 13C. Most 13C-labeled peptides were derived from proteins of Synechococcus spp. and Roseiflexus spp. Chaperones and proteins of carbohydrate metabolism were most abundantly labeled. Proteins involved in photosynthesis, Ci fixation, and N2 fixation were also labeled in Synechococcus spp. Importantly, most proteins of the 3-hydroxypropionate bi-cycle for Ci fixation in Roseiflexus spp. were labeled, establishing that members of this taxocene contribute to Ci fixation. Other taxa showed much lower [13C]bicarbonate incorporation. IMPORTANCE Yellowstone hot spring mats have been studied as natural models for understanding microbial community ecology and as modern analogs of stromatolites, the earliest community fossils on Earth. Stable-isotope probing of proteins (Pro-SIP) permitted short-term interrogation of the taxa that are involved in the important process of light-driven Ci fixation in this highly active community and will be useful in linking other metabolic processes to mat taxa. Here, evidence is presented that Roseiflexus spp., which use the 3-hydroxypropionate bi-cycle, are active in Ci fixation. Because this pathway imparts a lower degree of selection of isotopically heavy Ci than does the Calvin-Benson-Bassham cycle, the results suggest a mechanism to explain why the natural abundance of 13C in mat biomass is greater than expected if only the latter pathway were involved. Understanding how mat community members influence the 13C/12C ratios of mat biomass will help geochemists interpret the 13C/12C ratios of organic carbon in the fossil record.

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