scholarly journals Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11386
Author(s):  
Jose Luis Gonzalez-Pimentel ◽  
Tamara Martin-Pozas ◽  
Valme Jurado ◽  
Ana Zelia Miller ◽  
Ana Teresa Caldeira ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Major Elements ◽  
Morphological Characterization ◽  
Lava Tube ◽  
Ecological Functions ◽  
La Palma ◽  
Functional Profiling ◽  
Microbially Induced Carbonate Precipitation ◽  
Genome Annotations ◽  
Generation Sequencing

Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37–89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72–96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements.

scholarly journals Cyanobacterial Mats in Calcite-Precipitating Serpentinite-Hosted Alkaline Springs of the Voltri Massif, Italy

2020 ◽  
Vol 9 (1) ◽  
pp. 62
Author(s):  
Aysha Kamran ◽  
Kathrin Sauter ◽  
Andreas Reimer ◽  
Theresa Wacker ◽  
Joachim Reitner ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Microbial Mats ◽  
Environmental Dna ◽  
Cyanobacterial Mats ◽  
Cyanobacterial Community ◽  
Mineral Precipitation ◽  
Community Based ◽  
Specific Adaptation ◽  
Carbonate Buildups ◽  
Generation Sequencing

(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10–12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3–4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments.

scholarly journals Draft Genome Sequences of Two Streptomyces Strains, MZ03-37T and MZ03-48, Isolated from Lava Tube Speleothems

2020 ◽  
Vol 9 (25) ◽  
Author(s):  
Jose L. Gonzalez-Pimentel ◽  
Valme Jurado ◽  
Bernardo Hermosin ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
Canary Islands ◽  
Draft Genome ◽  
Bacterial Strains ◽  
Lava Tube ◽  
Genome Sequences ◽  
La Palma ◽  
Genomic Analyses

ABSTRACT Two Streptomyces strains were isolated from a lava tube in La Palma, Canary Islands. Genomic analyses suggest that the two strains could belong to the same species. Here, we report the draft genomes for these bacterial strains.

scholarly journals Multivariate statistical techniques for metagenomic analysis of microbial community recovered from environmental samples

2018 ◽  
Vol 24 ◽  
pp. 45-53 ◽  
Author(s):  
Z Akond ◽  
M Alam ◽  
MS Ahmed ◽  
MNH Mollah
Keyword(s):  
Microbial Communities ◽  
Microbial Mats ◽  
Statistical Techniques ◽  
Multivariate Statistical ◽  
Linear Discriminant ◽  
Metabolic Functions ◽  
Metabolic Variables ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Shed Light

High-throughput big dataset generated through next generation sequencing (NGS) of DNA samples helps identify key differences in the function and taxonomy between microbial communities as well as shed light on the diversity of microbes, cooperation and evolution in any particular ecosystem. During this study, three statistical techniques namely, Random Forest (RF), Multidimensional Scaling (MDS) and Linear Discriminant Analysis (LDA) approaches were employed for functional analysis of 212 publicly available metagenomic datasets within and between 10 environments against 27 metabolic functions. RF generates the 8 most important metabolic variables along with MDS and LDA among which Photosynthesis has the highest score (70.20); Phages, prophages has the second highest score (61.31) and Membrane Transport was found to have the eighth highest score (45.29). The MDS plot was found useful to visualize the separation of the microbes from human or animal hosts from other samples along the first dimension and the separation of the aquatic and mat communities along the second dimension. LDA analyses compared the extent of the microbial samples into three broad groups: the human and animal associated samples, the microbial mats, and the aquatic samples. RF showed that phage activity is a major difference between host-associated microbial communities and free-living. The MDS and LDA techniques suggest that mat communities were unique from both the animal associated metagenomes and the aquatic samples with differences in the vitamin and cofactor metabolism.J. bio-sci. 24: 45-53, 2016

Integrating microbiome, transcriptome and metabolome data to investigate gastric disease pathogenesis: a concise review

2021 ◽  
Vol 23 ◽  
Author(s):  
Dalla Doohan ◽  
Yudith Annisa Ayu Rezkitha ◽  
Langgeng Agung Waskito ◽  
Ratha-korn Vilaichone ◽  
Yoshio Yamaoka ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Human Microbiome Project ◽  
Gastric Disease ◽  
Disease Pathogenesis ◽  
Multiple Datasets ◽  
High Throughput Technology ◽  
Functional Profiling ◽  
Condition Indicator ◽  
The Relationship ◽  
Generation Sequencing

Abstract Microbiome, the study of microbial communities in specific environments, has developed significantly since the Human Microbiome Project began. Microbiomes have been associated with changes within environmental niches and the development of various diseases. The development of high-throughput technology such as next-generation sequencing has also allowed us to perform transcriptome studies, which provide accurate functional profiling data. Metabolome studies, which analyse the metabolites found in the environment, are the most direct environmental condition indicator. Although each dataset provides valuable information on its own, the integration of multiple datasets provides a deeper understanding of the relationship between the host, agent and environment. Therefore, network analysis using multiple datasets might give a clearer understanding of disease pathogenesis.

scholarly journals Bacterial and Fungal Diversity in Sediment and Water Column From the Abyssal Regions of the Indian Ocean

2021 ◽  
Vol 8 ◽  
Author(s):  
Natasha Maria Barnes ◽  
Samir R. Damare ◽  
Belle Damodara Shenoy
Keyword(s):  
Next Generation Sequencing ◽  
Indian Ocean ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Water Column ◽  
Deep Sea ◽  
Fungal Diversity ◽  
Ecological Functions ◽  
The Indian Ocean ◽  
Generation Sequencing

The deep sea is the largest environment on Earth, comprising important resources of commercial interest. It is composed of a wide variety of ecosystems, which is home to often unique organisms that are yet to be described. The deep-sea is one of the least studied environments, where research is strongly linked to technological access and advances. With the recent advances in the next-generation sequencing and bioinformatics tools, there is an enhanced understanding of microbial diversity and ecological functions in deep sea. Multidisciplinary programs are being undertaken to investigate into microbial communities in diverse marine environments. As compared to other Oceans, the deeper parts of Indian Ocean are still poorly sampled and studied for bacterial, and more so fungal diversity. The studies reporting usage of modern sequencing tools to describe uncultured microbial diversity have seen a rise in numbers in the last decade. In this review, we summarize the important findings of research works carried on bacterial and fungal diversity from the abyssal regions of the Indian Ocean and provide our views on possible future paths.

scholarly journals Ciguatera-Causing Dinoflagellate Gambierdiscus spp. (Dinophyceae) in a Subtropical Region of North Atlantic Ocean (Canary Islands): Morphological Characterization and Biogeography

Toxins ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 423 ◽  
Author(s):  
Isabel Bravo ◽  
Francisco Rodriguez ◽  
Isabel Ramilo ◽  
Pilar Rial ◽  
Santiago Fraga
Keyword(s):  
Canary Islands ◽  
Cultured Cells ◽  
North Atlantic Ocean ◽  
Morphological Variability ◽  
Molecular Data ◽  
Morphological Characterization ◽  
La Palma ◽  
Field Samples ◽  
Length Width ◽  
La Gomera

Dinoflagellates belonging to the genus Gambierdiscus produce ciguatoxins (CTXs), which are metabolized in fish to more toxic forms and subsequently cause ciguatera fish poisoning (CFP) in humans. Five species of Gambierdiscus have been described from the Canary Islands, where CTXs in fish have been reported since 2004. Here we present new data on the distribution of Gambierdiscus species in the Canary archipelago and specifically from two islands, La Palma and La Gomera, where the genus had not been previously reported. Gambierdiscus spp. concentrations were low, with maxima of 88 and 29 cells·g−1 wet weight in samples from La Gomera and La Palma, respectively. Molecular analysis (LSUrRNA gene sequences) revealed differences in the species distribution between the two islands: only G. excentricus was detected at La Palma whereas four species, G. australes, G. caribaeus, G. carolinianus, and G. excentricus, were identified from La Gomera. Morphometric analyses of cultured cells of the five Canary Islands species and of field specimens from La Gomera included cell size and a characterization of three thecal arrangement traits: (1) the shape of the 2′ plate, (2) the position of Po in the anterior suture of the 2′ plate, and (3) the length–width relationship of the 2″″ plate. Despite the wide morphological variability within the culture and field samples, the use of two or more variables allowed the discrimination of two species in the La Gomera samples: G. cf. excentricus and G. cf. silvae. A comparison of the molecular data with the morphologically based classification demonstrated important coincidences, such as the dominance of G. excentricus, but also differences in the species composition of Gambierdiscus, as G. caribaeus was detected in the study area only by using molecular methods.

Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Dapeng Li ◽  
Emmanuel Gaquerel
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Test Theory ◽  
Annual Review ◽  
Publication Date ◽  
Next Generation ◽  
Metabolic Diversity ◽  
Ecological Functions ◽  
Metabolome Data ◽  
Generation Sequencing

The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Morphological Characterization of Mycobacteriophage R1

1974 ◽  
Vol 32 ◽  
pp. 254-255
Author(s):  
B. L. Soloff ◽  
T. A. Rado
Keyword(s):  
Carbon Source ◽  
Stationary Phase ◽  
Growth Phase ◽  
Minimal Medium ◽  
Morphological Characterization ◽  
Logarithmic Growth Phase ◽  
Complete Lysis ◽  
Lysogenic Culture ◽  
Logarithmic Growth

Mycobacteriophage R1 was originally isolated from a lysogenic culture of M. butyricum. The virus was propagated on a leucine-requiring derivative of M. smegmatis, 607 leu−, isolated by nitrosoguanidine mutagenesis of typestrain ATCC 607. Growth was accomplished in a minimal medium containing glycerol and glucose as carbon source and enriched by the addition of 80 μg/ ml L-leucine. Bacteria in early logarithmic growth phase were infected with virus at a multiplicity of 5, and incubated with aeration for 8 hours. The partially lysed suspension was diluted 1:10 in growth medium and incubated for a further 8 hours. This permitted stationary phase cells to re-enter logarithmic growth and resulted in complete lysis of the culture.

Ultrastructural Localization of Acid Mucosubstance in Skeletal Muscle

1967 ◽  
Vol 25 ◽  
pp. 52-53 ◽  
Author(s):  
William J. Dougherty ◽  
Samuel S. Spicer
Keyword(s):  
Striated Muscle ◽  
Divalent Cations ◽  
Ultrastructural Localization ◽  
Major Elements ◽  
Frozen Sections ◽  
Thorium Dioxide ◽  
Iron Solution ◽  
Coupling System ◽  
Psoas Muscles ◽  
Formalin Fixed

In recent years, considerable attention has focused on the morphological nature of the excitation-contraction coupling system of striated muscle. Since the study of Porter and Palade, it has become evident that the sarcoplastic reticulum (SR) and transverse tubules constitute the major elements of this system. The problem still exists, however, of determining the mechamisms by which the signal to interdigitate is presented to the thick and thin myofilaments. This problem appears to center on the movement of Ca++ions between myofilaments and SR. Recently, Philpott and Goldstein reported acid mucosubstance associated with the SR of fish branchial muscle using the colloidal thorium dioxide technique, and suggested that this material may serve to bind or release divalent cations such as Ca++. In the present study, Hale's iron solution adapted to electron microscopy was applied to formalin-fixed myofibrils isolated from glycerol-extracted rabbit psoas muscles and to frozen sections of formalin-fixed rat psoas muscles.

A morphological and energy-dispersive x-ray spectroscopy (EDS) investigation of separator-grade cellophane

1994 ◽  
Vol 52 ◽  
pp. 430-431
Author(s):  
Michael E. Rock ◽  
Vern Kennedy ◽  
Bhaskar Deodhar ◽  
Thomas G. Stoebe
Keyword(s):  
Extrusion Process ◽  
Morphological Characterization ◽  
Energy Dispersive ◽  
Regenerated Cellulose ◽  
Battery System ◽  
X Ray ◽  
Functional Differences ◽  
Transmission Electron ◽  
Separator Material ◽  
Underwater Target

Cellophane is a composite polymer material, made up of regenerated cellulose (usually derived from wood pulp) which has been chemically transformed into "viscose", then formed into a (1 mil thickness) transparent sheet through an extrusion process. Although primarily produced for the food industry, cellophane's use as a separator material in the silver-zinc secondary battery system has proved to be another important market. We examined 14 samples from five producers of cellophane, which are being evaluated as the separator material for a silver/zinc alkaline battery system in an autonomous underwater target vehicle. Our intent was to identify structural and/or chemical differences between samples which could be related to the functional differences seen in the lifetimes of these various battery separators. The unused cellophane samples were examined by transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDS). Cellophane samples were cross sectioned (125-150 nm) using a diamond knife on a RMC MT-6000 ultramicrotome. Sections were examined in a Philips 430-T TEM at 200 kV. Analysis included morphological characterization, and EDS (for chemical composition). EDS was performed using an EDAX windowless detector.

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