scholarly journals Functional Metabolic Diversity of Bacterioplankton in Maritime Antarctic Lakes

2021 ◽  
Vol 9 (10) ◽  
pp. 2077
Author(s):  
Antonio Picazo ◽  
Juan Villaescusa ◽  
Carlos Rochera ◽  
Javier Miralles-Lorenzo ◽  
Antonio Quesada ◽  
...  
Keyword(s):  
Trophic Status ◽  
Carbon Sources ◽  
Anaerobic Respiration ◽  
Morphological Characteristics ◽  
Sequencing Data ◽  
Eutrophic Lakes ◽  
Biological Communities ◽  
Biolog Ecoplates ◽  
Metabolic Activities ◽  
Status Data

A summer survey was conducted on the bacterioplankton communities of seven lakes from Byers Peninsula (Maritime Antarctica), differing in trophic and morphological characteristics. Predictions of the metabolic capabilities of these communities were performed with FAPROTAX using 16S rRNA sequencing data. The versatility for metabolizing carbon sources was also assessed in three of the lakes using Biolog Ecoplates. Relevant differences among lakes and within lake depths were observed. A total of 23 metabolic activities associated to the main biogeochemical cycles were foreseen, namely, carbon (11), nitrogen (4), sulfur (5), iron (2), and hydrogen (1). The aerobic metabolisms dominated, although anaerobic respiration was also relevant near the lakes’ bottom as well as in shallow eutrophic lakes with higher nutrient and organic matter contents. Capacity for using carbon sources further than those derived from the fresh autochthonous primary production was detected. Clustering of the lakes based on metabolic capabilities of their microbial communities was determined by their trophic status, with functional diversity increasing with trophic status. Data were also examined using a co-occurrence network approach, indicating that the lakes and their catchments have to be perceived as connected and interacting macrosystems, where either stochastic or deterministic mechanisms for the assembling of communities may occur depending on the lake’s isolation. The hydrological processes within catchments and the potential metabolic plasticity of these biological communities must be considered for future climate scenarios in the region, which may extend the growing season and increase biomass circulation.

Application of Phenotype Microarray for Profiling Carbon Sources Utilization between Biofilm and Non-Biofilm of Pseudomonas aeruginosa from Clinical Isolates

2020 ◽  
Vol 21 (14) ◽  
pp. 1539-1550
Author(s):  
Nur S. Ismail ◽  
Suresh K. Subbiah ◽  
Niazlin M. Taib
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Carbon Sources ◽  
Anaerobic Respiration ◽  
Regulatory System ◽  
Negative Control ◽  
High Morbidity ◽  
Metabolic Profiles ◽  
Phenotype Microarray ◽  
Diverse Environment ◽  
Phenotype Microarrays

Background: This is the fastest work in obtaining the metabolic profiles of Pseudomonas aeruginosa in order to combat the infection diseases which leads to high morbidity and mortality rates. Pseudomonas aeruginosa is a high versatility of gram-negative bacteria that can undergo aerobic and anaerobic respiration. Capabilities in deploying different carbon sources, energy metabolism and regulatory system, ensure the survival of this microorganism in the diverse environment condition. Determination of differences in carbon sources utilization among biofilm and non-biofilm of Pseudomonas aeruginosa provides a platform in understanding the metabolic activity of the microorganism. Methods: The study was carried out from September 2017 to February 2019. Four archive isolates forming strong and intermediate biofilm and non-biofilms producer were subcultured from archive isolates. ATCC 27853 P. aeruginosa was used as a negative control or non-biofilm producing microorganism. Biofilm formation was confirmed by Crystal Violet Assay (CVA) and Congo Red Agar (CRA). Metabolic profiles of the biofilm and non-biofilms isolates were determined by phenotype microarrays (Biolog Omnilog). Results and Discussion: In this study, Pseudomonas aeruginosa biofilm isolates utilized uridine, L-threonine and L-serine while non-biofilm utilized adenosine, inosine, monomethyl, sorbic acid and succinamic acid. Conclusion: The outcome of this result will be used for future studies to improve detection or inhibit the growth of P. aeruginosa biofilm and non-biofilm respectively.

scholarly journals Genetic Diversity of Small Eukaryotes in Lakes Differing by Their Trophic Status

2005 ◽  
Vol 71 (10) ◽  
pp. 5935-5942 ◽  
Author(s):  
Marie Lefranc ◽  
Aurélie Thénot ◽  
Cécile Lepère ◽  
Didier Debroas
Keyword(s):  
Trophic Status ◽  
Eutrophic Lake ◽  
Rrna Genes ◽  
Eutrophic Lakes ◽  
Massif Central ◽  
Operational Taxonomic Units ◽  
Single Clone ◽  
18S Rrna Genes ◽  
Lake Pavin ◽  
Environmental Sequences

ABSTRACT Small eukaryotes, cells with a diameter of less than 5 μm, are fundamental components of lacustrine planktonic systems. In this study, small-eukaryote diversity was determined by sequencing cloned 18S rRNA genes in three libraries from lakes of differing trophic status in the Massif Central, France: the oligotrophic Lake Godivelle, the oligomesotrophic Lake Pavin, and the eutrophic Lake Aydat. This analysis shows that the least diversified library was in the eutrophic lake (12 operational taxonomic units [OTUs]) and the most diversified was in the oligomesotrophic lake (26 OTUs). Certain groups were present in at least two ecosystems, while the others were specific to one lake on the sampling date. Cryptophyta, Chrysophyceae, and the strictly heterotrophic eukaryotes, Ciliophora and fungi, were identified in the three libraries. Among the small eukaryotes found only in two lakes, Choanoflagellida and environmental sequences (LKM11) were not detected in the eutrophic system whereas Cercozoa were confined to the oligomesotrophic and eutrophic lakes. Three OTUs, linked to the Perkinsozoa, were detected only in the Aydat library, where they represented 60% of the clones of the library. Chlorophyta and Haptophyta lineages were represented by a single clone and were present only in Godivelle and Pavin, respectively. Of the 127 clones studied, classical pigmented organisms (autotrophs and mixotrophs) represented only a low proportion regardless of the library's origin. This study shows that the small-eukaryote community composition may differ as a function of trophic status; certain lineages could be detected only in a single ecosystem.

scholarly journals The usual anaerobic bacterial suspects extracted from a global metagenomic database of Covid19 patients from Peru, Cambodia, China, Brazil and the US - Prevotella, Veillonella, Capnocytophaga, Fusobacterium, Oribacterium and Bacteroides should be monitored for colonization

2020 ◽  
Author(s):  
Sandeep Chakraborty
Keyword(s):  
Anaerobic Bacteria ◽  
Anaerobic Respiration ◽  
Clinical Results ◽  
Cellular Level ◽  
Heme Binding ◽  
Sequencing Data ◽  
The Us ◽  
Hemoglobin Degradation ◽  
Mitochondrial Cytochrome Oxidase ◽  
Different Parts

The Covid19 pandemic [1], triggered by novel strain of a coronavirus SARS-Cov2 [2] has spread globally like a wildfire [3] after being first detected in Wuhan.Previous studies from China, Brazil and the US:Previously, several sequencing datasets - some of them published [4–9], others having sequencing data sub- mitted in NCBI (with no associated publications) [10–13] - have revealed the metagenome in these patients from different parts of the world. The overwhelming presence of anaerobic bacteria (very low concentration of oxygen kills them) in these patients has led to the theory that antibiotics (like doxycycline/Metronidazole) targeting these specific organisms may provide better clinical results [14].Two more studies added - patients from Peru and Cambodia:Here, two more studies from Peru (Table 1) and Cambodia (Table 2) provide further corroboration to the anaerobic bacteria theory. These anaerobic bacteria have virtually colonized the metagenome - pushing other aerobic species out of the niche, disrupting the homeostasis. Around 30% and 23% of the reads from Peru and Cambodia are bacterial, respectively. This is not observed in other patients, even when having chronic issues [15].Common opportunistic anaerobic bacteria in this global metagenomic Covid19 datasetHere, I enumerate common opportunistic anaerobic bacteria present in this global metagenomic Covid19 dataset (Table 3). Any or multiple of these might become the main colonizer after SARS-Cov2 infection in Covid19. The trigger of such an event is still elusive. However, once this happens, some of these bacte- ria express hemoglobin degrading proteins [16], heme-binding proteins sequestering heme after hemoglobin degradation [17], ‘plundering‘ iron, and thereby sequestering oxygen [18]. Hypoxia could also result from formate, the by-product of anaerobic respiration, which inhibits mitochondrial cytochrome oxidase, causing hypoxia at the cellular level [19].

scholarly journals Assessing the Microbial Communities in Four Different Daqusby Using PCR-DGGE, PLFA, and Biolog Analyses

2020 ◽  
Vol 69 (1) ◽  
pp. 27-37
Author(s):  
YUXI LING ◽  
WENYING LI ◽  
TONG TONG ◽  
ZUMING LI ◽  
QIAN LI ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Phospholipid Fatty Acid ◽  
Bacterial Species ◽  
Carbon Sources ◽  
Bacterial Biomass ◽  
Biolog Ecoplates ◽  
Different Types ◽  
Gradient Gel Electrophoresis ◽  
Plfa Analysis

Daqu made from raw wheat, barley or pea is used as an inoculum for the fermentation of Chinese Baijiu. In this study, the microbial communities of four different types of Daqus (sauce-flavor Wuling Daqu, sauce and strong-flavor Baisha Daqu, strong-flavor Deshan Daqu, and light-flavor Niulanshan Daqu) were analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), phospholipid fatty acid (PLFA) analysis, and Biolog EcoPlates analysis (Biolog). Clear differences were seen between the microbial communities of the four Daqus. PCR-DGGE showed differences in the number and brightness of bands between the Daqus, indicating the presence of unique bacterial species in Deshan Daqu, Wuling Daqu, and Niulanshan Daqu. Lactobacillus sanfranciscensis, Bacillus thermoamylovorans, and some unclassified bacteria were unique to Wuling Daqu, Deshan Daqu, and Niulanshan Daqu, respectively. Moreover, some bacterial species were observed in all four Daqus. A total of 26 PLFAs between C12 to C20 were detected from the four Daqus by PLFA analysis. Wuling Daqu had the highest total and fungal biomasses, Baisha Daqu had the highest bacterial biomass, and Niulanshan Daqu had the highest ratio of fungal biomass to bacterial biomass. The Biolog results indicated differences in the carbon source use and mode of the four Daqus, and also demonstrated that each Daqu had varying abilities to utilize different types of carbon sources. The cluster analysis of the three methods showed that the microbial communities of the four Daqus were different. This study also demonstrates the applicability of the three analytical methods in the evaluating of the microbial communities of Daqus.

scholarly journals Renewable Biodiesel Production from Oleaginous Yeast Biomass Using Industrial Wastes

2020 ◽  
Vol 141 ◽  
pp. 03010
Author(s):  
Sasithorn Kongruang ◽  
Sittiruk Roytrakul ◽  
Malinee Sriariyanun
Keyword(s):  
Fatty Acid ◽  
Second Generation ◽  
Carbon Sources ◽  
Morphological Characteristics ◽  
Rhodotorula Glutinis ◽  
Industrial Wastes ◽  
Biodiesel Production ◽  
Yeast Strains ◽  
Fatty Acid Profiling ◽  
Carbon Substrates

The accumulation lipid from oleaginous microorganisms is recognized as a second generation fuel. Biooil is known to as intracellular product of oily yeast utilizing various carbon substrates and converting different quantities of lipids in the form of triacylglycerols. This second generation fuel can be used to make biodiesel via a transesterification process. This study investigated the morphological characteristics of eight strains of Thai oleaginous yeasts via microscopy and analyzed the fatty acid profiling of yeasts cultured in three carbon sources: glucose, sugar cane molasses and crude glycerol in order to estimate biodiesel properties. To approach this goal, batch fermentations were used to culture eight yeast strains, Rhodosporidium toruloides TISTR 5123, TISTR 5154, TISTR 5149, Yarrowia lipolytica TISTR 5054, TISTR 5151, TISTR 5621, Rhodotorula glutinis TISTR 5159 and Rhodotorula graminis TISTR 5124 for 96 h under 30°C at 250 rpm. Result revealed that eight yeast strains contained significant amounts of fatty acids and lipids and accumulated mainly palmitic acid (C16:0), stearic acid (C18:0), oleic acid (C 18:1) and linoleic acid (C18:2), and they are suitable for the production of biodiesel. Fatty acid productions and profiles indicated that these yeast strains can be potentially used as the triacylglycerols producers for biodiesel production.

scholarly journals Phenotype profiling of white-nose syndrome pathogen Pseudogymnoascus destructans and closely-related Pseudogymnoascus pannorum reveals metabolic differences underlying fungal lifestyles

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 665 ◽  
Author(s):  
Vishnu Chaturvedi ◽  
Holland DeFiglio ◽  
Sudha Chaturvedi
Keyword(s):  
In Silico ◽  
Carbon Sources ◽  
The United States ◽  
Nitrogen Compounds ◽  
Pseudogymnoascus Destructans ◽  
White Nose Syndrome ◽  
Nutrient Supplements ◽  
Carbohydrate Degradation ◽  
Metabolic Activities ◽  
Phosphorous Compounds

Background: Pseudogymnoascus destructans, a psychrophile, causes bat white-nose syndrome (WNS). Pseudogymnoascus pannorum, a closely related fungus, causes human and canine diseases rarely. Both pathogens were reported from the same mines and caves in the United States, but only P. destructans caused WNS. Earlier genome comparisons revealed that P. pannorum contained more deduced proteins with ascribed enzymatic functions than P. destructans. Methods: We performed metabolic profiling with Biolog PM microarray plates to confirm in silico gene predictions. Results: P. pannorum utilized 78 of 190 carbon sources (41%), and 41 of 91 nitrogen compounds (43%) tested. P. destructans used 23 carbon compounds (12%) and 23 nitrogen compounds (24%). P. destructans exhibited more robust growth on the phosphorous compounds and nutrient supplements (83% and 15%, respectively) compared to P. pannorum (27% and 1%, respectively.). P. pannorum exhibited higher tolerance to osmolytes, pH extremes, and a variety of chemical compounds than P. destructans. Conclusions: An abundance of carbohydrate degradation pathways combined with robust stress tolerance provided clues for the soil distribution of P. pannorum. The limited metabolic profile of P. destructans was compatible with in silico predictions of far fewer proteins and enzymes. P. destructans ability to catabolize diverse phosphorous and nutrient supplements might be critical in the colonization and invasion of bat tissues. The present study of 1,047 different metabolic activities provides a framework for future gene-function investigations of the unique biology of the psychrophilic fungi.

scholarly journals Crude Oil Degrading Fingerprint and the Overexpression of Oxidase and Invasive Genes for n-hexadecane and Crude Oil Degradation in the Acinetobacter pittii H9-3 Strain

2019 ◽  
Vol 16 (2) ◽  
pp. 188 ◽  
Author(s):  
Yang Wang ◽  
Qiuyu Wang ◽  
Limei Liu
Keyword(s):  
Crude Oil ◽  
Carbon Sources ◽  
Morphological Characteristics ◽  
Oil Degradation ◽  
16S Rdna Sequence Analysis ◽  
Degrading Bacterium ◽  
Branched Alkanes ◽  
Crude Oil Degradation ◽  
Acinetobacter Pittii ◽  
The Difference

A crude oil-degrading bacterium named strain H9-3 was isolated from crude oil contaminated soil in the Northeastern area of China. Based on its morphological characteristics and 16S rDNA sequence analysis, strain H9-3 is affiliated to Acinetobacter pittii in the group of Gammaproteobacteria. The strain was efficient in removing 36.8% of the initial 10 g·L - 1 of crude oil within 21 days. GC-MS was performed and a preference was shown for n-C10, n-C11, i-C14, i-C17, i-C34, n-C12, n-C13, n-C14, n-C27, n-C32 and i-C13, over n-C16, n-C18–C22, n-C24–n-C31, and n-C36. This can be regarded as the specific fingerprint for crude oil degradation by strain H9-3 of Acinetobacter pittii. In addition to crude oil, it was shown that soybean oil and phenols can be utilized as carbon sources by strain H9-3. It was also shown that aniline and α -naphthol cannot be utilized for growth, but they can be tolerated by strain H9-3. Methylbenzene was neither utilized nor tolerated by strain H9-3. Although n-hexadecane was not preferentially consumed by strain H9-3, during culture with crude oil, it could be utilized for growth when it is the sole carbon source. The degradation of some branched alkanes (i-C14, i-C17 and i-C34) and the preferential degradation of crude oil over phenols could be used as a reference for distinguishing A. pittii from A. calcoaceticus. The difference in gene expression was very significant and was induced by diverse carbon sources, as shown in the qRT-PCR results. The oxidation and adhesion events occurred at high frequency during alkane degration by Acinetobacter pittii strain H9-3 cells.

scholarly journals Spatial and Seasonal Variations in the Abundance of Nitrogen-Transforming Genes and the Microbial Community Structure in Freshwater Lakes with Different Trophic Statuses

2019 ◽  
Vol 16 (13) ◽  
pp. 2298 ◽  
Author(s):  
Yu Wan ◽  
Xiaohong Ruan ◽  
Jie Wang ◽  
Xiaojun Shi
Keyword(s):  
Microbial Community ◽  
Trophic Status ◽  
Lake Taihu ◽  
Quantitative Polymerase Chain Reaction ◽  
Amoa Gene ◽  
Functional Markers ◽  
Ammonia Oxidizing Bacteria ◽  
Eutrophic Lakes ◽  
Nirs Gene ◽  
Transforming Genes

Identifying nitrogen-transforming genes and the microbial community in the lacustrine sedimentary environment is critical for revealing nitrogen cycle processes in eutrophic lakes. In this study, we examined the diversity and abundance of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), denitrifying bacteria (DNB), and anammox bacteria (AAOB) in different trophic status regions of Lake Taihu using the amoA, Arch-amoA, nirS, and hzo genes as functional markers. Quantitative Polymerase Chain Reaction (qPCR) results indicated that the abundance of the nirS gene was the highest, while the amoA gene had the lowest abundance in all regions. Except for the primary inflow area of Lake Taihu, Arch-amoA gene abundance was higher than the hzo gene in three lake bays, and the abundance of the nirS gene increased with decreasing trophic status. The opposite pattern was observed for the amoA, Arch-amoA, and hzo genes. Phylogenetic analyses showed that the predominant AOB and AOA were Nitrosomonas and Nitrosopumilus maritimus, respectively, and the proportion of Nitrosomonas in the eutrophic region (87.9%) was higher than that in the mesotrophic region (71.1%). Brocadia and Anammoxoglobus were the two predominant AAOB in Lake Taihu. Five novel unknown phylotypes of AAOB were observed, and Cluster AAOB-B was only observed in the inflow area with a proportion of 32%. In the DNB community, Flavobacterium occurred at a higher proportion (22.6–38.2%) in all regions, the proportion of Arthrobacter in the mesotrophic region (3.6%) was significantly lower than that in the eutrophic region (15.6%), and the proportions of Cluster DNB-E in the inflow area (24.5%) was significantly higher than that in the lake bay (7.3%). The canonical correspondence analysis demonstrated that the substrate concentration in sedimentary environments, such as NOx--N in the sediment, NH4+-N in the pore water, and the total organic matter, were the key factors that determined the nitrogen-transforming microbial community. However, the temperature was also a predominant factor affecting the AOA and AAOB communities.

Trophic Relationships in Freshwater Pelagic Ecosystems

1986 ◽  
Vol 43 (8) ◽  
pp. 1571-1581 ◽  
Author(s):  
Donald J. McQueen ◽  
John R. Post ◽  
Edward L. Mills
Keyword(s):  
Food Web ◽  
Trophic Status ◽  
Size Structure ◽  
Trophic Relationships ◽  
Top Down ◽  
Eutrophic Lakes ◽  
Bottom Up ◽  
Coefficients Of Variation ◽  
Step Down ◽  
Pelagic Ecosystems

Relative impacts of bottom-up (producer controlled) and top-down (consumer controlled) forces on the biomass and size structure of five major components of freshwater pelagic systems (piscivores, planktivores, zooplankton, phytoplankton, and total phosphorus availability) were estimated. Predictions that emerge are (1) maximum biomass at each trophic level is controlled from below (bottom-up) by nutrient availability, (2) this bottom-up regulation is strongest at the bottom of the food web (i.e. phosphorus → phytoplankton) and weakens by a factor of 2 with each succeeding step up the food web, (3) as energy moves up a food web, the predictability of bottom-up interactions decreases, (4) near the top of the food web, top-down (predator mediated) interactions are strong and have low coefficients of variation, but weaken with every step down the food web, (5) variability around the bottom-up regressions can always be explained by top-down forces, and (6) interplay between top-down and bottom-up effects changes with the trophic status of lakes. In eutrophic lakes, top-down effects are strong for piscivore → zooplankton, weaker for planktivore → zooplankton, and have little impact for zooplankton → phytoplankton. For oligotrophic lakes, the model predicts that top-down effects are not strongly buffered, so that zooplankton → phytoplankton interactions are significant.

scholarly journals Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach

2016 ◽  
Vol 55 (2) ◽  
pp. 81-90 ◽  
Author(s):  
M.A. Prieto-Calvo ◽  
M.K. Omer ◽  
O. Alvseike ◽  
M. López ◽  
A. Alvarez-Ordóñez ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Carbon Source ◽  
Carbon Sources ◽  
23S Rrna ◽  
Local Alignment ◽  
Taxonomic Structure ◽  
Sequencing Data ◽  
E Coli ◽  
Additional Information ◽  
Ft Ir

AbstractPhenotypic, chemotaxonomic and genotypic data from 12 strains ofEscherichia coli werecollected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS) and Fourier transform-infrared (FT-IR) spectroscopic profiles. The objectives were to compare several identification systems forE. coliand to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR), sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST) . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing ofE. colito species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy) for a more precise characterisation and identification ofE. coli. The results showed that identification ofE. colistrains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns.

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