scholarly journals Macroscopic Streamer Growths in Acidic, Metal-Rich Mine Waters in North Wales Consist of Novel and Remarkably Simple Bacterial Communities

2006 ◽  
Vol 72 (3) ◽  
pp. 2022-2030 ◽  
Author(s):  
Kevin B. Hallberg ◽  
Kris Coupland ◽  
Sakurako Kimura ◽  
D. Barrie Johnson
Keyword(s):  
Mine Drainage ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Fish Analysis ◽  
Microbial Composition ◽  
Mine Waters ◽  
Isolation Technique ◽  
Copper Mine ◽  
North Wales

ABSTRACT The microbial composition of acid streamers (macroscopic biofilms) in acidic, metal-rich waters in two locations (an abandoned copper mine and a chalybeate spa) in north Wales was studied using cultivation-based and biomolecular techniques. Known chemolithotrophic and heterotrophic acidophiles were readily isolated from disrupted streamers, but they accounted for only <1 to 7% of the total microorganisms present. Fluorescent in situ hybridization (FISH) revealed that 80 to 90% of the microbes in both types of streamers were β-Proteobacteria. Terminal restriction fragment length polymorphism analysis of the streamers suggested that a single bacterial species was dominant in the copper mine streamers, while two distinct bacteria (one of which was identical to the bacterium found in the copper mine streamers) accounted for about 90% of the streamers in the spa water. 16S rRNA gene clone libraries showed that the β-proteobacterium found in both locations was closely related to a clone detected previously in acid mine drainage in California and that its closest characterized relatives were neutrophilic ammonium oxidizers. Using a modified isolation technique, this bacterium was isolated from the copper mine streamers and shown to be a novel acidophilic autotrophic iron oxidizer. The β-proteobacterium found only in the spa streamers was closely related to the neutrophilic iron oxidizer Gallionella ferruginea. FISH analysis using oligonucleotide probes that targeted the two β-proteobacteria confirmed that the biodiversity of the streamers in both locations was very limited. The microbial compositions of the acid streamers found at the two north Wales sites are very different from the microbial compositions of the previously described acid streamers found at Iron Mountain, California, and the Rio Tinto, Spain.

Development of a Novel Biological System for Removing Manganese from Contaminated Waters

2007 ◽  
Vol 20-21 ◽  
pp. 267-270
Author(s):  
Richard Mariner ◽  
D. Barrie Johnson ◽  
Kevin B. Hallberg
Keyword(s):  
Mine Drainage ◽  
Low Cost ◽  
Bacterial Species ◽  
Rflp Analysis ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Domestic Water ◽  
Mine Waters ◽  
Water Stream ◽  
Set Up

Soluble manganese (Mn(II)) can cause nuisance and occasionally toxicity problems, both in surface and ground waters and in domestic water supplies. Many mine drainage waters contain highly elevated concentrations (often >100 mg l-1). Current systems for remediating mine waters, although effective for other metals, are often inefficient at removing manganese. This paper describes the development of self-sustaining, low-cost bioreactors that can be used in situ for passive removal of manganese from mine waters and other contaminated water courses of pH >4. A prototype bioreactor, set-up using Mn(IV)-coated pebbles from a fresh-water stream, was tested over one year and shown to be effective in removing Mn(II) from 10 to <0.25 mg l-1. Two species of fungi and one bacterial species were isolated from this system as Mn(II)-oxidizers. The fungi were identified as belonging to the order Pleosporales (Ascomycetes), and one was related (98 % 18S rRNA gene sequence identity) to a known Mn(II)-oxidising fungus. The bacterial isolate was closely related to the α-proteobacterium, Bosea thiooxidans. T-RFLP analysis showed that one or both of the fungal isolates were the dominant eukaryotes in the bioreactor community.

scholarly journals Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

2021 ◽  
Author(s):  
Artur Trzebny ◽  
Anna Slodkowicz-Kowalska ◽  
Johanna Björkroth ◽  
Miroslawa Dabert
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Microsporidian Infection ◽  
Functional Content

AbstractThe animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

scholarly journals Feeding a Low-protein Maternal Diet Affects Qinghai Bamei Piglet Jejunal Microbiome-metabolome Response

2021 ◽  
Author(s):  
Jipeng Jin ◽  
Liping Zhang ◽  
Qian Chen ◽  
Cunming Ma ◽  
Jianlei Jia ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Bacterial Species ◽  
Relative Weight ◽  
Integrated Approach ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Metabolic Profiles ◽  
Microbial Composition ◽  
Suckling Piglets

Abstract This experiment investigated the impacts of feeding a maternal low-CP concentration diet having iso-essential amino acids on new born suckling piglets intestinal microbial composition and metabolic profiles. The Bamei swine breed was selected due to high meat quality and flavor, but demonstrates slower growth rates which may be related to jejunal nutrient supply. Forty randomly selected purebred Bamei sows were divided into two groups and fed a low dietary CP (12%, LP) or a normal CP (14%, CON) diet, respectively, but formulated to contain similar (iso-) essential amino acid concentrations per current recommendations. At 21 days, 12 piglets were randomly selected from each treatment and euthanized with jejunum content samples collected. The 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling were combined as an integrated approach for evaluating the functional impact of maternal CP concentrations on piglet intestinal microbiome. Even though piglets demonstrated similar 0 to 21 d ADG among treatments, the jejunum relative weight, villus width, crypt depth and muscular thickness were increased (P < 0.05), while villus height, and villus height:crypt depth were reduced (P < 0.05) for the material LP compared to the maternal fed CON diet. Maternal CP concentrations can modify the intestinal microbial composition of Bamei suckling piglets. The relative abundances of the bacterial species Escherichia-Shigella, Actinobacillus, Clostridium_sensu_stricto_1, Veillonella, and Turicibacter were increased (P < 0.05) in the maternal LP fed diet compared with the maternal fed CON diet. Jejunal digesta metabolomics analysis indicated that several amino acids were metabolized (i.e. cys, met, tyr phe and trp), biosynthesized (arg phe, tyr, and trp), or degraded (lys) were enriched (P < 0.05) for the maternal fed LP compared with the maternal fed CON. Correlation analysis demonstrated that certain intestinal bacterial genera were highly related to the histomorphology and altered intestinal microbiota metabolites. In conclusion, maternal dietary CP concentrations in excess of protein and amino acid requirements not only altered suckling Bamei piglets histomorphology, microbial composition and function, but also modulated jejunum microbial metabolic profiles, which aids in understanding the beneficial effects when feeding a maternal LP diet on piglet intestinal health.

scholarly journals 16S rRNA Gene-Based Profiling of the Microbial Community in an Acid Mine Drainage Fe Precipitate at Libiola Mine (Liguria, Italy)

Minerals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1064
Author(s):  
Sirio Consani ◽  
Stefano Ghignone ◽  
Marina Pozzolini ◽  
Marco Giovine ◽  
Luigi Vezzulli ◽  
...  
Keyword(s):  
Microbial Community ◽  
Acid Mine Drainage ◽  
Mine Drainage ◽  
Bacterial Species ◽  
Ecological Niches ◽  
Rrna Gene ◽  
Acid Mine ◽  
Starting Point ◽  
Wide Range ◽  
Libiola Mine

Acid mine drainage (AMD) is a common environmental problem in many sulphide mines worldwide, and it is widely accepted that the microbial community plays a major role in keeping the process of acid generation active. The aim of this work is to describe, for the first time, the microbial community thriving in goethite and jarosite Fe precipitates from the AMD of the Libiola mine. The observed association is dominated by Proteobacteria (>50%), followed by Bacteroidetes (22.75%), Actinobacteria (7.13%), Acidobacteria (5.79%), Firmicutes (2.56%), and Nitrospirae (1.88%). Primary producers seem to be limited to macroalgae, with chemiolithotrophic strains being almost absent. A phylogenetic analysis of bacterial sequences highlighted the presence of heterotrophic bacteria, including genera actively involved in the AMD Fe cycle and genera (such as Cytophaga and Flavobacterium) that are able to reduce cellulose. The Fe precipitates constitute a microaerobic and complex environment in which many ecological niches are present, as proved by the wide range of bacterial species observed. This study is the first attempt to quantitatively characterize the microbial community of the studied area and constitutes a starting point to learn more about the microorganisms thriving in the AMD of the Libiola mine, as well as their potential applications.

scholarly journals Helicobacter pylori: Clonal Population Structure and Restricted Transmission within Families Revealed by Molecular Typing

2000 ◽  
Vol 38 (10) ◽  
pp. 3646-3651 ◽  
Author(s):  
Shan-Rui Han ◽  
Hans-Christoph E. Zschausch ◽  
Heinz-Georg W. Meyer ◽  
Thomas Schneider ◽  
Michael Loos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Helicobacter Pylori ◽  
Population Structure ◽  
Molecular Typing ◽  
Allelic Variation ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Chromosomal Dna ◽  
H Pylori

Helicobacter pylori infects up to 50% of the human population worldwide. The infection occurs predominantly in childhood and persists for decades or a lifetime. H. pylori is believed to be transmitted from person to person. However, tremendous genetic diversity has been reported for these bacteria. In order to gain insight into the epidemiological basis of this phenomenon, we performed molecular typing of H. pylori isolates from different families. Fifty-nine H. pylori isolates from 27 members of nine families were characterized by using restriction fragment length polymorphism analysis of five PCR-amplified genes, by pulsed-field gel electrophoresis (PFGE) of chromosomal DNA, and byvacA and cagA genotyping. The 16S rRNA gene exhibited little allelic variation, as expected for a unique bacterial species. In contrast, the vacA, flaA,ureAB, and lspA-glmM genes were highly polymorphic, with a mean genetic diversity of 0.83, which exceeds the levels recorded for all other bacterial species. In conjunction with PFGE, 59 H. pylori isolates could be differentiated into 21 clonal types. Each individual harbored only one clone, occasionally with a clonal variant. Identical strains were always found either between siblings or between a mother and her children. Statistical analysis revealed clonality of population structure in all isolates. The results of this study suggest the possible coexistence of a large array of clonal lineages that are evolving in each individual in isolation from one another. Transmission appears to occur primarily from mother to child and perhaps between siblings.

scholarly journals Assessment of commercial companion animal kefir products for label accuracy of microbial composition and quantity

2020 ◽  
Vol 98 (9) ◽  
Author(s):  
Breanna N Metras ◽  
Maxwell J Holle ◽  
Valerie J Parker ◽  
Michael J Miller ◽  
Kelly S Swanson
Keyword(s):  
Bacterial Species ◽  
Amplicon Sequencing ◽  
Companion Animal ◽  
Fermented Food ◽  
Health Claims ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Wide Range ◽  
Long Read ◽  
Number Of Microorganisms

Abstract Kefir is a fermented beverage containing yeast and bacteria produced by the fermentation of water or milk with kefir grains. Lack of regulation for probiotic-containing fermented food sold for companion dogs and cats creates the potential for misreporting on viable microbial counts, taxonomy, and label claims. In this study, the microbiota of six companion animal kefir products were measured quantitatively using standard plating techniques. Microbial composition of these products was also characterized by using high-resolution, long-read amplicon sequencing of the 16S rRNA gene. Five products (83%) listed specific microorganisms, and four products (66%) guaranteed colony forming units (CFU)/g on their label. To enumerate viable lactic acid bacteria (LAB), two lots of each homogenized product were plated upon opening and following 14 d on deMan Rogosa and Sharpe (MRS) agar and incubated under anaerobic and aerobic conditions. Results from point of opening revealed that all commercial kefir products with a guaranteed CFU/g overstated the number of microorganisms present by at least 1 log, with only one product exceeding 1 × 109 CFU/g. Sequencing results demonstrated that none of the labels claiming specific bacterial genera and species on their labels were correct, and all products contained at least three additional bacterial species above the minimum detectable threshold (0.001% relative abundance) that were not disclosed by the manufacturer. In addition to the incorrect viable CFU and bacterial taxonomies, several of the product labels and websites contained a wide range of health claims, none of which are supported by the companion animal literature. Our results demonstrate a low level of accuracy in the labeling of commercial kefir products intended for use in dogs and cats. Regulatory agencies, veterinarians, pet food professionals, and pet owners must scrutinize these products and demand a higher level of accuracy and quality in the future.

scholarly journals Heavy metal ions adsorption from mine waters by sawdust

2009 ◽  
Vol 15 (4) ◽  
pp. 237-249 ◽  
Author(s):  
Velizar Stankovic ◽  
Dragana Bozic ◽  
Milan Gorgievski ◽  
G. Bogdanovic
Keyword(s):  
Heavy Metal ◽  
Metal Ions ◽  
Mine Water ◽  
Heavy Metal Ions ◽  
Mine Drainage ◽  
Copper Ions ◽  
Supporting Electrolyte ◽  
Mine Waters ◽  
Copper Mine ◽  
Column Adsorption

In this work the results on the batch and column adsorption of copper and some associated ions by employing linden and poplar sawdust as a low-cost adsorbent are presented. The mine water from a local abandoned copper mine, as well as synthetic solutions of those ions which are the main constituents of the mine water were both used as a model-system in this study. The adsorption ability of the chosen sawdust to adsorb heavy metal ions is considered as a function of the initial pH of the solution and kind of metal ions. At lower pH of solutions the adsorption percentage (AD %) decreases leading to a zero AD % at pH < 1.1. Maximum AD % is achieved at 3.5 < pH < 5. It was found that poplar and linden sawdust have both almost equal adsorption capacities against copper ions. The highest AD % ( ?80%) was achieved for Cu2+, while for Fe2+ it was slightly above 10%. The other considered ions (Zn2+ and Mn2+) were within this interval. The results obtained in the batch mode were verified through the column test by using the real mine water originating from an acid mine drainage (AMD) of the copper mine 'Cerovo', RTB Bor. The breakthrough curves are presented as a function of the aqueous phase volume passed through the column allowing having an insight into the column adsorption features. Breakthrough points were determined for copper, manganese and zinc ions. A very high adsorption degree - higher than 99% was achieved in these experiments for all mentioned ions. After completing the adsorption, instead of desorption, the loaded sawdust was drained, dried and burned; the copper bearing ash was then leached with a controlled volume of sulphuric acid solution to concentrate copper therein. The obtained leach solution had the concentration of copper higher than 15 g dm-3 and the amount of H2SO4 high enough to serve as a supporting electrolyte suitable to be treated by the electrowinning for recovery of copper. The technology process based on the column adsorption is proposed and discussed.

scholarly journals Metagenomic Analysis of Bacteria Phylum Firmicutes and Bacteroidetes in Women with Type 2 Diabetes

2019 ◽  
Vol 26 (3) ◽  
pp. 110
Author(s):  
Zulhaerati Zulhaerati ◽  
Sri Budiarti ◽  
Rika Indri Astuti
Keyword(s):  
Insulin Resistance ◽  
Type 2 Diabetes ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Species ◽  
Metagenomic Analysis ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Microbial Composition ◽  
Uncultured Bacterium

Diabetes mellitus (DM) is a serious health problem in Indonesia. Type 2 diabetes is a metabolic disease which primarily caused by obesity-linked insulin resistance. There is a link between insulin resistance and bacterial populations in the gut. Therefore, the aims of this study was to analyze composition of bacteria belong to the phylum Firmicutes and Bacteroidetes in women with type 2 diabetes and non-diabetic persons as control. The study included five female adults type 2 diabetes patients and five healthy controls. The bacteria composition was analyzed for abundance by denaturing gradient gel electrophoresis (DGGE). Metagenomic analysis based on 16S rRNA gene was represented by 12 DGGE bands. The twelve respective bands showed the similarity ranging from 77 up to 98%. Diversity of microbial composition in women type 2 diabetes was represented by five DGGE bands are Bacteroides fragilis, Bacteroides vulgatus, uncultured Bacteroides sp. clone Lb4eF4, uncultured bacterium clone 16sms90-5g05, and uncultured bacterium clone Malaga 1F14. Four DGGE bands in women healthy controls are closely related to uncultured bacterium isolate DGGE gel band Eub42, uncultured bacterium isolate DGGE gel band K115, uncultured bacterium clone HFV04255, and Enterococcus sp. the finding shows bacterial species belong to the phylum Bacteroidetes was mostly found in women diabetic group, while those belong to the phylum Firmicutes was mostly found in healthy controls.

scholarly journals Comparative Analysis of Fecal Bacterial Microbiota of Six Bird Species

2021 ◽  
Vol 8 ◽  
Author(s):  
Li Gao ◽  
Li Liu ◽  
Chao Du ◽  
Qiangchuan Hou
Keyword(s):  
Gut Microbiota ◽  
Community Composition ◽  
Bacterial Species ◽  
Bird Species ◽  
Living Environment ◽  
Rrna Gene ◽  
Muscovy Duck ◽  
Microbial Composition ◽  
Gut Microbes ◽  
Whooper Swan

The gut microbiota contributes to host health by maintaining homeostasis and improving digestive efficiency. Therefore, identifying gut microbes will shed light on the annual life cycle of animals and in particular those that are threatened or endangered. Nonetheless, the gut microbial composition of the majority of bird species is still unknown. Here, for the first time, 16S rRNA gene sequencing was used to characterize and compare the community composition and diversity of gut microbiotas from six species of birds raised at the Wildlife Conservation Center in Baotou, China: relict gull (Larus relictus; n = 3), muscovy duck (Cairina moschata; n = 3), ruddy shelduck (Tadorna ferruginea; n = 3), demoiselle crane (Anthropoides virgo; n = 4), whooper swan (Cygnus cygnus; n = 3), and black swan (Cygnus atratus; n = 5). A total of 26,616 operational taxonomic units from 21 samples were classified into 32 phyla and 507 genera. Chao1, Shannon diversity, observed species, and Simpson index analysis revealed differences in the community richness and diversity between the different species. Proteobacteria was the dominant bacterial phylum in whooper swan and relict gull, whereas Firmicutes was the dominant bacterial phylum in the other species. At the genus level, 11 dominant genera were detected (Lactobacillus, Psychrobacter, Enterococcus, Carnobacterium, Weissella, Burkholderia, Escherichia/Shigella, Leuconostoc, Buttiauxella, Desemzia, and Staphylococcus). Principal component and cluster analyses revealed that, while the microbial community composition of different individuals of the same species clustered together, the gut microbial composition varied between the bird species. Furthermore, the most abundant bacterial species differed between bird species. Because many avian gut microbes are derived from the diet, the eating habits and natural living environment of birds may be important contributing factors to the observed differences. Short-term changes to the diet and living environment have little effect on the composition of the avian gut microbiota. This study provides a theoretical basis for bird protection, including disease prevention and control.

scholarly journals Uncovering the hidden bacterial ghost communities of yeast and experimental evidences demonstrates yeast as thriving hub for bacteria

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
B. Indu ◽  
Tallapragada Keertana ◽  
Sahu Ipsita ◽  
Uppada Jagadeeshwari ◽  
Chintalapati Sasikala ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Model Organism ◽  
Yeast Cells ◽  
Rrna Gene ◽  
Fish Analysis ◽  
Bacterial Cells ◽  
Introduced Fish ◽  
Yeast Cultures ◽  
As Species ◽  
Bacterial Ghost

AbstractOur major concern was to address “yeast endobacteria” which was based on a few reports in the recent past where bacteria may find yeast as a niche for survival. In this study, we report the microbiota of twenty-nine axenic yeast cultures recovered from different habitats based on their 16S rRNA gene-amplicon metagenomes. Yeasts were identified based on D1/D2 or ITS gene sequences. Bacterial diversity was widespread, varied and rich among all yeasts except for four strains. Taxa belonging to the phylum Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes and the genera; Streptococcus, Propionibacterium were common to all the yeasts. Candida tropicalis was used as a model organism to confirm bacteria through fluorescence in situ hybridization (FISH), isolating and re-introducing the isolated bacteria into the yeast. FISH analysis confirmed the endobacteria of C. tropicalis and we have successfully isolated four bacteria only after lysis and disruption of yeast cells. These bacteria were identified as species of Pseudomonas, Chryseobacterium, Lysinibacillus and Propionibacterium. Guestimates indicate 95% of bacterial species of C. tropicalis are yet-to-be-cultivated. We have successfully reintroduced mCherry tagged Pseudomonas into C. tropicalis. Also, auto-fluorescent Prochlorococcus and Rhodopseudomonas could be introduced into C. tropicalis while mCherry tagged E. coli or Salmonella could not be introduced. FISH analysis confirmed the presence of both native and infected bacterial cells present in C. tropicalis. Our findings unveil the insights into the ghost microbiota associated with yeast, which otherwise are considered to be axenic cultures. Their inherent occurrence, together with co-cultivation experiments under laboratory conditions suggests that yeasts are a thriving hub for bacterial communities.

Sign in / Sign up

Export Citation Format

Share Document