scholarly journals Subsurface Microbial Diversity in Deep-Granitic-Fracture Water in Colorado

2007 ◽  
Vol 74 (1) ◽  
pp. 143-152 ◽  
Author(s):  
Jason W. Sahl ◽  
Raleigh Schmidt ◽  
Elizabeth D. Swanner ◽  
Kevin W. Mandernack ◽  
Alexis S. Templeton ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Phospholipid Fatty Acid ◽  
Statistical Analyses ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Significant Shift ◽  
Clone Libraries ◽  
Borehole Water ◽  
Candidate Division

ABSTRACT A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This “Henderson candidate division” dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems.

scholarly journals Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Kärt Kanger ◽  
Nigel G H Guilford ◽  
HyunWoo Lee ◽  
Camilla L Nesbø ◽  
Jaak Truu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Solid State ◽  
Food Waste ◽  
Microbial Community Structure ◽  
Microbial Community Composition ◽  
Microbial Community Analysis ◽  
Waste Paper ◽  
Rrna Gene ◽  
Significant Shift

ABSTRACT Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.

scholarly journals Host–microbiome interactions in human type 2 diabetes following prebiotic fibre (galacto-oligosaccharide) intake

2016 ◽  
Vol 116 (11) ◽  
pp. 1869-1877 ◽  
Author(s):  
Camilla Pedersen ◽  
Edith Gallagher ◽  
Felicity Horton ◽  
Richard J. Ellis ◽  
Umer Z. Ijaz ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Community Structure ◽  
Microbial Community ◽  
Glucose Tolerance ◽  
Microbial Community Structure ◽  
Microbial Community Analysis ◽  
Intravenous Glucose ◽  
Intestinal Microbial Community ◽  
Human Type

AbstractAberrant microbiota composition and function have been linked to several pathologies, including type 2 diabetes. In animal models, prebiotics induce favourable changes in the intestinal microbiota, intestinal permeability (IP) and endotoxaemia, which are linked to concurrent improvement in glucose tolerance. This is the first study to investigate the link between IP, glucose tolerance and intestinal bacteria in human type 2 diabetes. In all, twenty-nine men with well-controlled type 2 diabetes were randomised to a prebiotic (galacto-oligosaccharide mixture) or placebo (maltodextrin) supplement (5·5 g/d for 12 weeks). Intestinal microbial community structure, IP, endotoxaemia, inflammatory markers and glucose tolerance were assessed at baseline and post intervention. IP was estimated by the urinary recovery of oral51Cr-EDTA and glucose tolerance by insulin-modified intravenous glucose tolerance test. Intestinal microbial community analysis was performed by high-throughput next-generation sequencing of 16S rRNA amplicons and quantitative PCR. Prebiotic fibre supplementation had no significant effects on clinical outcomes or bacterial abundances compared with placebo; however, changes in the bacterial family Veillonellaceae correlated inversely with changes in glucose response and IL-6 levels (r−0·90,P=0·042 for both) following prebiotic intake. The absence of significant changes to the microbial community structure at a prebiotic dosage/length of supplementation shown to be effective in healthy individuals is an important finding. We propose that concurrent metformin treatment and the high heterogeneity of human type 2 diabetes may have played a significant role. The current study does not provide evidence for the role of prebiotics in the treatment of type 2 diabetes.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

Microbial Community Analysis inside a Biooxidation Heap for Gold Recovery in Equador

2017 ◽  
Vol 262 ◽  
pp. 135-138 ◽  
Author(s):  
Carlos L. Aspiazu ◽  
Paulina Aguirre ◽  
Sabrina Hedrich ◽  
Axel Schippers
Keyword(s):  
Microbial Community ◽  
Fine Fraction ◽  
Community Analysis ◽  
Gold Recovery ◽  
Microbial Community Analysis ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Probable Number ◽  
Cell Numbers ◽  
Cell Counts

In a mine owned by the company Orenas S.A. (Equador), a biooxidation process for gold recovery has been developed. Refractory gold ore was crushed, milled and 500 ton of flotation concentrate was agglomerated by coating a support rock. This was piled up on a liner and the biooxidation process in the heap of 35x25x6 m3 was run for approximately 150 days. The oxidized material was subsequently removed for further processing. An outcrop allowed for depth dependent sampling of altogether 36 samples at three sites over the complete depth of 6 m. The fine fraction was removed from the host rock and sent to the laboratory for analysis of the microbial community. The pH ranged between 2.2 and 2.9. Total cell counts determined via counting under a fluorescence microscope after SYBR Green staining indicated a high microbial colonialization of the heap in all depths between 106 to 109 cells per g concentrate, however the highest cell numbers were mainly found in the upper 50 cm. Most-probable-number determination of living, acidophilic iron (II)-oxidizers for one site also revealed a decrease of cell numbers with depth (between 104 to 108 cells per g concentrate). Further molecular analyses of the community composition based on extracted DNA and 16S rRNA gene analyses by TRFLP and qPCR revealed a complex archaeal and bacterial community within the heap. It can be stated that an active community of acidophiles runs the biooxidation process in all sampled parts of the heap.

Linking Microbial Community Dynamics in BIOX® Leaching Tanks to Process Conditions: Integrating Lab and Commercial Experience

2017 ◽  
Vol 262 ◽  
pp. 38-42 ◽  
Author(s):  
Mariette Smart ◽  
Robert J. Huddy ◽  
Catherine J. Edward ◽  
Charl Fourie ◽  
Trust Shumba ◽  
...  
Keyword(s):  
South Africa ◽  
Community Structure ◽  
Microbial Community ◽  
Research University ◽  
Community Dynamics ◽  
Operating Conditions ◽  
Process Conditions ◽  
Significant Shift ◽  
Engineering Research ◽  
Microbial Community Dynamics

In the commercial BIOX® process, an acidophilic mixed bacterial and archaeal community dominated by iron and sulphur oxidising microorganisms is used to facilitate the recovery of precious metals from refractory gold-bearing sulphidic mineral concentrates. Characterisation of the microbial communities associated with commercial BIOX® reactors from four continents revealed a significant shift in the microbial community structure compared to that of the seed culture, maintained at SGS (South Africa). This has motivated more detailed study of the microbial community dynamics in the process. Microbial speciation of a subset of the BIOX® reactors at Fairview mines (Barberton, South Africa) and two laboratory maintained reactors housed at Centre for Bioprocess Engineering Research, University of Cape Town, has been performed tri-annually for three years by quantitative real-time polymerase chain reaction. The laboratory BIOX® culture maintained on Fairview concentrate was dominated by the desired iron oxidiser, Leptospirillum ferriphilum, and sulphur oxidiser, Acidithiobacillus caldus, when operated under standard BIOX® conditions. Shifts in the microbial community as a result of altered operating conditions were transient and did not result in a loss of the microbial diversity of the BIOX® culture. The community structure of the Fairview mines BIOX® reactor tanks showed archaeal dominance of these communities by organisms such as the iron oxidiser Ferroplasma acidiphilum and a Thermoplasma sp. for the period monitored. Shifts in the microbial community were observed across the monitoring period and mapped to changes in performance of the commercial process plant. Understanding the effect of changes in the plant operating conditions on the BIOX® community structure may assist in providing conditions that support the desired microbial consortium for optimal biooxidation to maximize gold recovery.

scholarly journals Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (Lactuca Species) Phyllosphere

2010 ◽  
Vol 76 (24) ◽  
pp. 8117-8125 ◽  
Author(s):  
Paul J. Hunter ◽  
Paul Hand ◽  
David Pink ◽  
John M. Whipps ◽  
Gary D. Bending
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Population Diversity ◽  
Microbial Interactions ◽  
Soluble Carbohydrates ◽  
Rrna Gene ◽  
Species Variation ◽  
Clone Libraries ◽  
Microbe Interactions

ABSTRACT Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.

Agriculturally relevant microbial community structure in long-term fertilized paddy soils as revealed by phospholipid fatty acid (PLFA) and pyrosequencing analyses

2018 ◽  
Vol 64 (10) ◽  
pp. 1379-1393 ◽  
Author(s):  
Saranya Kuppusamy ◽  
Aillen Rose Daquiado ◽  
Song Yeob Kim ◽  
Young-Eun Yoon ◽  
Jang Hwan Kim ◽  
...  
Keyword(s):  
Community Structure ◽  
Fatty Acid ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Paddy Soils

Microbial community structure analysis of euxinic sediments using phospholipid fatty acid biomarkers

1995 ◽  
Vol 51 (1) ◽  
pp. 21-38 ◽  
Author(s):  
Narasimmalu Rajendran ◽  
Osamu Matsuda ◽  
Norifumi Imamura ◽  
Yoshikuni Urushigawa
Keyword(s):  
Community Structure ◽  
Fatty Acid ◽  
Microbial Community ◽  
Structure Analysis ◽  
Microbial Community Structure ◽  
Phospholipid Fatty Acid ◽  
Fatty Acid Biomarkers
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