scholarly journals Analysis of the genetic potential and gene expression of microbial communities involved in the in situ bioremediation of uranium and harvesting electrical energy from organic matter

2004 ◽  
Author(s):  
D. Lovley
Keyword(s):  
Gene Expression ◽  
Organic Matter ◽  
Microbial Communities ◽  
Electrical Energy ◽  
In Situ Bioremediation ◽  
Genetic Potential

In Situ Gene Expression in Mixed-Culture Biofilms: Evidence of Metabolic Interactions between Community Members

1998 ◽  
Vol 64 (2) ◽  
pp. 721-732 ◽  
Author(s):  
Søren Møller ◽  
Claus Sternberg ◽  
Jens Bo Andersen ◽  
Bjarke Bak Christensen ◽  
Juan Luis Ramos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microbial Communities ◽  
Pure Culture ◽  
Fluorescent Protein ◽  
Confocal Laser ◽  
Specific Gene ◽  
Community Members ◽  
Metabolic Interactions ◽  
Green Fluorescent

ABSTRACT Microbial communities growing in laboratory-based flow chambers were investigated in order to study compartmentalization of specific gene expression. Among the community members studied, the focus was in particular on Pseudomonas putida and a strain of anAcinetobacter sp., and the genes studied are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and themeta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied inP. putida, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from thePu promoter was homogeneously induced by benzyl alcohol in both community and pure-culture biofilms, while the Pmpromoter was induced in the mixed community but not in a pure-culture biofilm. By sequentially adding community members, induction ofPm was shown to be a consequence of direct metabolic interactions between an Acinetobacter species and P. putida. Furthermore, in fixed biofilm samples organism identity was determined and gene expression was visualized at the same time by combining GFP expression with in situ hybridization with fluorescence-labeled 16S rRNA targeting probes. This combination of techniques is a powerful approach for investigating structure-function relationships in microbial communities.

scholarly journals Ooids forming in situ within microbial mats (Kiritimati atoll, central Pacific)

PalZ ◽  
2021 ◽  
Author(s):  
Pablo Suarez-Gonzalez ◽  
Joachim Reitner
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Microbial Mats ◽  
Formation Processes ◽  
Central Pacific ◽  
Environmental Processes ◽  
Definition Of ◽  
First Time

AbstractOoids (subspherical particles with a laminated cortex growing around a nucleus) are ubiquitous in the geological record since the Archean and have been widely studied for more than two centuries. However, various questions about them remain open, particularly about the role of microbial communities and organic matter in their formation and development. Although ooids typically occur rolling around in agitated waters, here, we describe for the first time aragonite ooids forming statically within microbial mats from hypersaline ponds of Kiritimati (Kiribati, central Pacific). Subspherical particles had been previously observed in these mats and classified as spherulites, but these particles grow around autochthonous micritic nuclei, and many of them have laminated cortices, with alternating radial fibrous laminae and micritic laminae. Thus, they are compatible with the definition of the term ‘ooid’ and are in fact very similar to many modern and fossil examples. Kiritimati ooids are more abundant and developed in some ponds and in some particular layers of the microbial mats, which leads to the discussion and interpretation of their formation processes as product of mat evolution, through a combination of organic and environmental factors. Radial fibrous laminae are formed during periods of increased supersaturation, either by metabolic or environmental processes. Micritic laminae are formed in closer association with the mat exopolymer (EPS) matrix, probably during periods of lower supersaturation and/or stronger EPS degradation. Therefore, this study represents a step forward in the understanding of ooid development as influenced by microbial communities, providing a useful analogue for explaining similar fossil ooids.

scholarly journals Detecting biogeochemical activity in basal ice using fluorescence spectroscopy

2010 ◽  
Vol 51 (56) ◽  
pp. 47-55 ◽  
Author(s):  
J.D. Barker ◽  
J.L. Klassen ◽  
M.J. Sharp ◽  
S.J. Fitzsimons ◽  
R.J. Turner
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Microbial Activity ◽  
Carbon Sink ◽  
Dry Valleys ◽  
Basal Ice ◽  
Fluorescence Characteristics ◽  
Glacier Ice ◽  
Aquatic Food

AbstractDissolved organic matter (DOM) is an important component of aquatic carbon and nutrient budgets and is a metabolic substrate for organisms at the base of aquatic food chains. Active microbial communities in glaciers affect the abundance and characteristics of organic matter (OM) that is exported to downstream ecosystems. However, how OM is biogeochemically altered in glaciers remains unknown and studies documenting active microbial activity by detecting in situ biogeochemical modifications of OM are lacking due to difficulties characterizing OM and the low concentrations of DOM typical of glacier environments. To address this issue, we measure the abundance and fluorescence characteristics of DOM in basal ice at Victoria Upper Glacier (VUG), McMurdo Dry Valleys, Antarctica. We compare these observations with the results of microbial incubations from the same basal ice samples to determine whether the occurrence of fluorophores indicative of recent microbial activity is linked to the presence of culturable microbial communities containing organisms that could have produced them. Psychrotolerant bacteria were isolated from basal ice samples and were associated with marine humic-like fluorescence. This is interpreted as being indicative of in situ microbial degradation of OM within basal ice at VUG. Marine humic-like material is a recalcitrant form of OM, and its biogeochemical transformation from a relatively labile form of OM in glacier ice may function as a carbon sink.

scholarly journals Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Manuel Kleiner
Keyword(s):  
Gene Expression ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Large Scale ◽  
Molecular Level ◽  
Carbon Sources ◽  
Community Members ◽  
Insight Into

ABSTRACT Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.

Molecular and Microscopic Analysis of Altered Gene Expression in Transgenic and Gene Targeted Mice

1996 ◽  
Vol 54 ◽  
pp. 12-13
Author(s):  
W. K. Jones ◽  
J. Robbins
Keyword(s):  
Gene Expression ◽  
Pulmonary Veins ◽  
Microscopic Analysis ◽  
Mouse Tissue ◽  
Adult Heart ◽  
Heavy Chains ◽  
Altered Gene Expression ◽  
Altered Gene ◽  
Pulmonary Myocardium

Two myosin heavy chains (MyHC) are expressed in the mammalian heart and are differentially regulated during development. In the mouse, the α-MyHC is expressed constitutively in the atrium. At birth, the β-MyHC is downregulated and replaced by the α-MyHC, which is the sole cardiac MyHC isoform in the adult heart. We have employed transgenic and gene-targeting methodologies to study the regulation of cardiac MyHC gene expression and the functional and developmental consequences of altered α-MyHC expression in the mouse.We previously characterized an α-MyHC promoter capable of driving tissue-specific and developmentally correct expression of a CAT (chloramphenicol acetyltransferase) marker in the mouse. Tissue surveys detected a small amount of CAT activity in the lung (Fig. 1a). The results of in situ hybridization analyses indicated that the pattern of CAT transcript in the adult heart (Fig. 1b, top panel) is the same as that of α-MyHC (Fig. 1b, lower panel). The α-MyHC gene is expressed in a layer of cardiac muscle (pulmonary myocardium) associated with the pulmonary veins (Fig. 1c). These studies extend our understanding of α-MyHC expression and delimit a third cardiac compartment.

In situ bioremediation of cyanide, PAHs and organic compounds using an engineered SEquenced REactive BARrier (SEREBAR)

2006 ◽  
Vol 14 (2) ◽  
pp. 478-482
Author(s):  
Jamie Robinson ◽  
Russell Thomas ◽  
Steve Wallace ◽  
Paddy Daly ◽  
Robert Kalin
Keyword(s):  
Organic Compounds ◽  
In Situ Bioremediation ◽  
Reactive Barrier
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