scholarly journals Molecular Analysis of Arsenate-Reducing Bacteria within Cambodian Sediments following Amendment with Acetate

2006 ◽  
Vol 73 (4) ◽  
pp. 1041-1048 ◽  
Author(s):  
G. Lear ◽  
B. Song ◽  
A. G. Gault ◽  
D. A. Polya ◽  
J. R. Lloyd
Keyword(s):  
Drinking Water ◽  
Organic Matter ◽  
Stable Isotope ◽  
Bacterial Communities ◽  
Microbial Reduction ◽  
Stable Isotope Probing ◽  
Direct Link ◽  
Present Evidence ◽  
Reducing Bacteria ◽  
Arsenate Reducing Bacteria

ABSTRACT The health of millions is threatened by the use of groundwater contaminated with sediment-derived arsenic for drinking water and irrigation purposes in Southeast Asia. The microbial reduction of sorbed As(V) to the potentially more mobile As(III) has been implicated in release of arsenic into groundwater, but to date there have been few studies of the microorganisms that can mediate this transformation in aquifers. With the use of stable isotope probing of nucleic acids, we present evidence that the introduction of a proxy for organic matter (13C-labeled acetate) stimulated As(V) reduction in sediments collected from a Cambodian aquifer that hosts arsenic-rich groundwater. This was accompanied by an increase in the proportion of prokaryotes closely related to the dissimilatory As(V)-reducing bacteria Sulfurospirillum strain NP-4 and Desulfotomaculum auripigmentum. As(V) respiratory reductase genes (arrA) closely associated with those found in Sulfurospirillum barnesii and Geobacter uraniumreducens were also detected in active bacterial communities utilizing 13C-labeled acetate in microcosms. This study suggests a direct link between inputs of organic matter and the increased prevalence and activity of organisms which transform As(V) to the potentially more mobile and thus hazardous As(III) via dissimilatory As(V) reduction.

scholarly journals Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

mBio ◽  
2014 ◽  
Vol 5 (4) ◽  
Author(s):  
Y. Verastegui ◽  
J. Cheng ◽  
K. Engel ◽  
D. Kolczynski ◽  
S. Mortimer ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Indicator Species ◽  
Bacterial Communities ◽  
Glycoside Hydrolase ◽  
Stable Isotope Probing ◽  
Glycoside Hydrolases ◽  
Metagenomic Analysis ◽  
Functional Metagenomics ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

ABSTRACTSoil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or stable-isotope-labeled (13C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa,Actinomycetales(Salinibacterium),Rhizobiales(Devosia),Rhodospirillales(Telmatospirillum), andCaulobacterales(PhenylobacteriumandAsticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. BothActinomycetalesandCaulobacterales(Phenylobacterium) were associated with metabolism of cellulose, andAlphaproteobacteriawere associated with the metabolism of arabinose; members of the orderRhizobialeswere strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the13C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes.IMPORTANCEThe ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential.

Metagenomics and stable isotope probing reveal the complementary contribution of fungal and bacterial communities in the recycling of dead biomass in forest soil

2020 ◽  
Vol 148 ◽  
pp. 107875 ◽  
Author(s):  
Rubén López-Mondéjar ◽  
Vojtěch Tláskal ◽  
Tomáš Větrovský ◽  
Martina Štursová ◽  
Rodolfo Toscan ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Forest Soil ◽  
Bacterial Communities ◽  
Stable Isotope Probing ◽  
Dead Biomass

Bio-signatures in metabasaltic glass of a Caledonian ophiolite, West Norway

2002 ◽  
Vol 139 (6) ◽  
pp. 601-608 ◽  
Author(s):  
HARALD FURNES ◽  
KARLIS MUEHLENBACHS ◽  
TERJE TORSVIK ◽  
OLE TUMYR ◽  
LANG SHI
Keyword(s):  
Organic Matter ◽  
Early Stage ◽  
Volcanic Rocks ◽  
Present Evidence ◽  
X Ray ◽  
Basaltic Rocks ◽  
Facies Metamorphism ◽  
Reducing Bacteria ◽  
Greenschist Facies Metamorphism

Evidence of bioalteration of natural basaltic rocks, presently receiving much attention, has so far been restricted to in situ oceanic crust and ophiolites in which fresh glass is still present. Here we present evidence of preserved bio-signatures in the chilled margin of pillow lavas of an old (443 Ma) ophiolite that has suffered pervasive lower greenschist facies metamorphism and deformation. X-ray mapping of initial alteration zones shows the remains of organic carbon associated with highly-concentrated Fe and S. Bioproduction of CO2 is further reflected in the low δ13C values of calcite extracted from pillow rims, compatible with microbe-induced fractionation during oxidation of organic matter. We attribute these effects to growth of sulphate-reducing bacteria at the early stage of ophiolite formation. During energy metabolism these bacteria reduce sulphate to H2S and oxidize organic matter to CO2 . Hydrogen sulphide will eventually react with iron and form pyrite, and carbon dioxide is precipitated as calcium carbonate. The results of this study may thus trigger the search for bio-signatures in glassy volcanic rocks of any age.

scholarly journals Stable Isotope Probing Identifies Bacterioplankton Lineages Capable of Utilizing Dissolved Organic Matter Across a Range of Bioavailability

2020 ◽  
Vol 11 ◽  
Author(s):  
Shuting Liu ◽  
Nicholas Baetge ◽  
Jacqueline Comstock ◽  
Keri Opalk ◽  
Rachel Parsons ◽  
...  
Keyword(s):  
Organic Matter ◽  
Stable Isotope ◽  
Dissolved Organic Matter ◽  
Stable Isotope Probing
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