Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer

Erwin, Daniel P.; Erickson, Issac K.; Delwiche, Mark E.; Colwell, Frederick S.; Strap, Janice L.; Crawford, Ronald L.

doi:10.1128/aem.71.4.2016-2025.2005

Cited by 70 publications

(42 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The clone library RFLP analysis revealed one major OTU (88% of clone library) with closest sequence similarity to a known Methylobacter pmoA gene sequence (AAF08210) (Costello and Lidstrom, 1999). The two remaining low-abundance OTUs, both with a relative abundance of 6%, were similar to pmoA clones from uncultivated bacteria collected from a river plain aquifer (AAZ06139) (Erwin et al, 2005) and a sand water filter (ABC59829) (Stoecker et al, 2006).…”

Section: Resultsmentioning

confidence: 83%

Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary

et al. 2008

View full text Add to dashboard Cite

The surface microlayer (SML) is the thin biogenic film found at the surface of a water body. The SML is poorly understood but has been shown to be important in biogeochemical cycling and sea-air gas exchange. We sampled the SML of the Blyth estuary at two sites (salinities 21 and 31 psu) using 47 mm polycarbonate membranes. DNA was extracted from the SML and corresponding subsurface water (0.4 m depth) and microbial (bacteria and archaea) community analysis was performed using denaturing gradient gel electrophoresis of 16S rRNA gene PCR amplicons. The diversity of bacterial functional genes that encode enzyme subunits for methane monooxygenase (pmoA and mmoX) and carbon monoxide dehydrogenase (coxL) was assessed using PCR, clone library construction and restriction fragment length polymorphism (RFLP) analysis. Methanotroph genes were present only in low copy numbers and pmoA was detected only in subsurface samples. Diversity of mmoX genes was low and most of the clone sequences detected were similar to those of mmoX from Methylomonas spp. Interestingly, some sequences detected in the SML were different from those detected in the subsurface. RFLP analysis of coxL clone libraries indicated a high diversity of carbon monoxide (CO)-utilizing bacteria in the estuary. The habitats of the closely related coxL sequences suggest that CO-utilizing bacteria in the estuary are recruited from both marine and freshwater/terrestrial inputs. In contrast, methanotroph recruitment appears to occur solely from freshwater input into the estuary.

show abstract

Section: Resultsmentioning

confidence: 83%

Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary

et al. 2008

View full text Add to dashboard Cite

show abstract

“…3) (32). Clone a3 (30% of total clones) was closely related to pmoA genes of the recently described yet uncultivated filamentous methanotroph Crenothrix polyspora (39) and to a large group of sequences recovered from the Eastern Snake River Plain aquifer, designated group II unculturables (16). While C. polyspora is a gammaproteobacterium, its pmoA sequence has been noted to be more closely related to amoA sequences and to the divergent alphaproteobacterial sequences (cluster 1) (39) than to gammaproteobacterial sequences.…”

Section: Resultsmentioning

confidence: 99%

“…Estimates of methanotroph abundance in natural samples are based on a number of complementary techniques, such as determination of methane oxidation rates (3,9,29,40), determination of the fatty acid composition of the total microbial population (9,29,40), PCR-based (2,14,15,19,25,26,28), quantitative PCR-based (5,27,29), or reverse transcriptase PCR (RT-PCR)-based (24,32) surveys, and direct counting using microscopy combined with fluorescence in situ hybridization (FISH) (6,8,10). The most widely used PCR primers for detecting type I and type II methanotrophic bacteria target rRNA genes (15,19) or functional genes encoding particulate methane monooxygenase (pmoA) (14), methanol dehydrogenase (mxaF) (14), formaldehyde-activating enzyme (fae) (25), or the D subunit of the formyltransferase/hydrolase complex (fhcD) (25), and large databases of these genes have been compiled from a variety of environments (5,11,14,16,19,24,26,28,31,33,39,40). The most widely used FISH probes target rRNA (15,19); however, several protocols have be...…”

mentioning

confidence: 99%

Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations

Kalyuzhnaya¹,

Zabinsky

Bowerman³

et al. 2006

Appl Environ Microbiol

108

View full text Add to dashboard Cite

A fluorescence in situ hybridization-flow cytometry (FISH/FC)-based method was optimized using artificial mixtures of pure cultures of methanotrophic bacteria. Traditional oligonucleotide probes targeting 16S rRNAs of type I (MG84/705 probe) and type II (MA450 probe) methanotrophs were labeled with fluorescein or Alexa fluor and used for FISH, followed by fluorescence-activated FC analysis and cell sorting (FACS). The method resulted in efficient separation of target cells (type I or type II methanotrophs) from the artificial mixtures. The method was then applied for detection and enrichment of type I and type II methanotroph populations from a natural sample, Lake Washington sediment. Cells were extracted from the sediment, fixed, and subjected to FISH/FC/FACS. The resulting subpopulations were analyzed by reverse transcriptase PCR surveys of 16S rRNA, pmoA (encoding a subunit of particulate methane monooxygenase), and fae (encoding formaldehydeactivating enzyme) genes. The functional gene analysis indicated specific separation of the type I and type II methanotroph populations. 16S rRNA gene analysis revealed that type I methanotrophs comprised 59% of the subpopulation separated using the type I-specific probe and that type II methanotrophs comprised 47.5% of the subpopulation separated using the type II-specific probe. Our data indicate that the FISH/FC/FACS protocol described can provide significant enrichment of microbial populations of interest from complex natural communities and that these can be used for genetic tests. We further tested the possibility of direct wholegenome amplification (WGA) from limited numbers of sorted cells, using artificial mixtures of microbes whose genome sequences are known. We demonstrated that efficient WGA can be achieved using 10 4 or more cells separated by 16S rRNA-specific FISH/FC/FACS, while fewer cells resulted in less specific WGA.

show abstract

“…The ESRPA is a deep basalt aquifer and is considered oligotrophic (4,22,29); however, previous work has demonstrated the presence of ureolytic microbes in this environment (11,13). Erwin et al also reported evidence of AOB during the analysis of methane monooxygenase clone libraries from ESRPA samples (7), but in general, the structure and function of ammonia-oxidizing microbial communities (and especially AOA) in deep aquifers like the ESRPA have been relatively unexplored.…”

mentioning

confidence: 99%

Responses of Ammonia-Oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater

Reed

Smith

Francis

et al. 2010

Appl Environ Microbiol

View full text Add to dashboard Cite

To evaluate the potential for organic nitrogen addition to stimulate the in situ growth of ammonia oxidizers during a field scale bioremediation trial, samples collected from the Eastern Snake River Plain Aquifer in Idaho before, during, and after the addition of molasses and urea were subjected to PCR analysis of ammonia monooxygenase subunit A (amoA) genes. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were present in all of the samples tested, with AOA amoA genes outnumbering AOB amoA genes in all of the samples. Following urea addition, nitrate levels rose and bacterial amoA copy numbers increased dramatically, suggesting that urea hydrolysis stimulated nitrification. Bacterial amoA diversity was limited to two Nitrosomonas phylotypes, whereas archaeal amoA analyses revealed 20 distinct operational taxonomic units, including several that were markedly different from all previously reported sequences. Results from this study demonstrate the likelihood of stimulating ammonia-oxidizing communities during field scale manipulation of groundwater conditions to promote urea hydrolysis.

show abstract

Diversity of Oxygenase Genes from Methane- and Ammonia-Oxidizing Bacteria in the Eastern Snake River Plain Aquifer

Cited by 70 publications

References 47 publications

Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary

Phylogenetic and functional gene analysis of the bacterial and archaeal communities associated with the surface microlayer of an estuary

Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations

Responses of Ammonia-Oxidizing Bacterial and Archaeal Populations to Organic Nitrogen Amendments in Low-Nutrient Groundwater

Contact Info

Product

Resources

About