Monday, January 16, 2017

New manuscript out in AEM led by collaborators at Penn State: 

Efficient low-pH iron removal by a microbial iron oxide mound ecosystem at Scalp Level Run

Acid mine drainage (AMD) is a major environmental problem affecting tens of thousands of km of waterways worldwide. Passive bioremediation of AMD relies on microbial communities to oxidize and remove iron from the system; however, iron-oxidation rates in AMD environments are highly variable across sites. At Scalp Level Run (Cambria County PA), first-order iron-oxidation rates are ten times faster than at other coal associated iron mounds in the Appalachians. We examined the bacterial community at Scalp Level Run to determine whether a unique community is responsible for the rapid iron oxidation rate. Despite strong geochemical gradients including an over 10-fold change in the concentration of ferrous iron from 57.3 mg/L at the emergence to 2.5 mg/L at the base of the coal tailings pile, the bacterial community composition was nearly constant with distance from the spring outflow. Scalp Level Run contains many of the same taxa present in other AMD sites, but the community is dominated by two strains of Ferrovum myxofaciens, a species that is associated with high rates of Fe(II) oxidation in laboratory studies.
Importance Acid mine drainage pollutes more than 19,300 km of rivers and streams and 72,000 ha of lakes worldwide (1). Remediation is frequently ineffective and costly, upwards of US$100 billion globally (2, 3, 4) and nearly US$5 billion in Pennsylvania alone (5). Microbial Fe(II) oxidation is more efficient than abiotic Fe(II) oxidation at low pH (6). Therefore, AMD bioremediation could harness microbial Fe(II) oxidation to fuel more cost-effective treatments. Advances will require a deeper understanding of the ecology of Fe(II)-oxidizing microbial communities and the factors that control their distribution and rates of Fe(II) oxidation. We investigated bacterial communities that inhabit an AMD site with rapid Fe(II) oxidation and found that they were dominated by two OTUs of Ferrovum myxofaciens, a taxon associated with high laboratory rates of iron-oxidation. This research represents a step forward in identifying taxa that can be used to enhance cost-effective AMD bioremediation.

Thursday, November 17, 2016

Tuesday, September 13, 2016

Fun new review paper up together with many collaborators and colleagues: 

Ten questions concerning the microbiomes of buildings

Buildings represent habitats for microorganisms that can have direct or indirect effects on the quality of our living spaces, health, and well-being. Over the last ten years, new research has employed sophisticated tools, including DNA sequencing-based approaches, to study microbes found in buildings and the overall built environment. These investigations have catalyzed new insights into and questions about the microbes that surround us in our daily lives. The emergence of the “microbiology of the built environment” field has required bridging disciplines, including microbiology, ecology, building science, architecture, and engineering. Early insights have included a fuller characterization of sources of microbes within buildings, important processes that structure the distributions and abundances of microbes, and a greater appreciation of the role that occupants can have on indoor microbiology. This ongoing work has also demonstrated that traditional culture- and microscopy-based approaches for studying microbiology vastly underestimate the types and quantity of microbes present in environmental samples. We offer ten questions that highlight important lessons learned regarding the microbiology of buildings and suggest future areas of investigation.

Friday, September 2, 2016

New in Genome Announcements: 

Draft Genome Sequence of Methanohalophilus mahii Strain DAL1 Reconstructed from a Hydraulic Fracturing-Produced Water Metagenome

We report here the 1,882,100-bp draft genome sequence of Methanohalophilus mahii strain DAL1, recovered from Marcellus Shale hydraulic fracturing-produced water using metagenomic contig binning. Genome annotation revealed several key methanogenesis genes and provides valuable information on archaeal activity associated with hydraulic fracturing-produced water environments.

Monday, July 25, 2016

New paper: Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale

Controlling microbial activity is a primary concern during the management of the large volumes of wastewater (produced water) generated during high-volume hydraulic fracturing. In this study we analyzed the transcriptional activity (metatranscriptomes) of three produced water samples from the Marcellus Shale. The goal of this study was to describe active metabolic pathways of industrial concern for produced water management and reuse, and to improve understanding of produced water microbial activity. Metatranscriptome analysis revealed active biofilm formation, sulfide production, and stress management mechanisms of the produced water microbial communities. Biofilm-formation and sulfate-reduction pathways were identified in all samples. Genes related to a diverse array of stress response mechanisms were also identified with implications for biocide efficacy. Additionally, active expression of a methanogenesis pathway was identified in a sample of produced water collected prior to holding pond storage. The active microbial community identified by metatranscriptome analysis was markedly different than the community composition as identified by 16S rRNA sequencing, highlighting the value of evaluating the active microbial fraction during assessments of produced water biofouling potential and evaluation of biocide application strategies. These results indicate biofouling and corrosive microbial processes are active in produced water and should be taken into consideration while designing produced water reuse strategies.

Tuesday, May 31, 2016

Welcome undergrad summer researchers Cassandra, Marissa, and Nicole! Glad to have you!