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- Anaerobic lignin degradation (3)
- DEGRADATION (3)
- Tropical forest soil isolate (3)
- CHEMICAL REPORTERS (2)
- Climate change (2)
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- Facultative anaerobe (2)
- Lignin (2)
- Metagenomics (2)
- Microbial ecology (2)
- Mycobacterium (2)
- Stress response (2)
- 4-hydroxyphenylacetate degradation pathway (1)
- ADENYLYL-CYCLASE (1)
- ALTERS (1)
- ANTIBIOTIC EFFICACY (1)
- AVAILABILITY (1)
- Anaerobic decomposition (1)
- Anaerobic metabolism (1)
- Archaea (1)
- BACILLUS-SUBTILIS (1)
- BACTERIAL COMMUNITIES (1)
- BENZYL ALCOHOL (1)
- BIOFILMS (1)
- BIOSYNTHESIS (1)
- BOREAL (1)
- Bacteria (1)
- Bio-Sep beads (1)
- Bioenergy (1)
- Biofuels (1)
- Biomass degradation (1)
Articles 1 - 30 of 46
Full-Text Articles in Life Sciences
Comparison Of Two 16s Rrna Primers (V3–V4 And V4–V5) For Studies Of Arctic Microbial Communities, Eduard Fadeev, Magda G. Cardozo-Mino, Josephine Z. Rapp, Christina Bienhold, Ian Salter, Verena Salman-Carvalho, Massimiliano Molari, Halina E. Tegetmeyer, Pier Luigi Buttigieg
Comparison Of Two 16s Rrna Primers (V3–V4 And V4–V5) For Studies Of Arctic Microbial Communities, Eduard Fadeev, Magda G. Cardozo-Mino, Josephine Z. Rapp, Christina Bienhold, Ian Salter, Verena Salman-Carvalho, Massimiliano Molari, Halina E. Tegetmeyer, Pier Luigi Buttigieg
Microbiology Department Faculty Publication Series
Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh environmental conditions, such as near-freezing temperatures and extreme seasonality. The gene for the small ribosomal subunit (16S rRNA) is commonly used to study the taxonomic composition of microbial communities in their natural environment. Several primer sets for this marker gene have been extensively tested across various sample sets, but these typically originated from low-latitude environments. An explicit evaluation …
Fungal Community Response To Long-Term Soil Warming With Potential Implications For Soil Carbon Dynamics, Gregory J. Pec, Linda T. A. Van Diepen, Melissa Knorr, A. Staurt Grandy, Jerry M. Melillo, Kristen M. Deangelis, Jeffery L. Blanchard, Serita D. Frey
Fungal Community Response To Long-Term Soil Warming With Potential Implications For Soil Carbon Dynamics, Gregory J. Pec, Linda T. A. Van Diepen, Melissa Knorr, A. Staurt Grandy, Jerry M. Melillo, Kristen M. Deangelis, Jeffery L. Blanchard, Serita D. Frey
Microbiology Department Faculty Publication Series
The direction and magnitude of climate warming effects on ecosystem processes such as carbon cycling remain uncertain. Soil fungi are central to these processes due to their roles as decomposers of soil organic matter, as mycorrhizal symbionts, and as determinants of plant diversity. Yet despite their importance to ecosystem functioning, we lack a clear understanding of the long-term response of soil fungal communities to warming. Toward this goal, we characterized soil fungal communities in two replicated soil warming experiments at the Harvard Forest (Petersham, Massachusetts, USA) which had experienced 5 degrees C above ambient soil temperatures for 5 and 20 …
Direct Observation Of Electrically Conductive Pili Emanating From Geobacter Sulfurreducens, Xinying Liu, David J. F. Walker, Stephen S. Nonnenmann, Dezhi Sun, Derek R. Lovley
Direct Observation Of Electrically Conductive Pili Emanating From Geobacter Sulfurreducens, Xinying Liu, David J. F. Walker, Stephen S. Nonnenmann, Dezhi Sun, Derek R. Lovley
Microbiology Department Faculty Publication Series
Geobacter sulfurreducens is a model microbe for elucidating the mechanisms for extracellular electron transfer in several biogeochemical cycles, bioelectrochemical applications, and microbial metal corrosion. Multiple lines of evidence previously suggested that electrically conductive pili (e-pili) are an essential conduit for long-range extracellular electron transport in G. sulfurreducens. However, it has recently been reported that G. sulfurreducens does not express e-pili and that filaments comprised of multi-heme c-type cytochromes are responsible for long-range electron transport. This possibility was directly investigated by examining cells, rather than filament preparations, with atomic force microscopy. Approximately 90% of the filaments emanating from wild-type cells had …
Trehalose Recycling Promotes Energy-Efficient Biosynthesis Of The Mycobacterial Cell Envelope, Amol Arunrao Pohane, Caleb R. Carr, Jaishree Garhyan, Benjamin M. Swarts, M. Sloan Siegrist
Trehalose Recycling Promotes Energy-Efficient Biosynthesis Of The Mycobacterial Cell Envelope, Amol Arunrao Pohane, Caleb R. Carr, Jaishree Garhyan, Benjamin M. Swarts, M. Sloan Siegrist
Microbiology Department Faculty Publication Series
The mycomembrane layer of the mycobacterial cell envelope is a barrier to environmental, immune, and antibiotic insults. There is considerable evidence of mycomembrane plasticity during infection and in response to host-mimicking stresses. Since mycobacteria are resource and energy limited under these conditions, it is likely that remodeling has distinct requirements from those of the well-characterized biosynthetic program that operates during unrestricted growth. Unexpectedly, we found that mycomembrane remodeling in nutrient-starved, nonreplicating mycobacteria includes synthesis in addition to turnover. Mycomembrane synthesis under these conditions occurs along the cell periphery, in contrast to the polar assembly of actively growing cells, and both …
Membrane-Partitioned Cell Wall Synthesis In Mycobacteria, Alam García-Heredia, Takehiro Kado, Caralyn E. Sein, Julia Puffal, Sarah H. Osman, Julius Judd, Todd A. Gray, Yasu S. Morita, M. Sloan Siegrist
Membrane-Partitioned Cell Wall Synthesis In Mycobacteria, Alam García-Heredia, Takehiro Kado, Caralyn E. Sein, Julia Puffal, Sarah H. Osman, Julius Judd, Todd A. Gray, Yasu S. Morita, M. Sloan Siegrist
Microbiology Department Faculty Publication Series
Many antibiotics target the assembly of cell wall peptidoglycan, an essential, heteropolymeric mesh that encases most bacteria. In rod-shaped bacteria, cell wall elongation is spatially precise yet relies on limited pools of lipid-linked precursors that generate and are attracted to membrane disorder. By tracking enzymes, substrates, and products of peptidoglycan biosynthesis in Mycobacterium smegmatis, we show that precursors are made in plasma membrane domains that are laterally and biochemically distinct from sites of cell wall assembly. Membrane partitioning likely contributes to robust, orderly peptidoglycan synthesis, suggesting that these domains help template peptidoglycan synthesis. The cell wall-organizing protein DivIVA and the …
Evidence For The Role Of Cyp51a And Xenobiotic Detoxification In Differential Sensitivity To Azole Fungicides In Boxwood Blight Pathogens, Stefanos Stravoravdis, Robert E. Marra, Nicholas R. Leblanc, Joanne Crouch, Jonathan P. Hulvey
Evidence For The Role Of Cyp51a And Xenobiotic Detoxification In Differential Sensitivity To Azole Fungicides In Boxwood Blight Pathogens, Stefanos Stravoravdis, Robert E. Marra, Nicholas R. Leblanc, Joanne Crouch, Jonathan P. Hulvey
Microbiology Department Faculty Publication Series
Boxwood blight, a fungal disease of ornamental plants (Buxus spp.), is caused by two sister species, Calonectria pseudonaviculata (Cps) and C. henricotiae (Che). Compared to Cps, Che is documented to display reduced sensitivity to fungicides, including the azole class of antifungals, which block synthesis of a key fungal membrane component, ergosterol. A previous study reported an ergosterol biosynthesis gene in Cps, CYP51A, to be a pseudogene, and RNA-Seq data confirm that a functional CYP51A is expressed only in Che. The lack of additional ergosterol biosynthesis genes showing significant differential expression suggests that the functional CYP51A in Che could contribute to …
Spatial Distribution Of Arctic Bacterioplankton Abundance Is Linked To Distinct Water Masses And Summertime Phytoplankton Bloom Dynamics (Fram Strait, 79°N), Magda G. Cardozo-Mino, Eduard Fadeev, Verena Salman-Carvalho, Antje Boetius
Spatial Distribution Of Arctic Bacterioplankton Abundance Is Linked To Distinct Water Masses And Summertime Phytoplankton Bloom Dynamics (Fram Strait, 79°N), Magda G. Cardozo-Mino, Eduard Fadeev, Verena Salman-Carvalho, Antje Boetius
Microbiology Department Faculty Publication Series
The Arctic is impacted by climate warming faster than any other oceanic region on Earth. Assessing the baseline of microbial communities in this rapidly changing ecosystem is vital for understanding the implications of ocean warming and sea ice retreat on ecosystem functioning. Using CARD-FISH and semi-automated counting, we quantified 14 ecologically relevant taxonomic groups of bacterioplankton (Bacteria and Archaea) from surface (0-30 m) down to deep waters (2,500 m) in summer ice-covered and ice-free regions of the Fram Strait, the main gateway for Atlantic inflow into the Arctic Ocean. Cell abundances of the bacterioplankton communities in surface waters varied from …
How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes For Lignin-Modifying Enzymes, Stefanos Stravoravdis, J. Reuben Shipway, Barry Goodell
How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes For Lignin-Modifying Enzymes, Stefanos Stravoravdis, J. Reuben Shipway, Barry Goodell
Microbiology Department Faculty Publication Series
Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin - a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin …
Stress-Induced Reorganization Of The Mycobacterial Membrane Domain, Jennifer M. Hayashi, Kirill Richardson, Emily S. Melzer, Steven J. Sandler, Bree B. Aldridge, M. Sloan Siegrist, Yasu S. Morita
Stress-Induced Reorganization Of The Mycobacterial Membrane Domain, Jennifer M. Hayashi, Kirill Richardson, Emily S. Melzer, Steven J. Sandler, Bree B. Aldridge, M. Sloan Siegrist, Yasu S. Morita
Microbiology Department Faculty Publication Series
Cell elongation occurs primarily at the mycobacterial cell poles, but the molecular mechanisms governing this spatial regulation remain elusive. We recently reported the presence of an intracellular membrane domain (IMD) that was spatially segregated from the conventional plasma membrane in Mycobacterium smegmatis. The IMD is enriched in the polar region of actively elongating cells and houses many essential enzymes involved in envelope biosynthesis, suggesting its role in spatially restricted elongation at the cell poles. Here, we examined reorganization of the IMD when the cells are no longer elongating. To monitor the IMD, we used a previously established reporter strain …
Genome Sequence Of Verrucomicrobium Sp. Strain Gas474, A Novel Bacterium Isolated From Soil, Grace Pold, Erin M. Conlon, Marcel Huntemann, Manoj Pillay, Natalia Mikhailova, Dimitrios Stamatis, T.B.K. Reddy, Chris Daum, Nicole Shapiro, Nikos Kyrpides, Tanja Woyke, Kristen Deangelis
Genome Sequence Of Verrucomicrobium Sp. Strain Gas474, A Novel Bacterium Isolated From Soil, Grace Pold, Erin M. Conlon, Marcel Huntemann, Manoj Pillay, Natalia Mikhailova, Dimitrios Stamatis, T.B.K. Reddy, Chris Daum, Nicole Shapiro, Nikos Kyrpides, Tanja Woyke, Kristen Deangelis
Microbiology Department Faculty Publication Series
Verrucomicrobium sp. strain GAS474 was isolated from the mineral soil of a temperate deciduous forest in central Massachusetts. Here, we present the complete genome sequence of this phylogenetically novel organism, which consists of a total of 3,763,444 bp on a single scaffold, with a 65.8% GC content and 3,273 predicted open reading frames.
Demethylmenaquinone Methyl Transferase Is A Membrane Domain-Associated Protein Essential For Menaquinone Homeostasis In Mycobacterium Smegmatis, Julia Puffal, Jacob A. Mayfield, D. Branch Moody, Yasu S. Morita
Demethylmenaquinone Methyl Transferase Is A Membrane Domain-Associated Protein Essential For Menaquinone Homeostasis In Mycobacterium Smegmatis, Julia Puffal, Jacob A. Mayfield, D. Branch Moody, Yasu S. Morita
Microbiology Department Faculty Publication Series
The intracellular membrane domain (IMD) in mycobacteria is a spatially distinct region of the plasma membrane with diverse functions. Previous comparative proteomic analysis of the IMD suggested that menaquinone biosynthetic enzymes are associated with this domain. In the present study, we determined the subcellular site of these enzymes using sucrose density gradient fractionation. We found that the last two enzymes, the methyltransferase MenG, and the reductase MenJ, are associated with the IMD in Mycobacterium smegmatis. MenA, the prenyltransferase that mediates the first membrane-associated step of the menaquinone biosynthesis, is associated with the conventional plasma membrane. For MenG, we additionally …
Multi-Time Series Rna-Seq Analysis Of Enterobacter Lignolyticus Scf1 During Growth In Lignin-Amended Medium, Roberto Orellana, Gina Chaput, Lye Meng Markillie, Hugh Mitchell, Matt Gaffrey, Gayla Orr, Kristen Deangelis
Multi-Time Series Rna-Seq Analysis Of Enterobacter Lignolyticus Scf1 During Growth In Lignin-Amended Medium, Roberto Orellana, Gina Chaput, Lye Meng Markillie, Hugh Mitchell, Matt Gaffrey, Gayla Orr, Kristen Deangelis
Microbiology Department Faculty Publication Series
The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth …
High-Quality Draft Genome Sequences Of Four Lignocellulose-Degrading Bacteria Isolated From Puerto Rican Forest Soil: Gordonia Sp., Paenibacillus Sp., Variovorax Sp., And Vogesella Sp., Hannah L. Woo, Kristen Deangelis, Hazuki Teshima, Karen Davenport, Hajnalka Daligault, Tracy Erkkila, Lynne Goodwin, Wei Gu, Chien-Chi Lo, Christine Munk, Matthew Scholz, Yan Xu, Patrick Chain, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Blake A. Simmons, Terry C. Hazen
High-Quality Draft Genome Sequences Of Four Lignocellulose-Degrading Bacteria Isolated From Puerto Rican Forest Soil: Gordonia Sp., Paenibacillus Sp., Variovorax Sp., And Vogesella Sp., Hannah L. Woo, Kristen Deangelis, Hazuki Teshima, Karen Davenport, Hajnalka Daligault, Tracy Erkkila, Lynne Goodwin, Wei Gu, Chien-Chi Lo, Christine Munk, Matthew Scholz, Yan Xu, Patrick Chain, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Blake A. Simmons, Terry C. Hazen
Microbiology Department Faculty Publication Series
Here, we report the high-quality draft genome sequences of four phylogenetically diverse lignocellulose-degrading bacteria isolated from tropical soil (Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the genetic basis of their ability to degrade lignocellulose. These isolates may provide novel enzymes for biofuel production.
Changes In Substrate Availability Drive Carbon Cycle Response To Chronic Warming, Grace Pold, A. Stuart Grandy, Jerry M. Melillo, Kristen Deangelis
Changes In Substrate Availability Drive Carbon Cycle Response To Chronic Warming, Grace Pold, A. Stuart Grandy, Jerry M. Melillo, Kristen Deangelis
Microbiology Department Faculty Publication Series
As earth's climate continues to warm, it is important to understand how the capacity of terrestrial ecosystems to retain carbon (C) will be affected. We combined measurements of microbial activity with the concentration, quality, and physical accessibility of soil carbon to microorganisms to evaluate the mechanisms by which more than two decades of experimental warming has altered the carbon cycle in a Northeast US temperate deciduous forest. We found that concentrations of soil organic matter were reduced in both the organic and mineral soil horizons. The molecular composition of the carbon was altered in the mineral soil with …
Hydrogen Production And Enzyme Activities In The Hyperthermophile Thermococcus Paralvinellae Grown On Maltose, Tryptone, And Agricultural Waste, Sarah A. Hensley, Emily Moreira, James F. Holden
Hydrogen Production And Enzyme Activities In The Hyperthermophile Thermococcus Paralvinellae Grown On Maltose, Tryptone, And Agricultural Waste, Sarah A. Hensley, Emily Moreira, James F. Holden
Microbiology Department Faculty Publication Series
Thermococcus may be an important alternative source of H2 in the hot subseafloor in otherwise low H2environments such as some hydrothermal vents and oil reservoirs. It may also be useful in industry for rapid agricultural waste treatment and concomitant H2 production. Thermococcus paralvinellae grown at 82°C without sulfur produced up to 5 mmol of H2 L−1 at rates of 5–36 fmol H2 cell−1 h−1 on 0.5% (wt vol−1) maltose, 0.5% (wt vol−1) tryptone, and 0.5% maltose + 0.05% tryptone media. Two potentially inhibiting conditions, the presence of 10 mM acetate and low pH (pH 5) in maltose-only medium, did not …
Long-Term Warming Alters Carbohydrate Degradation Potential In Temperate Forest Soils, Grace Pold, Andrew F. Billings, Jeff L. Blanchard, Daniel B. Burkhardt, Serita D. Frey, Jerry M. Melillo, Julia Schnabel, Linda T.A. Van Diepen, Kristen Deangelis
Long-Term Warming Alters Carbohydrate Degradation Potential In Temperate Forest Soils, Grace Pold, Andrew F. Billings, Jeff L. Blanchard, Daniel B. Burkhardt, Serita D. Frey, Jerry M. Melillo, Julia Schnabel, Linda T.A. Van Diepen, Kristen Deangelis
Microbiology Department Faculty Publication Series
As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with …
Two Decades Of Warming Increases Diversity Of A Potentially Lignolytic Bacterial Community, Grace Pold, Jerry M. Melillo, Kristen Deangelis
Two Decades Of Warming Increases Diversity Of A Potentially Lignolytic Bacterial Community, Grace Pold, Jerry M. Melillo, Kristen Deangelis
Microbiology Department Faculty Publication Series
As Earth's climate warms, the massive stores of carbon found in soil are predicted to become depleted, and leave behind a smaller carbon pool that is less accessible to microbes. At a long-term forest soil-warming experiment in central Massachusetts, soil respiration and bacterial diversity have increased, while fungal biomass and microbially-accessible soil carbon have decreased. Here, we evaluate how warming has affected the microbial community's capability to degrade chemically-complex soil carbon using lignin-amended BioSep beads. We profiled the bacterial and fungal communities using PCR-based methods and completed extracellular enzyme assays as a proxy for potential community function. We found that …
Genome Sequence And Description Of The Anaerobic Lignin-Degrading Bacterium Tolumonas Lignolytica Sp. Nov., Andrew F. Billings, Julian L. Fortney, Terry C. Hazen, Blake Simmons, Karen W. Davenport, Lynne Goodwin, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanya Woyke, Kristen Deangelis
Genome Sequence And Description Of The Anaerobic Lignin-Degrading Bacterium Tolumonas Lignolytica Sp. Nov., Andrew F. Billings, Julian L. Fortney, Terry C. Hazen, Blake Simmons, Karen W. Davenport, Lynne Goodwin, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanya Woyke, Kristen Deangelis
Microbiology Department Faculty Publication Series
Tolumonas lignolytica BRL6-1T sp. nov. is the type strain of T. lignolytica sp. nov., a proposed novel species of the Tolumonas genus. This strain was isolated from tropical rainforest soils based on its ability to utilize lignin as a sole carbon source. Cells of Tolumonas lignolytica BRL6-1T are mesophilic, non-spore forming, Gram-negative rods that are oxidase and catalase negative. The genome for this isolate was sequenced and returned in seven unique contigs totaling 3.6Mbp, enabling the characterization of several putative pathways for lignin breakdown. Particularly, we found an extracellular peroxidase involved in lignin depolymerization, as well as several enzymes involved …
Long-Term Forest Soil Warming Alters Microbial Communities In Temperate Forest Soils, Kristen Deangelis, Grace Pold, Begüm D. Topçuoğlu, Linda T.A. Van Diepen, Rebecca M. Varney, Jeffrey L. Blanchard, Jerry Melillo, Serita D. Frey
Long-Term Forest Soil Warming Alters Microbial Communities In Temperate Forest Soils, Kristen Deangelis, Grace Pold, Begüm D. Topçuoğlu, Linda T.A. Van Diepen, Rebecca M. Varney, Jeffrey L. Blanchard, Jerry Melillo, Serita D. Frey
Microbiology Department Faculty Publication Series
Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant …
Complete Genome Sequence Of The Lignin-Degrading Bacterium Klebsiella Sp. Strain Brl6-2, Hannah L. Woo, Nicholas R. Ballor, Terry C. Hazen, Julian L. Fortney, Blake Simmons, Karen Walston Davenport, Lynne Goodwin, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanja Woyke, Janet Jansson, Jeff Kimbrell, Kristen Deangelis
Complete Genome Sequence Of The Lignin-Degrading Bacterium Klebsiella Sp. Strain Brl6-2, Hannah L. Woo, Nicholas R. Ballor, Terry C. Hazen, Julian L. Fortney, Blake Simmons, Karen Walston Davenport, Lynne Goodwin, Natalia Ivanova, Nikos C. Kyrpides, Konstantinos Mavromatis, Tanja Woyke, Janet Jansson, Jeff Kimbrell, Kristen Deangelis
Microbiology Department Faculty Publication Series
In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated Klebsiella sp. strain BRL6-2 on minimal media with alkali lignin as the sole carbon source. This organism was isolated anaerobically from tropical forest soils collected from the Bisley watershed at the Ridge site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are characterized by cycles of iron oxidation and reduction. Genome sequencing was targeted because of its ability to grow on lignin anaerobically and lignocellulolytic …
Enzyme Activities Of Aerobic Lignocellulolytic Bacteria Isolated From Wet Tropical Forest Soils, Hannah L. Woo, Terry C. Hazen, Blake A. Simmons, Kristen Deangelis
Enzyme Activities Of Aerobic Lignocellulolytic Bacteria Isolated From Wet Tropical Forest Soils, Hannah L. Woo, Terry C. Hazen, Blake A. Simmons, Kristen Deangelis
Microbiology Department Faculty Publication Series
Lignocellulolytic bacteria have promised to be a fruitful source of new enzymes for next-generation lignocellulosic biofuel production. Puerto Rican tropical forest soils were targeted because the resident microbes decompose biomass quickly and to near-completion. Isolates were initially screened based on growth on cellulose or lignin in minimal media. 75 Isolates were further tested for the following lignocellulolytic enzyme activities: phenol oxidase, peroxidase, β-d-glucosidase, cellobiohydrolase, β-xylopyranosidase, chitinase, CMCase, and xylanase. Cellulose-derived isolates possessed elevated β-d-glucosidase, CMCase, and cellobiohydrolase activity but depressed phenol oxidase and peroxidase activity, while the contrary was true of lignin isolates, suggesting that these bacteria are specialized to …
Draft Genome Sequence Of The Lignin-Degrading Burkholderia Sp. Strain Lig30, Isolated From Wet Tropical Forest Soil, Hannah L. Woo, Sagar Utturkar, Dawn Klingeman, Blake A. Simmons, Kristen Deangelis, Steven D. Brown, Terry C. Hazen
Draft Genome Sequence Of The Lignin-Degrading Burkholderia Sp. Strain Lig30, Isolated From Wet Tropical Forest Soil, Hannah L. Woo, Sagar Utturkar, Dawn Klingeman, Blake A. Simmons, Kristen Deangelis, Steven D. Brown, Terry C. Hazen
Microbiology Department Faculty Publication Series
Burkholderia species are common soil Betaproteobacteria capable of degrading recalcitrant aromatic compounds and xenobiotics. Burkholderia sp. strain LIG30 was isolated from wet tropical forest soil and is capable of utilizing lignin as a sole carbon source. Here we report the draft genome sequence of Burkholderia sp. strain LIG30.
Fluctuations In Species-Level Protein Expression Occur During Element And Nutrient Cycling In The Subsurface, Michael Wilkins, Kelly Wrighton, Carrie Nicora, Kenneth Williams, Lee Mccue, Kim Handley, Chris Miller, Ludovic Giloteaux, Alison Montogomery, Derek Lovley, Jillian Banfield, Philip Long, Mary Lipton
Fluctuations In Species-Level Protein Expression Occur During Element And Nutrient Cycling In The Subsurface, Michael Wilkins, Kelly Wrighton, Carrie Nicora, Kenneth Williams, Lee Mccue, Kim Handley, Chris Miller, Ludovic Giloteaux, Alison Montogomery, Derek Lovley, Jillian Banfield, Philip Long, Mary Lipton
Microbiology Department Faculty Publication Series
While microbial activities in environmental systems play a key role in the utilization and cycling of essential elements and compounds, microbial activity and growth frequently fluctuates in response to environmental stimuli and perturbations. To investigate these fluctuations within a saturated aquifer system, we monitored a carbon-stimulated in situ Geobacter population while iron reduction was occurring, using 16S rRNA abundances and high-resolution tandem mass spectrometry proteome measurements. Following carbon amendment, 16S rRNA analysis of temporally separated samples revealed the rapid enrichment of Geobacter-like environmental strains with strong similarity to G. bemidjiensis. Tandem mass spectrometry proteomics measurements suggest high carbon flux through …
When Is A Microbial Culture "Pure"? Persistent Cryptic Contaminant Escapes Detection Even With Deep Genome Sequencing, Pravin Malla, Kelly Nevin, Minita Shrestha, Derek Lovley
When Is A Microbial Culture "Pure"? Persistent Cryptic Contaminant Escapes Detection Even With Deep Genome Sequencing, Pravin Malla, Kelly Nevin, Minita Shrestha, Derek Lovley
Microbiology Department Faculty Publication Series
Geobacter sulfurreducens strain KN400 was recovered in previous studies in which a culture of the DL1 strain of G. sulfurreducens served as the inoculum in investigations of microbial current production at low anode potentials (_400 mV versus Ag/AgCl). Differences in the genome sequences of KN400 and DL1 were too great to have arisen from adaptive evolution during growth on the anode. Previous deep sequencing (80-fold coverage) of the DL1 culture failed to detect sequences specific to KN400, suggesting that KN400 was an external contaminant inadvertently introduced into the anode culturing system. In order to evaluate this further, a portion of …
Aromatic Amino Acids Required For Pili Conductivity And Long-Range Extracellular Electron Transport In Geobacter Sulfurreducens, Madeline Vargas, Nikhil Malvankar, Pier-Luc Tremblay, Ching Leang, Jessica Smith, Pranav Patel, Oona Synoeyenbos-West, Kelly Nevin, Derek Lovley
Aromatic Amino Acids Required For Pili Conductivity And Long-Range Extracellular Electron Transport In Geobacter Sulfurreducens, Madeline Vargas, Nikhil Malvankar, Pier-Luc Tremblay, Ching Leang, Jessica Smith, Pranav Patel, Oona Synoeyenbos-West, Kelly Nevin, Derek Lovley
Microbiology Department Faculty Publication Series
It has been proposed that Geobacter sulfurreducens requires conductive pili for long-range electron transport to Fe(III) oxides and for high-density current production in microbial fuel cells. In order to investigate this further, we constructed a strain of G. sulfurreducens, designated Aro-5, which produced pili with diminished conductivity. This was accomplished by modifying the amino acid sequence of PilA, the structural pilin protein. An alanine was substituted for each of the five aromatic amino acids in the carboxyl terminus of PilA, the region in which G. sulfurreducens PilA differs most significantly from the PilAs of microorganisms incapable of long-range extracellular electron …
Evidence Supporting Dissimilatory And Assimilatory Lignin Degradation In Enterobacter Lignolyticus Scf1, Kristen Deangelis, Deepak Sharma, Rebecca Varney, Blake Simmons, Nancy G. Isern, Lye Meng Markillie, Carrie Nicora, Angela D. Norbeck, Ronald C. Taylor, Joshua T. Aldrich, Errol W. Robinson
Evidence Supporting Dissimilatory And Assimilatory Lignin Degradation In Enterobacter Lignolyticus Scf1, Kristen Deangelis, Deepak Sharma, Rebecca Varney, Blake Simmons, Nancy G. Isern, Lye Meng Markillie, Carrie Nicora, Angela D. Norbeck, Ronald C. Taylor, Joshua T. Aldrich, Errol W. Robinson
Microbiology Department Faculty Publication Series
Lignocellulosic biofuels are promising as sustainable alternative fuels, but lignin inhibits access of enzymes to cellulose, and by-products of lignin degradation can be toxic to cells. The fast growth, high efficiency and specificity of enzymes employed in the anaerobic litter deconstruction carried out by tropical soil bacteria make these organisms useful templates for improving biofuel production. The facultative anaerobe Enterobacter lignolyticus SCF1 was initially cultivated from Cloud Forest soils in the Luquillo Experimental Forest in Puerto Rico, based on anaerobic growth on lignin as sole carbon source. The source of the isolate was tropical forest soils that decompose litter rapidly …
Up Against The Wall: The Effects Of Climate Warming On Soil Microbial Diversity And The Potential For Feedbacks To The Carbon Cycle, Grace Pold, Kristen Deangelis
Up Against The Wall: The Effects Of Climate Warming On Soil Microbial Diversity And The Potential For Feedbacks To The Carbon Cycle, Grace Pold, Kristen Deangelis
Microbiology Department Faculty Publication Series
Earth’s climate is warming, and there is evidence that increased temperature alters soil C cycling, which may result in a self-reinforcing (positive), microbial mediated feedback to the climate system. Though soil microbes are major drivers of soil C cycling, we lack an understanding of how temperature affects SOM decomposition. Numerous studies have explored, to differing degrees, the extent to which climate change may affect biodiversity. While there is ample evidence that community diversity begets ecosystem stability and resilience, we know of keystone species that perform functions whose effects far outweigh their relative abundance. In this paper, we first review the …
Metagenomes Of Tropical Soil-Derived Anaerobic Switchgrass-Adapted Consortia With And Without Iron, Kristen Deangelis, Patrick D'Haeseleer, Dylan Chivian, Blake Simmons, Adam P. Arkin, Konstantinos Mavromatis, Stephanie Malfatti, Susannah Tringe, Terry C. Hazen
Metagenomes Of Tropical Soil-Derived Anaerobic Switchgrass-Adapted Consortia With And Without Iron, Kristen Deangelis, Patrick D'Haeseleer, Dylan Chivian, Blake Simmons, Adam P. Arkin, Konstantinos Mavromatis, Stephanie Malfatti, Susannah Tringe, Terry C. Hazen
Microbiology Department Faculty Publication Series
Tropical forest soils decompose litter rapidly with frequent episodes of anoxia, making it likely that bacteria using alternate terminal electron acceptors (TEAs) such as iron play a large role in supporting decomposition under these conditions. The prevalence of many types of metabolism in litter deconstruction makes these soils useful templates for improving biofuel production. To investigate how iron availability affects decomposition, we cultivated feedstock-adapted consortia (FACs) derived from iron-rich tropical forest soils accustomed to experiencing frequent episodes of anaerobic conditions and frequently fluctuating redox. One consortium was propagated under fermenting conditions, with switchgrass as the sole carbon source in minimal …
The Rnf Complex Of Clostridium Ljungdahlii Is A Proton-Translocating Ferredoxin: Nad+ Oxidoreductase Essential For Autotrophic Growth, Pier-Luc Tremblay, Tian Zhang, Shabir Dar, Ching Leang, Derek Lovley
The Rnf Complex Of Clostridium Ljungdahlii Is A Proton-Translocating Ferredoxin: Nad+ Oxidoreductase Essential For Autotrophic Growth, Pier-Luc Tremblay, Tian Zhang, Shabir Dar, Ching Leang, Derek Lovley
Microbiology Department Faculty Publication Series
It has been predicted that the Rnf complex of Clostridium ljungdahlii is a proton-translocating ferredoxin:NAD+ oxidoreductase which contributes to ATP synthesis by an H+-translocating ATPase under both autotrophic and heterotrophic growth conditions. The recent development of methods for genetic manipulation of C. ljungdahlii made it possible to evaluate the possible role of the Rnf complex in energy conservation. Disruption of the C. ljungdahlii rnf operon inhibited autotrophic growth. ATP synthesis, proton gradient, membrane potential, and proton motive force collapsed in the Rnf-deficient mutant with H2 as the electron source and CO2 as the electron acceptor. Heterotrophic growth was hindered in …
Analysis Of The Genome Of The Sexually Transmitted Insect Virus Helicoverpa Zea Nudivirus 2, John Burand, Woojin Kim, Claudio Afonso, Edan Tulman, Gerald Kutish, Zhiqiang Lu, Daniel Rock
Analysis Of The Genome Of The Sexually Transmitted Insect Virus Helicoverpa Zea Nudivirus 2, John Burand, Woojin Kim, Claudio Afonso, Edan Tulman, Gerald Kutish, Zhiqiang Lu, Daniel Rock
Microbiology Department Faculty Publication Series
The sexually transmitted insect virus Helicoverpa zea nudivirus 2 (HzNV-2) was determined to have a circular double-stranded DNA genome of 231,621 bp coding for an estimated 113 open reading frames (ORFs). HzNV-2 is most closely related to the nudiviruses, a sister group of the insect baculoviruses. Several putative ORFs that share homology with the baculovirus core genes were identified in the viral genome. However, HzNV-2 lacks several key genetic features of baculoviruses including the late transcriptional regulation factor, LEF-1 and the palindromic hrs, which serve as origins of replication. The HzNV-2 genome was found to code for three ORFs that …