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Articles 1 - 30 of 88
Full-Text Articles in Entire DC Network
High-Quality Genomes Of Paenibacillus Spp. Rc334 And Rc343, Isolated From A Long-Term Forest Soil Warming Experiment, Claire E. Kitzmiller, Wyatt C. Tran, Brendan Sullivan, Florencia Cortez, Mallory Choudoir, Rachel Simoes, Nipuni Dayarathne, Kristen M. Deangelis
High-Quality Genomes Of Paenibacillus Spp. Rc334 And Rc343, Isolated From A Long-Term Forest Soil Warming Experiment, Claire E. Kitzmiller, Wyatt C. Tran, Brendan Sullivan, Florencia Cortez, Mallory Choudoir, Rachel Simoes, Nipuni Dayarathne, Kristen M. Deangelis
Microbiology Department Faculty Publication Series
Paenibacillus spp. RC334 and RC343 were isolated from heated soil in a long-term soil warming experiment. Both genomes were 5.98 Mb and assembled as a single contig. We describe the assembly and annotation of the two high-quality draft genomes for these isolates here.
Detrimental Impact Of The Geobacter Metallireducens Type Vi Secretion System On Direct Interspecies Electron Transfer, Jessica A. Smith, Dawn E. Holmes, Trevor L. Woodard, Yang Li, Xingying Liu, Li-Ying Wang, David Meier, Ingrid A. Schwarz, Derek R. Lovley
Detrimental Impact Of The Geobacter Metallireducens Type Vi Secretion System On Direct Interspecies Electron Transfer, Jessica A. Smith, Dawn E. Holmes, Trevor L. Woodard, Yang Li, Xingying Liu, Li-Ying Wang, David Meier, Ingrid A. Schwarz, Derek R. Lovley
Microbiology Department Faculty Publication Series
Direct interspecies electron transfer (DIET) is important in anaerobic communities of environmental and practical significance. Other than the need for close physical contact for electrical connections, the interactions of DIET partners are poorly understood. Type VI secretion systems (T6SSs) typically kill competitive microbes. Surprisingly, Geobacter metallireducens highly expressed T6SS genes when DIET-based co-cultures were initiated with Geobacter sulfurreducens. T6SS gene expression was lower when the electron shuttle anthraquinone-2,6-disulfonate was added to alleviate the need for interspecies contact. Disruption of hcp, the G. metallireducens gene for the main T6SS needle-tube protein subunit, and the most highly upregulated gene in …
What A Tick Can Tell A Doctor: Using The Human-Biting Tick In The Clinical Management Of Tick-Borne Disease, Stephen M. Rich, Eric L. Siegel, Guang Xu
What A Tick Can Tell A Doctor: Using The Human-Biting Tick In The Clinical Management Of Tick-Borne Disease, Stephen M. Rich, Eric L. Siegel, Guang Xu
Microbiology Department Faculty Publication Series
With expanding concern about ticks, there is a general sense of uncertainty about the diagnosis and treatment of tick-borne diseases. The diagnosis process is often based on clinical judgment in conjunction with laboratory testing and can be pathogen specific. Treatments may require disease-dependent approaches, and co-infections complicate or increase the severity of the clinical picture. Measuring exposure indices in the tick has become popular among providers and their patients, though this practice is not universally understood, and certain public health agencies have voiced concerns regarding interpretation and rigor of testing. As many providers subscribe to or recommend these services to …
Fe(Iii) (Oxyhydr)Oxide Reduction By The Thermophilic Iron-Reducing Bacterium Desulfovulcanus Ferrireducens, Elizabeth C. Sklute, Deborah A. Leopo, Kaylee A. Neat, Kenneth J. T. Livi, M. Darby Dyar, James F. Holden
Fe(Iii) (Oxyhydr)Oxide Reduction By The Thermophilic Iron-Reducing Bacterium Desulfovulcanus Ferrireducens, Elizabeth C. Sklute, Deborah A. Leopo, Kaylee A. Neat, Kenneth J. T. Livi, M. Darby Dyar, James F. Holden
Microbiology Department Faculty Publication Series
Some thermophilic bacteria from deep-sea hydrothermal vents grow by dissimilatory iron reduction, but our understanding of their biogenic mineral transformations is nascent. Mineral transformations catalyzed by the thermophilic iron-reducing bacterium Desulfovulcanus ferrireducens during growth at 55°C were examined using synthetic nanophase ferrihydrite, akaganeite, and lepidocrocite separately as terminal electron acceptors. Spectral analyses using visible-near infrared (VNIR), Fourier-transform infrared attenuated total reflectance (FTIR-ATR), and Mössbauer spectroscopies were complemented with x-ray diffraction (XRD) and transmission electron microscopy (TEM) using selected area electron diffraction (SAED) and energy dispersive X-ray (EDX) analyses. The most extensive biogenic mineral transformation occurred with ferrihydrite, which produced a …
Differential Resistance Of Borrelia Burgdorferi Clones To Human Serum-Mediated Killing Does Not Correspond To Their Predicted Invasiveness, Patrick Pearson, Connor Rich, Eric L. Siegel, Dustin Brisson, Stephen M. Rich
Differential Resistance Of Borrelia Burgdorferi Clones To Human Serum-Mediated Killing Does Not Correspond To Their Predicted Invasiveness, Patrick Pearson, Connor Rich, Eric L. Siegel, Dustin Brisson, Stephen M. Rich
Microbiology Department Faculty Publication Series
Reservoir host associations have been observed among and within Borrelia genospecies, and host complement-mediated killing is a major determinant in these interactions. In North America, only a subset of Borrelia burgdorferi lineages cause the majority of disseminated infections in humans. We hypothesize that differential resistance to human complement-mediated killing may be a major phenotypic determinant of whether a lineage can establish systemic infection. As a corollary, we hypothesize that borreliacidal action may differ among human subjects. To test these hypotheses, we isolated primary B. burgdorferi clones from field-collected ticks and determined whether the killing effects of human serum differed among …
Inositol Acylation Of Phosphatidylinositol Mannosides: A Rapid Mass Response To Membrane Fluidization In Mycobacteria, Peter P. Nguyen, Takehiro Kado, M Sloan Siegrist, Yasu S. Morita
Inositol Acylation Of Phosphatidylinositol Mannosides: A Rapid Mass Response To Membrane Fluidization In Mycobacteria, Peter P. Nguyen, Takehiro Kado, M Sloan Siegrist, Yasu S. Morita
Microbiology Department Faculty Publication Series
Mycobacteria share an unusually complex, multilayered cell envelope, which contributes to adaptation to changing environments. The plasma membrane is the deepest layer of the cell envelope and acts as the final permeability barrier against outside molecules. There is an obvious need to maintain the plasma membrane integrity, but the adaptive responses of the plasma membrane to stress exposure remain poorly understood. Using chemical treatment and heat stress to fluidize the membrane, we show here that phosphatidylinositol (PI)-anchored plasma membrane glycolipids known as PI mannosides (PIMs) are rapidly remodeled upon membrane fluidization in Mycobacterium smegmatis. Without membrane stress, PIMs are …
Spatial Repellents Transfluthrin And Metofluthrin Affect The Behavior Of Dermacentor Variabilis, Amblyomma Americanum, And Ixodes Scapularis In An In Vitro Vertical Climb Assay, Eric L. Siegel, Marcos Olivera, Esteban Martinez Roig, Melynda Perry, Andrew Y. Li, Sebastián D'Hers, Stephen M. Rich
Spatial Repellents Transfluthrin And Metofluthrin Affect The Behavior Of Dermacentor Variabilis, Amblyomma Americanum, And Ixodes Scapularis In An In Vitro Vertical Climb Assay, Eric L. Siegel, Marcos Olivera, Esteban Martinez Roig, Melynda Perry, Andrew Y. Li, Sebastián D'Hers, Stephen M. Rich
Microbiology Department Faculty Publication Series
Repellents serve an important role in bite protection. Tick repellents largely rely on biomechanisms that induce responses with direct contact, but synthetic pyrethroids used as spatial repellents against insects have received recent attention for potential use in tick protection systems. An in vitro vertical climb assay was designed to assess spatial repellency against Dermacentor variabilis, Amblyomma americanum, and Ixodes scapularis adult, female ticks. Climbing behavior was assessed with and without the presence of two spatial repellents, transfluthrin and metofluthrin. Repellency parameters were defined to simulate the natural questing behavior of ambushing ticks, including measures of detachment, pseudo-questing duration, …
Microbe-Mineral Interaction And Novel Proteins For Iron Oxide Mineral Reduction In The Hyperthermophilic Crenarchaeon Pyrodictium Delaneyi, Srishti Kashyap, James F. Holden
Microbe-Mineral Interaction And Novel Proteins For Iron Oxide Mineral Reduction In The Hyperthermophilic Crenarchaeon Pyrodictium Delaneyi, Srishti Kashyap, James F. Holden
Microbiology Department Faculty Publication Series
Dissimilatory iron reduction by hyperthermophilic archaea occurs in many geothermal environments and generally relies on microbe-mineral interactions that transform various iron oxide minerals. In this study, the physiology of dissimilatory iron and nitrate reduction was examined in the hyperthermophilic crenarchaeon type strain Pyrodictium delaneyi Su06. Iron barrier experiments showed that P. delaneyi required direct contact with the Fe(III) oxide mineral ferrihydrite for reduction. The separate addition of an exogenous electron shuttle (anthraquinone-2,6-disulfonate), a metal chelator (nitrilotriacetic acid), and 75% spent cell-free supernatant did not stimulate growth with or without the barrier. Protein electrophoresis showed that the c-type cytochrome and …
Mechanisms For Electron Uptake By Methanosarcina Acetivorans During Direct Interspecies Electron Transfer, Dawn E. Holmes, Jinjie Zhou, Toshiyuki Ueki, Trevor Woodard, Derek Lovley
Mechanisms For Electron Uptake By Methanosarcina Acetivorans During Direct Interspecies Electron Transfer, Dawn E. Holmes, Jinjie Zhou, Toshiyuki Ueki, Trevor Woodard, Derek Lovley
Microbiology Department Faculty Publication Series
Direct interspecies electron transfer (DIET) between bacteria and methanogenic archaea appears to be an important syntrophy in both natural and engineered methanogenic environments. However, the electrical connections on the outer surface of methanogens and the subsequent processing of electrons for carbon dioxide reduction to methane are poorly understood. Here, we report that the genetically tractable methanogen Methanosarcina acetivorans can grow via DIET in coculture with Geobacter metallireducens serving as the electron-donating partner. Comparison of gene expression patterns in M. acetivorans grown in coculture versus pure-culture growth on acetate revealed that transcripts for the outer-surface multiheme c-type cytochrome MmcA were …
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 …
Mechanisms For Electron Uptake By Methanosarcina Acetivorans During Direct Interspecies Electron Transfer, Dawn E. Holmes, Jinjie Zhou, Toshiyuki Ueki, Derek R. Lovley
Mechanisms For Electron Uptake By Methanosarcina Acetivorans During Direct Interspecies Electron Transfer, Dawn E. Holmes, Jinjie Zhou, Toshiyuki Ueki, Derek R. Lovley
Microbiology Department Faculty Publication Series
Direct interspecies electron transfer (DIET) between bacteria and methanogenic archaea appears to be an important syntrophy in both natural and engineered methanogenic environments. However, the electrical connections on the outer surface of methanogens and the subsequent processing of electrons for carbon dioxide reduction to methane are poorly understood. Here, we report that the genetically tractable methanogen Methanosarcina acetivorans can grow via DIET in coculture with Geobacter metallireducens serving as the electron-donating partner. Comparison of gene expression patterns in M. acetivorans grown in coculture versus pure-culture growth on acetate revealed that transcripts for the outer-surface multiheme c-type cytochrome MmcA were higher …
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 …
Draft Genome Sequence Of Desulfurobacterium Thermolithotrophum Strain Hr11, A Novel Thermophilic Autotrophic Subspecies From A Deep-Sea Hydrothermal Vent, James F. Holden, Collin P. Bardwell, Srishti Kashyap
Draft Genome Sequence Of Desulfurobacterium Thermolithotrophum Strain Hr11, A Novel Thermophilic Autotrophic Subspecies From A Deep-Sea Hydrothermal Vent, James F. Holden, Collin P. Bardwell, Srishti Kashyap
Microbiology Department Faculty Publication Series
Desulfurobacterium sp. strain HR11 was isolated from a hydrothermal vent on the Juan de Fuca Ridge. We present the 1.55-Mb genome sequence of HR11, which contains 1,624 putative protein-coding sequences. Overall genome relatedness index analyses indicate that HR11 is a novel subspecies of D. thermolithotrophum.
Genome Sequences Of Frankineae Sp. Strain Mt45 And Jatrophihabitans Sp. Strain Gas493, Two Actinobacteria Isolated From Forest Soil, Kristen M. Deangelis, Grace Pold
Genome Sequences Of Frankineae Sp. Strain Mt45 And Jatrophihabitans Sp. Strain Gas493, Two Actinobacteria Isolated From Forest Soil, Kristen M. Deangelis, Grace Pold
Microbiology Department Faculty Publication Series
Frankiaceae are bacterial endosymbionts that are also found free-living in soil. Here, we present the genome sequences of two novel bacterial members of the order Frankiales, class Actinobacteria, isolated from temperate terrestrial forest soils. The genomes for MT45 and GAS493 indicate a genetic capacity for carbohydrate degradation but not nitrogen fixation.
Draft Genome Sequence Of A Terrestrial Planctomycete, Singulisphaera Sp. Strain Gp 187, Isolated From Forest Soil, Maureen A. Morrow, Grace Pold, Kristen M. Deangelis
Draft Genome Sequence Of A Terrestrial Planctomycete, Singulisphaera Sp. Strain Gp 187, Isolated From Forest Soil, Maureen A. Morrow, Grace Pold, Kristen M. Deangelis
Microbiology Department Faculty Publication Series
Here we present the draft genome sequence of a novel species of the genus Singulisphaera (phylum Planctomycetes, family Isosphaeraceae), isolated from soil. Singulisphaera sp. strain GP 187 has a relatively large mobilome and numerous novel genes that may contriubte to the production of bioactive molecules.
Rainforest-To-Pasture Conversion Stimulates Soil Methanogenesis Across The Brazilian Amazon, Marie E. Kroeger, Laura K. Meredith, Kyle M. Meyer, Kevin D. Webster, Plinio Barbosa De Camargo, Leandro Fonseca De Souza, Siu Mui Tsai, Joost Van Haren, Scott Saleska, Brendan J. M. Bohannan, Jorge L. Mazza Rodrigues, Erika Berenguer, Klaus Nüsslein
Rainforest-To-Pasture Conversion Stimulates Soil Methanogenesis Across The Brazilian Amazon, Marie E. Kroeger, Laura K. Meredith, Kyle M. Meyer, Kevin D. Webster, Plinio Barbosa De Camargo, Leandro Fonseca De Souza, Siu Mui Tsai, Joost Van Haren, Scott Saleska, Brendan J. M. Bohannan, Jorge L. Mazza Rodrigues, Erika Berenguer, Klaus Nüsslein
Microbiology Department Faculty Publication Series
The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a …
Transcriptome Analysis Of The Brown Rot Fungus Gloeophyllum Trabeum During Lignocellulose Degradation, Kiwamu Umezawa, Mai Niikura, Yuka Kojima, Barry Goodell, Makoto Yoshida
Transcriptome Analysis Of The Brown Rot Fungus Gloeophyllum Trabeum During Lignocellulose Degradation, Kiwamu Umezawa, Mai Niikura, Yuka Kojima, Barry Goodell, Makoto Yoshida
Microbiology Department Faculty Publication Series
Brown rot fungi have great potential in biorefinery wood conversion systems because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. Some studies have shown that wood degradation mechanisms of brown rot fungi have diversity in their substrate selectivity. Gloeophyllum trabeum, one of the most studied brown rot species, has broad substrate selectivity and even can degrade …
Stealing The Show: Kshv Hijacks Host Rna Regulatory Pathways To Promote Infection, Daniel Macveigh-Fierro, William Rodriguez, Jacob Miles, Mandy Muller
Stealing The Show: Kshv Hijacks Host Rna Regulatory Pathways To Promote Infection, Daniel Macveigh-Fierro, William Rodriguez, Jacob Miles, Mandy Muller
Microbiology Department Faculty Publication Series
Kaposi’s sarcoma-associated herpesvirus (KSHV) induces life-long infections and has evolved many ways to exert extensive control over its host’s transcriptional and post-transcriptional machinery to gain better access to resources and dampened immune sensing. The hallmark of this takeover is how KSHV reshapes RNA fate both to control expression of its own gene but also that of its host. From the nucleus to the cytoplasm, control of RNA expression, localization, and decay is a process that is carefully tuned by a multitude of factors and that can adapt or react to rapid changes in the environment. Intriguingly, it appears that KSHV …
Hydrothermal Chimney Distribution On The Endeavour Segment, Juan De Fuca Ridge, David A. Clague, Julie F. Martin, Jennifer B. Paduan, David A. Butterfield, John W. Jamieson, Morgane Le Saout, David W. Caress, Hans Thomas, James F. Holden, Deborah S. Kelley
Hydrothermal Chimney Distribution On The Endeavour Segment, Juan De Fuca Ridge, David A. Clague, Julie F. Martin, Jennifer B. Paduan, David A. Butterfield, John W. Jamieson, Morgane Le Saout, David W. Caress, Hans Thomas, James F. Holden, Deborah S. Kelley
Microbiology Department Faculty Publication Series
The Endeavour Segment of the Juan de Fuca Ridge is well known for its abundance of hydrothermal vents and chimneys. One-meter scale multibeam mapping data collected by an autonomous undersea vehicle revealed 572 chimneys along the central 14 km of the segment, although only 47 are named and known to be active. Hydrothermal deposits are restricted to the axial graben and the near-rims of the graben above a seismically mapped axial magma lens. The sparse eruptive activity on the segment during the last 4,300 years has not buried inactive chimneys, as occurs at more magmatically robust mid-ocean ridges.
Fluid Geochemistry, Local Hydrology, And Metabolic Activity Define Methanogen Community Size And Composition In Deep-Sea Hydrothermal Vents, Lucy C. Stewart, Christopher K. Algar, Caroline S. Fortunato, Benjamin I. Larson, Joseph J. Vallino, Julie A. Huber, David A. Butterfield, James F. Holden
Fluid Geochemistry, Local Hydrology, And Metabolic Activity Define Methanogen Community Size And Composition In Deep-Sea Hydrothermal Vents, Lucy C. Stewart, Christopher K. Algar, Caroline S. Fortunato, Benjamin I. Larson, Joseph J. Vallino, Julie A. Huber, David A. Butterfield, James F. Holden
Microbiology Department Faculty Publication Series
The size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH4 production kinetics based on chemostat H2 availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H2, …
Growth Kinetics, Carbon Isotope Fractionation, And Gene Expression In The Hyperthermophile Methanocaldococcus Jannaschii During Hydrogen-Limited Growth And Interspecies Hydrogen Transfer, Begüm D. Topçuoğlu, Cem Meydan, Tran B. Nguyen, Susan Q. Lang, James F. Holden
Growth Kinetics, Carbon Isotope Fractionation, And Gene Expression In The Hyperthermophile Methanocaldococcus Jannaschii During Hydrogen-Limited Growth And Interspecies Hydrogen Transfer, Begüm D. Topçuoğlu, Cem Meydan, Tran B. Nguyen, Susan Q. Lang, James F. Holden
Microbiology Department Faculty Publication Series
Hyperthermophilic methanogens are often H2 limited in hot subseafloor environments, and their survival may be due in part to physiological adaptations to low H2 conditions and interspecies H2 transfer. The hyperthermophilic methanogen Methanocaldococcus jannaschii was grown in monoculture at high (80 to 83 μM) and low (15 to 27 μM) aqueous H2 concentrations and in coculture with the hyperthermophilic H2 producer Thermococcus paralvinellae. The purpose was to measure changes in growth and CH4 production kinetics, CH4 fractionation, and gene expression in M. jannaschii with changes in H2 flux. Growth and cell-specific …
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.
Geobacter Strains Expressing Poorly Conductive Pili Reveal Constraints On Direct Interspecies Electron Transfer Mechanisms, Toshiyuki Ueki, Kelly P. Nevin, Amelia-Elena Rotaru, Li-Ying Wang, Joy E. Ward, Trevor L. Woodard, Derek R. Lovley
Geobacter Strains Expressing Poorly Conductive Pili Reveal Constraints On Direct Interspecies Electron Transfer Mechanisms, Toshiyuki Ueki, Kelly P. Nevin, Amelia-Elena Rotaru, Li-Ying Wang, Joy E. Ward, Trevor L. Woodard, Derek R. Lovley
Microbiology Department Faculty Publication Series
Cytochrome-to-cytochrome electron transfer and electron transfer along conduits of multiple extracellular magnetite grains are often proposed as strategies for direct interspecies electron transfer (DIET) that do not require electrically conductive pili (e-pili). However, physical evidence for these proposed DIET mechanisms has been lacking. To investigate these possibilities further, we constructed Geobacter metallireducens strain Aro-5, in which the wild-type pilin gene was replaced with the aro-5 pilin gene that was previously shown to yield poorly conductive pili in Geobacter sulfurreducens strain Aro-5. G. metallireducens strain Aro-5 did not reduce Fe(III) oxide and produced only low current densities, phenotypes consistent with expression …