DeAngelis, Kristen

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Assistant Professor, Department of Microbiology
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I am a microbiologist trained in microbial ecology and bioinformatics. My research is focused on microbial traits and emergent properties of microbial communities. Climate change is the most pressing issue facing people today, and our work seeks to understand microbial feedbacks with climate, and applying this understanding to improve lignocellulosic biofuels production. 

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Now showing 1 - 10 of 20
  • Publication
    Complete genome sequence of “Enterobacter lignolyticus” SCF1
    (2011-01-01) DeAngelis, Kristen; D'Haeseleer, Patrick; Chivian, Dylan; Fortney, Julian L.; Khudyakov, Jane; Simmons, Blake; Woo, Hannah; Arkin, Adam P.; Davenport, Karen Walston; Goodwin, Lynne; Chen, Amy; Ivanova, Natalia; Kyrpides, Nikos C.; Mavromatis, Konstantinos; Woyke, Tanja; Hazen, Terry C.
    In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated “Enterobacter lignolyticus”SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest 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 net methane producers. Because of its ability to grow on lignin anaerobically, we sequenced the genome. The genome of “E. lignolyticus” SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohydrate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degradation pathway encoded in a single gene cluster.
  • Publication
    Microbiology 562: D. Batch Fermentation Module
    (2017-01-01) DeAngelis, Kristen; Prado, Cecilia
    In this module, we set up a fermentation of grains by yeast with hops to brew beer (D1). We make media and pour plates to grow and identify microbial contaminants (D2). Two weeks after setting up the primary fermentation, we prime and condition the fermentation (D3). While we wait for the priming and conditioning to finish, we do a bioinformatics analysis of microbial communities turning ethanol (a product of fermentation) to n-caproic acid, (D4), to illustrate the power of metagenomic sequencing in resolving microorganisms and their potential physiology. Then we identify and examine the microbial contaminants cultured in the primary fermentation (D5). When the beer is finished, we perform a sensory analysis (D6) followed by a field trip to the Berkshire Brewing Company in South Deerfield, MA, where we will tour their brewing facilities and microbiology lab.
  • Publication
    Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils
    (2016-01-01) Pold, Grace; Billings, Andrew F.; Blanchard, Jeff L.; Burkhardt, Daniel B.; Frey, Serita D.; Melillo, Jerry M.; Schnabel, Julia; van Diepen, Linda T.A.; DeAngelis, Kristen
    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 carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.
  • Publication
    Two decades of warming increases diversity of a potentially lignolytic bacterial community
    (2015-01-01) Pold, Grace; Melillo, Jerry M.; DeAngelis, Kristen
    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 lignin-amended beads selected for a distinct community containing bacterial taxa closely related to known lignin degraders, as well as members of many genera not previously noted as capable of degrading lignin. Warming tended to drive bacterial community structure more strongly in the lignin beads, while the effect on the fungal community was limited to unamended beads. Of those bacterial operational taxonomic units (OTUs) enriched by the warming treatment, many were enriched uniquely on lignin-amended beads. These taxa may be contributing to enhanced soil respiration under warming despite reduced readily available C availability. In aggregate, these results suggest that there is genetic potential for chemically complex soil carbon degradation that may lead to extended elevated soil respiration with long-term warming.
  • Publication
    Genome sequence and description of the anaerobic lignin-degrading bacterium Tolumonas lignolytica sp. nov.
    (2015-01-01) Billings, Andrew F.; Fortney, Julian L.; Hazen, Terry C.; Simmons, Blake; Davenport, Karen W.; Goodwin, Lynne; Ivanova, Natalia; Kyrpides, Nikos C.; Mavromatis, Konstantinos; Woyke, Tanya; DeAngelis, Kristen
    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 in β-aryl ether bond cleavage, which is the most abundant linkage between lignin monomers. We also found genes for enzymes involved in ferulic acid metabolism, which is a common product of lignin breakdown. By characterizing pathways and enzymes employed in the bacterial breakdown of lignin in anaerobic environments, this work should assist in the efficient engineering of biofuel production from lignocellulosic material.
  • Publication
    Long-term forest soil warming alters microbial communities in temperate forest soils
    (2015-01-01) DeAngelis, Kristen; Pold, Grace; Topçuoğlu, Begüm D.; van Diepen, Linda T.A.; Varney, Rebecca M.; Blanchard, Jeffrey L.; Melillo, Jerry; Frey, Serita D.
    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 change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.
  • Publication
    Genome Sequences of Frankineae sp. Strain MT45 and Jatrophihabitans sp. Strain GAS493, Two Actinobacteria Isolated from Forest Soil
    (2020-01-01) DeAngelis, Kristen M.; Pold, Grace
    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.
  • Publication
    Draft Genome Sequence of a Terrestrial Planctomycete, Singulisphaera sp. Strain GP 187, Isolated from Forest Soil
    (2020-01-01) Morrow, Maureen A.; Pold, Grace; DeAngelis, Kristen M.
    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.
  • Publication
    Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2
    (2014-01-01) Woo, Hannah L.; Ballor, Nicholas R.; Hazen, Terry C.; Fortney, Julian L.; Simmons, Blake; Davenport, Karen Walston; Goodwin, Lynne; Ivanova, Natalia; Kyrpides, Nikos C.; Mavromatis, Konstantinos; Woyke, Tanja; Jansson, Janet; Kimbrell, Jeff; DeAngelis, Kristen
    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 activity via in vitro enzyme assays. The genome of Klebsiella sp. strain BRL6-2 is 5.80 Mbp with no detected plasmids, and includes a relatively small arsenal of genes encoding lignocellulolytic carbohydrate active enzymes. The genome revealed four putative peroxidases including glutathione and DyP-type peroxidases, and a complete protocatechuate pathway encoded in a single gene cluster. Physiological studies revealed Klebsiella sp. strain BRL6-2 to be relatively stress tolerant to high ionic strength conditions. It grows in increasing concentrations of ionic liquid (1-ethyl-3-methyl-imidazolium acetate) up to 73.44 mM and NaCl up to 1.5 M.
  • Publication
    Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium
    (2017-01-01) Orellana, Roberto; Chaput, Gina; Markillie, Lye Meng; Mitchell, Hugh; Gaffrey, Matt; Orr, Gayla; DeAngelis, Kristen
    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 conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.