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Dissertation Implementing Organic Amendments To
DISSERTATION IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE Submitted by Erika J. Foster Graduate Degree Program in Ecology In partial fulfillment of the requirements For the Degree of Doctor of Philosophy Colorado State University Fort Collins, Colorado Summer 2018 Doctoral Committee: Advisor: M. Francesca Cotrufo Louise Comas Charles Rhoades Matthew D. Wallenstein Copyright by Erika J. Foster 2018 All Rights Reserved i ABSTRACT IMPLEMENTING ORGANIC AMENDMENTS TO ENHANCE MAIZE YIELD, SOIL MOISTURE, AND MICROBIAL NUTRIENT CYCLING IN TEMPERATE AGRICULTURE To sustain agricultural production into the future, management should enhance natural biogeochemical cycling within the soil. Strategies to increase yield while reducing chemical fertilizer inputs and irrigation require robust research and development before widespread implementation. Current innovations in crop production use amendments such as manure and biochar charcoal to increase soil organic matter and improve soil structure, water, and nutrient content. Organic amendments also provide substrate and habitat for soil microorganisms that can play a key role cycling nutrients, improving nutrient availability for crops. Additional plant growth promoting bacteria can be incorporated into the soil as inocula to enhance soil nutrient cycling through mechanisms like phosphorus solubilization. Since microbial inoculation is highly effective under drought conditions, this technique pairs well in agricultural systems using limited irrigation to save water, particularly in semi-arid regions where climate change and population growth exacerbate water scarcity. The research in this dissertation examines synergistic techniques to reduce irrigation inputs, while building soil organic matter, and promoting natural microbial function to increase crop available nutrients. The research was conducted on conventional irrigated maize systems at the Agricultural Research Development and Education Center north of Fort Collins, CO. -
Phylogenetic Conservation of Bacterial Responses to Soil Nitrogen Addition Across Continents
ARTICLE https://doi.org/10.1038/s41467-019-10390-y OPEN Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents Kazuo Isobe1,2, Steven D. Allison 1,3, Banafshe Khalili1, Adam C. Martiny 1,3 & Jennifer B.H. Martiny1 Soil microbial communities are intricately linked to ecosystem functioning such as nutrient cycling; therefore, a predictive understanding of how these communities respond to envir- onmental changes is of great interest. Here, we test whether phylogenetic information can 1234567890():,; predict the response of bacterial taxa to nitrogen (N) addition. We analyze the composition of soil bacterial communities in 13 field experiments across 5 continents and find that the N response of bacteria is phylogenetically conserved at each location. Remarkably, the phylo- genetic pattern of N responses is similar when merging data across locations. Thus, we can identify bacterial clades – the size of which are highly variable across the bacterial tree – that respond consistently to N addition across locations. Our findings suggest that a phylogenetic approach may be useful in predicting shifts in microbial community composition in the face of other environmental changes. 1 Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA. 2 Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan. 3 Department of Earth System Science, University of California, Irvine, CA 92697, USA. Correspondence and requests for materials should be addressed to K.I. (email: [email protected]) or to J.B.H.M. (email: [email protected]) NATURE COMMUNICATIONS | (2019) 10:2499 | https://doi.org/10.1038/s41467-019-10390-y | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-10390-y t is well established that environmental changes such as soil up the signal of vertical inherence and result in a random dis- warming and nutrient addition alter the composition of bac- tribution of response across the phylogeny6. -
Marine Sediments Illuminate Chlamydiae Diversity and Evolution
Supplementary Information for: Marine sediments illuminate Chlamydiae diversity and evolution Jennah E. Dharamshi1, Daniel Tamarit1†, Laura Eme1†, Courtney Stairs1, Joran Martijn1, Felix Homa1, Steffen L. Jørgensen2, Anja Spang1,3, Thijs J. G. Ettema1,4* 1 Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden 2 Department of Earth Science, Centre for Deep Sea Research, University of Bergen, N-5020 Bergen, Norway 3 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, NL-1790 AB Den Burg, The Netherlands 4 Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands. † These authors contributed equally * Correspondence to: Thijs J. G. Ettema, Email: [email protected] Supplementary Information Supplementary Discussions ............................................................................................................................ 3 1. Evolutionary relationships within the Chlamydiae phylum ............................................................................. 3 2. Insights into the evolution of pathogenicity in Chlamydiaceae ...................................................................... 8 3. Secretion systems and flagella in Chlamydiae .............................................................................................. 13 4. Phylogenetic diversity of chlamydial nucleotide transporters. .................................................................... -
Downloaded from the Genome NCBI
bioRxiv1 preprint doi: https://doi.org/10.1101/765248; this version posted July 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Groundwater Elusimicrobia are metabolically diverse compared to gut microbiome Elusimicrobia 2 and some have a novel nitrogenase paralog. 3 4 Raphaël Méheust1,2, Cindy J. Castelle1,2, Paula B. Matheus Carnevali1,2, Ibrahim F. Farag3, Christine He1, 5 Lin-Xing Chen1,2, Yuki Amano4, Laura A. Hug5, and Jillian F. Banfield1,2,*. 6 7 1Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA 94720, 8 USA 9 2Innovative Genomics Institute, Berkeley, CA 94720, USA 10 3School of Marine Science and Policy, University of Delaware, Lewes, DE 19968, USA 11 4Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Ibaraki, Japan 12 5Department of Biology, University of Waterloo, ON, Canada 13 *Corresponding author: Email: [email protected] 14 15 Abstract 16 Currently described members of Elusimicrobia, a relatively recently defined phylum, are animal- 17 associated and rely on fermentation. However, free-living Elusimicrobia have been detected in sediments, 18 soils and groundwater, raising questions regarding their metabolic capacities and evolutionary 19 relationship to animal-associated species. Here, we analyzed 94 draft-quality, non-redundant genomes, 20 including 30 newly reconstructed genomes, from diverse animal-associated and natural environments. 21 Genomes group into 12 clades, 10 of which previously lacked reference genomes. Groundwater- 22 associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, reliant on 23 oxygen or nitrate/nitrite-dependent respiration, or a variety of organic compounds and Rhodobacter 24 nitrogen fixation-dependent (Rnf-dependent) acetogenesis with hydrogen and carbon dioxide as the 25 substrates. -
Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones
International Journal of Environmental Research and Public Health Article Activated Sludge Microbial Community and Treatment Performance of Wastewater Treatment Plants in Industrial and Municipal Zones Yongkui Yang 1,2 , Longfei Wang 1, Feng Xiang 1, Lin Zhao 1,2 and Zhi Qiao 1,2,* 1 School of Environmental Science and Engineering, Tianjin University, Tianjin 300350, China; [email protected] (Y.Y.); [email protected] (L.W.); [email protected] (F.X.); [email protected] (L.Z.) 2 China-Singapore Joint Center for Sustainable Water Management, Tianjin University, Tianjin 300350, China * Correspondence: [email protected]; Tel.: +86-22-87402072 Received: 14 November 2019; Accepted: 7 January 2020; Published: 9 January 2020 Abstract: Controlling wastewater pollution from centralized industrial zones is important for reducing overall water pollution. Microbial community structure and diversity can adversely affect wastewater treatment plant (WWTP) performance and stability. Therefore, we studied microbial structure, diversity, and metabolic functions in WWTPs that treat industrial or municipal wastewater. Sludge microbial community diversity and richness were the lowest for the industrial WWTPs, indicating that industrial influents inhibited bacterial growth. The sludge of industrial WWTP had low Nitrospira populations, indicating that influent composition affected nitrification and denitrification. The sludge of industrial WWTPs had high metabolic functions associated with xenobiotic and amino acid metabolism. Furthermore, bacterial richness was positively correlated with conventional pollutants (e.g., carbon, nitrogen, and phosphorus), but negatively correlated with total dissolved solids. This study was expected to provide a more comprehensive understanding of activated sludge microbial communities in full-scale industrial and municipal WWTPs. Keywords: activated sludge; industrial zone; metabolic function; microbial community; wastewater treatment 1. -
Genome-Reconstruction for Eukaryotes from Complex Natural Microbial Communities
bioRxiv preprint doi: https://doi.org/10.1101/171355; this version posted August 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Genome-reconstruction for eukaryotes from complex natural microbial communities Patrick T. West1, Alexander J. Probst2, Igor V. Grigoriev1,5, Brian C. Thomas2, Jillian F. Banfield2,3,4* 1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. 2Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. 3Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. 4Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. 5US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. * Corresponding Author Running title Metagenomic Reconstruction of Eukaryotic Genomes Keywords metagenomics, eukaryotes, genome, gene prediction Corresponding author contact info Jillian Banfield Department of Environmental Science, Policy, & Management UC Berkeley 130 Mulford Hall #3114 Berkeley, CA 94720 [email protected] (510) 643-2155 1 bioRxiv preprint doi: https://doi.org/10.1101/171355; this version posted August 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Microbial eukaryotes are integral components of natural microbial communities and their inclusion is critical for many ecosystem studies yet the majority of published metagenome analyses ignore eukaryotes. -
Experimental Warming Reduces Survival, Cold Tolerance, and Gut Prokaryotic Diversity of the Eastern Subterranean Termite, Reticulitermes flavipes (Kollar)
fmicb-12-632715 May 11, 2021 Time: 20:32 # 1 ORIGINAL RESEARCH published: 17 May 2021 doi: 10.3389/fmicb.2021.632715 Experimental Warming Reduces Survival, Cold Tolerance, and Gut Prokaryotic Diversity of the Eastern Subterranean Termite, Reticulitermes flavipes (Kollar) Rachel A. Arango1*†, Sean D. Schoville2, Cameron R. Currie3 and Camila Carlos-Shanley4*† 1 USDA Forest Service, Forest Products Laboratory, Madison, WI, United States, 2 Department of Entomology, University of Wisconsin-Madison, Madison, WI, United States, 3 Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States, 4 Department of Biology, Texas State University, San Marcos, TX, United States Edited by: Understanding the effects of environmental disturbances on insects is crucial in Brian Weiss, predicting the impact of climate change on their distribution, abundance, and ecology. Yale University, United States As microbial symbionts are known to play an integral role in a diversity of functions within Reviewed by: Ellen Decaestecker, the insect host, research examining how organisms adapt to environmental fluctuations KU Leuven, Belgium should include their associated microbiota. In this study, subterranean termites Elizabeth Ottesen, University of Georgia, United States [Reticulitermes flavipes (Kollar)] were exposed to three different temperature treatments ◦ ◦ ◦ *Correspondence: characterized as low (15 C), medium (27 C), and high (35 C). Results suggested that Rachel A. Arango pre-exposure to cold allowed termites to stay active longer in decreasing temperatures [email protected] but caused termites to freeze at higher temperatures. High temperature exposure Camila Carlos-Shanley [email protected]. had the most deleterious effects on termites with a significant reduction in termite †These authors have contributed survival as well as reduced ability to withstand cold stress. -
Bacterial Communities Associated with Cell Phones and Shoes
A peer-reviewed version of this preprint was published in PeerJ on 9 June 2020. View the peer-reviewed version (peerj.com/articles/9235), which is the preferred citable publication unless you specifically need to cite this preprint. Coil DA, Neches RY, Lang JM, Jospin G, Brown WE, Cavalier D, Hampton- Marcell J, Gilbert JA, Eisen JA. 2020. Bacterial communities associated with cell phones and shoes. PeerJ 8:e9235 https://doi.org/10.7717/peerj.9235 Bacterial communities associated with cell phones and shoes David A Coil Corresp., 1 , Russell Y Neches 1 , Jenna M Lang 1 , Guillaume Jospin 1 , Wendy E Brown 2, 3 , Darlene Cavalier 3, 4 , Jarrad Hampton-Marcell 5 , Jack A Gilbert 6 , Jonathan A Eisen Corresp. 7 1 Genome Center, UC Davis, Davis, California, United States 2 Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States 3 Science Cheerleaders, Inc, United States 4 SciStarter.org, United States 5 Argonne National Laboratory, University of Chicago, Lemont, Illinois, United States 6 Department of Surgery, University of Chicago, Chicago, Illinois, United States 7 Genome Center, Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, Davis, California, United States Corresponding Authors: David A Coil, Jonathan A Eisen Email address: [email protected], [email protected] Background: Every human being carries with them a collection of microbes, a collection that is likely both unique to that person, but also dynamic as a result of significant flux with the surrounding environment. The interaction of the human microbiome (i.e., the microbes that are found directly in contact with a person in places such as the gut, mouth, and skin) and the microbiome of accessory objects (e.g., shoes, clothing, phones, jewelry) is of potential interest to both epidemiology and the developing field of microbial forensics. -
Metagenomic Views of Microbial Dynamics Influenced By
www.nature.com/scientificreports OPEN Metagenomic views of microbial dynamics infuenced by hydrocarbon seepage in sediments of the Gulf of Mexico Rui Zhao1, Zarath M. Summers2, Glenn D. Christman1, Kristin M. Yoshimura1 & Jennifer F. Biddle1* Microbial cells in the seabed are thought to persist by slow population turnover rates and extremely low energy requirements. External stimulations such as seafoor hydrocarbon seeps have been demonstrated to signifcantly boost microbial growth; however, the microbial community response has not been fully understood. Here we report a comparative metagenomic study of microbial response to natural hydrocarbon seeps in the Gulf of Mexico. Subsurface sediments (10–15 cm below seafoor) were collected from fve natural seep sites and two reference sites. The resulting metagenome sequencing datasets were analyzed with both gene-based and genome-based approaches. 16S rRNA gene-based analyses suggest that the seep samples are distinct from the references by both 16S rRNA fractional content and phylogeny, with the former dominated by ANME-1 archaea (~50% of total) and Desulfobacterales, and the latter dominated by the Deltaproteobacteria, Planctomycetes, and Chlorofexi phyla. Sulfate-reducing bacteria (SRB) are present in both types of samples, with higher relative abundances in seep samples than the references. Genes for nitrogen fxation were predominantly found in the seep sites, whereas the reference sites showed a dominant signal for anaerobic ammonium oxidation (anammox). We recovered 49 metagenome-assembled genomes and assessed the microbial functional potentials in both types of samples. By this genome-based analysis, the seep samples were dominated by ANME-1 archaea and SRB, with the capacity for methane oxidation coupled to sulfate reduction, which is consistent with the 16S rRNA-gene based characterization. -
Dramatic Expansion of Microbial Groups That Shape the Global Sulfur Cycle 2 3 Authors: Karthik Anantharaman1*, Sean P
bioRxiv preprint doi: https://doi.org/10.1101/166447; this version posted July 21, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Title: Dramatic expansion of microbial groups that shape the global sulfur cycle 2 3 Authors: Karthik Anantharaman1*, Sean P. Jungbluth2, Rose S. Kantor3, Adi Lavy1, Lesley A. 4 Warren4, Michael S. Rappé5, Brian C. Thomas1, and Jillian F. Banfield1,6,7* 5 Affiliations: 6 1Department of Earth and Planetary Sciences, Berkeley, CA, USA 7 2DOE Joint Genome Institute, Walnut Creek, CA, USA 8 3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA 9 4Department of Civil Engineering, University of Toronto, Ontario, CANADA 10 5Hawaii Institute of Marine Biology, University of Hawaii at Manoa, Kaneohe, HI, USA 11 6Department of Environmental Science, Policy, and Management, Berkeley, CA, USA 12 7Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 13 USA 14 15 *Corresponding author 16 Email: [email protected] 17 Address: 307 McCone Hall, Berkeley, CA 94720 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 1 bioRxiv preprint doi: https://doi.org/10.1101/166447; this version posted July 21, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Alpha-Carbonic Anhydrases from Hydrothermal Vent Sources As Potential Carbon Dioxide Sequestration Agents: in Silico Sequence, Structure and Dynamics Analyses
International Journal of Molecular Sciences Article Alpha-Carbonic Anhydrases from Hydrothermal Vent Sources as Potential Carbon Dioxide Sequestration Agents: In Silico Sequence, Structure and Dynamics Analyses Colleen Varaidzo Manyumwa 1 , Reza Zolfaghari Emameh 2 and Özlem Tastan Bishop 1,* 1 Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown 6140, South Africa; [email protected] 2 Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran; [email protected] * Correspondence: [email protected]; Tel.: +27-46-603-8072; Fax: +27-46-603-7576 Received: 28 September 2020; Accepted: 27 October 2020; Published: 29 October 2020 Abstract: With the increase in CO2 emissions worldwide and its dire effects, there is a need to reduce CO2 concentrations in the atmosphere. Alpha-carbonic anhydrases (α-CAs) have been identified as suitable sequestration agents. This study reports the sequence and structural analysis of 15 α-CAs from bacteria, originating from hydrothermal vent systems. Structural analysis of the multimers enabled the identification of hotspot and interface residues. Molecular dynamics simulations of the homo-multimers were performed at 300 K, 363 K, 393 K and 423 K to unearth potentially thermostable α-CAs. Average betweenness centrality (BC) calculations confirmed the relevance of some hotspot and interface residues. The key residues responsible for dimer thermostability were identified by comparing fluctuating interfaces with stable ones, and were part of conserved motifs. Crucial long-lived hydrogen bond networks were observed around residues with high BC values. Dynamic cross correlation fortified the relevance of oligomerization of these proteins, thus the importance of simulating them in their multimeric forms. -
Mean and SD Archaea Bacteria Genome Size (Mb)
Distributions for kingdom level Primer score mean and SD Genomic GC (%) mean and SD 60 3 2 50 1 Primer score 40 0 Genomic GC (%) Bacteria Bacteria Archaea Archaea kingdom kingdom 16S GC (%) mean and SD Genome size (Mb) mean and SD 65 5 60 4 55 3 16S GC (%) 2 Genome size (Mb) Genome size 50 Bacteria Bacteria Archaea Archaea kingdom kingdom 16S GC (%) Primer score 45 50 55 60 65 0 1 2 3 4 Acidobacteria Acidobacteria Actinobacteria Actinobacteria Aquificae Aquificae Bacteroidetes Bacteroidetes Caldiserica Caldiserica Chlamydiae Chlamydiae Chlorobi Primer scoremeanandSD Chlorobi 16S GC(%)meanandSD Chloroflexi Chloroflexi Chrysiogenetes Chrysiogenetes Crenarchaeota Crenarchaeota Cyanobacteria Cyanobacteria Deferribacteres Deferribacteres Deinococcus−Thermus Deinococcus−Thermus Dictyoglomi Dictyoglomi Elusimicrobia Elusimicrobia phylum phylum Euryarchaeota Euryarchaeota Fibrobacteres Fibrobacteres Firmicutes Firmicutes Fusobacteria Fusobacteria Gemmatimonadetes Gemmatimonadetes Ignavibacteria Ignavibacteria Ignavibacteriae Ignavibacteriae Korarchaeota Korarchaeota Lentisphaerae Lentisphaerae Nanoarchaeota Nanoarchaeota Nitrospirae Nitrospirae Planctomycetes Planctomycetes level phylum for Distributions Proteobacteria Proteobacteria Spirochaetes Spirochaetes Synergistetes Synergistetes Tenericutes Tenericutes Thaumarchaeota Thaumarchaeota Thermodesulfobacteria Thermodesulfobacteria Thermotogae Thermotogae unclassified unclassified Verrucomicrobia Verrucomicrobia Genome size (Mb) Genomic GC (%) 10.0 30 40 50 60 70 2.5 5.0 7.5 Acidobacteria Acidobacteria