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Avila-Herrera A, Kimbrel JA, Manuel Martí J, Thissen J, Saada EA, Weisenberger T, Arrildt KT, Segelke BW, Allen JE, Zemla A, Borucki MK. Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies. PLoS One 2024; 19:e0289198. [PMID: 38271318 PMCID: PMC10810540 DOI: 10.1371/journal.pone.0289198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays. Thus, mAb assessment assays that utilize a more genetically diverse, biologically relevant, virus stock may yield data that are relevant for prediction of mAb efficacy and for enhancing biosurveillance.
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Affiliation(s)
- Aram Avila-Herrera
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Jeffrey A. Kimbrel
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jose Manuel Martí
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - James Thissen
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Edwin A. Saada
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Tracy Weisenberger
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Kathryn T. Arrildt
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Brent W. Segelke
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
| | - Jonathan E. Allen
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Adam Zemla
- Lawrence Livermore National Laboratory, Computing Directorate, Global Security Computing Applications Division, Livermore, California, United States of America
| | - Monica K. Borucki
- Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Biosciences and Biotechnology Division, Livermore, California, United States of America
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2
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Li W, Baliu-Rodriguez D, Premathilaka SH, Thenuwara SI, Kimbrel JA, Samo TJ, Ramon C, Kiledal EA, Rivera SR, Kharbush J, Isailovic D, Weber PK, Dick GJ, Mayali X. Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures. ISME J 2024; 18:wrae082. [PMID: 38718148 PMCID: PMC11126159 DOI: 10.1093/ismejo/wrae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/01/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
Nutrient-induced blooms of the globally abundant freshwater toxic cyanobacterium Microcystis cause worldwide public and ecosystem health concerns. The response of Microcystis growth and toxin production to new and recycled nitrogen (N) inputs and the impact of heterotrophic bacteria in the Microcystis phycosphere on these processes are not well understood. Here, using microbiome transplant experiments, cyanotoxin analysis, and nanometer-scale stable isotope probing to measure N incorporation and exchange at single cell resolution, we monitored the growth, cyanotoxin production, and microbiome community structure of several Microcystis strains grown on amino acids or proteins as the sole N source. We demonstrate that the type of organic N available shaped the microbial community associated with Microcystis, and external organic N input led to decreased bacterial colonization of Microcystis colonies. Our data also suggest that certain Microcystis strains could directly uptake amino acids, but with lower rates than heterotrophic bacteria. Toxin analysis showed that biomass-specific microcystin production was not impacted by N source (i.e. nitrate, amino acids, or protein) but rather by total N availability. Single-cell isotope incorporation revealed that some bacterial communities competed with Microcystis for organic N, but other communities promoted increased N uptake by Microcystis, likely through ammonification or organic N modification. Our laboratory culture data suggest that organic N input could support Microcystis blooms and toxin production in nature, and Microcystis-associated microbial communities likely play critical roles in this process by influencing cyanobacterial succession through either decreasing (via competition) or increasing (via biotransformation) N availability, especially under inorganic N scarcity.
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Affiliation(s)
- Wei Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - David Baliu-Rodriguez
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States
| | - Sanduni H Premathilaka
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States
| | - Sharmila I Thenuwara
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Erik Anders Kiledal
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48104, United States
| | - Sara R Rivera
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48104, United States
| | - Jenan Kharbush
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48104, United States
| | - Dragan Isailovic
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48104, United States
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI 48104, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States
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3
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Maillard F, Michaud TJ, See CR, DeLancey LC, Blazewicz SJ, Kimbrel JA, Pett-Ridge J, Kennedy PG. Melanization slows the rapid movement of fungal necromass carbon and nitrogen into both bacterial and fungal decomposer communities and soils. mSystems 2023; 8:e0039023. [PMID: 37338274 PMCID: PMC10469842 DOI: 10.1128/msystems.00390-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 06/21/2023] Open
Abstract
Microbial necromass contributes significantly to both soil carbon (C) persistence and ecosystem nitrogen (N) availability, but quantitative estimates of C and N movement from necromass into soils and decomposer communities are lacking. Additionally, while melanin is known to slow fungal necromass decomposition, how it influences microbial C and N acquisition as well as elemental release into soils remains unclear. Here, we tracked decomposition of isotopically labeled low and high melanin fungal necromass and measured 13C and 15N accumulation in surrounding soils and microbial communities over 77 d in a temperate forest in Minnesota, USA. Mass loss was significantly higher from low melanin necromass, corresponding with greater 13C and 15N soil inputs. A taxonomically and functionally diverse array of bacteria and fungi was enriched in 13C and/or 15N at all sampling points, with enrichment being consistently higher on low melanin necromass and earlier in decomposition. Similar patterns of preferential C and N enrichment of many bacterial and fungal genera early in decomposition suggest that both microbial groups co-contribute to the rapid assimilation of resource-rich soil organic matter inputs. While overall richness of taxa enriched in C was higher than in N for both bacteria and fungi, there was a significant positive relationship between C and N in co-enriched taxa. Collectively, our results demonstrate that melanization acts as a key ecological trait mediating not only fungal necromass decomposition rate but also necromass C and N release and that both elements are rapidly co-utilized by diverse bacterial and fungal decomposers in natural settings. IMPORTANCE Recent studies indicate that microbial dead cells, particularly those of fungi, play an important role in long-term carbon persistence in soils. Despite this growing recognition, how the resources within dead fungal cells (also known as fungal necromass) move into decomposer communities and soils are poorly quantified, particularly in studies based in natural environments. In this study, we found that the contribution of fungal necromass to soil carbon and nitrogen availability was slowed by the amount of melanin present in fungal cell walls. Further, despite the overall rapid acquisition of carbon and nitrogen from necromass by a diverse range of both bacteria and fungi, melanization also slowed microbial uptake of both elements. Collectively, our results indicate that melanization acts as a key ecological trait mediating not only fungal necromass decomposition rate, but also necromass carbon and nitrogen release into soil as well as microbial resource acquisition.
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Affiliation(s)
- François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Talia J. Michaud
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Craig R. See
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Lang C. DeLancey
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Peter G. Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
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Riley R, Bowers RM, Camargo AP, Campbell A, Egan R, Eloe-Fadrosh EA, Foster B, Hofmeyr S, Huntemann M, Kellom M, Kimbrel JA, Oliker L, Yelick K, Pett-Ridge J, Salamov A, Varghese NJ, Clum A. Terabase-Scale Coassembly of a Tropical Soil Microbiome. Microbiol Spectr 2023; 11:e0020023. [PMID: 37310219 PMCID: PMC10434106 DOI: 10.1128/spectrum.00200-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.
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Affiliation(s)
- Robert Riley
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Robert M. Bowers
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Antonio Pedro Camargo
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Ashley Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Rob Egan
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | | | - Brian Foster
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Steven Hofmeyr
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcel Huntemann
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Matthew Kellom
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Leonid Oliker
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Katherine Yelick
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Asaf Salamov
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Neha J. Varghese
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Alicia Clum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
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5
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Yancey CE, Kiledal EA, Chaganti SR, Denef VJ, Errera RM, Evans JT, Hart LN, Isailovic D, James WS, Kharbush JJ, Kimbrel JA, Li W, Mayali X, Nitschky H, Polik CA, Powers MA, Premathilaka SH, Rappuhn NA, Reitz LA, Rivera SR, Zwiers CC, Dick GJ. The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome. Harmful Algae 2023; 126:102440. [PMID: 37290887 DOI: 10.1016/j.hal.2023.102440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/10/2023]
Abstract
Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L⁻¹) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.
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Affiliation(s)
- Colleen E Yancey
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - E Anders Kiledal
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Vincent J Denef
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Reagan M Errera
- National Oceanic and Atmospheric Administration (NOAA), Great Lakes Environmental Research Laboratory (GLERL), 4840 S State Road, Ann Arbor, MI 48108, United States of America
| | - Jacob T Evans
- Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Lauren N Hart
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, United States of America; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Dragan Isailovic
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - William S James
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jenan J Kharbush
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Wei Li
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, United States of America
| | - Helena Nitschky
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Catherine A Polik
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - McKenzie A Powers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sanduni H Premathilaka
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, United States of America
| | - Nicole A Rappuhn
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Laura A Reitz
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Sara R Rivera
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Claire C Zwiers
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Gregory J Dick
- Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, United States of America; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, 4840 S State Road, Ann Arbor, MI 48108, United States of America.
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6
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Nuccio EE, Blazewicz SJ, Lafler M, Campbell AN, Kakouridis A, Kimbrel JA, Wollard J, Vyshenska D, Riley R, Tomatsu A, Hestrin R, Malmstrom RR, Firestone M, Pett-Ridge J. HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. Microbiome 2022; 10:199. [PMID: 36434737 PMCID: PMC9700909 DOI: 10.1186/s40168-022-01391-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling. RESULTS Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to 13C-AMF hyphosphere DNA from a 13CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% 13C), even though the soils' overall enrichment was low (1.8 atom% 13C). We assembled 212 13C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera. CONCLUSIONS Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.
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Affiliation(s)
- Erin E. Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Steven J. Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Marissa Lafler
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Ashley N. Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Anne Kakouridis
- Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | | | | | | | - Rachel Hestrin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA USA
| | | | - Mary Firestone
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA USA
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7
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Kimbrel JA, Jeffrey BM, Ward CS. Prokaryotic Genome Annotation. Methods Mol Biol 2021; 2349:193-214. [PMID: 34718997 DOI: 10.1007/978-1-0716-1585-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
In the last decade, the high-throughput and relatively low cost of short-read sequencing technologies have revolutionized prokaryotic genomics. This has led to an exponential increase in the number of bacterial and archaeal genome sequences available, as well as corresponding increase of genome assembly and annotation tools developed. Together, these hardware and software technologies have given scientists unprecedented options to study their chosen microbial systems without the need for large teams of bioinformaticists or supercomputing facilities. While these analysis tools largely fall into only a few categories, each may have different requirements, caveats and file formats, and some may be rarely updated or even abandoned. And so, despite the apparent ease in sequencing and analyzing a prokaryotic genome, it is no wonder that the budding genomicist may quickly find oneself overwhelmed. Here, we aim to provide the reader with an overview of genome annotation and its most important considerations, as well as an easy-to-follow protocol to get started with annotating a prokaryotic genome.
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Affiliation(s)
- Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Brendan M Jeffrey
- Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MA, USA
| | - Christopher S Ward
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
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8
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Trubl G, Kimbrel JA, Liquet-Gonzalez J, Nuccio EE, Weber PK, Pett-Ridge J, Jansson JK, Waldrop MP, Blazewicz SJ. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 2021; 9:208. [PMID: 34663463 PMCID: PMC8522061 DOI: 10.1186/s40168-021-01154-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/19/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). RESULTS We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. CONCLUSIONS Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Jeffrey A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jose Liquet-Gonzalez
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Department of Life and Environmental Sciences, University of California, Merced, CA, 95343, USA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Mark P Waldrop
- U.S. Geological Survey, Geology, Minerals, Energy, and Geophysics Science Center, Menlo Park, CA, USA
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
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9
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber M, Best AA, DeJongh M, Kimbrel JA, D’haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2021; 49:D575-D588. [PMID: 32986834 PMCID: PMC7778927 DOI: 10.1093/nar/gkaa746] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/25/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical 'Rosetta Stone' to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org/biochem and KBase.
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Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D’haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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10
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2021; 49:D1555. [PMID: 33179751 DOI: 10.1101/2020.03.31.018663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
ABSTRACTFor over ten years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions;; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical “Rosetta Stone” to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies, and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.
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Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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11
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2020; 49:D1555. [PMID: 33179751 PMCID: PMC7778962 DOI: 10.1093/nar/gkaa1143] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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12
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Fisher CL, Ward CS, Lane PD, Kimbrel JA, Sale KL, Stuart RK, Mayali X, Lane TW. Bacterial communities protect the alga Microchloropsis salina from grazing by the rotifer Brachionus plicatilis. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Griesemer M, Kimbrel JA, Zhou CE, Navid A, D'haeseleer P. Combining multiple functional annotation tools increases coverage of metabolic annotation. BMC Genomics 2018; 19:948. [PMID: 30567498 PMCID: PMC6299973 DOI: 10.1186/s12864-018-5221-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/05/2018] [Indexed: 12/15/2022] Open
Abstract
Background Genome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional annotations. Annotated genomes typically contain 30–50% of genes without functional annotation, severely limiting our knowledge of the “parts lists” that the organisms have at their disposal. These incomplete annotations may be sufficient to derive a model of a core set of well-studied metabolic pathways that support growth in pure culture. However, pathways important for growth on unusual metabolites exchanged in complex microbial communities are often less understood, resulting in missing functional annotations in newly sequenced genomes. Results Here, we present results on a comprehensive reannotation of 27 bacterial reference genomes, focusing on enzymes with EC numbers annotated by KEGG, RAST, EFICAz, and the BRENDA enzyme database, and on membrane transport annotations by TransportDB, KEGG and RAST. Our analysis shows that annotation using multiple tools can result in a drastically larger metabolic network reconstruction, adding on average 40% more EC numbers, 3–8 times more substrate-specific transporters, and 37% more metabolic genes. These results are even more pronounced for bacterial species that are phylogenetically distant from well-studied model organisms such as E. coli. Conclusions Metabolic annotations are often incomplete and inconsistent. Combining multiple functional annotation tools can greatly improve genome coverage and metabolic network size, especially for non-model organisms and non-core pathways. Electronic supplementary material The online version of this article (10.1186/s12864-018-5221-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc Griesemer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
| | - Carol E Zhou
- Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
| | - Ali Navid
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA
| | - Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA. .,Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA.
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14
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Samo TJ, Kimbrel JA, Nilson DJ, Pett-Ridge J, Weber PK, Mayali X. Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions. Environ Microbiol 2018; 20:4385-4400. [PMID: 30022580 DOI: 10.1111/1462-2920.14357] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 05/15/2018] [Accepted: 07/08/2018] [Indexed: 01/25/2023]
Abstract
The surface and surroundings of microalgal cells (phycosphere) are critical interaction zones but have been difficult to functionally interrogate due to methodological limitations. We examined effects of phycosphere-associated bacteria for two biofuel-relevant microalgal species (Phaeodactylum tricornutum and Nannochloropsis salina) using stable isotope tracing and high spatial resolution mass spectrometry imaging (NanoSIMS) to quantify elemental exchanges at the single-cell level. Each algal species responded differently to bacterial attachment. In P. tricornutum, a high percentage of cells had attached bacteria (92%-98%, up to eight bacteria per alga) and fixed 64% more carbon with attached bacteria compared to axenic cells. In contrast, N. salina cells were less commonly associated with bacteria (42%-63%), harboured fewer bacteria per alga, and fixed 10% more carbon without attached bacteria compared to axenic cells. An uncultivated bacterium related to Haliscomenobacter sp. was identified as an effective mutualist; it increased carbon fixation when attached to P. tricornutum and incorporated 71% more algal-fixed carbon relative to other bacteria. Our results illustrate how phylogenetic identity and physical location of bacteria and algae facilitate diverse metabolic responses. Phycosphere-mediated, mutualistic chemical exchanges between autotrophs and heterotrophs may be a fruitful means to increase microalgal productivity for applied engineering efforts.
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Affiliation(s)
- Ty J Samo
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
| | - Jeffrey A Kimbrel
- Lawrence Livermore National Laboratory, Bioscience and Biotechnology Division, 7000 East Avenue, Livermore, California
| | - Daniel J Nilson
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
| | - Xavier Mayali
- Lawrence Livermore National Laboratory, Nuclear and Chemical, Sciences Division, 7000 East Avenue, Livermore, California
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15
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Kimbrel JA, Ballor N, Wu YW, David MM, Hazen TC, Simmons BA, Singer SW, Jansson JK. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Front Microbiol 2018; 9:1492. [PMID: 30042744 PMCID: PMC6048260 DOI: 10.3389/fmicb.2018.01492] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/15/2018] [Indexed: 11/13/2022] Open
Abstract
Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.
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Affiliation(s)
- Jeffrey A Kimbrel
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Ballor
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yu-Wei Wu
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maude M David
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Terry C Hazen
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Blake A Simmons
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Steven W Singer
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
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16
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Di Y, Emerson SC, Schafer DW, Kimbrel JA, Chang JH. Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data. Stat Appl Genet Mol Biol 2013; 12:49-70. [PMID: 23502340 DOI: 10.1515/sagmb-2012-0071] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
RNA sequencing (RNA-Seq) is the current method of choice for characterizing transcriptomes and quantifying gene expression changes. This next generation sequencing-based method provides unprecedented depth and resolution. The negative binomial (NB) probability distribution has been shown to be a useful model for frequencies of mapped RNA-Seq reads and consequently provides a basis for statistical analysis of gene expression. Negative binomial exact tests are available for two-group comparisons but do not extend to negative binomial regression analysis, which is important for examining gene expression as a function of explanatory variables and for adjusted group comparisons accounting for other factors. We address the adequacy of available large-sample tests for the small sample sizes typically available from RNA-Seq studies and consider a higher-order asymptotic (HOA) adjustment to likelihood ratio tests. We demonstrate that 1) the HOA-adjusted likelihood ratio test is practically indistinguishable from the exact test in situations where the exact test is available, 2) the type I error of the HOA test matches the nominal specification in regression settings we examined via simulation, and 3) the power of the likelihood ratio test does not appear to be affected by the HOA adjustment. This work helps clarify the accuracy of the unadjusted likelihood ratio test and the degree of improvement available with the HOA adjustment. Furthermore, the HOA test may be preferable even when the exact test is available because it does not require ad hoc library size adjustments.
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Affiliation(s)
- Yanming Di
- Department of Statistics, Oregon State University, Corvallis, OR 97330,USA.
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17
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Fox SE, Preece J, Kimbrel JA, Marchini GL, Sage A, Youens-Clark K, Cruzan MB, Jaiswal P. Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae). Appl Plant Sci 2013; 1:apps.1200011. [PMID: 25202520 PMCID: PMC4105277 DOI: 10.3732/apps.1200011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/07/2013] [Indexed: 05/03/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. • METHODS AND RESULTS More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum. The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs) and >20,000 simple sequence repeat (SSR) DNA sites. • CONCLUSIONS To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.
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Affiliation(s)
- Samuel E. Fox
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| | - Justin Preece
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| | - Jeffrey A. Kimbrel
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Fourth Floor, Emeryville, California 94608 USA
| | - Gina L. Marchini
- Department of Biology, Portland State University, Portland, Oregon 97201 USA
| | - Abigail Sage
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
| | - Ken Youens-Clark
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 USA
| | - Mitchell B. Cruzan
- Department of Biology, Portland State University, Portland, Oregon 97201 USA
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, 2082 Cordley Hall, Oregon State University, Corvallis, Oregon 97331 USA
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Kimbrel JA, Thomas WJ, Jiang Y, Creason AL, Thireault CA, Sachs JL, Chang JH. Mutualistic co-evolution of type III effector genes in Sinorhizobium fredii and Bradyrhizobium japonicum. PLoS Pathog 2013; 9:e1003204. [PMID: 23468637 PMCID: PMC3585131 DOI: 10.1371/journal.ppat.1003204] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/08/2013] [Indexed: 12/16/2022] Open
Abstract
Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing model, conflicts between mutualist and host are largely resolved and the interaction is characterized by evolutionary stasis. We tested these opposing frameworks in two lineages of mutualistic rhizobia, Sinorhizobium fredii and Bradyrhizobium japonicum. To examine genes demonstrably important for host-interactions we coupled the mining of genome sequences to a comprehensive functional screen for type III effector genes, which are necessary for many Gram-negative pathogens to infect their hosts. We demonstrate that the rhizobial type III effector genes exhibit a surprisingly high degree of conservation in content and sequence that is in contrast to those of a well characterized plant pathogenic species. This type III effector gene conservation is particularly striking in the context of the relatively high genome-wide diversity of rhizobia. The evolution of rhizobial type III effectors is inconsistent with the molecular arms race paradigm. Instead, our results reveal that these loci are relatively static in rhizobial lineages and suggest that fitness conflicts between rhizobia mutualists and their host plants have been largely resolved.
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Affiliation(s)
- Jeffrey A. Kimbrel
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - William J. Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Allison L. Creason
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Caitlin A. Thireault
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Joel L. Sachs
- Department of Biology, University of California-Riverside, Riverside, California, United States of America
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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19
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Cumbie JS, Kimbrel JA, Di Y, Schafer DW, Wilhelm LJ, Fox SE, Sullivan CM, Curzon AD, Carrington JC, Mockler TC, Chang JH. GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences. PLoS One 2011; 6:e25279. [PMID: 21998647 PMCID: PMC3188579 DOI: 10.1371/journal.pone.0025279] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 08/30/2011] [Indexed: 12/12/2022] Open
Abstract
GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM)-compliant program of preference. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO) terms. Results are transparent and data are systematically stored in a MySQL relational database to facilitate additional analyses as well as quality assessment. We used next generation sequencing to generate a small-scale RNA-Seq dataset derived from the heavily studied defense response of Arabidopsis thaliana and used GENE-counter to process the data. Collectively, the support from analysis of microarrays as well as the observed and substantial overlap in results from each of the three statistics packages demonstrates that GENE-counter is well suited for handling the unique characteristics of small sample sizes and high variability in gene counts.
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Affiliation(s)
- Jason S. Cumbie
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Jeffrey A. Kimbrel
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Yanming Di
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Daniel W. Schafer
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Larry J. Wilhelm
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Samuel E. Fox
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Christopher M. Sullivan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Aron D. Curzon
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - James C. Carrington
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Todd C. Mockler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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Kimbrel JA, Givan SA, Temple TN, Johnson KB, Chang JH. Genome sequencing and comparative analysis of the carrot bacterial blight pathogen, Xanthomonas hortorum pv. carotae M081, for insights into pathogenicity and applications in molecular diagnostics. Mol Plant Pathol 2011; 12:580-94. [PMID: 21722296 PMCID: PMC6640479 DOI: 10.1111/j.1364-3703.2010.00694.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Xanthomonas hortorum pv. carotae (Xhc) is an economically important pathogen of carrots. Its ability to epiphytically colonize foliar surfaces and infect seeds can result in bacterial blight of carrots when grown in warm and humid regions. We used high-throughput sequencing to determine the genome sequence of isolate M081 of Xhc. The short reads were de novo assembled and the resulting contigs were ordered using a syntenic reference genome sequence from X. campestris pv. campestris ATCC 33913. The improved, high-quality draft genome sequence of Xhc M081 is the first for its species. Despite its distance from other sequenced xanthomonads, Xhc M081 still shared a large inventory of orthologous genes, including many clusters of virulence genes common to other foliar pathogenic species of Xanthomonas. We also mined the genome sequence and identified at least 21 candidate type III effector genes. Two were members of the avrBs2 and xopQ families that demonstrably elicit effector-triggered immunity. We showed that expression in planta of these two type III effectors from Xhc M081 was sufficient to elicit resistance gene-mediated hypersensitive responses in heterologous plants, indicating a possibility for resistance gene-mediated control of Xhc. Finally, we identified regions unique to the Xhc M081 genome sequence, and demonstrated their potential in the design of molecular diagnostics for this pathogen.
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Affiliation(s)
- Jeffrey A Kimbrel
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, USA
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Sayavedra-Soto LA, Hamamura N, Liu CW, Kimbrel JA, Chang JH, Arp DJ. The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family. Environ Microbiol Rep 2011; 3:390-396. [PMID: 23761285 DOI: 10.1111/j.1758-2229.2010.00239.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The Gram-positive bacterium Nocardioides sp. strain CF8 uses a membrane-associated monooxygenase (pBMO) to grow on butane. The nucleotide sequences of the genes encoding this novel monooxygenase were revealed through analysis of a de novo assembled draft genome sequence determined by high-throughput sequencing of the whole genome. The pBMO genes were in a similar arrangement to the genes for ammonia monooxygenase (AMO) from the ammonia-oxidizing bacteria and for particulate methane monooxygenase (pMMO) from the methane-oxidizing bacteria. The pBMO genes likely constitute an operon in the order bmoC, bmoA and bmoB. The nucleotide sequence was less than 50% similar to the genes for AMO and pMMO. The operon for pBMO was confirmed to be a single copy in the genome by Southern and computational analyses. In an incubation on butane the increase of transcriptional activity of the pBmoA gene was congruent with the increase of pBMO activity and suggested correspondence between gene expression and the utilization of butane. Phylogenetic comparison revealed distant but significant similarity of all three pBMO subunits to homologous members of the AMO/pMMO family and indicated that the pBMO represents a deeply branching third lineage of this group of particulate monooxygenases. No other bmoCAB-like genes were found to cluster with pBMO lineage in phylogenetic analysis by database searches including genomic and metagenomic sequence databases. pBMO is the first example of the AMO/pMMO-like monooxygenase from Gram-positive bacteria showing similarities to proteobacterial pMMO and AMO sequences.
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Affiliation(s)
- Luis A Sayavedra-Soto
- Department of Botany and Plant Pathology Molecular and Cellular Biology Program Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA. Center for Marine Environmental Studies, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan. Department of Chemical Engineering, National Taiwan University, Taipei, 106, Taiwan
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Kimbrel JA, Givan SA, Halgren AB, Creason AL, Mills DI, Banowetz GM, Armstrong DJ, Chang JH. An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6. BMC Genomics 2010; 11:522. [PMID: 20920191 PMCID: PMC2997014 DOI: 10.1186/1471-2164-11-522] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 09/28/2010] [Indexed: 12/20/2022] Open
Abstract
Background Pseudomonas fluorescens is a genetically and physiologically diverse species of bacteria present in many habitats and in association with plants. This species of bacteria produces a large array of secondary metabolites with potential as natural products. P. fluorescens isolate WH6 produces Germination-Arrest Factor (GAF), a predicted small peptide or amino acid analog with herbicidal activity that specifically inhibits germination of seeds of graminaceous species. Results We used a hybrid next-generation sequencing approach to develop a high-quality draft genome sequence for P. fluorescens WH6. We employed automated, manual, and experimental methods to further improve the draft genome sequence. From this assembly of 6.27 megabases, we predicted 5876 genes, of which 3115 were core to P. fluorescens and 1567 were unique to WH6. Comparative genomic studies of WH6 revealed high similarity in synteny and orthology of genes with P. fluorescens SBW25. A phylogenomic study also placed WH6 in the same lineage as SBW25. In a previous non-saturating mutagenesis screen we identified two genes necessary for GAF activity in WH6. Mapping of their flanking sequences revealed genes that encode a candidate anti-sigma factor and an aminotransferase. Finally, we discovered several candidate virulence and host-association mechanisms, one of which appears to be a complete type III secretion system. Conclusions The improved high-quality draft genome sequence of WH6 contributes towards resolving the P. fluorescens species, providing additional impetus for establishing two separate lineages in P. fluorescens. Despite the high levels of orthology and synteny to SBW25, WH6 still had a substantial number of unique genes and represents another source for the discovery of genes with implications in affecting plant growth and health. Two genes are demonstrably necessary for GAF and further characterization of their proteins is important for developing natural products as control measure against grassy weeds. Finally, WH6 is the first isolate of P. fluorescens reported to encode a complete T3SS. This gives us the opportunity to explore the role of what has traditionally been thought of as a virulence mechanism for non-pathogenic interactions with plants.
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Affiliation(s)
- Jeffrey A Kimbrel
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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Thomas WJ, Thireault CA, Kimbrel JA, Chang JH. Recombineering and stable integration of the Pseudomonas syringae pv. syringae 61 hrp/hrc cluster into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1. Plant J 2009; 60:919-28. [PMID: 19682294 DOI: 10.1111/j.1365-313x.2009.03998.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Many Gram-negative bacteria use a type III secretion system (T3SS) to establish associations with their hosts. The T3SS is a conduit for direct injection of type-III effector proteins into host cells, where they manipulate the host for the benefit of the infecting bacterium. For plant-associated pathogens, the variations in number and amino acid sequences of type-III effectors, as well as their functional redundancy, make studying type-III effectors challenging. To mitigate this challenge, we developed a stable delivery system for individual or defined sets of type-III effectors into plant cells. We used recombineering and Tn5-mediated transposition to clone and stably integrate, respectively, the complete hrp/hrc region from Pseudomonas syringae pv. syringae 61 into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1. We describe our development of Effector-to-Host Analyzer (EtHAn), and demonstrate its utility for studying effectors for their in planta functions.
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Affiliation(s)
- William J Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
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Cohu CM, Abdel-Ghany SE, Gogolin Reynolds KA, Onofrio AM, Bodecker JR, Kimbrel JA, Niyogi KK, Pilon M. Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant. Mol Plant 2009; 2:1336-50. [PMID: 19969519 DOI: 10.1093/mp/ssp084] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Copper (Cu) is an important mineral nutrient found in chloroplasts as a cofactor associated with plastocyanin and Cu/Zn superoxide dismutase (Cu/ZnSOD). Superoxide dismutases are metallo-enzymes found in most oxygenic organisms with proposed roles in reducing oxidative stress. Several recent studies in Arabidopsis have shown that microRNAs and a SQUAMOSA promoter binding protein-like7 (SPL7) transcription factor function to down-regulate the expression of many Cu-proteins, including Cu/ZnSOD in both plastids and the cytosol, during growth on low Cu. Plants contain the Cu Chaperone for SOD (CCS) that delivers Cu to Cu/ZnSODs, and, in Arabidopsis, both cytosolic and plastidic CCS versions are encoded by one gene. In this study, we demonstrate that Arabidopsis CCS transcript levels are regulated by Cu, mediated by microRNA 398 that was not previously predicted to target CCS. The microRNA target site is conserved in CCS of Oryza sativa. The data suggest that Cu-regulated microRNAs may have more mRNA targets than was previously predicted. A CCS null mutant has no measurable SOD activity in the chloroplast and cytosol, indicating an absolute requirement for CCS. When the CCS null mutant was grown on high Cu media, it lacked both Fe superoxide dismutase (FeSOD) and Cu/ZnSOD activity. However, this did not lead to a visual phenotype and no photosynthetic deficiencies were detected, even after high light stress. These results indicate that Cu/ZnSOD is not a pivotal component of the photosynthetic anti-oxidant system during growth in laboratory conditions.
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Affiliation(s)
- Christopher M Cohu
- Biology Department, Colorado State University, Fort Collins, CO 80523-1878, USA
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