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Bledsoe RB, Goodwillie C, Peralta AL. Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres. mSphere 2020; 5:e00035-20. [PMID: 32434837 PMCID: PMC7380569 DOI: 10.1128/msphere.00035-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/07/2020] [Indexed: 12/04/2022] Open
Abstract
In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling.IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways.
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Affiliation(s)
- Regina B Bledsoe
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Carol Goodwillie
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
| | - Ariane L Peralta
- Department of Biology, East Carolina University, Greenville, North Carolina, USA
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Costa OY, Zerillo MM, Zühlke D, Kielak AM, Pijl A, Riedel K, Kuramae EE. Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses. Microorganisms 2020; 8:E244. [PMID: 32059463 PMCID: PMC7074687 DOI: 10.3390/microorganisms8020244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 01/18/2023] Open
Abstract
The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.
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Affiliation(s)
- Ohana Y.A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Marcelo M. Zerillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Anna M. Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
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Akita H, Matsushika A, Kimura ZI. Enterobacter oligotrophica sp. nov., a novel oligotroph isolated from leaf soil. Microbiologyopen 2019; 8:e00843. [PMID: 31066221 PMCID: PMC7650607 DOI: 10.1002/mbo3.843] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 12/01/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
A novel oligotrophic bacterium, designated strain CCA6, was isolated from leaf soil collected in Japan. Cells of the strain were found to be a Gram‐negative, non‐sporulating, motile, rod‐shaped bacterium. Strain CCA6 grew at 10–45°C (optimum 20°C) and pH 4.5–10.0 (optimum pH 5.0). The strain was capable of growth in poor‐nutrient (oligotrophic) medium, and growth was unaffected by high‐nutrient medium. The major fatty acid and predominant quinone system were C16:0 and ubiquinone‐8. Phylogenetic analysis based on 16S rRNA gene sequences indicated strain CCA6 presented as a member of the family Enterobacteriaceae. Multilocus sequence analysis (MLSA) based on fragments of the atpD, gyrB, infB, and rpoB gene sequences was performed to further identify strain CCA6. The MLSA showed clear branching of strain CCA6 with respect to Enterobacter type strains. The complete genome of strain CCA6 consisted of 4,476,585 bp with a G+C content of 54.3% and comprising 4,372 predicted coding sequences. The genome average nucleotide identity values between strain CCA6 and the closest related Enterobacter type strain were <88.02%. Based on its phenotypic, chemotaxonomic and phylogenetic features, strain CCA6 (=HUT 8142T =KCTC 62525T) can be considered as a novel species within the genus Enterobacter with the proposed name Enterobacter oligotrophica.
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Affiliation(s)
- Hironaga Akita
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Japan
| | - Akinori Matsushika
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Hiroshima, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, Japan
| | - Zen-Ichiro Kimura
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, Kure, Japan
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Abstract
Rhodococcus erythropolis N9T-4 grows on an inorganic solid-state medium with no additional carbon and energy sources; however, it is unable to grow well in a liquid culture medium under the oligotrophic conditions. We examined submerged cultivations of N9T-4 using a polyurethane foam sponge to achieve approximately 10 times of the oligotrophic growth of the bacterium in the liquid culture medium.
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Affiliation(s)
- Tomohiro Matsuoka
- a Applied Chemistry and Biochemical Engineering Course, Department of Engineering , Graduate School of Integrated Science and Technology, Shizuoka University , Hamamatsu , Japan
| | - Nobuyuki Yoshida
- a Applied Chemistry and Biochemical Engineering Course, Department of Engineering , Graduate School of Integrated Science and Technology, Shizuoka University , Hamamatsu , Japan
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Gibbons SM, Lekberg Y, Mummey DL, Sangwan N, Ramsey PW, Gilbert JA. Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem. mSystems 2017; 2:e00178-16. [PMID: 28289729 PMCID: PMC5340861 DOI: 10.1128/msystems.00178-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/06/2017] [Indexed: 11/24/2022] Open
Abstract
Plant invasions often reduce native plant diversity and increase net primary productivity. Invaded soils appear to differ from surrounding soils in ways that impede restoration of diverse native plant communities. We hypothesize that invader-mediated shifts in edaphic properties reproducibly alter soil microbial community structure and function. Here, we take a holistic approach, characterizing plant, prokaryotic, and fungal communities and soil physicochemical properties in field sites, invasion gradients, and experimental plots for three invasive plant species that cooccur in the Rocky Mountain West. Each invader had a unique impact on soil physicochemical properties. We found that invasions drove shifts in the abundances of specific microbial taxa, while overall belowground community structure and functional potential were fairly constant. Forb invaders were generally enriched in copiotrophic bacteria with higher 16S rRNA gene copy numbers and showed greater microbial carbohydrate and nitrogen metabolic potential. Older invasions had stronger effects on abiotic soil properties, indicative of multiyear successions. Overall, we show that plant invasions are idiosyncratic in their impact on soils and are directly responsible for driving reproducible shifts in the soil environment over multiyear time scales. IMPORTANCE In this study, we show how invasive plant species drive rapid shifts in the soil environment from surrounding native communities. Each of the three plant invaders had different but consistent effects on soils. Thus, there does not appear to be a one-size-fits-all strategy for how plant invaders alter grassland soil environments. This work represents a crucial step toward understanding how invaders might be able to prevent or impair native reestablishment by changing soil biotic and abiotic properties.
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Affiliation(s)
- Sean M. Gibbons
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, USA
- Bioscience Division, The Microbiome Center, Argonne National Laboratory, Argonne, Illinois, USA
- MPG Ranch, Missoula, Montana, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ylva Lekberg
- MPG Ranch, Missoula, Montana, USA
- Department of Ecosystem and Conservation Science, University of Montana, Missoula, Montana, USA
| | | | - Naseer Sangwan
- Bioscience Division, The Microbiome Center, Argonne National Laboratory, Argonne, Illinois, USA
| | | | - Jack A. Gilbert
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois, USA
- Bioscience Division, The Microbiome Center, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Surgery, The Microbiome Center, University of Chicago, Chicago, Illinois, USA
- Marine Biological Laboratory, The Microbiome Center, Woods Hole, Massachusetts, USA
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Abstract
A microbe's growth rate helps to set its ecological success and its contribution to food web dynamics and biogeochemical processes. Growth rates at the community level are constrained by biomass and trophic interactions among bacteria, phytoplankton, and their grazers. Phytoplankton growth rates are approximately 1 d(-1), whereas most heterotrophic bacteria grow slowly, close to 0.1 d(-1); only a few taxa can grow ten times as fast. Data from 16S rRNA and other approaches are used to speculate about the growth rate and the life history strategy of SAR11, the most abundant clade of heterotrophic bacteria in the oceans. These strategies are also explored using genomic data. Although the methods and data are imperfect, the available data can be used to set limits on growth rates and thus on the timescale for changes in the composition and structure of microbial communities.
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Affiliation(s)
- David L Kirchman
- School of Marine Science and Policy, University of Delaware, Lewes, Delaware 19958;
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Lipson DA. The complex relationship between microbial growth rate and yield and its implications for ecosystem processes. Front Microbiol 2015; 6:615. [PMID: 26136742 PMCID: PMC4468913 DOI: 10.3389/fmicb.2015.00615] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 06/03/2015] [Indexed: 01/15/2023] Open
Affiliation(s)
- David A. Lipson
- Department of Biology, San Diego State UniversitySan Diego, CA, USA
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Spring S, Scheuner C, Göker M, Klenk HP. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Front Microbiol 2015; 6:281. [PMID: 25914684 PMCID: PMC4391266 DOI: 10.3389/fmicb.2015.00281] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [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: 01/17/2015] [Accepted: 03/21/2015] [Indexed: 11/13/2022] Open
Abstract
In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.
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Affiliation(s)
- Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Carmen Scheuner
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Markus Göker
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany
| | - Hans-Peter Klenk
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures Braunschweig, Germany ; School of Biology, Newcastle University Newcastle upon Tyne, UK
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Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N. The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Soil Biol Biochem 2011; 43:1450-1455. [PMID: 22267877 PMCID: PMC3260529 DOI: 10.1016/j.soilbio.2011.03.012] [Citation(s) in RCA: 348] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples). Data collected from surface horizons indicate that Verrucomicrobia average 23% of bacterial sequences, making them far more abundant than had been estimated. We show that this underestimation is likely due to primer bias, as many of the commonly used PCR primers appear to exclude verrucomicrobial 16S rRNA genes during amplification. Verrucomicrobia were detected in 180 out of 181 soils examined, with members of the class Spartobacteria dominating verrucomicrobial communities in nearly all biomes and soil depths. The relative abundance of Verrucomicrobia was highest in grasslands and in subsurface soil horizons, where they were often the dominant bacterial phylum. Although their ecology remains poorly understood, Verrucomicrobia appear to be dominant in many soil bacterial communities across the globe, making additional research on their ecology clearly necessary.
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Affiliation(s)
- Gaddy T. Bergmann
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
| | - Scott T. Bates
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
| | - Kathryn G. Eilers
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
| | - Christian L. Lauber
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
| | - J. Gregory Caporaso
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, Colorado 80309-0215, USA
| | - William A. Walters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Campus Box 347, Boulder, Colorado 80309-0347, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, Colorado 80309-0215, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309-0216, USA
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Campus Box 334, Boulder, Colorado 80309-0334, USA
- Corresponding author: Dr. Noah Fierer Assistant professor University of Colorado at Boulder Department of Ecology and Evolutionary Biology CIRES Box 216 UCB Boulder, CO 80309-0216, USA Office: 303-492-5615 Lab: 303-492-2099 Fax: 303-492-1149
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