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Vanreppelen G, Wuyts J, Van Dijck P, Vandecruys P. Sources of Antifungal Drugs. J Fungi (Basel) 2023; 9:jof9020171. [PMID: 36836286 PMCID: PMC9965926 DOI: 10.3390/jof9020171] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Due to their eukaryotic heritage, the differences between a fungal pathogen's molecular makeup and its human host are small. Therefore, the discovery and subsequent development of novel antifungal drugs are extremely challenging. Nevertheless, since the 1940s, researchers have successfully uncovered potent candidates from natural or synthetic sources. Analogs and novel formulations of these drugs enhanced the pharmacological parameters and improved overall drug efficiency. These compounds ultimately became the founding members of novel drug classes and were successfully applied in clinical settings, offering valuable and efficient treatment of mycosis for decades. Currently, only five different antifungal drug classes exist, all characterized by a unique mode of action; these are polyenes, pyrimidine analogs, azoles, allylamines, and echinocandins. The latter, being the latest addition to the antifungal armamentarium, was introduced over two decades ago. As a result of this limited arsenal, antifungal resistance development has exponentially increased and, with it, a growing healthcare crisis. In this review, we discuss the original sources of antifungal compounds, either natural or synthetic. Additionally, we summarize the existing drug classes, potential novel candidates in the clinical pipeline, and emerging non-traditional treatment options.
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2
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Halamka TA, Raberg JH, McFarlin JM, Younkin AD, Mulligan C, Liu X, Kopf SH. Production of diverse brGDGTs by Acidobacterium Solibacter usitatus in response to temperature, pH, and O 2 provides a culturing perspective on brGDGT proxies and biosynthesis. GEOBIOLOGY 2023; 21:102-118. [PMID: 36150122 PMCID: PMC10087280 DOI: 10.1111/gbi.12525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/08/2022] [Accepted: 08/24/2022] [Indexed: 05/04/2023]
Abstract
Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are bacterial membrane lipids that are frequently employed as paleoenvironmental proxies because of the strong empirical correlations between their relative abundances and environmental temperature and pH. Despite the ubiquity of brGDGTs in modern and paleoenvironments, the source organisms of these enigmatic compounds have remained elusive, requiring paleoenvironmental applications to rely solely on observed environmental correlations. Previous laboratory and environmental studies have suggested that the globally abundant bacterial phylum of the Acidobacteria may be an important brGDGT producer in nature. Here, we report on experiments with a cultured Acidobacterium, Solibacter usitatus, that makes a large portion of its cellular membrane (24 ± 9% across all experiments) out of a structurally diverse set of tetraethers including the common brGDGTs Ia, IIa, IIIa, Ib, and IIb. Solibacter usitatus was grown across a range of conditions including temperatures from 15 to 30°C, pH from 5.0 to 6.5, and O2 from 1% to 21%, and demonstrated pronounced shifts in the degree of brGDGT methylation across these growth conditions. The temperature response in culture was in close agreement with trends observed in published environmental datasets, supporting a physiological basis for the empirical relationship between brGDGT methylation number and temperature. However, brGDGT methylation at lower temperatures (15 and 20°C) was modulated by culture pH with higher pH systematically increasing the degree of methylation. In contrast, pH had little effect on brGDGT cyclization, supporting the hypothesis that changes in bacterial community composition may underlie the link between cyclization number and pH observed in environmental samples. Oxygen concentration likewise affected brGDGT methylation highlighting the potential for this environmental parameter to impact paleotemperature reconstruction. Low O2 culture conditions further resulted in the production of uncommon brGDGT isomers that could be indicators of O2 limitation. Finally, the production of brGTGTs (trialkyl tetraethers) in addition to the previously discovered iso-C15-based mono- and diethers in S. usitatus suggests a potential biosynthetic pathway for brGDGTs that uses homologs of the archaeal tetraether synthase (Tes) enzyme for tetraether synthesis from diethers.
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Affiliation(s)
- Toby A. Halamka
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
| | - Jonathan H. Raberg
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
- Faculty of Earth SciencesUniversity of IcelandReykjavikIceland
| | - Jamie M. McFarlin
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
| | - Adam D. Younkin
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
| | | | - Xiao‐Lei Liu
- School of GeosciencesUniversity of OklahomaNormanOklahomaUSA
| | - Sebastian H. Kopf
- Department of Geological SciencesUniversity of Colorado BoulderDenverCOUSA
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3
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Moon TS. SynMADE: synthetic microbiota across diverse ecosystems. Trends Biotechnol 2022; 40:1405-1414. [PMID: 36117027 DOI: 10.1016/j.tibtech.2022.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 01/21/2023]
Abstract
The past two decades have witnessed rapid advances in engineering individual microbial strains to produce biochemicals and biomaterials. However, engineering microbial consortia has been relatively slow. Using systems and synthetic biology approaches, researchers have been developing tools for engineering complex microbiota. In this opinion article, I discuss future directions and visions regarding developing microbiota as a biomanufacturing host. Specifically, I propose that we can develop the soil microbial community itself as a huge bioreactor. Ultimately, researchers will provide a generalizable system that enables us to understand a microbial consortium's interaction and metabolism on diverse temporal and spatial scales to address global problems, including the climate crisis, food inequality, the issue of waste, and sustainable bioproduction.
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Affiliation(s)
- Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Division of Biology and Biomedical Sciences, Washington University in St Louis, St Louis, MO 63130, USA.
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4
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Huber KJ, Pester M, Eichorst SA, Navarrete AA, Foesel BU. Editorial: Acidobacteria – Towards Unraveling the Secrets of a Widespread, Though Enigmatic, Phylum. Front Microbiol 2022; 13:960602. [PMID: 35814658 PMCID: PMC9267355 DOI: 10.3389/fmicb.2022.960602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katharina J. Huber
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Stephanie A. Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Acacio A. Navarrete
- Graduate Program in Environmental Sciences, University Brazil, São Paulo, Brazil
| | - Bärbel U. Foesel
- Working Group Biobank, Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- *Correspondence: Bärbel U. Foesel
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5
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Yamamoto K, Toya S, Sabidi S, Hoshiko Y, Maeda T. Diluted Luria-Bertani medium vs. sewage sludge as growth media: comparison of community structure and diversity in the culturable bacteria. Appl Microbiol Biotechnol 2021; 105:3787-3798. [PMID: 33856534 DOI: 10.1007/s00253-021-11248-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/27/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
Because colony formation is essential to seek bacterial functions by the direct observation of phenotype, the diversification of colony formation for culturable bacteria is a big challenge in the research field of Environmental Biotechnology. In this study, the biodiversity of cultivable bacteria (colony or liquid culture) was compared by using Luria-Bertani (LB) medium and waste sewage sludge (WSS) under different dilutions and temperatures. When WSS was used as a bacterial source, whereas the highest number of colonies was found at the concentration of WSS (5%), a particular concentration of LB (10%) or WSS (1%) as a growth medium showed the best number of the operational taxonomic units (OTUs) of colonies. The results of bacterial community structure indicated that there are 1, 8, and 12 bacterial genera found uniquely in the agar plates of LB, 10% LB, and 5% WSS. By contrast, when palm oil mill effluent sludge was used as a bacterial source, the effect of dilution was different with WSS. When comparing the biodiversity between colonies and liquid culture, a high OTU value was observed in the colonies on the plate. In addition, 30°C showed the highest number of colonies in LB, 10% LB, and 5% WSS whereas the best OTUs were observed at 37°C for LB and 10% LB, and at 25°C for 5% WSS. This study demonstrates the diversification of cultivable bacteria through the number of OTUs in diluted LB medium and WSS, which is beneficial to isolate a unique bacterial strain.Key points• Impacts of diluted LB medium and WSS for colony formation were determined.• Difference of concentration of LB and WSS made different effects on colony formation.• Temperature change affected on diluted LB and WSS as media.
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Affiliation(s)
- Kazuo Yamamoto
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Wakamatsu-Ku, Kitakyushu, Japan
| | - Shotaro Toya
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Wakamatsu-Ku, Kitakyushu, Japan
| | - Sarah Sabidi
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Wakamatsu-Ku, Kitakyushu, Japan
| | - Yuki Hoshiko
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Wakamatsu-Ku, Kitakyushu, Japan
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Wakamatsu-Ku, Kitakyushu, Japan.
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6
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Oberpaul M, Zumkeller CM, Culver T, Spohn M, Mihajlovic S, Leis B, Glaeser SP, Plarre R, McMahon DP, Hammann P, Schäberle TF, Glaeser J, Vilcinskas A. High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests. Front Microbiol 2020; 11:597628. [PMID: 33240253 PMCID: PMC7677567 DOI: 10.3389/fmicb.2020.597628] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/19/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial communities in the immediate environment of socialized invertebrates can help to suppress pathogens, in part by synthesizing bioactive natural products. Here we characterized the core microbiomes of three termite species (genus Coptotermes) and their nest material to gain more insight into the diversity of termite-associated bacteria. Sampling a healthy termite colony over time implicated a consolidated and highly stable microbiome, pointing toward the fact that beneficial bacterial phyla play a major role in termite fitness. In contrast, there was a significant shift in the composition of the core microbiome in one nest during a fungal infection, affecting the abundance of well-characterized Streptomyces species (phylum Actinobacteria) as well as less-studied bacterial phyla such as Acidobacteria. High-throughput cultivation in microplates was implemented to isolate and identify these less-studied bacterial phylogenetic group. Amplicon sequencing confirmed that our method maintained the bacterial diversity of the environmental samples, enabling the isolation of novel Acidobacteriaceae and expanding the list of cultivated species to include two strains that may define new species within the genera Terracidiphilus and Acidobacterium.
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Affiliation(s)
- Markus Oberpaul
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Celine M. Zumkeller
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Tanja Culver
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Marius Spohn
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Sanja Mihajlovic
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Benedikt Leis
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Stefanie P. Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Rudy Plarre
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
| | - Dino P. McMahon
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
- Institute of Biology, Free University of Berlin, Berlin, Germany
| | - Peter Hammann
- Sanofi-Aventis Deutschland GmbH, R&D Integrated Drug Discovery, Hoechst Industrial Park, Frankfurt am Main, Germany
| | - Till F. Schäberle
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Jens Glaeser
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
| | - Andreas Vilcinskas
- Branch for Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
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7
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Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, Suriani NL. Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review. Front Microbiol 2020; 11:580024. [PMID: 33193209 PMCID: PMC7661733 DOI: 10.3389/fmicb.2020.580024] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/08/2020] [Indexed: 11/13/2022] Open
Abstract
Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.
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Affiliation(s)
- Sadaf Kalam
- Department of Biochemistry, St. Ann's College for Women, Hyderabad, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, India
| | - R Z Sayyed
- Department of Microbiology, PSGVP Mandal's, Arts, Science and Commerce College, Shahada, India
| | - Hesham Ali El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,City of Scientific Research and Technological Applications, New Borg El-Arab, Egypt
| | - Daniel Joe Dailin
- Institute of Bioproduct Development, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia.,School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Malaysia
| | - Ni Luh Suriani
- Biology Department, Faculty of Mathematics and Natural Science, Udayana University, Bali, Indonesia
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8
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Chaudhary DK, Kim J. Experimental Setup for a Diffusion Bioreactor to Isolate Unculturable Soil Bacteria. Bio Protoc 2019; 9:e3388. [PMID: 33654882 DOI: 10.21769/bioprotoc.3388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 11/02/2022] Open
Abstract
Unculturable bacteria are those bacteria which proliferate in their native habitat but unable to grow or thrive in the normal laboratory media and conditions. The molecular techniques have revealed the significance of these uncultured bacteria in terms of their functional diversity and potential to produce secondary metabolites. To achieve these benefits, scientists have attempted to isolate and cultivate unculturable bacteria in the laboratory using transwell plates, optical tweezers, laser microdissection, microbioreactors, and diffusions bioreactors. However, these techniques are still inadequate to resolve the difficulties of cultivating unculturable bacteria. Therefore, it is essential to develop new cultivation method that enables growth of diverse range of bacteria in the laboratory conditions. Diffusion bioreactor is a membrane bound chamber which allows microbes to proliferate in their native environment by providing the excess to naturally occurring nutrients and signaling compounds. This paper presents efficient and reliable protocol to construct a diffusion bioreactor and its utilization to isolate and cultivate unculturable soil bacteria in laboratory.
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Affiliation(s)
| | - Jaisoo Kim
- Ecology Laboratory, Department of Life Science, Kyonggi University, Suwon, South Korea
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9
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Chaudhary DK, Khulan A, Kim J. Development of a novel cultivation technique for uncultured soil bacteria. Sci Rep 2019; 9:6666. [PMID: 31040339 PMCID: PMC6491550 DOI: 10.1038/s41598-019-43182-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/16/2019] [Indexed: 01/18/2023] Open
Abstract
In this study, a new diffusion bioreactor was developed to cultivate hidden bacterial communities in their natural environment. The newly developed method was investigated to cultivate microbial communities from the forest soil, and the results were evaluated against traditional culture methods and compared to the results of a pyrosequencing-based molecular survey. The molecular analysis revealed that a diverse bacterial population was present in the soil sample. However, both the newly developed method and the traditional method recovered more than 400 isolates, which belonged to only four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Although these isolates were distributed over only four major phyla, the use of the newly developed technique resulted in the successful cultivation of 35 previously uncultured strains, whereas no such strains were successfully cultivated by the traditional method. Furthermore, the study also found that the recovery of uncultured bacteria and novel isolates was related to sampling season, incubation period, and cultivation media. The use of soil collected in summer, a prolonged incubation period, and low-substrate modified media increased the recovery of uncultured and novel isolates. Overall, the results indicate that the newly designed diffusion bioreactor can mimic the natural environment, which permits the cultivation of previously uncultured bacteria.
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Affiliation(s)
| | - Altankhuu Khulan
- Ecology Laboratory, Department of Life Science, Kyonggi University, Suwon, South Korea
| | - Jaisoo Kim
- Ecology Laboratory, Department of Life Science, Kyonggi University, Suwon, South Korea.
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10
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Baldrian P. The known and the unknown in soil microbial ecology. FEMS Microbiol Ecol 2019; 95:5281230. [DOI: 10.1093/femsec/fiz005] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/08/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220 Praha 4, Czech Republic
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11
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Santini TC, Raudsepp M, Hamilton J, Nunn J. Extreme Geochemical Conditions and Dispersal Limitation Retard Primary Succession of Microbial Communities in Gold Tailings. Front Microbiol 2018; 9:2785. [PMID: 30546349 PMCID: PMC6279923 DOI: 10.3389/fmicb.2018.02785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
Microbial community succession in tailings materials is poorly understood at present, and likely to be substantially different from similar processes in natural primary successional environments due to the unusual geochemical properties of tailings and the isolated design of tailings storage facilities. This is the first study to evaluate processes of primary succession in microbial communities colonizing unamended tailings, and compare the relative importance of stochastic (predominantly dust-borne dispersal) and deterministic (strong selection pressures from extreme geochemical properties) processes in governing community assembly rates and trajectories to those observed in natural environments. Dispersal-based recruitment required > 6 months to shift microbial community composition in unamended, field-weathered gold tailings; and in the absence of targeted inoculants, recruitment was dominated by salt- and alkali-tolerant species. In addition, cell numbers were less than 106 cells/g tailings until > 6 months after deposition. Laboratory experiments simulating microbial cell addition via dust revealed that high (>6 months' equivalent) dust addition rates were required to effect stabilization of microbial cell counts in tailings. In field-weathered tailings, topsoil addition during rehabilitation works exerted a double effect, acting as a microbial inoculant and correcting geochemical properties of tailings. However, microbial communities in rehabilitated tailings remained compositionally distinct from those of reference soils in surrounding environments. pH, water extractable Mg, and water extractable Fe emerged as major controls on microbial community composition in the field-weathered gold tailings. Overall, this study highlights the need for application of targeted microbial inoculants to accelerate rates of microbial community succession in tailings, which are limited primarily by slow dispersal due to physical and spatial isolation of tailings facilities from inoculant sources; and for geochemical properties of tailings to be amended to moderate values to encourage microbial community diversification and succession.
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Affiliation(s)
- Talitha C Santini
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia.,School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maija Raudsepp
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jessica Hamilton
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Jasmine Nunn
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
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12
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Sarhan MS, Patz S, Hamza MA, Youssef HH, Mourad EF, Fayez M, Murphy B, Ruppel S, Hegazi NA. G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla. Microbes Environ 2018; 33:317-325. [PMID: 30210099 PMCID: PMC6167109 DOI: 10.1264/jsme2.me18023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022] Open
Abstract
The rapid development of high-throughput techniques and expansion of bacterial databases have accelerated efforts to bring plant microbiomes into cultivation. We introduced plant-only-based culture media as a successful candidate to mimic the nutritional matrices of plant roots. We herein employed a G3 PhyloChip microarray to meticulously characterize the culture-dependent and -independent bacterial communities of the maize root compartments, the endo- and ecto-rhizospheres. An emphasis was placed on the preference of the growth of unculturable candidate divisions/phyla on plant-only-based culture media over standard culture media (nutrient agar). A total of 1,818 different operational taxonomic units (OTUs) were resolved representing 67 bacterial phyla. Plant-only-based culture media displayed particular affinity towards recovering endophytic over ectophytic rhizobacteria. This was shown by the slightly higher recovery of CFUs for endophytes on plant-only-based culture media (26%) than on standard culture media (10%) as well as the higher taxa richness and numbers of exclusive families of unculturable divisions/phyla. Out of 30 bacterial phyla (comprising >95% of the whole population), 13 were of a significantly higher incidence on plant-only-based culture media, 6 phyla of which were not-yet-cultured (Atribacteria, OP9; Dependentiae, TM6; Latescibacteria, WS3; Marinimicrobia, SAR406; Omnitrophica, OP3; BRC1). Furthermore, plant-only-based culture media significantly enriched less abundant and/or hard-to-culture bacterial phyla (Acidobacteria, Gemmatimonadetes, and Tenericutes). These results present conclusive evidence of the ability of plant-only-based culture media to bring the plant-fed in situ microbiome into the status of plant-fed in vitro cultures, and to widen the scope of cultivation of heretofore-unculturable bacterial divisions/phyla.
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Affiliation(s)
- Mohamed S. Sarhan
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Sascha Patz
- Algorithms in Bioinformatics, Center for Bioinformatics, University of TübingenTübingen, 72076Germany
| | - Mervat A. Hamza
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Hanan H. Youssef
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Elhussein F. Mourad
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
| | - Brian Murphy
- Department of Botany, School of Natural Sciences, Trinity College DublinDublin 2Ireland
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/Erfurt e.V. (IGZ)Großbeeren, 14979Germany
| | - Nabil A. Hegazi
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo UniversityGiza, 12613Egypt
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13
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Huber KJ, Overmann J. Vicinamibacteraceae fam. nov., the first described family within the subdivision 6 Acidobacteria. Int J Syst Evol Microbiol 2018; 68:2331-2334. [PMID: 29809123 DOI: 10.1099/ijsem.0.002841] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Acidobacteria constitute a globally widespread phylum and mainly inhabit soil environments. Despite their high abundance and activity, only 60 species from seven of the 26 acidobacterial subdivisions (sds; corresponding to class level) are (validly) described. Thus, only a low number of higher taxonomic ranks is currently distinguished within the Acidobacteria. Additionally, the distribution of the known acidobacterial species within the described families of the Acidobacteriaceae (sd1), Bryobacteraceae (sd3), Blastocatellaceae (sd4), Pyrinomonadaceae (sd4), Holophagaceae (sd8) and Acanthopleuribacteraceae (sd8) is extremely biased as most strains are affiliated with the Acidobacteriaceae. Members of this family are characteristic for acidic soils. In contrast, culture-independent analysis of microbial communities worldwide revealed that sd6 Acidobacteria prevail in soils with neutral pH. To improve the existing acidobacterial taxonomy, we here formally describe the first family within sd6 Acidobacteria, the Vicinamibacteraceae. Members of the Vicinamibacteraceae are aerobic, neutrophilic, psychrotolerant to mesophilic chemoheterotrophs. Their cells stain Gram-negative, do not form capsules or spores, and are non-motile. They occur as single cells or in aggregates and divide by binary fission. Growth occurs on sugars or complex proteinaceous compounds. MK-8 is the major quinone. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C18 : 1ω7c or ω9c, iso-C17 : 1ω9c, C16 : 0 and iso-C17 : 0. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol are the major polar lipids. Unidentified glycolipids or unknown phospholipids might also be present. The G+C content of the DNA ranges from 64.7 to 65.9 mol%. Within the Vicinamibacteraceae fam. nov., Vicinamibacter and Luteitalea are the only genera described so far.
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Affiliation(s)
- Katharina J Huber
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Braunschweig University of Technology, Braunschweig, Germany
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Pulschen AA, Bendia AG, Fricker AD, Pellizari VH, Galante D, Rodrigues F. Isolation of Uncultured Bacteria from Antarctica Using Long Incubation Periods and Low Nutritional Media. Front Microbiol 2017; 8:1346. [PMID: 28769908 PMCID: PMC5509766 DOI: 10.3389/fmicb.2017.01346] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 07/03/2017] [Indexed: 12/16/2022] Open
Abstract
Uncultured microorganisms comprise most of the microbial diversity existing on our planet. Despite advances in environmental sequencing and single-cell genomics, in-depth studies about bacterial metabolism and screening of novel bioproducts can only be assessed by culturing microbes in the laboratory. Here we report uncultured, or recalcitrant, microorganisms from an Antarctic soil sample, using relatively simple methods: oligotrophic media, extended incubation periods, observation under stereo microscopy, and selection of slow-growing bacteria. We managed to isolate several rare microorganisms belonging to infrequently isolated or recently described genera, for example Lapillicoccus, Flavitalea, Quadrisphaera, Motilibacter, and Polymorphobacter. Additionally, we obtained isolates presenting 16S rRNA sequence similarity ranging from 92.08 to 94.46% with any other known cultured species, including two distinct isolates from the class Thermoleophilia, that although common in Antarctic soils (as identified by metagenomics), was never reported to be isolated from such samples. Our data indicates that simple methods are still useful for cultivating recalcitrant microorganisms, even when dealing with samples from extreme environments.
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Affiliation(s)
| | - Amanda G Bendia
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São PauloButantã, Brazil
| | | | - Vivian H Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São PauloButantã, Brazil
| | - Douglas Galante
- Laboratório Nacional de Luz Síncrotron, Centro Nacional de Pesquisa em Energia e MateriaisCampinas, Brazil
| | - Fabio Rodrigues
- Departamento de Química Fundamental, Instituto de Química, Universidade de São PauloButantã, Brazil
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15
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Hegazi NA, Sarhan MS, Fayez M, Patz S, Murphy BR, Ruppel S. Plant-fed versus chemicals-fed rhizobacteria of Lucerne: Plant-only teabags culture media not only increase culturability of rhizobacteria but also recover a previously uncultured Lysobacter sp., Novosphingobium sp. and Pedobacter sp. PLoS One 2017; 12:e0180424. [PMID: 28686606 PMCID: PMC5501534 DOI: 10.1371/journal.pone.0180424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 06/15/2017] [Indexed: 11/19/2022] Open
Abstract
In an effort to axenically culture the previously uncultivable populations of the rhizobacteria of Lucerne (Medicago sativa L.), we propose plant-only teabags culture media to mimic the nutritional matrix available in the rhizosphere. Here, we show that culture media prepared from Lucerne powder teabags substantially increased the cultivability of Lucerne rhizobacteria compared with a standard nutrient agar, where we found that the cultivable populations significantly increased by up to 60% of the total bacterial numbers as estimated by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR). Cluster analysis of 16S rDNA Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) of cultivable Colony-Forming Units (CFUs) revealed a more distinct composition and separation of bacterial populations recovered on the plant-only teabags culture media than those developed on a standard nutrient agar. Further, the new plant medium gave preference to the micro-symbiont Sinorhizobium meliloti, and succeeded in isolating a number of not-yet-cultured bacteria, most closely matched to Novosphingobium sp., Lysobacter sp. and Pedobacter sp. The present study may encourage other researchers to consider moving from the well-established standard culture media to the challenging new plant-only culture media. Such a move may reveal previously hidden members of rhizobacteria, and help to further explore their potential environmental impacts.
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Affiliation(s)
- Nabil A. Hegazi
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
- * E-mail:
| | - Mohamed S. Sarhan
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed Fayez
- Environmental Studies and Research Unit (ESRU), Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Sascha Patz
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/ Erfurt e.V. (IGZ), Großbeeren, Germany
| | - Brian R. Murphy
- Department of Botany, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops Großbeeren/ Erfurt e.V. (IGZ), Großbeeren, Germany
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Vandermaesen J, Lievens B, Springael D. Isolation and identification of culturable bacteria, capable of heterotrophic growth, from rapid sand filters of drinking water treatment plants. Res Microbiol 2017; 168:594-607. [DOI: 10.1016/j.resmic.2017.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 03/08/2017] [Accepted: 03/29/2017] [Indexed: 10/19/2022]
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17
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Vieira S, Luckner M, Wanner G, Overmann J. Luteitalea pratensis gen. nov., sp. nov. a new member of subdivision 6 Acidobacteria isolated from temperate grassland soil. Int J Syst Evol Microbiol 2017; 67:1408-1414. [PMID: 28141504 DOI: 10.1099/ijsem.0.001827] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Albeit being widespread and abundant in soils worldwide, bacteria of the phylum Acidobacteria have remained grossly understudied due to difficulties in their cultivation and isolation. To date, only 48 species have been validly described, including a single member of the phylogenetically diverse Acidobacteria subdivision 6. Here, we report the polyphasic characterization of strain HEG_-6_39T, a novel representative of Acidobacteria subdivision 6 isolated from a grassland soil in Thuringia, Germany. Cells of HEG_-6_39T are Gram-stain-negative, non-motile, non-spore-forming, non-capsulated short rods that form small dark yellow colonies. This slow growing bacterium is psychrotolerant and grows between 0 and 36 °C. It displays a narrower pH tolerance (5.3-8.3) than most acidobacteria. The strain is an aerobe that grows chemo-organotrophically utilizing mostly sugars and proteinaceous substrates such as peptone, yeast extract, casein hydrolysate and casamino acids as substrates. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and two unknown phospholipids are identified as polar lipids. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), C18 : 1ω9c and iso-C17 : 1ω9c. The major respiratory quinone is MK-8. The G+C content of the genomic DNA is 64.7 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Vicinamibacter silvestris Ac_5_C6T with 93.6 % sequence similarity. Based on the present taxonomic characterization, strain HEG_-6_39T represents a new species of a novel genus for which the name Luteitalea pratensis gen. nov., sp. nov., is proposed. The type strain of the type species is HEG_-6_39T (=DSM 100886T=KCTC 52215T).
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Affiliation(s)
- Selma Vieira
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Manja Luckner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.,Braunschweig University of Technology, Braunschweig, Germany
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18
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Matsuo H, Kudo C, Li J, Tonouchi A. Acidicapsa acidisoli sp. nov., from the acidic soil of a deciduous forest. Int J Syst Evol Microbiol 2016; 67:862-867. [PMID: 27902281 DOI: 10.1099/ijsem.0.001688] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated strain SK-11T was isolated from the acidic soil of a deciduous forest in the Shirakami Mountains in Japan. Cells of strain SK-11T were aerobic, non-motile, Gram-stain-negative rods, 0.7-1.0 µm in width and 1.0-1.4 µm in length. The pH range for growth was between pH 4.0 and 5.5, with an optimum at pH 5.0. The temperature range for growth was between 10 and 35 °C, with an optimum at around 25-30 °C. Strain SK-11T utilized various carbohydrates as growth substrates as well as yeast extract and protein hydrolysates. The major cellular fatty acids (>10 % of total fatty acid contents) were iso-C15 : 0 (55.4 %), iso-C17 : 0 (16.7 %) and iso-C17 : 1ω9c/10 methyl-hexadecanoic acid (17.7 %). The major respiratory quinone was MK-8. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and an unidentified polar lipid. The DNA G+C content of strain SK-11T was 56.9 %. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SK-11T belonged to the family Acidobacteriaceae within subdivision 1 of the phylum Acidobacteria, and the closest relatives of strain SK-11T were Acidicapsa ligni WH120T and Acidicapsa borealis KA1T, with 16S rRNA gene sequence similarities of 96.6 and 96.5 %, respectively. On the basis of the evidence from our polyphasic study, we concluded that strain SK-11T represents a novel species of the genus Acidicapsa, and propose the name Acidicapsa acidisoli sp. nov. The type strain of Acidicapsaacidisolisp nov. is SK-11T (=DSM 100508T=NBRC 111227T).
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Affiliation(s)
- Heizo Matsuo
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Chisaki Kudo
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Juan Li
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
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19
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Seuradge BJ, Oelbermann M, Neufeld JD. Depth-dependent influence of different land-use systems on bacterial biogeography. FEMS Microbiol Ecol 2016; 93:fiw239. [PMID: 27915285 DOI: 10.1093/femsec/fiw239] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/15/2016] [Accepted: 11/29/2016] [Indexed: 11/12/2022] Open
Abstract
Despite progress in understanding microbial biogeography of surface soils, few studies have investigated depth-dependent distributions of terrestrial microorganisms in subsoils. We leveraged high-throughput sequencing of 16S rRNA genes obtained from soils collected from the RARE: Charitable Research Reserve (Cambridge, ON, Canada) to assess the influence of depth on bacterial communities across various land-use types. Although bacterial communities were strongly influenced by depth across all sites, the magnitude of this influence was variable and demonstrated that land-use attributes also played a significant role in shaping soil bacterial communities. Soil pH exhibited a large gradient across samples and strongly influenced shifts in bacterial communities with depth and across different land-use systems, especially considering that physicochemical conditions showed generally consistent trends with depth. We observed significant (p ≤ 0.001) and strongly correlated taxa with depth and pH, with a strong predominance of positively depth-correlated OTUs without cultured representatives. These findings highlight the importance of depth in soil biogeographical surveys and that subsurface soils harbour understudied bacterial members with potentially unique and important functions in deeper soil horizons that remain to be characterized.
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Affiliation(s)
- Brent J Seuradge
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Maren Oelbermann
- School of Environment, Resources and Sustainability, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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20
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Campanharo JC, Kielak AM, Castellane TCL, Kuramae EE, Lemos EGDM. Optimized medium culture forAcidobacteriasubdivision 1 strains. FEMS Microbiol Lett 2016; 363:fnw245. [DOI: 10.1093/femsle/fnw245] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/04/2016] [Accepted: 10/25/2016] [Indexed: 11/13/2022] Open
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21
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de Menezes AB, Müller C, Clipson N, Doyle E. The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment. MICROBIOLOGY-SGM 2016; 162:1572-1582. [PMID: 27459857 DOI: 10.1099/mic.0.000341] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The soil bacterial community at the Giessen free-air CO2 enrichment (Gi-FACE) experiment was analysed by tag sequencing of the 16S rRNA gene. No substantial effects of CO2 levels on bacterial community composition were detected. However, the soil moisture gradient at Gi-FACE had a significant effect on bacterial community composition. Different groups within the Acidobacteria and Verrucomicrobia phyla were affected differently by soil moisture content. These results suggest that modest increases in atmospheric CO2 may cause only minor changes in soil bacterial community composition and indicate that the functional responses of the soil community to CO2 enrichment previously reported at Gi-FACE are due to factors other than changes in bacterial community composition. The effects of the moisture gradient revealed new information about the relationships between poorly known Acidobacteria and Verrucomicrobia and soil moisture content. This study contrasts with the relatively small number of other temperate grassland free-air CO2 enrichment microbiome studies in the use of moderate CO2 enrichment and the resulting minor changes in the soil microbiome. Thus, it will facilitate the development of further climate change mitigation studies. In addition, the moisture gradient found at Gi-FACE contributes new knowledge in soil microbial ecology, particularly regarding the abundance and moisture relationships of the soil Verrucomicrobia.
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Affiliation(s)
- Alexandre B de Menezes
- Peel Building, School of Environment & Life Sciences, University of Salford, Salford M5 4WT, UK
| | - Christoph Müller
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Department of Plant Ecology, Justus-Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Nicholas Clipson
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Evelyn Doyle
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
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22
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Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE. The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Front Microbiol 2016; 7:744. [PMID: 27303369 PMCID: PMC4885859 DOI: 10.3389/fmicb.2016.00744] [Citation(s) in RCA: 442] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 05/03/2016] [Indexed: 12/01/2022] Open
Abstract
The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Cristine C Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília Brasília, Brazil
| | - George A Kowalchuk
- Ecology and Biodiversity Group, University of Utrecht Utrecht, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, The Netherlands Institute of Ecology - Koninklijke Nederlandse Akademie van Wetenschappen Wageningen, Netherlands
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23
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Huber KJ, Geppert AM, Wanner G, Fösel BU, Wüst PK, Overmann J. The first representative of the globally widespread subdivision 6 Acidobacteria,Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil. Int J Syst Evol Microbiol 2016; 66:2971-2979. [PMID: 27150379 DOI: 10.1099/ijsem.0.001131] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Members of the phylum Acidobacteria are abundant in a wide variety of soil environments. Despite this, previous cultivation attempts have frequently failed to retrieve representative phylotypes of Acidobacteria, which have, therefore, been discovered by culture-independent methods (13175 acidobacterial sequences in the SILVA database version 123; NR99) and only 47 species have been described so far. Strain Ac_5_C6T represents the first isolate of the globally widespread and abundant subdivision 6 Acidobacteria and is described in the present study. Cells of strain Ac_5_C6T were Gram-stain-negative, immotile rods that divided by binary fission. They formed yellow, extremely cohesive colonies and stable aggregates even in rapidly shaken liquid cultures. Ac_5_C6T was tolerant of a wide range of temperatures (12-40 °C) and pH values (4.7-9.0). It grew chemoorganoheterotrophically on a broad range of substrates including different sugars, organic acids, nucleic acids and complex proteinaceous compounds. The major fatty acids of Ac_5_C6T were iso-C17 : 1 ω9c, C18 : 1 ω7c and iso-C15 : 0. Summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), iso-C17 : 0 and C16 : 0 were also detected. Phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid were identified as polar lipids. The major quinone was MK-8. The DNA G+C content of Ac_5_C6T was 65.9 mol%. With 16S rRNA gene sequence similarities of 83-84 %, the closest described relatives were Acidicapsa borealis KA1T, Acidobacterium capsulatum 161T, Granulicella pectinovorans TPB6011T, Occallatibacter riparius 277T and Paludibaculum fermentans P105T. According to the morphological, physiological and molecular characteristics, the novel genus Vicinamibacter gen. nov., and the novel species, Vicinamibacter silvestris sp. nov. (type strain Ac_5_C6T = DSM 29464T = LMG 29035T) are proposed.
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Affiliation(s)
- Katharina J Huber
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alicia M Geppert
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Bärbel U Fösel
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K Wüst
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Technical University Braunschweig, Braunschweig, Germany
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24
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Conjugative transfer of broad host range plasmids to an acidobacterial strain, Edaphobacter aggregans. J Biotechnol 2016; 221:107-13. [DOI: 10.1016/j.jbiotec.2016.01.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 01/19/2023]
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25
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Newman MM, Hoilett N, Lorenz N, Dick RP, Liles MR, Ramsier C, Kloepper JW. Glyphosate effects on soil rhizosphere-associated bacterial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 543:155-160. [PMID: 26580738 DOI: 10.1016/j.scitotenv.2015.11.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 04/15/2023]
Abstract
Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community.
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Affiliation(s)
- Molli M Newman
- Department of Entomology and Plant Pathology, Auburn University, CASIC Building, Auburn, AL 36849, USA.
| | - Nigel Hoilett
- Department of Agricultural Sciences, Northwest Missouri State University, 800 University Drive, Maryville, MO 64468, USA
| | - Nicola Lorenz
- School of Environment and Natural Resources, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, USA
| | - Richard P Dick
- School of Environment and Natural Resources, The Ohio State University, 2021 Coffey Road, Columbus, OH 43210, USA
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, CASIC Building, Auburn, AL 36849, USA
| | - Cliff Ramsier
- Ag Spectrum, 428 East 11th Street, DeWitt, IA 52742, USA
| | - Joseph W Kloepper
- Department of Entomology and Plant Pathology, Auburn University, CASIC Building, Auburn, AL 36849, USA
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26
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van der Voort M, Kempenaar M, van Driel M, Raaijmakers JM, Mendes R. Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression. Ecol Lett 2016; 19:375-82. [PMID: 26833547 DOI: 10.1111/ele.12567] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/29/2015] [Accepted: 12/08/2015] [Indexed: 02/05/2023]
Abstract
The rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 °C, 1 h) of a soil suppressive to the root pathogenic fungus Rhizoctonia solani caused significant increase in alpha diversity of the rhizobacterial community and led to partial or complete loss of disease protection. A reassembly model is proposed where bacterial families that are heat tolerant and have high growth rates significantly increase in relative abundance after heat disturbance, while temperature-sensitive and slow-growing bacteria have a disadvantage. The results also pointed to a potential role of slow-growing, heat-tolerant bacterial families from Actinobacteria and Acidobacteria phyla in plant disease protection. In conclusion, short heat disturbance of soil results in rearrangement of rhizobacterial communities and this is correlated with changes in the ecosystem service disease suppression.
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Affiliation(s)
- Menno van der Voort
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Marcel Kempenaar
- The Netherlands Bioinformatics Centre (NBIC), Nijmegen, Netherlands
| | - Marc van Driel
- The Netherlands Bioinformatics Centre (NBIC), Nijmegen, Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO/KNAW), Wageningen, Netherlands.,Institute of Biology, Leiden University, Wageningen, Netherlands
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariuna, Brazil
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García-Fraile P, Benada O, Cajthaml T, Baldrian P, Lladó S. Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation. Appl Environ Microbiol 2016; 82:560-9. [PMID: 26546425 PMCID: PMC4711116 DOI: 10.1128/aem.03353-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 11/02/2015] [Indexed: 01/22/2023] Open
Abstract
Understanding the activity of bacteria in coniferous forests is highly important, due to the role of these environments as a global carbon sink. In a study of the microbial biodiversity of montane coniferous forest soil in the Bohemian Forest National Park (Czech Republic), we succeeded in isolating bacterial strain S55(T), which belongs to one of the most abundant operational taxonomic units (OTUs) in active bacterial populations, according to the analysis of RNA-derived 16S rRNA amplicons. The 16S rRNA gene sequence analysis showed that the species most closely related to strain S55(T) include Bryocella elongata SN10(T) (95.4% identity), Acidicapsa ligni WH120(T) (95.2% identity), and Telmatobacter bradus TPB6017(T) (95.0% identity), revealing that strain S55(T) should be classified within the phylum Acidobacteria, subdivision 1. Strain S55(T) is a rod-like bacterium that grows at acidic pH (3 to 6). Its phylogenetic, genotypic, phenotypic, and chemotaxonomic characteristics indicate that strain S55(T) corresponds to a new genus within the phylum Acidobacteria; thus, we propose the name Terracidiphilus gabretensis gen. nov., sp. nov. (strain S55(T) = NBRC 111238(T) = CECT 8791(T)). This strain produces extracellular enzymes implicated in the degradation of plant-derived biopolymers. Moreover, analysis of the genome sequence of strain S55(T) also reveals the presence of enzymatic machinery required for organic matter decomposition. Soil metatranscriptomic analyses found 132 genes from strain S55(T) being expressed in the forest soil, especially during winter. Our results suggest an important contribution of T. gabretensis S55(T) in the carbon cycle in the Picea abies coniferous forest.
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Affiliation(s)
- Paula García-Fraile
- Institute of Microbiology ASCR, Laboratory of Fungal Genetics and Metabolism, Prague, Czech Republic
| | - Oldrich Benada
- Institute of Microbiology ASCR, Laboratory of Molecular Structure Characterization, Prague, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology ASCR, Laboratory of Environmental Biotechnology, Prague, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology ASCR, Laboratory of Environmental Microbiology, Prague, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology ASCR, Laboratory of Environmental Microbiology, Prague, Czech Republic
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Lladó S, Benada O, Cajthaml T, Baldrian P, García-Fraile P. Silvibacterium bohemicum gen. nov. sp. nov., an acidobacterium isolated from coniferous soil in the Bohemian Forest National Park. Syst Appl Microbiol 2015; 39:14-9. [PMID: 26774420 DOI: 10.1016/j.syapm.2015.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 12/10/2015] [Accepted: 12/12/2015] [Indexed: 12/24/2022]
Abstract
During the course of a study assessing the bacterial diversity of a coniferous forest soil (pH 3.8) in the Bohemian Forest National Park (Czech Republic), we isolated strain S15(T) which corresponded to one of the most abundant soil OTUs. Strain S15(T) is represented by Gram-negative, motile, rod-like cells that are 0.3-0.5μm in diameter and 0.9-1.1μm in length. Its pH range for growth was 3-6, with optimal conditions found at approximately 4-5. It can grow at temperatures between 20°C and 28°C, with optimum growth at 22-24°C. Its respiratory quinone is MK-8, and its main fatty acid is iso-C15:0 (73.7%). The G+C DNA content was 58.2mol%. According to the 16S rRNA gene sequence analysis, strain S15(T) belongs to subdivision 1 of the phylum Acidobacteria, being affiliated to the cluster of Acidipila rosea AP8(T) and Acidobacterium capsulatum ATCC 51196(T). Analysis of the S15(T) genome revealed the presence of 404 genes that are involved in carbohydrate metabolism, which indicates the metabolic potential to degrade polysaccharides of plant and fungal origin. Based on genotypic and phenotypic characteristics, the strain S15(T) represents a new genus and species within the family Acidobacteriaceae, for which the name Silvibacterium bohemicum gen. nov., sp. nov. is proposed (type strain S15(T)=LMG 28607(T)=CECT 8790(T)).
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Affiliation(s)
- Salvador Lladó
- Institute of Microbiology ASCR, Laboratory of Environmental Microbiology, Prague, Czech Republic
| | - Oldrich Benada
- Institute of Microbiology ASCR, Laboratory of Molecular Structure Characterization, Prague, Czech Republic
| | - Tomáš Cajthaml
- Institute of Microbiology ASCR, Laboratory of Environmental Biotechnology, Prague, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology ASCR, Laboratory of Environmental Microbiology, Prague, Czech Republic
| | - Paula García-Fraile
- Institute of Microbiology ASCR, Laboratory of Fungal Genetics and Metabolism, Prague, Czech Republic.
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Mukherjee S, Juottonen H, Siivonen P, Lloret Quesada C, Tuomi P, Pulkkinen P, Yrjälä K. Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site. ISME JOURNAL 2014; 8:2131-42. [PMID: 25105905 DOI: 10.1038/ismej.2014.151] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/16/2014] [Accepted: 05/21/2014] [Indexed: 11/09/2022]
Abstract
Restoration of polluted sites via in situ bioremediation relies heavily on the indigenous microbes and their activities. Spatial heterogeneity of microbial populations, contaminants and soil chemical parameters on such sites is a major hurdle in optimizing and implementing an appropriate bioremediation regime. We performed a grid-based sampling of an aged creosote-contaminated site followed by geostatistical modelling to illustrate the spatial patterns of microbial diversity and activity and to relate these patterns to the distribution of pollutants. Spatial distribution of bacterial groups unveiled patterns of niche differentiation regulated by patchy distribution of pollutants and an east-to-west pH gradient at the studied site. Proteobacteria clearly dominated in the hot spots of creosote pollution, whereas the abundance of Actinobacteria, TM7 and Planctomycetes was considerably reduced from the hot spots. The pH preferences of proteobacterial groups dominating in pollution could be recognized by examining the order and family-level responses. Acidobacterial classes came across as generalists in hydrocarbon pollution whose spatial distribution seemed to be regulated solely by the pH gradient. Although the community evenness decreased in the heavily polluted zones, basal respiration and fluorescein diacetate hydrolysis rates were higher, indicating the adaptation of specific indigenous microbial populations to hydrocarbon pollution. Combining the information from the kriged maps of microbial and soil chemistry data provided a comprehensive understanding of the long-term impacts of creosote pollution on the subsurface microbial communities. This study also highlighted the prospect of interpreting taxa-specific spatial patterns and applying them as indicators or proxies for monitoring polluted sites.
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Affiliation(s)
- Shinjini Mukherjee
- Department of Biosciences, MEM Group, University of Helsinki, Helsinki, Finland
| | - Heli Juottonen
- Department of Biosciences, MEM Group, University of Helsinki, Helsinki, Finland
| | - Pauli Siivonen
- Department of Biosciences, MEM Group, University of Helsinki, Helsinki, Finland
| | | | | | | | - Kim Yrjälä
- Department of Biosciences, MEM Group, University of Helsinki, Helsinki, Finland
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Ambardar S, Sangwan N, Manjula A, Rajendhran J, Gunasekaran P, Lal R, Vakhlu J. Identification of bacteria associated with underground parts of Crocus sativus by 16S rRNA gene targeted metagenomic approach. World J Microbiol Biotechnol 2014; 30:2701-9. [PMID: 24989343 DOI: 10.1007/s11274-014-1694-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/21/2014] [Indexed: 11/28/2022]
Abstract
Saffron (Crocus sativus L), an autumn-flowering perennial sterile plant, reproduces vegetatively by underground corms. Saffron has biannual corm-root cycle that makes it an interesting candidate to study microbial dynamics in its rhizosphere and cormosphere (area under influence of corm). Culture independent 16S rRNA gene metagenomic study of rhizosphere and cormosphere of Saffron during flowering stage revealed presence of 22 genera but none of the genus was common in all the three samples. Bulk soil bacterial community was represented by 13 genera with Acidobacteria being dominant. In rhizosphere, out of eight different genera identified, Pseudomonas was the most dominant genus. Cormosphere bacteria comprised of six different genera, dominated by the genus Pantoea. This study revealed that the bacterial composition of all the three samples is significantly different (P < 0.05) from each other. This is the first report on the identification of bacteria associated with rhizosphere, cormosphere and bulk soil of Saffron, using cultivation independent 16S rRNA gene targeted metagenomic approach.
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Huber KJ, Wüst PK, Rohde M, Overmann J, Foesel BU. Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil. Int J Syst Evol Microbiol 2014; 64:1866-1875. [DOI: 10.1099/ijs.0.060236-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Acidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the
Acidobacteria
are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the
Acidobacteria
were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4HT and Ac_23_E3T were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4HT and Ac_23_E3T were aerobic mesophiles with a broad range of tolerance towards pH (4.0–9.5 and 3.5–10.0, respectively) and temperature (15–44 and 12–47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4HT and Ac_23_E3T were iso-C15 : 0, summed feature 1 (C13 : 0 3-OH/iso-C15 : 1 H), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and anteiso-C17 : 0. The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4HT and Ac_23_E3T were 53.2 and 52.6 mol%, respectively. The closest described relative was
Blastocatella fastidiosa
A2-16T, with 16S rRNA gene sequence identity of 93.2 and 93.3 %, respectively. Strains A22_HD_4HT and Ac_23_E3T displayed 16S rRNA gene sequence similarity of 97.4 % to each other. On the basis of the low DNA–DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4HT = DSM 26555T = LMG 27985T) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3T = DSM 26558T = LMG 27597T).
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Affiliation(s)
- Katharina J. Huber
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K. Wüst
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- Department of Medical Microbiology, Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jörg Overmann
- Technical University Braunschweig, Braunschweig, Germany
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Bärbel U. Foesel
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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HIDAYATI ERNIN, TRI WAHYUDI ARIS, SUWANTO ANTONIUS, WIDYASTUTI RAHAYU. Abundance of Culturable Bacteria Isolated from Maize Rhizosphere Soil Using Four Different Culture Media. MICROBIOLOGY INDONESIA 2014. [DOI: 10.5454/mi.8.1.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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The rhizosphere selects for particular groups of acidobacteria and verrucomicrobia. PLoS One 2013; 8:e82443. [PMID: 24349285 PMCID: PMC3862674 DOI: 10.1371/journal.pone.0082443] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 10/25/2013] [Indexed: 11/23/2022] Open
Abstract
There is a lack in our current understanding on the putative interactions of species of the phyla of Acidobacteria and Verrucomicrobia with plants. Moreover, progress in this area is seriously hampered by the recalcitrance of members of these phyla to grow as pure cultures. The purpose of this study was to investigate whether particular members of Acidobacteria and Verrucomicrobia are avid colonizers of the rhizosphere. Based on previous work, rhizosphere competence was demonstrated for the Verrucomicrobia subdivision 1 groups of Luteolibacter and Candidatus genus Rhizospheria and it was hypothesized that the rhizosphere is a common habitat for Acidobacteria subdivision 8 (class Holophagae). We assessed the population densities of Bacteria, Verrucomicrobia subdivision 1 groups Luteolibacter and Candidatus genus Rhizospheria and Acidobacteria subdivisions 1, 3, 4, 6 and Holophagae in bulk soil and in the rhizospheres of grass, potato and leek in the same field at different points in time using real-time quantitative PCR. Primers of all seven verrucomicrobial, acidobacterial and holophagal PCR systems were based on 16S rRNA gene sequences of cultivable representatives of the different groups. Luteolibacter, Candidatus genus Rhizospheria, subdivision 6 acidobacteria and Holophaga showed preferences for one or more rhizospheres. In particular, the Holophaga 16S rRNA gene number were more abundant in the leek rhizosphere than in bulk soil and the rhizospheres of grass and potato. Attraction to, and colonization of, leek roots by Holophagae strain CHC25 was further shown in an experimental microcosm set-up. In the light of this remarkable capacity, we propose to coin strain CHC25 Candidatus Porrumbacterium oxyphilus (class Holophagae, Phylum Acidobacteria), the first cultured representative with rhizosphere competence.
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Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile. PLoS One 2013; 8:e64659. [PMID: 23741360 PMCID: PMC3669403 DOI: 10.1371/journal.pone.0064659] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance of known Fe reducing species at all depths in the profile. The abundance of sequences associated with anaerobic metabolic processes generally increased with depth, while aerobic cytochrome c oxidases decreased. Methanogenesis genes and methanogen genomes followed the pattern of CH4 fluxes : they increased steeply with depth into the active layer, but declined somewhat over the transition zone between the lower active layer and the upper permafrost. The latter was relatively enriched in fermentative and anaerobic respiratory pathways. A survey of decaheme cytochromes (MtrA, MtrC and their homologs) revealed that this is a promising approach to identifying potential reducers of Fe(III) or HS, and indicated a possible role for Acidobacteria as Fe reducers in these soils. Methanogens appear to coexist in the same layers, though in lower abundance, with Fe reducing bacteria and other potential competitors, including acetogens. These observations provide a rich set of hypotheses for further targeted study.
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Blastocatella fastidiosa gen. nov., sp. nov., isolated from semiarid savanna soil – The first described species of Acidobacteria subdivision 4. Syst Appl Microbiol 2013; 36:82-9. [DOI: 10.1016/j.syapm.2012.11.002] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 11/15/2012] [Accepted: 11/19/2012] [Indexed: 11/18/2022]
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Isolation of a substantial proportion of forest soil bacterial communities detected via pyrotag sequencing. Appl Environ Microbiol 2013; 79:2096-8. [PMID: 23315727 DOI: 10.1128/aem.03112-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated 1,264 bacterial strains from forest soils previously surveyed via pyrosequencing of rRNA gene amplicons. Conventional culturing techniques recovered a substantial proportion of the community, with isolates representing 22% of 98,557 total pyrotags. Growth characteristics of isolates indicated that ecological traits were associated with relative abundances of corresponding pyrotag operational taxonomic units.
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Geothrix fermentans secretes two different redox-active compounds to utilize electron acceptors across a wide range of redox potentials. Appl Environ Microbiol 2012; 78:6987-95. [PMID: 22843516 DOI: 10.1128/aem.01460-12] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The current understanding of dissimilatory metal reduction is based primarily on isolates from the proteobacterial genera Geobacter and Shewanella. However, environments undergoing active Fe(III) reduction often harbor less-well-studied phyla that are equally abundant. In this work, electrochemical techniques were used to analyze respiratory electron transfer by the only known Fe(III)-reducing representative of the Acidobacteria, Geothrix fermentans. In contrast to previously characterized metal-reducing bacteria, which typically reach maximal rates of respiration at electron acceptor potentials of 0 V versus standard hydrogen electrode (SHE), G. fermentans required potentials as high as 0.55 V to respire at its maximum rate. In addition, G. fermentans secreted two different soluble redox-active electron shuttles with separate redox potentials (-0.2 V and 0.3 V). The compound with the lower midpoint potential, responsible for 20 to 30% of electron transfer activity, was riboflavin. The behavior of the higher-potential compound was consistent with hydrophilic UV-fluorescent molecules previously found in G. fermentans supernatants. Both electron shuttles were also produced when cultures were grown with Fe(III), but not when fumarate was the electron acceptor. This study reveals that Geothrix is able to take advantage of higher-redox-potential environments, demonstrates that secretion of flavin-based shuttles is not confined to Shewanella, and points to the existence of high-potential-redox-active compounds involved in extracellular electron transfer. Based on differences between the respiratory strategies of Geothrix and Geobacter, these two groups of bacteria could exist in distinctive environmental niches defined by redox potential.
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Faoro H, Glogauer A, Couto GH, de Souza EM, Rigo LU, Cruz LM, Monteiro RA, Pedrosa FDO. Characterization of a new Acidobacteria-derived moderately thermostable lipase from a Brazilian Atlantic Forest soil metagenome. FEMS Microbiol Ecol 2012; 81:386-94. [PMID: 22428990 DOI: 10.1111/j.1574-6941.2012.01361.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 02/25/2012] [Accepted: 03/06/2012] [Indexed: 11/28/2022] Open
Abstract
A clone (LP001) expressing a new lipase gene was isolated from a metagenomic library of the Brazilian Atlantic Forest soil. The DNA insert of LP001 was fully sequenced, and 38 ORFs were identified. Comparison of ORFs, %G + C content and gene organization with sequenced bacterial genomes suggested that the fosmid DNA insert belongs to an organism of the Acidobacteria phylum. Protein domain analysis and inactivation by transposon insertion showed that the protein encoded by ORF29 was responsible for the lipase activity and was named LipAAc. The purified LipAAc lipase was capable of hydrolyzing a broad range of substrates, showing the highest activity against p-nitrophenol (pNP) decanoate. The lipase was active over a pH range of 5.0-10.0 and was insensitive to divalent cations. LipAAc is moderately thermostable with optimum temperature between 50 and 60 °C and was thermally activated (80% activity increase) after 1 h incubation at 50 °C. Phylogenetic analysis suggested that the LipAAc is a member of family I of bacterial lipases and clusters with other moderately thermostable lipases of this group. Comparisons of the DNA insert of fosmid LP001 with other acidobacterial genomes and sequence database suggest that lipAAc gene has a fungal origin and was acquired by horizontal transfer.
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Affiliation(s)
- Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, PR, Brazil
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