Cargando…
Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments
Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet the limited number of isolates makes it difficult to understand the physiology and ecological impact of the microorganisms involved. Here, two-stage cultiva...
Autores principales: | , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419728/ https://www.ncbi.nlm.nih.gov/pubmed/25999927 http://dx.doi.org/10.3389/fmicb.2015.00386 |
_version_ | 1782369634095202304 |
---|---|
author | Hori, Tomoyuki Aoyagi, Tomo Itoh, Hideomi Narihiro, Takashi Oikawa, Azusa Suzuki, Kiyofumi Ogata, Atsushi Friedrich, Michael W. Conrad, Ralf Kamagata, Yoichi |
author_facet | Hori, Tomoyuki Aoyagi, Tomo Itoh, Hideomi Narihiro, Takashi Oikawa, Azusa Suzuki, Kiyofumi Ogata, Atsushi Friedrich, Michael W. Conrad, Ralf Kamagata, Yoichi |
author_sort | Hori, Tomoyuki |
collection | PubMed |
description | Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet the limited number of isolates makes it difficult to understand the physiology and ecological impact of the microorganisms involved. Here, two-stage cultivation was implemented to selectively enrich and isolate crystalline iron(III) oxide reducing microorganisms in soils and sediments. Firstly, iron reducers were enriched and other untargeted eutrophs were depleted by 2-years successive culture on a crystalline ferric iron oxide (i.e., goethite, lepidocrocite, hematite, or magnetite) as electron acceptor. Fifty-eight out of 136 incubation conditions allowed the continued existence of microorganisms as confirmed by PCR amplification. High-throughput Illumina sequencing and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures on each of the ferric iron oxides contained bacteria belonging to the Deltaproteobacteria (mainly Geobacteraceae), followed by Firmicutes and Chloroflexi, which also comprised most of the operational taxonomic units (OTUs) identified. Venn diagrams indicated that the core OTUs enriched with all of the iron oxides were dominant in the Geobacteraceae while each type of iron oxides supplemented selectively enriched specific OTUs in the other phylogenetic groups. Secondly, 38 enrichment cultures including novel microorganisms were transferred to soluble-iron(III) containing media in order to stimulate the proliferation of the enriched iron reducers. Through extinction dilution-culture and single colony isolation, six strains within the Deltaproteobacteria were finally obtained; five strains belonged to the genus Geobacter and one strain to Pelobacter. The 16S rRNA genes of these isolates were 94.8–98.1% identical in sequence to cultured relatives. All the isolates were able to grow on acetate and ferric iron but their physiological characteristics differed considerably in terms of growth rate. Thus, the novel strategy allowed to enrich and isolate novel iron(III) reducers that were able to thrive by reducing crystalline ferric iron oxides. |
format | Online Article Text |
id | pubmed-4419728 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-44197282015-05-21 Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments Hori, Tomoyuki Aoyagi, Tomo Itoh, Hideomi Narihiro, Takashi Oikawa, Azusa Suzuki, Kiyofumi Ogata, Atsushi Friedrich, Michael W. Conrad, Ralf Kamagata, Yoichi Front Microbiol Microbiology Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet the limited number of isolates makes it difficult to understand the physiology and ecological impact of the microorganisms involved. Here, two-stage cultivation was implemented to selectively enrich and isolate crystalline iron(III) oxide reducing microorganisms in soils and sediments. Firstly, iron reducers were enriched and other untargeted eutrophs were depleted by 2-years successive culture on a crystalline ferric iron oxide (i.e., goethite, lepidocrocite, hematite, or magnetite) as electron acceptor. Fifty-eight out of 136 incubation conditions allowed the continued existence of microorganisms as confirmed by PCR amplification. High-throughput Illumina sequencing and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures on each of the ferric iron oxides contained bacteria belonging to the Deltaproteobacteria (mainly Geobacteraceae), followed by Firmicutes and Chloroflexi, which also comprised most of the operational taxonomic units (OTUs) identified. Venn diagrams indicated that the core OTUs enriched with all of the iron oxides were dominant in the Geobacteraceae while each type of iron oxides supplemented selectively enriched specific OTUs in the other phylogenetic groups. Secondly, 38 enrichment cultures including novel microorganisms were transferred to soluble-iron(III) containing media in order to stimulate the proliferation of the enriched iron reducers. Through extinction dilution-culture and single colony isolation, six strains within the Deltaproteobacteria were finally obtained; five strains belonged to the genus Geobacter and one strain to Pelobacter. The 16S rRNA genes of these isolates were 94.8–98.1% identical in sequence to cultured relatives. All the isolates were able to grow on acetate and ferric iron but their physiological characteristics differed considerably in terms of growth rate. Thus, the novel strategy allowed to enrich and isolate novel iron(III) reducers that were able to thrive by reducing crystalline ferric iron oxides. Frontiers Media S.A. 2015-05-05 /pmc/articles/PMC4419728/ /pubmed/25999927 http://dx.doi.org/10.3389/fmicb.2015.00386 Text en Copyright © 2015 Hori, Aoyagi, Itoh, Narihiro, Oikawa, Suzuki, Ogata, Friedrich, Conrad and Kamagata. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Hori, Tomoyuki Aoyagi, Tomo Itoh, Hideomi Narihiro, Takashi Oikawa, Azusa Suzuki, Kiyofumi Ogata, Atsushi Friedrich, Michael W. Conrad, Ralf Kamagata, Yoichi Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments |
title | Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments |
title_full | Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments |
title_fullStr | Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments |
title_full_unstemmed | Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments |
title_short | Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments |
title_sort | isolation of microorganisms involved in reduction of crystalline iron(iii) oxides in natural environments |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419728/ https://www.ncbi.nlm.nih.gov/pubmed/25999927 http://dx.doi.org/10.3389/fmicb.2015.00386 |
work_keys_str_mv | AT horitomoyuki isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments AT aoyagitomo isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments AT itohhideomi isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments AT narihirotakashi isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments AT oikawaazusa isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments AT suzukikiyofumi isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments AT ogataatsushi isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments AT friedrichmichaelw isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments AT conradralf isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments AT kamagatayoichi isolationofmicroorganismsinvolvedinreductionofcrystallineironiiioxidesinnaturalenvironments |