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Murakami C, Tanaka AR, Sato Y, Morimoto K. Buffer-free CAS assay using a diluted growth medium efficiently detects siderophore production and microbial growth. Biometals 2024; 37:223-232. [PMID: 37848652 DOI: 10.1007/s10534-023-00544-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
Siderophores are iron chelators and low-molecular-weight compounds secreted by various microorganisms under low-iron conditions. Many microorganisms produce siderophores in the natural environment as iron is an essential element for many of them. CAS assays are widely used to detect siderophores in cultures of various microorganisms; however, it is necessary to improve their sensitivity for the efficient application to fastidious microorganisms. We developed a simple, high-throughput CAS assay employing a buffer-free CAS reagent and diluted growth medium (10% dR2A) in a 96-well microplate. Using a diluted growth medium in agar plates suitable for iron-restricted conditions supported siderophore production by microorganisms from activated sludge. A buffer-free CAS reagent combined with a diluted growth medium revealed that these microorganisms tended to produce more siderophores or iron chelators than microorganisms under iron-rich conditions. Moreover, this buffer-free CAS assay easily and efficiently detected not only siderophore production but also the growth of fastidious microorganisms.
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Affiliation(s)
- Chiho Murakami
- Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Hiroshima City, Hiroshima Prefecture, 731-0153, Japan.
| | - Arowu R Tanaka
- Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Hiroshima City, Hiroshima Prefecture, 731-0153, Japan
| | - Yuichiro Sato
- Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Hiroshima City, Hiroshima Prefecture, 731-0153, Japan
| | - Kinjiro Morimoto
- Faculty of Pharmacy, Yasuda Women's University, 6-13-1 Yasuhigashi, Hiroshima City, Hiroshima Prefecture, 731-0153, Japan
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2
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Boonmak C, Kettongruang S, Buranathong B, Morikawa M, Duangmal K. Duckweed-associated bacteria as plant growth-promotor to enhance growth of Spirodela polyrhiza in wastewater effluent from a poultry farm. Arch Microbiol 2023; 206:43. [PMID: 38148332 DOI: 10.1007/s00203-023-03778-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
Duckweed has been highlighted as an invaluable resource because of its abilities to remove nitrogen and phosphorus from wastewater coupling with the production of high starch/protein-containing plant biomass. Duckweed recruits microbes and particularly forms a stable "core" bacterial microbiota, which greatly reduces the colonization efficiency of plant growth-promoting bacteria (PGPB). In this study, natural duckweeds were enriched in a sterilized-partially treated wastewater effluent from a poultry farm. After 24 days of cultivation, the duckweed-associated bacteria (DAB) were isolated and evaluated for their plant growth-promoting (PGP) potentials by co-cultivation with axenic Spirodela polyrhiza. Ten species were found in more than one location and could be considered candidates for the stable "core" DAB. Among them, all isolates of Acinetobacter soli, Acidovorax kalamii, Brevundimonas vesicularis, Pseudomonas toyotomiensis, and Shinella curvata increased duckweed growth in Hoagland medium. The highest PGP ability was observed in Sh. curvata W12-8 (with EPG value of 208.72%), followed by Paracoccus marcusii W7-16 (171.31%), Novosphingobium subterraneum W5-13 (156.96%), and Ac. kalamii W7-18 (156.96%). However, the highest growth promotion in the wastewater was observed when co-cultured with W7-16, which was able to increase biomass dry weight and root length of duckweed by 3.17 and 2.26 folds, respectively.
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Affiliation(s)
- Chanita Boonmak
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Biodiversity Center Kasetsart University (BDCKU), Kasetsart University, Bangkok, 10900, Thailand.
- Duckweed Holobiont Resource and Research Center (DHbRC), Kasetsart University, Bangkok, 10900, Thailand.
| | - Sirapat Kettongruang
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Buranaporn Buranathong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Kasetsart University, Bangkok, 10900, Thailand
- Duckweed Holobiont Resource and Research Center (DHbRC), Kasetsart University, Bangkok, 10900, Thailand
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3
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Singh P, Jani K, Sharma S, Rale V, Souche Y, Prakash S, Jogdeo P, Patil Y, Dhanorkar MN. Microbial Population Dynamics in Lemnaceae (Duckweed)-Based Wastewater Treatment System. Curr Microbiol 2022; 80:56. [PMID: 36585971 DOI: 10.1007/s00284-022-03149-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 12/11/2022] [Indexed: 01/01/2023]
Abstract
The dynamic microflora associated within, and in the surrounding aquatic environment, has been found to be responsible for the functional properties of many aquatic plants. The aim of the current work was to evaluate the effectiveness of Lemnaceae-based wastewater treatment system under tropical conditions and investigate the changes in the aquatic microflora upon plant growth. A biological wastewater treatment system was designed and investigated using mixed Lemnaceae culture comprising Lemna minor and Spirodela polyrhiza in a batch mode. A significant reduction in total solids (31.8%), biochemical oxygen demand (93.5%), and chemical oxygen demand (73.2%) was observed after seven days of duckweed growth using a low inoculum. A preliminary study on the change in the microbial population diversity and functionality, in the wastewater before and after treatment, revealed an increase in the denitrifying microflora in wastewater post-Lemnaceae treatment. Dominance of 10 bacterial phyla, contributing for 98.3% of the total bacterial communities, was recorded, and ~ 50.6% loss of diversity post-treatment of wastewater was revealed by the Shannon Index. Among 16 bacterial families showing relative abundance of ≥ 1% in untreated wastewater, Methylobacteriaceae, Pseudomonadaceae, Brucellaceae, Rhodobacteraceae, and Acetobacteraceae prevailed in the water post-treatment by duckweeds. This is a novel work done on the dynamics of aquatic microflora associated with Lemnaceae under tropical Indian conditions. It confirms the application of Lemnaceae-based wastewater treatment system as effective biofilter and calls for further studies on the active involvement of the endophytic and aquatic microflora in the functions of these plant.
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Affiliation(s)
- Pooja Singh
- Symbiosis Centre for Waste Resource Management, Symbiosis International (Deemed University), Lavale, Pune, 412115, India
| | - Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Pashan, Pune, India
| | - Shreyansh Sharma
- Symbiosis Centre for Waste Resource Management, Symbiosis International (Deemed University), Lavale, Pune, 412115, India.,Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Vinay Rale
- Symbiosis Centre for Research and Innovation, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Yogesh Souche
- National Centre for Microbial Resource, National Centre for Cell Science, Pashan, Pune, India
| | - Sumit Prakash
- Symbiosis Centre for Waste Resource Management, Symbiosis International (Deemed University), Lavale, Pune, 412115, India
| | | | - Yogesh Patil
- Symbiosis Centre for Research and Innovation, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Manikprabhu N Dhanorkar
- Symbiosis Centre for Waste Resource Management, Symbiosis International (Deemed University), Lavale, Pune, 412115, India.
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4
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Makino A, Nakai R, Yoneda Y, Toyama T, Tanaka Y, Meng XY, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. Isolation of Aquatic Plant Growth-Promoting Bacteria for the Floating Plant Duckweed (Lemna minor). Microorganisms 2022; 10:microorganisms10081564. [PMID: 36013982 PMCID: PMC9416352 DOI: 10.3390/microorganisms10081564] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/15/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) can exert beneficial growth effects on their host plants. Little is known about the phylogeny and growth-promoting mechanisms of PGPB associated with aquatic plants, although those of terrestrial PGPB have been well-studied. Here, we report four novel aquatic PGPB strains, MRB1–4 (NITE P-01645–P-01648), for duckweed Lemna minor from our rhizobacterial collection isolated from Lythrum anceps. The number of L. minor fronds during 14 days co-culture with the strains MRB1–4 increased by 2.1–3.8-fold, compared with an uninoculated control; the plant biomass and chlorophyll content in co-cultures also increased. Moreover, all strains possessed an indole-3-acetic acid production trait in common with a plant growth-promoting trait of terrestrial PGPB. Phylogenetic analysis showed that three strains, MRB-1, -3, and -4, were affiliated with known proteobacterial genera (Bradyrhizobium and Pelomonas); this report is the first to describe a plant-growth promoting activity of Pelomonas members. The gammaproteobacterial strain MRB2 was suggested to be phylogenetically novel at the genus level. Under microscopic observation, the Pelomonas strain MRB3 was epiphytic and adhered to both the root surfaces and fronds of duckweed. The duckweed PGPB obtained here could serve as a new model for understanding unforeseen mechanisms behind aquatic plant-microbe interactions.
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Affiliation(s)
- Ayaka Makino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Hokkaido, Japan; (A.M.); (R.N.)
| | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Hokkaido, Japan; (A.M.); (R.N.)
| | - Yasuko Yoneda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
| | - Tadashi Toyama
- Graduate School of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Yasuhiro Tanaka
- Graduate School of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan;
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
| | - Kazuhiro Mori
- Graduate School of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Michihiko Ike
- Graduate School of Engineering, Osaka University, Suita 565-0871, Osaka, Japan;
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan;
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (X.-Y.M.); (Y.K.)
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan
- Biotechnology Research Center, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Correspondence: ; Tel.: +81-29-861-6592
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5
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Degradation of Three Microcystin Variants in the Presence of the Macrophyte Spirodela polyrhiza and the Associated Microbial Communities. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19106086. [PMID: 35627623 PMCID: PMC9142107 DOI: 10.3390/ijerph19106086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/07/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022]
Abstract
Cyanobacteria, which form water blooms all over the world, can produce a wide range of cyanotoxins such as hepatotoxic microcystins (MCs) and other biologically active metabolites harmful to living organisms, including humans. Microcystin biodegradation, particularly caused by bacteria, has been broadly documented; however, studies in this field focus mainly on strains isolated from natural aquatic environments. In this paper, the biodegradation of microcystin-RR (MC-RR), microcystin-LR (MC-LR), and microcystin-LF (MC-LF) after incubation with Spirodela polyrhiza and the associated microorganisms (which were cultured under laboratory conditions) is shown. The strongest MC biodegradation rate after nine days of incubation was observed for MC-RR, followed by MC-LR. No statistically significant decrease in the concentration of MC-LF was noted. Products of MC decomposition were detected via the HPLC method, and their highest number was found for MC-RR (six products with the retention time between 5.6 and 16.2 min), followed by MC-LR (two products with the retention time between 19.3 and 20.2 min). Although the decrease in MC-LF concentration was not significant, four MC-LF degradation products were detected with the retention time between 28.9 and 33.0 min. The results showed that MC-LF was the most stable and resistant MC variant under experimental conditions. No accumulation of MCs or their biodegradation products in S. polyrhiza was found. The findings suggest that the microorganisms (bacteria and algae) associated with S. polyrhiza could be responsible for the MC biodegradation observed. Therefore, there is a need to broaden the research on the biodegradation products detected and potential MC-degraders associated with plants.
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Acosta K, Appenroth KJ, Borisjuk L, Edelman M, Heinig U, Jansen MAK, Oyama T, Pasaribu B, Schubert I, Sorrels S, Sree KS, Xu S, Michael TP, Lam E. Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era. THE PLANT CELL 2021; 33:3207-3234. [PMID: 34273173 PMCID: PMC8505876 DOI: 10.1093/plcell/koab189] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/18/2021] [Indexed: 05/05/2023]
Abstract
The aquatic Lemnaceae family, commonly called duckweed, comprises some of the smallest and fastest growing angiosperms known on Earth. Their tiny size, rapid growth by clonal propagation, and facile uptake of labeled compounds from the media were attractive features that made them a well-known model for plant biology from 1950 to 1990. Interest in duckweed has steadily regained momentum over the past decade, driven in part by the growing need to identify alternative plants from traditional agricultural crops that can help tackle urgent societal challenges, such as climate change and rapid population expansion. Propelled by rapid advances in genomic technologies, recent studies with duckweed again highlight the potential of these small plants to enable discoveries in diverse fields from ecology to chronobiology. Building on established community resources, duckweed is reemerging as a platform to study plant processes at the systems level and to translate knowledge gained for field deployment to address some of society's pressing needs. This review details the anatomy, development, physiology, and molecular characteristics of the Lemnaceae to introduce them to the broader plant research community. We highlight recent research enabled by Lemnaceae to demonstrate how these plants can be used for quantitative studies of complex processes and for revealing potentially novel strategies in plant defense and genome maintenance.
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Affiliation(s)
- Kenneth Acosta
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Klaus J Appenroth
- Plant Physiology, Matthias Schleiden Institute, University of Jena, Jena 07737, Germany
| | - Ljudmilla Borisjuk
- The Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben D-06466, Germany
| | - Marvin Edelman
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uwe Heinig
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marcel A K Jansen
- School of Biological, Earth and Environmental Sciences, Environmental Research Institute, University College Cork, Cork T23 TK30, Ireland
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Buntora Pasaribu
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Ingo Schubert
- The Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben D-06466, Germany
| | - Shawn Sorrels
- Department of Plant Biology, Rutgers the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - K Sowjanya Sree
- Department of Environmental Science, Central University of Kerala, Periye 671320, India
| | - Shuqing Xu
- Institute for Evolution and Biodiversity, University of Münster, Münster 48149, Germany
| | | | - Eric Lam
- Author for correspondence: (E.L.), (T.P.M.)
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7
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Easy detection of siderophore production in diluted growth media using an improved CAS reagent. J Microbiol Methods 2021; 189:106310. [PMID: 34428498 DOI: 10.1016/j.mimet.2021.106310] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 11/24/2022]
Abstract
Siderophores are low molecular weight organic compounds produced by various microorganisms, especially pathogenic bacteria including rhizobacteria, and have a high affinity for iron. Although most microorganisms are thought to secrete siderophores under iron-depleted conditions, it is unclear how many microorganisms produce siderophores in the natural environment. Also, the chrome azurol sulfonate (CAS) assay, which is widely used for the detection of siderophores, needs to be improved for wider applicability. We developed a simple, high-throughput CAS assay in a 96-well microplate with a concentrated CAS reagent and commonly used diluted growth media in the absence of artificial iron depletion. The improved microplate CAS shuttle assay revealed that it could easily detect siderophores released from Pseudomonas (P.) fluorescence, P. putida, Burlkholderia stabilis, and Ottowia oryzae, as models of siderophore-producing bacteria. This CAS shuttle assay employed along with diluted growth media is a promising tool to screen new siderophore-producing bacteria.
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8
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Yoneda Y, Yamamoto K, Makino A, Tanaka Y, Meng XY, Hashimoto J, Shin-ya K, Satoh N, Fujie M, Toyama T, Mori K, Ike M, Morikawa M, Kamagata Y, Tamaki H. Novel Plant-Associated Acidobacteria Promotes Growth of Common Floating Aquatic Plants, Duckweeds. Microorganisms 2021; 9:1133. [PMID: 34074043 PMCID: PMC8225144 DOI: 10.3390/microorganisms9061133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 05/20/2021] [Indexed: 11/17/2022] Open
Abstract
Duckweeds are small, fast growing, and starch- and protein-rich aquatic plants expected to be a next generation energy crop and an excellent biomaterial for phytoremediation. Despite such an importance, very little is known about duckweed-microbe interactions that would be a key biological factor for efficient industrial utilization of duckweeds. Here we first report the duckweed growth promoting ability of bacterial strains belonging to the phylum Acidobacteria, the members of which are known to inhabit soils and terrestrial plants, but their ecological roles and plant-microbe interactions remain largely unclear. Two novel Acidobacteria strains, F-183 and TBR-22, were successfully isolated from wild duckweeds and phylogenetically affiliated with subdivision 3 and 6 of the phylum, respectively, based on 16S rRNA gene sequence analysis. In the co-culture experiments with aseptic host plants, the F-183 and TBR-22 strains visibly enhanced growth (frond number) of six duckweed species (subfamily Lemnoideae) up to 1.8-5.1 times and 1.6-3.9 times, respectively, compared with uninoculated controls. Intriguingly, both strains also increased the chlorophyll content of the duckweed (Lemna aequinoctialis) up to 2.4-2.5 times. Under SEM observation, the F-183 and TBR-22 strains were epiphytic and attached to the surface of duckweed. Taken together, our findings suggest that indigenous plant associated Acidobacteria contribute to a healthy growth of their host aquatic plants.
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Affiliation(s)
- Yasuko Yoneda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
| | - Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
- Bioproduction Research Institute, AIST, Sapporo 062-8517, Hokkaido, Japan
| | - Ayaka Makino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
| | - Yasuhiro Tanaka
- Department of Environmental Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan;
| | - Xian-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
| | - Junko Hashimoto
- Japan Biological Informatics Consortium (JBiC), Koto-ku, Tokyo 135-0064, Japan;
| | - Kazuo Shin-ya
- Cellular and Molecular Biotechnology Research Institute, AIST, Koto-ku, Tokyo 135-0064, Japan;
| | - Noriyuki Satoh
- Okinawa Institute of Science, Technology Graduate University (OIST), Kunigami-gun 904-0495, Okinawa, Japan; (N.S.); (M.F.)
| | - Manabu Fujie
- Okinawa Institute of Science, Technology Graduate University (OIST), Kunigami-gun 904-0495, Okinawa, Japan; (N.S.); (M.F.)
| | - Tadashi Toyama
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Kazuhiro Mori
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi, Kofu 400-8511, Yamanashi, Japan; (T.T.); (K.M.)
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, Suita 565-0871, Osaka, Japan;
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan;
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan; (Y.Y.); (K.Y.); (A.M.); (X.-Y.M.); (Y.K.)
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
- Biotechnology Research Center, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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9
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Iwashita T, Tanaka Y, Tamaki H, Yoneda Y, Makino A, Tateno Y, Li Y, Toyama T, Kamagata Y, Mori K. Comparative Analysis of Microbial Communities in Fronds and Roots of Three Duckweed Species: Spirodela polyrhiza, Lemna minor, and Lemna aequinoctialis. Microbes Environ 2021; 35. [PMID: 32684532 PMCID: PMC7511783 DOI: 10.1264/jsme2.me20081] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The microbial communities inhabiting the fronds of duckweeds have not been investigated in as much detail as those on the roots. We herein examined the microbial communities in three duckweed species using 16S rRNA amplicon sequencing and compared them to those on the roots. The microbial compositions of the fronds were distinct from those of the roots in the three species. Various types of taxonomic bacteria, including rarely cultivated phyla, Acidobacteria, Armatimonadetes, and Verrucomicrobia, were also isolated from the fronds, but at a slightly lower abundance than those from the roots. These results suggest that duckweed fronds are an alternative source for isolating rare and novel microbes, which may otherwise be recalcitrant to cultivation using conventional strategies.
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Affiliation(s)
| | - Yasuhiro Tanaka
- Graduate School of Life and Environmental Sciences, University of Yamanashi
| | | | | | | | - Yuka Tateno
- Graduate School of Engineering, University of Yamanashi
| | - Yan Li
- Graduate School of Engineering, University of Yamanashi
| | | | | | - Kazuhiro Mori
- Graduate School of Engineering, University of Yamanashi
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10
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Wu X, Spencer S, Gushgari-Doyle S, Yee MO, Voriskova J, Li Y, Alm EJ, Chakraborty R. Culturing of "Unculturable" Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater. Front Microbiol 2020; 11:610001. [PMID: 33391234 PMCID: PMC7773641 DOI: 10.3389/fmicb.2020.610001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/19/2020] [Indexed: 11/23/2022] Open
Abstract
Recovery and cultivation of diverse environmentally-relevant microorganisms from the terrestrial subsurface remain a challenge despite recent advances in modern molecular technology. Here, we applied complex carbon (C) sources, i.e., sediment dissolved organic matter (DOM) and bacterial cell lysate, to enrich groundwater microbial communities for 30 days. As comparisons, we also included enrichments amended with simple C sources including glucose, acetate, benzoate, oleic acid, cellulose, and mixed vitamins. Our results demonstrate that complex C is far more effective in enriching diverse and distinct microorganisms from groundwater than simple C. Simple C enrichments yield significantly lower biodiversity, and are dominated by few phyla (e.g., Proteobacteria and Bacteroidetes), while microcosms enriched with complex C demonstrate significantly higher biodiversity including phyla that are poorly represented in published culture collections (e.g., Verrucomicrobia, Planctomycetes, and Armatimonadetes). Subsequent isolation from complex C enrichments yielded 228 bacterial isolates representing five phyla, 17 orders, and 56 distinct species, including candidate novel, rarely cultivated, and undescribed organisms. Results from this study will substantially advance cultivation and isolation strategies for recovering diverse and novel subsurface microorganisms. Obtaining axenic representatives of “once-unculturable” microorganisms will enhance our understanding of microbial physiology and function in different biogeochemical niches of terrestrial subsurface ecosystems.
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Affiliation(s)
- Xiaoqin Wu
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sarah Spencer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sara Gushgari-Doyle
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mon Oo Yee
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jana Voriskova
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yifan Li
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Romy Chakraborty
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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11
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Chen D, Zhang H, Wang Q, Shao M, Li X, Chen D, Zeng R, Song Y. Intraspecific variations in cadmium tolerance and phytoaccumulation in giant duckweed (Spirodela polyrhiza). JOURNAL OF HAZARDOUS MATERIALS 2020; 395:122672. [PMID: 32305716 DOI: 10.1016/j.jhazmat.2020.122672] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 05/25/2023]
Abstract
Duckweeds are widely recognized for the heavy metal phytoremediation. However, the intraspecific variations in biological responses of duckweeds to heavy metal remain largely unknown. Here, the toxicity and phytoaccumulation of cadmium (Cd) were synchronously evaluated in 30 accessions of giant duckweed (Spirodela polyrhiza) collected from different provenances in Southern China. Exposure to 1 μM Cd decreased relative growth rates of dry weight, fronds number and fronds area, as well as photosynthetic pigment contents, while it increased H2O2 accumulation, lipid peroxidation and activities of anti-oxidant enzymes in the majority of accessions. Cd treatment led to remarkable Cd accumulation but little changes in the starch content in giant duckweed. The biological responses to Cd varied among the accessions. Further correlation analysis indicated that growth traits and Cd concentration were positively correlated with Cd accumulation, while the contents of chlorophyll, H2O2 and MDA were negatively associated with Cd accumulation. Our results proved the great intraspecific variation in Cd tolerance of giant duckweed, suggesting a valuable natural resource for Cd phytoremediation. Moreover, different mechanisms may be exploited by S. polyrhiza for phytoaccumulation, but growth maintenance, Cd uptake and antioxidative enzyme-independent ROS-scavenging under Cd exposure are the common mechanisms contributing to Cd accumulation ability.
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Affiliation(s)
- Daoqian Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Hao Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Qiongli Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Min Shao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Xinyu Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Dongmei Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Yuanyuan Song
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China.
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12
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Tamaki H. Cultivation Renaissance in the Post-Metagenomics Era: Combining the New and Old. Microbes Environ 2019; 34:117-120. [PMID: 31243255 PMCID: PMC6594738 DOI: 10.1264/jsme2.me3402rh] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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13
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Ishizawa H, Kuroda M, Inoue K, Inoue D, Morikawa M, Ike M. Colonization and Competition Dynamics of Plant Growth-Promoting/Inhibiting Bacteria in the Phytosphere of the Duckweed Lemna minor. MICROBIAL ECOLOGY 2019; 77:440-450. [PMID: 30603770 DOI: 10.1007/s00248-018-1306-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/11/2018] [Indexed: 05/22/2023]
Abstract
Despite the considerable role of aquatic plant-associated bacteria in host plant growth and nutrient cycling in aquatic environments, the mode of their plant colonization has hardly been understood. This study examined the colonization and competition dynamics of a plant growth-promoting bacterium (PGPB) and two plant growth-inhibiting bacteria (PGIB) in the aquatic plant Lemna minor (common duckweed). When inoculated separately to L. minor, each bacterial strain quickly colonized at approximately 106 cells per milligram (plant fresh weight) and kept similar populations throughout the 7-day cultivation time. The results of two-membered co-inoculation assays revealed that the PGPB strain Aquitalea magnusonii H3 consistently competitively excluded the PGIB strain Acinetobacter ursingii M3, and strain H3 co-existed at almost 1:1 proportion with another PGIB strain, Asticcacaulis excentricus M6, regardless of the inoculation ratios (99:1-1:99) and inoculation order. We also found that A. magnusonii H3 exerted its growth-promoting effect over the negative effects of the two PGIB strains even when only a small amount was inoculated, probably due to its excellent competitive colonization ability. These experimental results demonstrate that there is a constant ecological equilibrium state involved in the bacterial colonization of aquatic plants.
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Affiliation(s)
- Hidehiro Ishizawa
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masashi Kuroda
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kanako Inoue
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Osaka, Ibaraki, 567-0047, Japan
| | - Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masaaki Morikawa
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, N10-W5, Kita-ku, Sapporo, 060-0810, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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14
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Tanaka Y, Tamaki H, Tanaka K, Tozawa E, Matsuzawa H, Toyama T, Kamagata Y, Mori K. "Duckweed-Microbe Co-Cultivation Method" for Isolating a Wide Variety of Microbes Including Taxonomically Novel Microbes. Microbes Environ 2018; 33:402-406. [PMID: 30404972 PMCID: PMC6308005 DOI: 10.1264/jsme2.me18067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We herein described a new microbial isolation method using the interaction between the floating aquatic plant, duckweed, and microbes. We harvested microbial cells from Japanese loosestrife roots and co-cultivated these cells with aseptic duckweed using artificial inorganic medium for the plant for four weeks. During the co-cultivation, some duckweeds were collected every week, and the roots were used for microbial isolation using a low-nutrient plate medium. As a result, diverse microbial isolates, the compositions of which differed from those of the original source (Japanese loosestrife root), were obtained when the roots of duckweed were collected after 2 weeks of cultivation. We also successfully isolated a wide variety of novel microbes, including two strains within the rarely cultivated phylum, Armatimonadetes. The present study shows that a duckweed-microbe co-cultivation approach together with a conventional technique (direct isolation from a microbial source) effectively obtains more diverse microbes from a sole environmental sample.
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Affiliation(s)
- Yasuhiro Tanaka
- Graduate School of Life and Environmental Sciences, University of Yamanashi
| | | | - Kazuya Tanaka
- Graduate School of Engineering, University of Yamanashi
| | - Erina Tozawa
- Graduate School of Life and Environmental Sciences, University of Yamanashi
| | - Hiroaki Matsuzawa
- International Research Centre for River Basin Environment, University of Yamanashi
| | - Tadashi Toyama
- Graduate School of Engineering, University of Yamanashi.,International Research Centre for River Basin Environment, University of Yamanashi
| | | | - Kazuhiro Mori
- Graduate School of Engineering, University of Yamanashi
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15
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Gu YQ, Li TT, Li HQ. Biofilm formation monitored by confocal laser scanning microscopy during startup of MBBR operated under different intermittent aeration modes. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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16
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Gentès S, Taupiac J, Colin Y, André JM, Guyoneaud R. Bacterial periphytic communities related to mercury methylation within aquatic plant roots from a temperate freshwater lake (South-Western France). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:19223-19233. [PMID: 28664497 DOI: 10.1007/s11356-017-9597-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/20/2017] [Indexed: 06/07/2023]
Abstract
Macrophyte floating roots are considered as hotspots for methylmercury (MeHg) production in aquatic ecosystems through microbial activity. Nevertheless, very little is known about periphyton bacterial communities and mercury (Hg) methylators in such ecological niches. The ability to methylate inorganic Hg is broadly distributed among prokaryotes; however, sulfate-reducers have been reported to be the most important MeHg producers in macrophyte floating roots. In the present work, the periphyton bacterial communities colonizing Ludwigia sp. floating roots were investigated through molecular methods. Among the 244 clones investigated, anaerobic microorganisms associated with the sulfur biogeochemical cycle were identified. Notably, members of the sulfur-oxidizing prokaryotes and the anoxygenic, purple non-sulfur bacteria (Rhodobacteraceae, Comamonadaceae, Rhodocyclaceae, Hyphomicrobiaceae) and the sulfate reducers (Desulfobacteraceae, Syntrophobacteraceae, and Desulfobulbaceae) were detected. In addition, 15 sulfate-reducing strains related to the Desulfovibrionaceae family were isolated and their Hg-methylation capacity was tested using a biosensor. The overall results confirmed that Hg methylation is a strain-specific process since the four strains identified as new Hg-methylators were closely related to non-methylating isolates. This study highlights the potential involvement of periphytic bacteria in Hg methylation when favorable environmental conditions are present in such ecological micro-niches.
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Affiliation(s)
- Sophie Gentès
- Equipe Environnement et Microbiologie, UMR IPREM5254 Université de Pau et des Pays de l'Adour, Bâtiment IBEAS, BP1153, 64013, Pau Cedex, France.
- Université de Bordeaux, EPOC, UMR CNRS 5805, 33120, Arcachon, France.
| | - Julie Taupiac
- Equipe Environnement et Microbiologie, UMR IPREM5254 Université de Pau et des Pays de l'Adour, Bâtiment IBEAS, BP1153, 64013, Pau Cedex, France
| | - Yannick Colin
- Equipe Environnement et Microbiologie, UMR IPREM5254 Université de Pau et des Pays de l'Adour, Bâtiment IBEAS, BP1153, 64013, Pau Cedex, France
| | - Jean-Marc André
- Equipe CIH, IMS UMR 5218, Ecole Nationale Supérieure de Cognitique, 109 Avenue Roul, 33400, Talence, France
| | - Rémy Guyoneaud
- Equipe Environnement et Microbiologie, UMR IPREM5254 Université de Pau et des Pays de l'Adour, Bâtiment IBEAS, BP1153, 64013, Pau Cedex, France
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17
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Tanaka Y, Matsuzawa H, Tamaki H, Tagawa M, Toyama T, Kamagata Y, Mori K. Isolation of Novel Bacteria Including Rarely Cultivated Phyla, Acidobacteria and Verrucomicrobia, from the Roots of Emergent Plants by Simple Culturing Method. Microbes Environ 2017; 32:288-292. [PMID: 28740039 PMCID: PMC5606700 DOI: 10.1264/jsme2.me17027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A number of novel bacteria including members of rarely cultivated phyla, Acidobacteria and Verrucomicrobia, were successfully isolated from the roots of two emergent plants, Iris pseudacorus and Scirpus juncoides, by a simple culturing method. A total of 47.1% (66 strains) for I. pseudacorus and 42.1% (59 strains) for S. juncoides of all isolates (140 strains from each sample) were phylogenetically novel. Furthermore, Acidobacteria and Verrucomicrobia occupied 10.7% (15 strains) and 2.9% (4 strains) of I. pseudacorus isolates, and 2.1% (3 strains) and 3.6% (5 strains) of S. juncoides isolates, respectively, indicating that plant roots are attractive sources for isolating rarely cultivated microbes.
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Affiliation(s)
- Yasuhiro Tanaka
- Department of Environmental Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi
| | - Hiroaki Matsuzawa
- International Research Centre for River Basin Environment, University of Yamanashi
| | | | | | - Tadashi Toyama
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi
| | | | - Kazuhiro Mori
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi
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18
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Doherty M, Yager PL, Moran MA, Coles VJ, Fortunato CS, Krusche AV, Medeiros PM, Payet JP, Richey JE, Satinsky BM, Sawakuchi HO, Ward ND, Crump BC. Bacterial Biogeography across the Amazon River-Ocean Continuum. Front Microbiol 2017; 8:882. [PMID: 28588561 PMCID: PMC5440517 DOI: 10.3389/fmicb.2017.00882] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and >2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.
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Affiliation(s)
- Mary Doherty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, CambridgeMD, United States
| | - Patricia L Yager
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Victoria J Coles
- Horn Point Laboratory, University of Maryland Center for Environmental Science, CambridgeMD, United States
| | - Caroline S Fortunato
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods HoleMA, United States
| | - Alex V Krusche
- Center of Nuclear Energy in Agriculture, University of São PauloPiracicaba, Brazil
| | - Patricia M Medeiros
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Jérôme P Payet
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, CorvallisOR, United States
| | - Jeffrey E Richey
- School of Oceanography, University of Washington, SeattleWA, United States
| | | | - Henrique O Sawakuchi
- Center of Nuclear Energy in Agriculture, University of São PauloPiracicaba, Brazil
| | - Nicholas D Ward
- Marine Sciences Laboratory, Pacific Northwest National Laboratory, SequimWA, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, CorvallisOR, United States
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19
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Ishizawa H, Kuroda M, Morikawa M, Ike M. Evaluation of environmental bacterial communities as a factor affecting the growth of duckweed Lemna minor. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:62. [PMID: 28293292 PMCID: PMC5345205 DOI: 10.1186/s13068-017-0746-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/28/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Duckweed (family Lemnaceae) has recently been recognized as an ideal biomass feedstock for biofuel production due to its rapid growth and high starch content, which inspired interest in improving their productivity. Since microbes that co-exist with plants are known to have significant effects on their growth according to the previous studies for terrestrial plants, this study has attempted to understand the plant-microbial interactions of a duckweed, Lemna minor, focusing on the growth promotion/inhibition effects so as to assess the possibility of accelerated duckweed production by modifying co-existing bacterial community. RESULTS Co-cultivation of aseptic L. minor and bacterial communities collected from various aquatic environments resulted in changes in duckweed growth ranging from -24 to +14% compared to aseptic control. A number of bacterial strains were isolated from both growth-promoting and growth-inhibitory communities, and examined for their co-existing effects on duckweed growth. Irrespective of the source, each strain showed promotive, inhibitory, or neutral effects when individually co-cultured with L. minor. To further analyze the interactions among these bacterial strains in a community, binary combinations of promotive and inhibitory strains were co-cultured with aseptic L. minor, resulting in that combinations of promotive-promotive or inhibitory-inhibitory strains generally showed effects similar to those of individual strains. However, combinations of promotive-inhibitory strains tended to show inhibitory effects while only Aquitalea magnusonii H3 exerted its plant growth-promoting effect in all combinations tested. CONCLUSION Significant change in biomass production was observed when duckweed was co-cultivated with environmental bacterial communities. Promotive, neutral, and inhibitory bacteria in the community would synergistically determine the effects. The results indicate the possibility of improving duckweed biomass production via regulation of co-existing bacterial communities.
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Affiliation(s)
- Hidehiro Ishizawa
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Masashi Kuroda
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
| | - Masaaki Morikawa
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, N10-W5, Kita-ku, Sapporo, 060-0810 Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871 Japan
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20
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Zhao Y, Fang Y, Jin Y, Huang J, Ma X, He K, He Z, Wang F, Zhao H. Microbial community and removal of nitrogen via the addition of a carrier in a pilot-scale duckweed-based wastewater treatment system. BIORESOURCE TECHNOLOGY 2015; 179:549-558. [PMID: 25579229 DOI: 10.1016/j.biortech.2014.12.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 06/04/2023]
Abstract
Carriers were added to a pilot-scale duckweed-based (Lemna japonica 0223) wastewater treatment system to immobilize and enhance microorganisms. This system and another parallel duckweed system without carriers were operated for 1.5 years. The results indicated the addition of the carrier did not significantly affect the growth and composition of duckweed, the recovery of total nitrogen (TN), total phosphorus (TP) and CO2 or the removal of TP. However, it significantly improved the removal efficiency of TN and NH4(+)-N (by 19.97% and 15.02%, respectively). The use of 454 pyrosequencing revealed large differences of the microbial communities between the different components within a system and similarities within the same components between the two systems. The carrier biofilm had the highest bacterial diversity and relative abundance of nitrifying bacteria (3%) and denitrifying bacteria (24% of Rhodocyclaceae), which improved nitrogen removal of the system. An efficient N-removal duckweed system with enhanced microorganisms was established.
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Affiliation(s)
- Yonggui Zhao
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China; Institute of Environmental Sciences and Ecological Restoration, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yanling Jin
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China.
| | - Jun Huang
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China.
| | - Xinrong Ma
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China.
| | - Kaize He
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China.
| | - Zhiming He
- Yunnan Light Industrial Academy of Science, Kunming 650034, China.
| | - Feng Wang
- Chengdu Gusheng Technology Development Co. Ltd., Chengdu 610041, China.
| | - Hai Zhao
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China.
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21
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Tsementzi D, Poretsky R, Rodriguez-R LM, Luo C, Konstantinidis KT. Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:640-655. [PMID: 25756118 DOI: 10.1111/1758-2229.12180] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Metatranscriptomics of environmental samples enables the identification of community activities without a priori knowledge of taxonomic or functional composition. However, several technical challenges associated with the RNA preparation protocols can affect the relative representation of transcripts and data interpretation. Here, seven replicate metatranscriptomes from planktonic freshwater samples (Lake Lanier, USA) were sequenced to evaluate technical and biological reproducibility of different RNA extraction protocols. Organic versus bead-beating extraction showed significant enrichment for low versus high G + C% mRNA populations respectively. The sequencing data were best modelled by a negative binomial distribution to account for the large technical and biological variation observed. Despite the variation, the transcriptional activities of populations that persisted in year-round metagenomes from the same site consistently showed distinct expression patterns, reflecting different ecologic strategies and allowing us to test prevailing models on the contribution of both rare biosphere and abundant members to community activity. For instance, abundant members of the Verrucomicrobia phylum systematically showed low transcriptional activity compared with other abundant taxa. Our results provide a practical guide to the analysis of metatranscriptomes and advance understanding of the activity and ecology of abundant and rare members of temperate freshwater microbial communities.
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22
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Zhao Y, Fang Y, Jin Y, Huang J, Bao S, Fu T, He Z, Wang F, Zhao H. Potential of duckweed in the conversion of wastewater nutrients to valuable biomass: a pilot-scale comparison with water hyacinth. BIORESOURCE TECHNOLOGY 2014; 163:82-91. [PMID: 24787320 DOI: 10.1016/j.biortech.2014.04.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 04/04/2014] [Accepted: 04/05/2014] [Indexed: 05/15/2023]
Abstract
The application potential of duckweed (Lemna japonica 0234) and water hyacinth (Eichhornia crassipes) were compared in two pilot-scale wastewater treatment systems for more than one year. The results indicated duckweed had the same total nitrogen (TN) recovery rate as water hyacinth (0.4 g/m(2)/d) and a slightly lower total phosphorus (TP) recovery rate (approximately 0.1g/m(2)/d) even though its biomass production was half that of water hyacinth. The higher content of crude protein (33.34%), amino acids (25.80%), starch (40.19%), phosphorus (1.24%), flavonoids (2.91%) and lower fiber content provided duckweed with more advantages in resource utilization. Additionally, microbial community discovered by 454 pyrosequencing indicated that less nitrifying bacteria and more nitrogen-fixing bacteria in rhizosphere of duckweed provided it with higher nitrogen recovery efficiency (60%) than water hyacinth (47%). Under the presented condition, duckweed has more application advantages than water hyacinth because it more effectively converted the wastewater nutrients into valuable biomass.
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Affiliation(s)
- Yonggui Zhao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yang Fang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
| | - Yanling Jin
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
| | - Jun Huang
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
| | - Shu Bao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Tian Fu
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
| | - Zhiming He
- Yunnan Light Industrial Academy of Science, Kunming 650034, China.
| | - Feng Wang
- Chengdu Gusheng Technology Development Co. Ltd., Chengdu 610041, China.
| | - Hai Zhao
- Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences (CAS), Chengdu 610041, China; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu 610041, China.
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Okazaki K, Iino T, Kuroda Y, Taguchi K, Takahashi H, Ohwada T, Tsurumaru H, Okubo T, Minamisawa K, Ikeda S. An assessment of the diversity of culturable bacteria from main root of sugar beet. Microbes Environ 2014; 29:220-3. [PMID: 24789987 PMCID: PMC4103529 DOI: 10.1264/jsme2.me13182] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The partial sequences of the 16S rRNA genes of 531 bacteria isolated from the main root of the sugar beet (Beta vulgaris L.) were determined and subsequently grouped into 155 operational taxonomic units by clustering analysis (≥99% identity). The most abundant phylum was Proteobacteria (72.5–77.2%), followed by Actinobacteria (9.8–16.6%) and Bacteroidetes (4.3– 15.4%). Alphaproteobacteria (46.7–64.8%) was the most dominant class within Proteobacteria. Four strains belonging to Verrucomicrobia were also isolated. Phylogenetic analysis revealed that the Verrucomicrobia bacterial strains were closely related to Haloferula or Verrucomicrobium.
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Affiliation(s)
- Kazuyuki Okazaki
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization
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24
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Fabisch M, Beulig F, Akob DM, Küsel K. Surprising abundance of Gallionella-related iron oxidizers in creek sediments at pH 4.4 or at high heavy metal concentrations. Front Microbiol 2013; 4:390. [PMID: 24385973 PMCID: PMC3866512 DOI: 10.3389/fmicb.2013.00390] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/29/2013] [Indexed: 11/13/2022] Open
Abstract
We identified and quantified abundant iron-oxidizing bacteria (FeOB) at three iron-rich, metal-contaminated creek sites with increasing sediment pH from extremely acidic (R1, pH 2.7), to moderately acidic (R2, pH 4.4), to slightly acidic (R3, pH 6.3) in a former uranium-mining district. The geochemical parameters showed little variations over the 1.5 year study period. The highest metal concentrations found in creek sediments always coincided with the lowest metal concentrations in creek water at the slightly acidic site R3. Sequential extractions of R3 sediment revealed large portions of heavy metals (Ni, Cu, Zn, Pb, U) bound to the iron oxide fraction. Light microscopy of glass slides exposed in creeks detected twisted stalks characteristic of microaerobic FeOB of the family Gallionellaceae at R3 but also at the acidic site R2. Sequences related to FeOB such as Gallionella ferruginea, Sideroxydans sp. CL21, Ferritrophicum radicicola, and Acidovorax sp. BrG1 were identified in the sediments. The highest fraction of clone sequences similar to the acidophilic "Ferrovum myxofaciens" was detected in R1. Quantitative PCR using primer sets specific for Gallionella spp., Sideroxydans spp., and "Ferrovum myxofaciens" revealed that ~72% (R2 sediment) and 37% (R3 sediment) of total bacterial 16S rRNA gene copies could be assigned to groups of FeOB with dominance of microaerobic Gallionella spp. at both sites. Gallionella spp. had similar and very high absolute and relative gene copy numbers in both sediment communities. Thus, Gallionella-like organisms appear to exhibit a greater acid and metal tolerance than shown before. Microaerobic FeOB from R3 creek sediment enriched in newly developed metal gradient tubes tolerated metal concentrations of 35 mM Co, 24 mM Ni, and 1.3 mM Cd, higher than those in sediments. Our results will extend the limited knowledge of FeOB at contaminated, moderately to slightly acidic environments.
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Affiliation(s)
- Maria Fabisch
- Aquatic Geomicrobiology Group, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
| | - Felix Beulig
- Aquatic Geomicrobiology Group, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
| | - Denise M. Akob
- Aquatic Geomicrobiology Group, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
- U.S. Geological Survey, National Research ProgramReston, VA, USA
| | - Kirsten Küsel
- Aquatic Geomicrobiology Group, Institute of Ecology, Friedrich Schiller University JenaJena, Germany
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25
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From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules. Antonie van Leeuwenhoek 2013; 104:551-67. [PMID: 23982431 DOI: 10.1007/s10482-013-0007-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/14/2013] [Indexed: 01/19/2023]
Abstract
Most members of the phylum Planctomycetes share many unusual traits that are unique for bacteria, since they divide independent of FtsZ through asymmetric budding, possess a complex life cycle and comprise a compartmentalized cell plan. Besides their complex cell biological features Planctomycetes are environmentally important and play major roles in global matter fluxes. Such features have been successfully employed in biotechnological applications such as the anaerobic oxidation of ammonium in wastewater treatment plants or the utilization of enzymes for biotechnological processes. However, little is known about planctomycetal secondary metabolites. This is surprising as Planctomycetes have several key features in common with known producers of small bioactive molecules such as Streptomycetes or Myxobacteria: a complex life style and large genome sizes. Planctomycetal genomes with an average size of 6.9 MB appear as tempting targets for drug discovery approaches. To enable the hunt for bioactive molecules from Planctomycetes, we performed a comprehensive genome mining approach employing the antiSMASH secondary metabolite identification pipeline and found 102 candidate genes or clusters within the analyzed 13 genomes. However, as most genes and operons related to secondary metabolite production are exclusively expressed under certain environmental conditions, we optimized Phenotype MicroArray protocols for Rhodopirellula baltica and Planctomyces limnophilus to allow high throughput screening of putative stimulating carbon sources. Our results point towards a previously postulated relationship of Planctomycetes with algae or plants, which secrete compounds that might serve as trigger to stimulate the secondary metabolite production in Planctomycetes. Thus, this study provides the necessary starting point to explore planctomycetal small molecules for drug development.
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Tanaka Y, Tamaki H, Matsuzawa H, Nigaya M, Mori K, Kamagata Y. Microbial community analysis in the roots of aquatic plants and isolation of novel microbes including an organism of the candidate phylum OP10. Microbes Environ 2012; 27:149-57. [PMID: 22791047 PMCID: PMC4036017 DOI: 10.1264/jsme2.me11288] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A number of molecular ecological studies have revealed complex and unique microbial communities in various terrestrial plant roots; however, little is known about the microbial communities of aquatic plant roots in spite of their potential use for water quality improvement in aquatic environments (e.g. floating treatment wetland system). Here, we report the microbial communities inhabiting the roots of emerged plants, reed (Phragmites australis) and Japanese loosestrife (Lythrum anceps), collected from a floating treatment wetland in a pond by both culture-independent and culture-dependent approaches. Culture-independent analysis based on 16S rRNA gene sequences revealed that the microbial compositions between the two aquatic plant roots were clearly different (e.g. the predominant microbe was Betaproteobacteria for reed and Alphaproteobacteria for Japanese loosestrife). In comparisons of microbial communities between the plant roots and pond water taken from near the plants, the microbial diversity in the plant roots (e.g. 4.40-4.26 Shannon-Weiner index) were higher than that of pond water (e.g. 3.15 Shannon-Weiner index). Furthermore, the plant roots harbored 2.5-3.5 times more phylogenetically novel clone phylotypes than pond water. The culture-dependent approach also revealed differences in the microbial composition and diversity among the two plant roots and pond water. More importantly, compared to pond water, we succeeded in isolating approximately two times more novel isolate phylotypes, including a bacterium of candidate phylum OP10 (recently named Armatimonadetes) from the plant roots. These findings suggest that aquatic plants roots are significant sources for a variety of novel organisms.
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Affiliation(s)
- Yasuhiro Tanaka
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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Wang Y, Hayatsu M, Fujii T. Extraction of bacterial RNA from soil: challenges and solutions. Microbes Environ 2012; 27:111-21. [PMID: 22791042 PMCID: PMC4036013 DOI: 10.1264/jsme2.me11304] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Detection of bacterial gene expression in soil emerged in the early 1990s and provided information on bacterial responses in their original soil environments. As a key procedure in the detection, extraction of bacterial RNA from soil has attracted much interest, and many methods of soil RNA extraction have been reported in the past 20 years. In addition to various RT-PCR-based technologies, new technologies for gene expression analysis, such as microarrays and high-throughput sequencing technologies, have recently been applied to examine bacterial gene expression in soil. These technologies are driving improvements in RNA extraction protocols. In this mini-review, progress in the extraction of bacterial RNA from soil is summarized with emphasis on the major difficulties in the development of methodologies and corresponding strategies to overcome them.
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Affiliation(s)
- Yong Wang
- Environmental Biofunction Division, National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan.
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28
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Puspita ID, Kamagata Y, Tanaka M, Asano K, Nakatsu CH. Are uncultivated bacteria really uncultivable? Microbes Environ 2012; 27:356-66. [PMID: 23059723 PMCID: PMC4103542 DOI: 10.1264/jsme2.me12092] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 06/20/2012] [Indexed: 11/16/2022] Open
Abstract
Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency.
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Affiliation(s)
- Indun Dewi Puspita
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2–17 Tsukisamu-Higashi, Toyohira, Sapporo, Hokkaido 062–8517,
Japan
| | - Michiko Tanaka
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
| | - Kozo Asano
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
| | - Cindy H. Nakatsu
- Graduate School of Agriculture, Hokkaido University, N9 W9, Kita-ku, Sapporo, Hokkaido 060–8589,
Japan
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907,
USA
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29
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Subrahmanyam G, Vaghela R, Bhatt NP, Archana G. Carbonate-dissolving bacteria from 'miliolite', a bioclastic limestone, from Gopnath, Gujarat, Western India. Microbes Environ 2012; 27:334-7. [PMID: 22446314 PMCID: PMC4036042 DOI: 10.1264/jsme2.me11347] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In the present investigation, the abundance and molecular phylogeny of part of the culturable bacterial population involved in the dissolution of “miliolite”, a bioclastic limestone, from Gopnath, India, was studied. Carbonate-dissolving bacteria were isolated, enumerated and screened for their ability to dissolve miliolite. Amplified ribosomal DNA restriction analysis (ARDRA) indicated 14 operational taxonomic units (OTUs) to be distributed in 5 different clades at a similarity coefficient of 0.85. Then, 16S rRNA sequence analysis helped to decipher that the majority of carbonate-dissolving bacteria were affiliated to phyla Firmicutes (Families Bacillaceae and Staphylococcaceae) and Actinobacteria (Family Promicromonosporaceae) indicating their role in miliolite weathering.
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Affiliation(s)
- Gangavarapu Subrahmanyam
- Department of Microbiology & Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara-390002, Gujarat, India
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Fujii K, Kuwahara A, Nakamura K, Yamashita Y. Development of a simple cultivation method for isolating hitherto-uncultured cellulase-producing microbes. Appl Microbiol Biotechnol 2011; 91:1183-92. [DOI: 10.1007/s00253-011-3376-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 05/02/2011] [Accepted: 05/03/2011] [Indexed: 11/30/2022]
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