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Nemr RA, Patz S, Abdelwakeel SM, Khalil M, Ben Djadid A, Abdelfadeel MR, Morsi AT, Goda HA, Youssef HH, Hamza M, Abbas M, Fayez M, El-Sahhar KF, Becker M, Ruppel S, Hegazi NA. Culture Media Based on Leaf Strips/Root Segments Create Compatible Host/Organ Setup for in vitro Cultivation of Plant Microbiota. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.660790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Plant microbiota have co-evolved with their associated plants in the entire holobiont, and their assemblages support diversity and productivity on our planet. Of importance is in vitro cultivation and identification of their hub taxa for possible core microbiome modification. Recently, we introduced the in situ-similis culturing strategy, based on the use of plant leaves as a platform for in vitro growth of plant microbiota. Here, the strategy is further extended by exploring plant organ compatible cultivation of plant microbiota when grown on corresponding leaf/root-based culture media. Pooling the advantages of MPN enrichment methodology together with natural plant-only-based culture media, the introduced method efficiently constructed a nutritional milieu governed by vegan nutrients of plant origin, i.e., leaf strips/root segments, immersed in plain semi-solid water agar. MPN estimates exceeded log 7.0 and 4.0 g−1 of endo-rhizosphere and endo-phyllosphere, respectively, of maize and sunflower; being proportionate to those obtained for standard culture media. With sunflower, PCR-DGGE analyses indicated divergence in community composition of cultivable endophytes primarily attributed to culture media, signaling a certain degree of plant organ affinity/compatibility. Based on 16S rRNA gene sequencing of bacterial isolates, 20 genera comprising 32 potential species were enriched; belonged to Bacteroidetes, Firmicutes, and Alpha-/Gammaproteobacteria. The described cultivation strategy furnished diversified nutritive platform in terms of homologous/heterologous plant organ-based medium and ambient/limited oxygenic cultivation procedure. Duly, cultivability extended to > 8 genera: Bosea, Brevundimonas, Chitinophaga, Pseudoxanthomonas, Sphingobacterium Caulobacter, Scandinavium, and Starkeya; the latter three genera were not yet reported for Sunflower, and possible unknown species or even one new putative genus. Thus, both potential members of the major microbiome and rare isolates of satellite microbiomes can be isolated using the presented method. It is a feasible addition to traditional cultivation methods to explore new potential resources of PGPB for future biotechnological applications.
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Abstract
The brines of natural salt lakes with total salt concentrations exceeding 30% are often colored red by dense communities of halophilic microorganisms. Such red brines are found in the north arm of Great Salt Lake, Utah, in the alkaline hypersaline lakes of the African Rift Valley, and in the crystallizer ponds of coastal and inland salterns where salt is produced by evaporation of seawater or some other source of saline water. Red blooms were also reported in the Dead Sea in the past. Different types of pigmented microorganisms may contribute to the coloration of the brines. The most important are the halophilic archaea of the class Halobacteria that contain bacterioruberin carotenoids as well as bacteriorhodopsin and other retinal pigments, β-carotene-rich species of the unicellular green algal genus Dunaliella and bacteria of the genus Salinibacter (class Rhodothermia) that contain the carotenoid salinixanthin and the retinal protein xanthorhodopsin. Densities of prokaryotes in red brines often exceed 2-3×107 cells/mL. I here review the information on the biota of the red brines, the interactions between the organisms present, as well as the possible roles of the red halophilic microorganisms in the salt production process and some applied aspects of carotenoids and retinal proteins produced by the different types of halophiles inhabiting the red brines.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Goh F, Allen MA, Leuko S, Kawaguchi T, Decho AW, Burns BP, Neilan BA. Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay. ISME JOURNAL 2008; 3:383-96. [PMID: 19092864 DOI: 10.1038/ismej.2008.114] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The stromatolites at Shark Bay, Western Australia, are analogues of some of the oldest evidence of life on Earth. The aim of this study was to identify and spatially characterize the specific microbial communities associated with Shark Bay intertidal columnar stromatolites. Conventional culturing methods and construction of 16S rDNA clone libraries from community genomic DNA with both universal and specific PCR primers were employed. The estimated coverage, richness and diversity of stromatolite microbial populations were compared with earlier studies on these ecosystems. The estimated coverage for all clone libraries indicated that population coverage was comprehensive. Phylogenetic analyses of stromatolite and surrounding seawater sequences were performed in ARB with the Greengenes database of full-length non-chimaeric 16S rRNA genes. The communities identified exhibited extensive diversity. The most abundant sequences from the stromatolites were alpha- and gamma-proteobacteria (58%), whereas the cyanobacterial community was characterized by sequences related to the genera Euhalothece, Gloeocapsa, Gloeothece, Chroococcidiopsis, Dermocarpella, Acaryochloris, Geitlerinema and Schizothrix. All clones from the archaeal-specific clone libraries were related to the halophilic archaea; however, no archaeal sequence was identified from the surrounding seawater. Fluorescence in situ hybridization also revealed stromatolite surfaces to be dominated by unicellular cyanobacteria, in contrast to the sub-surface archaea and sulphate-reducing bacteria. This study is the first to compare the microbial composition of morphologically similar stromatolites over time and examine the spatial distribution of specific microorganismic groups in these intertidal structures and the surrounding seawater at Shark Bay. The results provide a platform for identifying the key microbial physiology groups and their potential roles in modern stromatolite morphogenesis and ecology.
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Affiliation(s)
- Falicia Goh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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Goh F, Leuko S, Allen MA, Bowman JP, Kamekura M, Neilan BA, Burns BP. Halococcus hamelinensis sp. nov., a novel halophilic archaeon isolated from stromatolites in Shark Bay, Australia. Int J Syst Evol Microbiol 2006; 56:1323-1329. [PMID: 16738110 DOI: 10.1099/ijs.0.64180-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several halophilic archaea belonging to the genus Halococcus were isolated from stromatolites from Hamelin Pool, Shark Bay, Western Australia, collected during field trips in 1996 and 2002. This is the first incidence of halophilic archaea being isolated from this environment. Stromatolites are biosedimentary structures that have been formed throughout the earth's evolutionary history and have been preserved in the geological record for over 3 billion years. The stromatolites from Hamelin Pool, Western Australia, are the only known example of extant stromatolites forming in hypersaline coastal environments. Based on their 16S rRNA gene sequences and morphology, the isolates belong to the genus Halococcus. Strain 100NA1, isolated from stromatolites collected in 2002, was closely related to strain 100A6(T) that was isolated from the stromatolites collected in 1996, with a DNA-DNA hybridization value of 94 +/- 8 %. DNA-DNA hybridization values of strain 100A6(T) with Halococcus morrhuae NRC 16008 and Halococcus saccharolyticus ATCC 49257(T) were 17 +/- 6 and 11 +/-7 %, respectively. The DNA G + C content of strain 100A6(T) was 60.5 mol% (T(m)). The main polar lipid was S-DGA-1, a sulphated glycolipid that has been detected in all strains of the genus Halococcus. Whole-cell protein profiles, enzyme composition and utilization of various carbon sources were distinct from those of all previously characterized Halococcus species. The recognition of this strain as representing a novel species within the genus Halococcus is justified, and the name Halococcus hamelinensis sp. nov. is proposed. The type strain is 100A6(T) (=JCM 12892(T) = ACM 5227(T)).
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Affiliation(s)
- Falicia Goh
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Stefan Leuko
- Australian Centre for Astrobiology, Macquarie University, Building E8C 153, Sydney, NSW 2109, Australia
| | - Michelle A Allen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - John P Bowman
- Australian Food Safety Centre, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia
| | - Masahiro Kamekura
- Noda Institute for Scientific Research, 399 Noda, Noda-shi, Chiba-ken 278-0037, Japan
| | - Brett A Neilan
- Australian Centre for Astrobiology, Macquarie University, Building E8C 153, Sydney, NSW 2109, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Brendan P Burns
- Australian Centre for Astrobiology, Macquarie University, Building E8C 153, Sydney, NSW 2109, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Bae JW, Rhee SK, Park JR, Kim BC, Park YH. Isolation of uncultivated anaerobic thermophiles from compost by supplementing cell extract of Geobacillus toebii in enrichment culture medium. Extremophiles 2005; 9:477-85. [PMID: 16041476 DOI: 10.1007/s00792-005-0467-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Accepted: 06/20/2005] [Indexed: 10/25/2022]
Abstract
Several researchers have reported that microorganisms can be cultivated only in the presence of other microorganisms. We suggest that a portion of uncultivated microorganisms might be cultivated in the presence of cellular components released from bacteria in their natural environments. In this study, the cell extract of Geobacillus toebii was used to enrich uncultivated thermophiles from compost. In the process of enrichment cultures, cell extract supplementation apparently changed the community composition. This change was monitored by PCR-DGGE targeting 16S rRNA gene. Five novel groups of microorganisms (similarity of 16S rRNA gene to the closest relative <96%) were specifically isolated from enrichment cultures by using cell extract-supplemented culture media. Their growth was found to be dependent on the addition of extract of G. toebii. Putting these findings together, we suggest that the extracts of bacteria could be one of the growth factors in the thermal ecosystem with a possibility of extending other ecological niches.
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Affiliation(s)
- Jin-Woo Bae
- Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Eundong 52, Yusong, Daejeon, Korea
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Improved Most-Probable-Number Method To Detect Sulfate-Reducing Bacteria with Natural Media and a Radiotracer. Appl Environ Microbiol 1998; 64:1700-7. [PMID: 9572939 PMCID: PMC106218 DOI: 10.1128/aem.64.5.1700-1707.1998] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A greatly improved most-probable-number (MPN) method for selective enumeration of sulfate-reducing bacteria (SRB) is described. The method is based on the use of natural media and radiolabeled sulfate (35SO42-). The natural media used consisted of anaerobically prepared sterilized sludge or sediment slurries obtained from sampling sites. The densities of SRB in sediment samples from Kysing Fjord (Denmark) and activated sludge were determined by using a normal MPN (N-MPN) method with synthetic cultivation media and a tracer MPN (T-MPN) method with natural media. The T-MPN method with natural media always yielded significantly higher (100- to 1,000-fold-higher) MPN values than the N-MPN method with synthetic media. The recovery of SRB from environmental samples was investigated by simultaneously measuring sulfate reduction rates (by a 35S-radiotracer method) and bacterial counts by using the T-MPN and N-MPN methods, respectively. When bacterial numbers estimated by the T-MPN method with natural media were used, specific sulfate reduction rates (qSO42-) of 10(-14) to 10(-13) mol of SO42- cell-1 day-1 were calculated, which is within the range of qSO42- values previously reported for pure cultures of SRB (10(-15) to 10(-14) mol of SO42- cell-1 day-1). qSO42- values calculated from N-MPN values obtained with synthetic media were several orders of magnitude higher (2 x 10(-10) to 7 x 10(-10) mol of SO42- cell-1 day-1), showing that viable counts of SRB were seriously underestimated when standard enumeration media were used. Our results demonstrate that the use of natural media results in significant improvements in estimates of the true numbers of SRB in environmental samples.
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Characterization of the halophilic archaeal community in saltern crystallizer ponds by means of polar lipid analysis. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf01990639] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Oren A, Gurevich P. Characterization of the dominant halophilic archaea in a bacterial bloom in the dead sea. FEMS Microbiol Ecol 1993. [DOI: 10.1111/j.1574-6941.1993.tb00037.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Oren A. The use of protein synthesis inhibitors in the estimation of the contribution of halophilic archaebacteria to bacterial activity in hypersaline environments. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb03940.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Oren A. Estimation of the contribution of halobacterial to the bacterial biomass and activity in solar salterns by the use of bile salts. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb03923.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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