Diversity and biotechnological potential of culturable bacteria from Brazilian mangrove sediment
14 Mar 2009-World Journal of Microbiology & Biotechnology (Springer Netherlands)-Vol. 25, Iss: 7, pp 1305-1311
TL;DR: The diversity of culturable bacteria present over the seasons at two depths in a mangrove sediment and in a transect area from the land to the sea is assessed.
Abstract: Mangrove ecosystems are environments subject to substantial degradation by anthropogenic activities. Its location, in coastal area, interfacing the continents and the oceans makes it substantially important in the prospection for biotechnological applications. In this study, we assessed the diversity of culturable bacteria present over the seasons at two depths (0–10 and 30–40 cm) in a mangrove sediment and in a transect area from the land to the sea. In total, 238 bacteria were isolated, characterized by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and further identified, by Fatty Acid Methyl Esther (FAME-MIDI), into the orders of Vibrionales, Actinomycetales and Bacillales. Also the ability of the isolates in producing economically important enzymes (amylases, proteases, esterases and lipases) was evaluated and the order Vibrionales was the main enzymatic source.
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TL;DR: A deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology revealed that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteria.
Abstract: Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments.
229 citations
Cites background from "Diversity and biotechnological pote..."
...More specifically, researches conducted by our group are based on mangrove sediments along the coastline of Sao Paulo State in Brazil, where several descriptions of the microbiology found in mangrove were made based on culture-dependent [12] and culture-independent approaches [13,20]; see these references for descriptions of the chemical and physical features of the analysed mangroves....
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TL;DR: The present paper makes an attempt to review the microbial diversity in mangrove ecosystems and explore their potential applications in various fields such as agriculture, pharmaceutical, industrial, environmental and medical sciences.
Abstract: Mangrove forests occurring at the interface of terrestrial and marine ecosystems represent a rich biological diversity of plants, animals and microorganisms. Microbes, being an important component of the mangrove environment, not only play a very critical role in creating and maintaining this biosphere but also serve as a source of biotechnologically valuable and important products. By participating in various steps of decomposition and mineralization of leaf litter, microbes make an essential contribution to the productivity of the mangrove ecosystem. They able to recycle nutrients, produce and consume gases that affect global climate, destroy pollutants, treat anthropogenic wastes and can also be used for biological control of plant and animal pests. Microorganisms from mangrove environments are a major source of antimicrobial agents and also produce a wide range of important medicinal compounds, including enzymes, antitumor agents, insecticides, vitamins, immunosuppressants, and immune modulators. However, the phylogenetic and functional description of microbial diversity in mangrove ecosystems has not been addressed to the same extent as for other environments. Even though the mangrove ecosystem is very rich in microbial diversity, less than 5% of species have been described; in many cases neither their ecological role nor their application potential is known. Recently developed technologies in molecular biology and genetics offer great promise to explore the potential of microbial diversity. Hence, the present paper makes an attempt to review the microbial diversity in mangrove ecosystems and explore their potential applications in various fields such as agriculture, pharmaceutical, industrial, environmental and medical sciences.
179 citations
Cites background from "Diversity and biotechnological pote..."
...…sp. Industrial application Mishra 2010 Amylase, protease, esterase and lipases Vibrionales, Actinomycetales and Bacillales Industrial application Armando et al. 2009 Phytase Bacillus circulans, B. licheniformis, B. pantothenicus Industrial application Joseph and Paul Raj 2007 Lipopeptides and…...
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TL;DR: The results indicated that the culturable halophilic/halotolerant bacteria inhabiting salty and arid ecosystems have a potential to contribute to promoting plant growth under the harsh salinity and drought conditions.
Abstract: Soil salinity and drought are among the environmental stresses that most severely affect plant growth and production around the world. In this study the rhizospheres of Salicornia plants and bulk soils were collected from Sebkhet and Chott hypersaline ecosystems in Tunisia. Depiction of bacterial microbiome composition by Denaturing Gradient Gel Electrophoresis unveiled the occurrence of a high bacterial diversity associated with Salicornia root system. A large collection of 475 halophilic and halotolerant bacteria was established from Salicornia rhizosphere and the surrounding bulk soil, and the bacteria were characterized for the resistance to temperature, osmotic and saline stresses, and plant growth promotion (PGP) features. Twenty Halomonas strains showed resistance to a wide set of abiotic stresses and were able to perform different PGP activities in vitro at 5% NaCl, including ammonia and indole-3-acetic acid production, phosphate solubilisation, and potential nitrogen fixation. By using a gfp-labelled strain it was possible to demonstrate that Halomonas is capable of successfully colonising Salicornia roots in the laboratory conditions. Our results indicated that the culturable halophilic/halotolerant bacteria inhabiting salty and arid ecosystems have a potential to contribute to promoting plant growth under the harsh salinity and drought conditions. These halophilic/halotolerant strains could be exploited in biofertilizer formulates to sustain crop production in degraded and arid lands.
153 citations
Cites background from "Diversity and biotechnological pote..."
...Both Oceanobacillus picturae, and Nesterenkonia halobia were previously isolated from a different saline ecosystem, namely, mangrove sediments [43, 44], where O....
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TL;DR: Two Gram (+) bacterial strains, BSB6 and BSB12, showing resistance and potential for Se(IV) reduction among 26 moderately halotolerant isolates from the Bhitarkanika mangrove soil were characterized by biochemical and 16S rDNA sequence analyses.
127 citations
TL;DR: This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings.
Abstract: Actinobacteria are one of the most important and efficient groups of natural metabolite producers. The genus Streptomyces have been recognized as prolific producers of useful natural compounds as they produced more than half of the naturally-occurring antibiotics isolated to-date and continue as the primary source of new bioactive compounds. Lately, Streptomyces groups isolated from different environments produced the same types of compound, possibly due to frequent genetic exchanges between species. As a result, there is a dramatic increase in demand to look for new compounds which have pharmacological properties from another group of Actinobacteria, known as rare actinobacteria; which is isolated from special environments such as mangrove. Recently, mangrove ecosystem is becoming a hot spot for studies of bioactivities and the discovery of natural products. Many novel compounds discovered from the novel rare actinobacteria have been proven as potential new drugs in medical and pharmaceutical industries such as antibiotics, antimicrobials, antibacterials, anticancer, and antifungals. This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings.
125 citations
Cites background from "Diversity and biotechnological pote..."
...Different genera such as Brevibacterium, Dermabacter, Kytococcus, Microbacterium, Nesterenkonia, and Rothia were isolated from mangrove sediments in Brazil (Dias et al., 2009b)....
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...The metagenomic data from Thompson et al. (2013) showed similar predominant bacterial phyla in two different mangrove areas in Brazil, namely Rio de Janeiro and Bahia; were Proteobacteria (57.8% and 44.6%), Firmicutes (11% and 12.3%), and Actinobacteria (8.4% and 7.5%)....
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...The description of mangrove microbiology has been made on the basis of pyrosequencing, based on DNA extracted directly from the sediment of four distinct mangrove areas along the coast of the Sao Paulo State in Brazil (Andreote et al., 2012)....
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References
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Book•
01 Jan 1994
TL;DR: Methodology for General and Molecular Microbiology Morphology Light microscopy Determinative and cytological light microscopy Electron microscopy Cell fractionation Antigen-antibody reactions Growth: Physicochemical factors in growth Nutrition and media Enrichment and isolation Solid, liquid/solid and semisolid culture Liquid culture Growth measurement Culture preservation Molecular Genetics: Gene mutation Gene transfer in Gram-negative bacteria Gene transferIn Gram-positive bacteria Plasmids Transposon mutagenesis
Abstract: Methodology for General and Molecular Microbiology Morphology Light microscopy Determinative and cytological light microscopy Electron microscopy Cell fractionation Antigen-antibody reactions Growth: Physicochemical factors in growth Nutrition and media Enrichment and isolation Solid, liquid/solid and semisolid culture Liquid culture Growth measurement Culture preservation Molecular Genetics: Gene mutation Gene transfer in Gram-negative bacteria Gene transfer in Gram-positive bacteria Plasmids Transposon mutagenesis Gene cloning and expression Polymerase chain reaction Nucleic acid analysis Metabolism: Physical analysis Chemical analysis Enzymatic activity Permeability and transport Systematics: Phenotypic characterization DNA sequence similarities Ribosomal RNA hybridization and gene sequencing Nucleic acid probes General Methods: Laboratory safety Photography Records and reports
3,742 citations
TL;DR: A group-specific primer, F243 (positions 226 to 243, Escherichia coli numbering), was developed by comparison of sequences of genes encoding 16S rRNA for the detection of actinomycetes in the environment with PCR and temperature or denaturing gradient gel electrophoresis (TGGE or DGGE, respectively).
Abstract: A group-specific primer, F243 (positions 226 to 243, Escherichia coli numbering), was developed by comparison of sequences of genes encoding 16S rRNA (16S rDNA) for the detection of actinomycetes in the environment with PCR and temperature or denaturing gradient gel electrophoresis (TGGE or DGGE, respectively). The specificity of the forward primer in combination with different reverse ones was tested with genomic DNA from a variety of bacterial strains. Most actinomycetes investigated could be separated by TGGE and DGGE, with both techniques giving similar results. Two strategies were employed to study natural microbial communities. First, we used the selective amplification of actinomycete sequences (E. coli positions 226 to 528) for direct analysis of the products in denaturing gradients. Second, a nested PCR providing actinomycete-specific fragments (E. coli positions 226 to 1401) was used which served as template for a PCR when conserved primers were used. The products (E. coli positions 968 to 1401) of this indirect approach were then separated by use of gradient gels. Both approaches allowed detection of actinomycete communities in soil. The second strategy allowed the estimation of the relative abundance of actinomycetes within the bacterial community. Mixtures of PCR-derived 16S rDNA fragments were used as model communities consisting of five actinomycetes and five other bacterial species. Actinomycete products were obtained over a 100-fold dilution range of the actinomycete DNA in the model community by specific PCR; detection of the diluted actinomycete DNA was not possible when conserved primers were used. The methods tested for detection were applied to monitor actinomycete community changes in potato rhizosphere and to investigate actinomycete diversity in different soils.
1,433 citations
"Diversity and biotechnological pote..." refers methods in this paper
...The 16S rDNA gene was amplified from DNA extracted from each strain using the primers 27F and 1378R (Heuer et al. 1997)....
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TL;DR: Vibrios harbour a wealth of diverse genomes as revealed by different genomic techniques including amplified fragment length polymorphism, multilocus sequence typing, repetetive extragenic palindrome PCR, ribotyping, and whole-genome sequencing, which are probably important driving forces in the evolution and speciation of vibrios.
Abstract: Vibrios are ubiquitous and abundant in the aquatic environment. A high abundance of vibrios is also detected in tissues and/or organs of various marine algae and animals, e.g., abalones, bivalves, corals, fish, shrimp, sponges, squid, and zooplankton. Vibrios harbour a wealth of diverse genomes as revealed by different genomic techniques including amplified fragment length polymorphism, multilocus sequence typing, repetetive extragenic palindrome PCR, ribotyping, and whole-genome sequencing. The 74 species of this group are distributed among four different families, i.e., Enterovibrionaceae, Photobacteriaceae, Salinivibrionaceae, and Vibrionaceae. Two new genera, i.e., Enterovibrio norvegicus and Grimontia hollisae, and 20 novel species, i.e., Enterovibrio coralii, Photobacterium eurosenbergii, V. brasiliensis, V. chagasii, V. coralliillyticus, V. crassostreae, V. fortis, V. gallicus, V. hepatarius, V. hispanicus, V. kanaloaei, V. neonatus, V. neptunius, V. pomeroyi, V. pacinii, V. rotiferianus, V. superstes, V. tasmaniensis, V. ezurae, and V. xuii, have been described in the last few years. Comparative genome analyses have already revealed a variety of genomic events, including mutations, chromosomal rearrangements, loss of genes by decay or deletion, and gene acquisitions through duplication or horizontal transfer (e.g., in the acquisition of bacteriophages, pathogenicity islands, and super-integrons), that are probably important driving forces in the evolution and speciation of vibrios. Whole-genome sequencing and comparative genomics through the application of, e.g., microarrays will facilitate the investigation of the gene repertoire at the species level. Based on such new genomic information, the taxonomy and the species concept for vibrios will be reviewed in the next years.
1,136 citations
"Diversity and biotechnological pote..." refers background in this paper
...The order Vibrionales was previously described from marine environments responding to variations in weather or to environmental factors such as salinity (Thompson et al. 2004; Sousa et al. 2006)....
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...The bacterial groups that were detected in the mangrove sediment are commonly found in marine and estuarine environments (Holguin and Bashan 1996; Thompson et al. 2004; Sousa et al. 2006; Stevens et al. 2007)....
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TL;DR: It is shown that the lipase formation of various strains is adaptive, and is demonstrated by adding water-soluble Tweens to a nutrient medium, which is necessary in those cases in which the formation of lipase is adaptive.
Abstract: A simple method to detect lipolytic activity of micro-organisms is described. The formation of lipase is demonstrated by adding water-soluble Tweens to a nutrient medium. Around the colonies with lipolytic activity there appears a well visible halo which is due to crystals of the calcium salt of the fatty acid liberated by lipolysis. The three chief advantages of the use of Tweens are that:
1.
there is an optimum contact between the growing cells and the fatty substrate, which is necessary in those cases in which the formation of lipase is adaptive.
2.
they can be used in studies on the specificity of the lipase.
3.
the results are directly visible.
792 citations
"Diversity and biotechnological pote..." refers background or methods in this paper
...The presence of a degradation zone was noted after bacterial growth (Sierra 1957)....
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...Determination of esterase activity Esterase activity was detected using a culture medium described by Sierra (1957)....
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...Esterase activity was detected using a culture medium described by Sierra (1957) ....
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...In order to detect lipolytic activity, a similar methodology was used as described above for esterase activity, with the exception that Tween 80 was replaced by Tween 20. The presence of a degradation zone was noted after bacterial growth ( Sierra 1957 )....
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TL;DR: Solid media are described on which the production of the extracellular enzymes amylase, lipase, DNA- and RNAase, pectinase, protease, urease, and chitinase were detected.
Abstract: Solid media are described on which the production of the extracellular enzymes amylase, lipase, DNA- and RNAase, pectinase, protease, urease, and chitinase were detected. The media were tested with...
644 citations
Additional excerpts
...After bacterial growth, 5 ml of 1% iodine solution was added to each plate and the presence of a stainless zone around the colony indicated amylase production (Hankin and Anagnostakis 1975)....
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