Isolation of bacteria capable of growth with 2-methylisoborneol and geosmin as the sole carbon and energy sources

Undesirable odour substances (geosmin and 2-methylisoborneol) in water environment: Sources, impacts and removal strategies

Off-flavours in fish products generated from recirculating aquaculture systems (RAS) are a major problem in the fish farming industry affecting the market demand and prices. A particular concern is the muddy or musty odour and taste in fish due to the presence of secondary metabolites geosmin and 2-methylisoborneol (2-MIB), produced by actinobacteria (mainly Streptomyces), myxobacteria and cyanobacteria. Off-flavours have deteriorated the quality of fish, rendering their products unfit for human consumption. The process of odour removal requires purification for several days to weeks in clean water; thus this leads to additional production costs. Geosmin and 2-MIB, detected at extremely low odour thresholds, are the most widespread off-flavour metabolites in aquaculture, entering through fish gills and accumulating in the fish adipose tissues. In this review, we aimed to determine the diversity and identity of geosmin- and 2-MIB-producing bacteria in aquaculture and provide possible strategies for their elimination.

Occurrences of 2-methylisoborneol and geosmin -degrading bacteria in a eutrophic reservoir and the role of cell-bound versus dissolved fractions

As taste-and-odor outbreaks are common in surface waters worldwide, extensive studies have focused on the identification of microorganisms involved in the production of 2-methylisoborneol (MIB) and geosmin (GSM). However, fewer studies have tried to identify potential degraders in natural environments. Eagle Creek Reservoir, a temperate and eutrophic water body, experienced two major seasonal odorous outbreaks in 2013 with maximal concentrations of 99.1 (MIB) and 77.3 ng L^-1 (GSM). Fractionation analyses of the odorous compounds showed that MIB was found more frequently in the dissolved fraction while GSM was mostly cell-bound. This difference likely impacts taste-and-odor (T&O) compound susceptibility to biodegradation by bacteria. Spearman relationships of epilimnetic samples collected between spring and early fall linked dissolved MIB occurrences to higher abundances of Bacteroidetes like Flavobacterium resistens, F. granuli, F. saliperosum (p < 0.001), F. kamogawaensis (p < 0.01) capable of MIB degradation. Occurrences of cell-bound GSM were correlated to two α-Proteobacteria Novosphingobium hassiacum (p < 0.001) and Sphingomonas oligophenolica (p < 0.01), both identified as potential degraders of GSM. The roles of Pseudomonas and Bacillus were ambiguous, and these genera might have been involved in both compound biodegradations (p < 0.05).

Biofloc Systems for Sustainable Production of Economically Important Aquatic Species: A Review

The increasing global population has led to an increase in food demand; consequently, aquaculture is one of the food production sectors that has offered opportunities to alleviate hunger, malnutrition, and poverty. However, the development of a sustainable aquaculture industry has been hindered by the limited availability of natural resources as well as its negative impact on the surrounding environment. Hence, there is an urgent need to search for better aquacultural production systems that, despite their high productivity and profitability, utilize fewer resources such as water, energy, land, and capital in conjunction with a negligible impact on the environment. Biofloc technology (BFT) is one of the most exciting and promising sustainable aquaculture systems; it takes into account the intensive culture of aquatic species, zero water exchange, and improved water quality as a result of beneficial microbial biomass activity, which, at the same time, can be utilized as a nutritious aquaculture feed, thus lowering the costs of production. Furthermore, BFT permits the installation of integrated multi-trophic aquaculture (IMTA) systems in which the wastes of one organism are utilized as feed by another organism, without a detrimental effect on co-cultured species. This review, therefore, highlights the basics of BFT, factors associated with BFT for the successful production of aquatic species, the significance of this food production system for the sustainable production of economically important aquatic species, its economic aspects, drawbacks, limitations, and recommended management aspects for sustainable aquaculture.

A novel cyanobacterial geosmin producer, revising GeoA distribution and dispersion patterns in Bacteria

Cyanobacteria are ubiquitous organisms with a relevant contribution to primary production in all range of habitats. Cyanobacteria are well known for their part in worldwide occurrence of aquatic blooms while producing a myriad of natural compounds, some with toxic potential, but others of high economical impact, as geosmin. We performed an environmental survey of cyanobacterial soil colonies to identify interesting metabolic pathways and adaptation strategies used by these microorganisms and isolated, sequenced and assembled the genome of a cyanobacterium that displayed a distinctive earthy/musty smell, typical of geosmin, confirmed by GC-MS analysis of the culture's volatile extract. Morphological studies pointed to a new Oscillatoriales soil ecotype confirmed by phylogenetic analysis, which we named Microcoleus asticus sp. nov. Our studies of geosmin gene presence in Bacteria, revealed a scattered distribution among Cyanobacteria, Actinobacteria, Delta and Gammaproteobacteria, covering different niches. Careful analysis of the bacterial geosmin gene and gene tree suggests an ancient bacterial origin of the gene, that was probably successively lost in different time frames. The high sequence similarities in the cyanobacterial geosmin gene amidst freshwater and soil strains, reinforce the idea of an evolutionary history of geosmin, that is intimately connected to niche adaptation.

Heptachlor degradation characteristics of a novel strain and its application

With heptachlor as the sole carbon source, an effective heptachlor-degrading microorganism (named strain H) was isolated from the sludge of heptachlor-polluted sewage of a chemical plant, via enrichment, screening and purification. Strain H was identified as a facultative anaerobic Gram-negative bacterial strain belonging to genus Shigella based on the physiological-biochemical characteristics and the similarity analysis of its 16S rDNA gene sequence with the sequences logged in the Ribosomal Database Project and GenBank databases. When the optimal inoculation volume and the pH were 20% and 7.1-7.6, respectively, strain H was able to degrade heptachlor by more than 88.2% after130 h, with initial concentration of heptachlor being 300 μg/L at 30 ± 0.5 °C. It was also shown that strain H can grow on the degradation products of heptachlor such as 1-hydroxychlordene or heptachlor epoxide. Furthermore, additional carbon sources can accelerate the degradation rate of heptachlor because of co-metabolism. The degradation dynamics could be described by a first-order reaction model. A real-world field experiment demonstrated that strain H was effective in practical applications of heptachlor biodegradation in contaminated soil.

Conversion mechanism of heptachlor by a novel bacterial strain

Microbial treatment is the preferred method for the remediation of soil and water contaminated by heptachlor. We collected sludge samples from the sewage biological treatment pool of Shaanxi Insecticide Factory in Xi'an, China, which were used as bacteria source. With heptachlor as the substrate, at 30–35 °C, an effective microorganism (named strain H) for heptachlor degradation was isolated successfully after a long period of acclimation, screening and purification. Strain H was able to use heptachlor as a carbon source and had a good capacity for biodegradation of heptachlor. Strain H was preliminarily identified as a Gram-negative, short rod-shaped, single-cell bacterial strain that was similar to the genus Escherichia or Shigella, according to the analysis of its morphology and physiological–biochemical characteristics. Then, strain H was further identified as a novel bacterium based on the similarity analysis of its 16S rDNA gene sequence with the sequences logged in the RDP and GenBank databases. The 16S rDNA of this bacterium has never been reported before. When the inoculation volume and the pH were 20% and 7.1–7.6, respectively, the degradation rate of heptachlor can reach more than 88.2% in 130 h, with the initial concentration of heptachlor being 300 μg L⁻¹ at 30–35 °C. Identification of the metabolites by GC/MS showed that strain H degrades heptachlor via two pathways simultaneously, i.e., pathway (1) hydroxylation at the C1 position of heptachlor to 1-hydroxychlordene followed by epoxidation and dechlorination to chlordene epoxide; and pathway (2) epoxidation at the C2 and C3 positions of heptachlor to heptachlor epoxide, and then heptachlor epoxide was further transformed to chlordene epoxide by dechlorination reaction, or degraded to heptachlor diol by hydrolysis reaction. The biodegradation of heptachlor indicated that heptachlor and its metabolites can be converted into less-toxic small molecular metabolites by a series of reactions such as epoxidation, hydrolysis and dechlorination reactions.

Microbial treatment is the preferred method for the remediation of soil and water contaminated by heptachlor.

Combined adsorption and degradation of the off-flavor compound 2-methylisoborneol in sludge derived from a recirculating aquaculture system

Off-flavor in fish poses a serious threat for the aquaculture industry. In the present study, removal of 2-methylisoborneol (MIB), an off-flavor causing compound, was found to be mediated by adsorption and bacterial degradation in sludge derived from an aquaculture system. A numerical model was developed which augmented Langmuir equations of kinetics of adsorption/desorption of MIB with first order degradation kinetics. When laboratory-scale reactors, containing sludge from the aquaculture system, were operated in a recirculating mode, MIB in solution was depleted to undetectable levels within 6 days in reactors with untreated sludge, while its depletion was incomplete in reactors with sterilized sludge. When operated in an open flow mode, removal of MIB was significantly faster in reactors with untreated sludge. Efficient MIB removal was evident under various conditions, including ambient MIB levels, flow velocities and sludge loads. When operated in an open flow mode, the model successfully predicted steady MIB removal rates with time. During steady state conditions, most of the MIB removal was found to be due to microbial degradation of the adsorbed MIB. Findings obtained in this study can be used in the design of reactors for removal of off-flavor compounds from recirculating aquaculture systems.

Isolation and characterization of a cold-resistant PCB209-degrading bacterial strain from river sediment and its application in bioremediation of contaminated soil

A cold-resistant bacterium (strain QL) that can degrade 2,2',3,3',4,4',5,5',6,6'-decachlorobiphenyl (PCB209) was isolated from Wei-he River sediment. Strain QL was identified as a rod-shaped gram-negative bacterial strain, which was further identified as Comamonas testosteroni. C. testosteroni has never been reported to be capable of degrading PCB209 at low temperatures. In this study, the degradation characteristics showed that strain QL could grow with PCB209 as the sole carbon source at low temperatures (10 ± 0.5 °C). More significantly, strain QL of 40% inoculation volume was able to completely degrade PCB209 in 140 h (initial concentration of PCB209 was 100-500 µg L(-1) at 10 ± 0.5 °C and pH 7-8). The degradation process proceeded with zero-order reaction kinetics. Moreover, both laboratory simulation and real-world field experiments demonstrated that strain QL was effective in practical applications of PCB209 biodegradation in contaminated soil.

Metabolic characteristics of the species Variovorax paradoxus

This review outlines information about the Gram-negative, aerobic bacterium Variovorax paradoxus. The genomes of these species have G+C contents of 66.5-69.4 mol%, and the cells form yellow colonies. Some strains of V. paradoxus are facultative lithoautotrophic, others are chemoorganotrophic. Many of them are associated with important catabolic processes including the degradation of toxic and/or complex chemical compounds. The degradation pathways or other skills related to the following compounds, respectively, are described in this review: sulfolane, 3-sulfolene, 2-mercaptosuccinic acid, 3,3'-thiodipropionic acid, aromatic sulfonates, alkanesulfonates, amino acids and other sulfur sources, polychlorinated biphenyls, dimethyl terephthalate, linuron, 2,4-dinitrotoluene, homovanillate, veratraldehyde, 2,4-dichlorophenoxyacetic acid, anthracene, poly(3-hydroxybutyrate), chitin, cellulose, humic acids, metal-EDTA complexes, yttrium, rare earth elements, As(III), trichloroethylene, capsaicin, 3-nitrotyrosine, acyl-homoserine lactones, 1-aminocyclopropane-1-carboxylate, methyl tert-butyl ether, geosmin, and 2-methylisoborneol. Strains of V. paradoxus are also engaged in mutually beneficial interactions with other plant and bacterial species in various ecosystems. This species comprises probably promising strains for bioremediation and other biotechnical applications. Lately, the complete genomes of strains S110 and EPS have been sequenced for further investigations.