| 1. |
- Lobanov, Victor P., et al.
(author)
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Ecosystem-specific microbiota and microbiome databases in the era of big data
- 2022
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In: Environmental Microbiome. - : Springer Science and Business Media LLC. - 2524-6372. ; 17:1
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Journal article (peer-reviewed)abstract
- The rapid development of sequencing methods over the past decades has accelerated both the potential scope and depth of microbiota and microbiome studies. Recent developments in the field have been marked by an expansion away from purely categorical studies towards a greater investigation of community functionality. As in-depth genomic and environmental coverage is often distributed unequally across major taxa and ecosystems, it can be difficult to identify or substantiate relationships within microbial communities. Generic databases containing datasets from diverse ecosystems have opened a new era of data accessibility despite costs in terms of data quality and heterogeneity. This challenge is readily embodied in the integration of meta-omics data alongside habitat-specific standards which help contextualise datasets both in terms of sample processing and background within the ecosystem. A special case of large genomic repositories, ecosystem-specific databases (ES-DB's), have emerged to consolidate and better standardise sample processing and analysis protocols around individual ecosystems under study, allowing independent studies to produce comparable datasets. Here, we provide a comprehensive review of this emerging tool for microbial community analysis in relation to current trends in the field. We focus on the factors leading to the formation of ES-DB's, their comparison to traditional microbial databases, the potential for ES-DB integration with meta-omics platforms, as well as inherent limitations in the applicability of ES-DB's.
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| 2. |
- Lobanov, Victor P., et al.
(author)
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Improving Plant Health Through Nutrient Remineralization in Aquaponic Systems
- 2021
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In: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 12
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Journal article (peer-reviewed)abstract
- The exploitation of readily bioavailable fish excreta as a source of plant nutrients lies at the cornerstone of aquaponics farming. Research on nutrient cycling in aquaponic systems has devoted considerable attention to the plant uptake of dissolved nutrients in fish excreta, however, the integration of particulate-bound nutrients into downstream hydroponic farming has remained elusive. The high amount of organic carbon present in fish sludge may lead to biofouling if directly incorporated into hydroponic circulation systems, reducing the utility of incorporating fish solids on a large scale. In this study, we implemented a novel treatment system capable of reducing the carbon and nitrogen load of fish solids to produce a liquid fertilizer for a downstream hydroponics unit. Lettuce (Lactuca sativa) fertilized with exclusively a commercial nutrient solution, the biofilter effluent (coupled aquaponic system), effluent from the solids treatment system, or the latter two combined were grown in nutrient flow technique gutters downstream of a recirculating aquaculture system stocked with rainbow trout (Oncorhynchus mykiss). While crop yields were lower for the aquaponic treatments compared to lettuce grown in a commercial nutrient solution, plant sap analysis demonstrated a contrasting picture with respect to internal nutrient concentrations. Lettuce grown in the commercial hydroponic solution were deficient in several mineral nutrients (Mg, Ca, Na, and Si) nor did they have higher iron concentrations despite the significantly higher EDTA-chelated aqueous iron (460 x greater than other treatments) in the nutrient solution. Nutrient uptake in the rhizosphere was not investigated on a molecular level, although stunted rhizosphere growth in the commercial nutrient solution control suggests a weakened capacity for nutrient uptake in comparison to other treatments. Alongside the remineralization of micronutrients, the solids treatment system addressed the common issue of excess carbon leading to biofouling via a total suspended solids reduction of 87.27% +/- 9.95 during the coupled aquaponics cultivation period. Ultimately, these data lead to two important conclusions. Firstly, optimizing nutrient bioavailability is not synonymous to increasing the presence of a nutrient in the water column. Secondly, estimating ideal nutrient solution concentrations involves both preventing nutrient blocking and improving bioavailability.
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| 3. |
- Lobanov, Victor P.
(author)
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Nutrient Transfer in Aquaponic Systems – Optimizing microbial processes for greater circularity and economic viability
- 2023
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Doctoral thesis (other academic/artistic)abstract
- The trend towards sustainable process design in modern industries combines the goal of improving process efficiency with a conscientious shift towards resource conservation. Aquaponics, a system that involves co-cultivating fish and plants, is a waste-conscious food production system. The primary system inputs - water and fish feed - are supplied to the aquaculture component and then transferred downstream to an area of plant cultivation. The upstream aquaculture component is organized in the form of a recirculating aquaculture system (RAS), while the downstream portion is most often a hydroponic greenhouse and as such takes the form of two recirculating loops that have a variable degree of connectivity. Aquaponics, just as its parent fields of aquaculture and hydroponics, falls under the umbrella of closed environment agriculture (CEA) systems. Unlike aquaculture and hydroponic cultivation systems, aquaponics relies heavily on endogenous microbial communities to remineralize nutrients and eliminate fish-toxic waste products. To date, efforts to improve nutrient use efficiency in aquaponic systems have primarily focused on nitrogen metabolism within the biofilter, with research around the utilization of other nutrient streams (solid waste) relegated to waste disposal. This dissertation addresses this shortcoming by investigating the processes underlying microbial colonization and nutrient remineralization in aquaponics, along with an analysis of the potential to improve system efficiency and sustainability through solids revalorization. These efforts demonstrate the capacity of bioprocess innovation to bridge the commercialization gap that has thus far limited widespread adoption of this type of high intensity, yet sustainable, food production systems. While there are already hundreds of aquaponics operations developing globally, achieving industrial scale production at similar scales to land-based aquaculture and hydroponic facilities has yet to be accomplished. Therefore, this dissertation aims to better understand nutrient flows and remineralization and how they can be utilized to improve food production and resource-use efficiency. Chapter 2 discusses how plants can guide microbial colonization in aquaponic systems, Chapter 3 reviews the advent of ecosystem-specific microbiota and microbiome databases, Chapter 4 introduces a novel nutrient remineralization system that converts fish solids into a fertilizer for CEA, and finally, Chapter 5 expands this technology to include the generation of methane from fish solids. In conclusion to these four chapters, a discussion section contextualizes the experiments within the larger umbrella of microbial and nutrient flow and how this relates to sustainable process design.
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| 4. |
- Lobanov, Victor P., et al.
(author)
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Simultaneous biomethane production and nutrient remineralization from aquaculture solids
- 2023
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In: Aquacultural Engineering. - : Elsevier BV. - 0144-8609. ; 101
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Journal article (peer-reviewed)abstract
- The rapid expansion of the aquaculture industry has brought about a heightened focus on the waste produced by high intensity fish farming. In closed-containment, recirculating aquaculture systems (RAS), fish solids are mechanically separated and/or coagulated before being disposed as waste. Subsequent revalorization is typically limited to the direct dispersal of aquaculture solids onto agricultural fields. Here, we developed a novel, continuous flow, low-cost solids waste treatment system for freshwater and saline RAS. Rotating drum filter backwash was collected as the primary feedstock for anaerobic digestion. A laboratory scale set up was used to monitor the conversion of the solids into a methane-rich (60-80% purity) biogas stream. Iron supplementation (ferric iron at 100 mg/L and 1000 mg/L) improved salt tolerance of the methanogenic community, leading to higher methane yields in a supplemented (FeCl3 at 1000 mg/L) saline treatment than the saline control. The application of iron additionally improves pH stability and volatile fatty acid utilization. The methane yield ranged from 0.1 to 0.4 NL CH4/ g VS across the three freshwater treatments and the iron-supplemented saline treatment, however, it was significantly lower for the saltwater control: ranging between 0.08 and 0.25 NL CH4/ g VS. These values correspond to a percentage yield of 57-86% of the total biomethane potential. Overall, implementing anaerobic digestion for RAS waste valorization may generate significant amounts of biomethane to be used in electricity and heating for large-scale aquaculture facilities, while even for smaller facilities it may off-set costs and mitigate environmental impacts of the waste streams.
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| 5. |
- Lobanov, Victor P., et al.
(author)
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Sturgeon and paddlefish: Review of research on broodstock and early life stage management
- 2023
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In: Aquaculture and Fisheries. - 2096-1758 .- 2468-550X.
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Research review (peer-reviewed)abstract
- Sturgeon aquaculture has taken a parallel yet unique path relative to other teleost rearing. One of the driving factors has been the fact that virtually all extant species are facing extinction; thus, laws concerning the transport and processing of sturgeon are stringent. As a result, most sturgeon companies vertically integrate the farming process from hatchery to harvest, in contrast to the production of other commercial fish species (e.g., trout, sea bass, salmon), where farmers tend to purchase fry from producers specialized only in the production of that life stage and sell product to unaffiliated fish processors. Sturgeon aquaculture is furthermore unique in the extremely high value of the main product (caviar). The secondary product (meat) also surpasses other finfish aquaculture products' average price per weight. These expensive outputs reveal the greatest challenge in production — an exceptionally long time to market from larvae to harvestable adults. For all their rigor and robustness as juveniles and adults, sturgeon species are highly fragile during larval stages. Due to the unique legal framework around sturgeon cultivation, aquaculturists often specialize in regional species, although some hybrids have achieved global popularity. This lends to a heterogenous swath of literature on best cultivation and management practices, especially at early growth stages. Nonetheless, the role of aquaculture as both a food source and restocking program to thwart further extinction of sturgeon species has hardly been fully tapped. In light of the many challenges, this review examines recent advances in sturgeon farming with an emphasis on broodstock and early life-stage management to summarize studies that can help researchers and farmers assess the industry's current state.
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| 6. |
- Lobanov, Victor, et al.
(author)
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Plants Dictate Root Microbial Composition in Hydroponics and Aquaponics
- 2022
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In: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
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Journal article (peer-reviewed)abstract
- The role of the microbial community in mediating fish and plant co-culture is often considered the black box of aquaponics. Despite widespread recognition regarding the dependency of plants on their rhizosphere, the extent to which upstream aquaculture influences downstream hydroponic root communities has been poorly described in the literature. In this study we performed a taxonomic survey (16S rRNA metabarcoding) of microbial communities originating in the facility water source, hydroponic nutrient solution (HNS) sump, nutrient supplemented biofilter effluent (BF) sump, and recirculating aquaculture system tanks stocked with Nile tilapia (Oreochromis niloticus). Lettuce (Lactuca sativa) was then grown using the HNS and BF effluent under sterilized or mature (prior aquaponics/hydroponics lettuce culture water) conditions, likewise, the influence of probiotic addition or inoculation with soil-grown lettuce rhizosphere was assessed. Compositional similarities across treatments suggest that under soil-less conditions, plants are able to exert a stronger discriminatory influence on their rhizosphere composition than is done by colonization from upstream sources. Furthermore, cluster dendrograms grouped the sterilized and unsterilized treatments more consistently together than hydroponics and aquaponics treatments. These findings contradict conventional beliefs that microbial communities in the water column colonize roots based on their presence alone, ignoring the role that plants play in rhizosphere community selection.
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| 7. |
- Mougin, Julia, 1994, et al.
(author)
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Effects of dietary co-exposure to fungal and herbal functional feed additives on immune parameters and microbial intestinal diversity in rainbow trout (Oncorhynchus mykiss)
- 2023
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In: Fish & Shellfish Immunology. - 1050-4648. ; 137
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Journal article (peer-reviewed)abstract
- Misuse and overuse of antibiotics in aquaculture has proven to be an unsustainable practice leading to increased bacterial resistance. An alternative strategy involves the inclusion of immunostimulants in fish diets, especially fungal and herbal compounds already authorized for human consumption, hence without environmental or public health concerns. In this study, we used a holistic and cross-disciplinary pipeline to assess the immunos-timulatory properties of two fungi: Trametes versicolor and Ganoderma lucidum; one herbal supplement, capsaicin in the form of Espelette pepper (Capsicum annuum), and a combination of these fungal and herbal additives on rainbow trout (Oncorhynchus mykiss). We investigated the impact of diet supplementation for 7 weeks on sur-vival, growth performance, cellular, humoral, and molecular immune parameters, as well as the intestinal mi-crobial composition of the fish. Uptake of herbal and fungal compounds influenced the expression of immune related genes, without generating an inflammatory response. Significant differences were detected in the spleen-tlr2 gene expression. Supplementation with herbal additives correlated with structural changes in the fish in-testinal microbiota and enhanced overall intestinal microbial diversity. Results demonstrated that the different treatments had no adverse effect on growth performance and survival, suggesting the safety of the different feed additives at the tested concentrations. While the mechanisms and multifactorial interactions remain unclear, this study provides insights not only in regard to nutrition and safety of these compounds, but also how a combined immune and gut microbiota approach can shed light on efficacy of immunostimulant compounds for potential commercial inclusion as feed supplements.
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