Remember me on this computer. Enter the email address you signed up with and we'll email you a reset link. Need an account? Click here to sign up. Download Free PDF. A short summary of this paper. Ocampo-Velazquez, Juan F.
Garcia-Trejo, and Ramon G. Guevara-Gonzalez C. Guevara-Gonzalez; ramon. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components.
The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. This approach can also be useful to understand complex interactions of living components in the system.
Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems RAS. However, microbial community composition of aquaponics is still unknown. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications.
Introduction innovations in the field, it has been possible to develop economically feasible systems capable to cultivate species at The continuous rise in global human population makes the high densities, even with unfavorable climatic regime and expansion and intensification of our current food production limited water availability [3, 4].
These kinds of proposals are systems necessary. In addition, in order to mitigate negative nowadays considered as culture models for sustainable food environmental impacts, it is also desirable to design new production systems [5]. RAS allows a reduction system. From this approach, traditional food production of water consumption due to waste management and nutrient systems have been under public eyes being questioned about recycling [3].
Historically, the concept of practical and effi- its sustainability [1, 2]. One example is the case of aquaculture cient food production systems is not new. Cultures of China, industry. In the XX century, the first attempts to create practical, growing rate [3].
These systems are known with the term organisms [26]. Moreover, using these tools, the production with integration of hydroponics [10]. The final vast prokaryotic diversity must be more revealed than with byproduct of fish protein metabolism is ammonia NH3 traditional techniques. Metagenomic techniques combined [11].
Ammonia accumulates in aquaculture ponds and it can with next generations sequencing NGS and bioinformatic be dangerous to fish at specific temperature and pH levels tools have boosted microbial ecology. Wastes of ammoniacal nitrogen genomics approaches has allowed the discovery of large array are transformed into less harmful compounds like nitrate by of genes [26].
This modern approach allows knowledge of the biological filtration [13, 14]. In contrast, aquaponics do and emergent properties [27]. With these studies it is possible not require water replacement; addition of make-up water is to evaluate the potential of aquaponic microbial community for losses because evaporation or replacement volume is less for future biotechnological uses.
These nutrients are enough for vegetable consumption [20]. Then, dissolved nutrients 2. Microbial Community in RAS in the media are absorbed by root plants, optimizing the use of nutrients and water, and reduce wastes for fish and In RAS environment, aquaponic system is very important environmental impact [19].
On this way, the system allows microbial community in the same order of magnitude as minimizing resources as land, water, and energy [15]. The system provides different quality for both aquatic species and plants. For maintaince microniches for the microbial populations according to a dif- of water quality RAS have been utilized for solid removal ferential gradient of oxygen and nutrients.
Every microniche and biological filtration. For this purpose, there are two or supports development of specific microbial populations [28]. In aquaponics, both solids removal and biolog- differences on microbial diversity [24, 29]. Biofilter compo- ical filtration are in the same component. Accumulation nent presents the most abundant content of microbes [22].
However, the need of different excreted by fish, and carbon and nitrogen accumulated from physicochemical conditions in water for living components uneaten food and fecal matter. One of the most important makes the management of the system very complex. The conversions is carried out by nitrifying bacteria; they are recommended pH for aquaculture systems is 6. The and denitrification processes [16, 22, 30].
Other microbial pH is a parameter that can limit the development for plants, metabolisms are involved in proteolysis and sulfate reduction fish, or bacteria [14, 23]. Populations of microorganisms [30]. The populations are distributed according to respiratory or microbial community in biofilter of aquaponics have metabolism determined in strict aerobic or microaerophilic an essential role in aquaponic systems development [21].
In general, ammonia oxidizing and nitrate oxidizing. Each reaction the most common approach for nitrogen removal from water involved different species of bacteria: Nitrosomonas and is based on the processes of aerobic autotrophic nitrification Nitrobacter [10, 24]. Probably best studied group of environmental impor- Autotrophic and heterotrophic microorganisms are tance in this type of ecosystems are nitrifying prokaryotes present in RAS.
Autotrophic organisms use CO2 as carbon including both the ammonium oxidizing and the nitrite source and inorganic nitrogen, sulphur, or iron compounds as oxidizing prokaryotes [25]. However, microbial community energy source. Plants, algae, and some bacteria in aquaponic in aquaponic system is not characterized. Due to biological systems present this metabolism. Heterotrophic organisms interactions in biofilter of aquaponic system, microbial com- use carbohydrates, amino acids, peptides, and lipids as munities are very interesting to analyze.
In the system, organic matter The most important revolution in microbial ecology was from uneaten feeds, excreta of aquatic species, and detritus the use of molecular techniques and DNA sequencing in are mineralized by this type of microorganisms [22, 32].
BioMed Research International 3 Autotrophic nitrification removes ammonia at sufficient Plant culture rate to maintain water quality at a level to prevent ammonia toxicity to the fish [33]. Heterotrophic NOB-Nitrospira sp. To overcome nitrifiers and -Nitrobacter sp. On the other hand, heterotrophic bacteria constitute an Fish culture important factor in terms of O2 consumption and com- pete with autotrophic bacteria, diseases in fish and later in Heterotrophic human.
Some populations of these bacteria are suspected bacteria Pump of having a positive effect against pathogenic bacteria [33]. Heterotrophic microorganisms exhibit higher growth rates Figure 1: General distribution of microbial populations in than autotrophs and can use organic substrates as source of aquaponic systems.
The main source of heterotrophic bacteria is within the 1. Free ammonia is NH3 , the toxic form biofilter. Bacteria of heterotrophic nitrification are probably of ammoniacal N. High free ammonia NH3 might inhibit ideal prokaryotes for coupled nitrification-denitrification in the heterotrophic nitrification activity but not the growth. The dissolved ing to pH conditions. Highest removal of ammonium At lower heterotrophic bacteria. High concentration of organic carbon pH values or at more alkalinity, the growth of heterotrophic affects negatively nitrate production; it means concentration bacteria of group Acinetobacter increased.
Efficient removal of nitrite was always very low [28, 35]. Some strains of of ammonium at the slightly alkaline environment may be heterotrophic nitrifiers had the capability to use nitrite NO2 caused by more free ammonia contained in medium, which and nitrate NO3 as the source for nitrogen for growth and is preferentially by ammonia monooxygenase amoA [34].
It means that bacterial correlated with oxygen content. On the 34]. These bac- 2. Microbial Diversity Characterization. In decade, teria integrate more open aggregations but may also be found some species have been characterized in diverse components distributed in the biofilm systems.
Another general obser- of RAS and mainly on biofilters [30, 37—39]. Considering vation is that Nitrospira spp. Average CFU in although in lower numbers and using small amounts of biological filter was 7. The aforementioned theoretical distribu- in the outlet. Concentration of bacteria on the biofilter media tion of autotrophic and heterotrophic bacteria in aquaponic was 5.
Thus, bacterial systems is showed in Figure 1. The heterotrophic bacteria will concentration does not depend of fish stocking density [28]. These studies the pond culture near to sediment. Autotrophic bacteria revealed that the main bacterial groups presented in fresh- like strains of AOB-Nitrosomonas sp. From these bacterial groups -Nitrospira will be in open aggregations in a portion of the only Hyphomicrobium facilis, Rhizobium sp.
Ammonia Oxidizers Bacteria ibacter sp. Group Microorganism Process References Actinobacteria Microbacterium imperiale [30] Mycobacterium chitae [30] Corynebacterium tuberculostearicum Pathogen in humans [39] Propionibacterium acnes [39] Acidobacteria Acidobacteria bacterium [39] Bacteroidetes Chryseobacterium sp. Some strains pathogen in humans [37] Flavobacteriales bacterium Sulfate reduction [37] Flavobacterium columnare Pathogen in fish [39] Flavobacterium sp.
Heterotrophic denitrification [38, 39] Bacteroides plebeius Sulfate reduction [39] Myroides sp. Pathogen in humans [37] Sphingobacterium sp. Heterotrophic denitrification [30] Nitrobacter winogradskyi Nitrite oxidation [30, 40] Nordella oligomobilis [30] Ochrobactrum anthropi [30] Rhizobium sp. Nitrogen fixation [30, 37, 39] Rhodopseudomonas acidophila [30] Rhodovulum euryhalinum Denitrification [30] Bradyrhizobium japonicum [39] Woodsholea maritima [39] Rhodobacter sp.
Heterotrophic bacteria [37, 39] Aeromonas sp. Pathogen in fish [37] Lactobacillus paraplantarum [30] Lactococcus lactis [39] Macrococcus brunensis [30] Macrococcus lamae [30] Sarcina sp. Anammox [38] Planctomyces maris Anammox [38] Planctomicetes sp. Nitrite oxidation [38] Nitrospirae Nitrospira moscoviensis Nitrite oxidation [30, 38, 39] All microorganisms of this table were analysed with 16S rRNA clone library method, denaturing gradient gel electrophoresis DGGE , and few cases with biochemical procedures.
PCR-based molecular techniques have mainly been used relationship with higher plants in humidity environments. The last molecular technique is the order to determine the presence of bacterial pathogens for most common for study of microbial communities in RAS human and for aquatic species [5, 51, 52].
Pathogens in Aquaponic Systems subunit of monooxygenase , nirK nitrite reductase gen , and norB nitric oxide reductase [25, 43]. Aquaponic systems have been used as sustainable agricultural The analysis using 16S rRNA genes as a phylogenetic systems [5, 51]. With the same volume of water for fish marker was a revolutionary strategy for microbial ecol- production can be produced edible vegetables.
These systems ogy with cultured-independent method being developed are discussed as regards their utilization in improving sus- since 90s, after the work of Lane and collaborators [44]. Many species of bacteria and coliforms and variable interspersed regions that allow a reliable and are inherently present in aquaponic recirculating biofilter detailed microbial classification. For this molecular technique carrying out transformations of organic matter and wastes the correct selection of primers is critical.
Some pairs of of fishes. This implies the presence of many microorganisms primers can overestimate or underestimate species richness; that can be pathogens for plants, fishes, and, mostly, human. This happened One of the most important considerations for this food when primers selected do not anneal equally to DNA target in production system is food safety. In agricultural systems, all members of community and the amplification was carried the evaluation of food safety is emerging as a critical out on certain taxonomic group [45].
Some particular regions procedure in harvesting and management operations. For are recommended to obtain representational characterization this purpose, some microorganisms have been considered in complex microbial community [45, 46]. Some of these safety-indicators are Escherichia unique and complex environments [16]. Microbial commu- coli and Salmonella spp. These microorganisms are typi- nities in aquatic system or in RAS are as complex as changes cally found in the intestines of warm-blooded animals like in environmental variables according to period of time [30, birds, mice, cattle, and others.
They are common indicators 39, 47]. Besides, every aquatic species in a RAS introduces of fecal contamination and microbial water quality. These its own unique microbial flora [30]. Aquaponic RAS system bacteria are zoonotic enteric bacteria transient in fish gut introduces additional living component compared to other microflora from contaminated water in open systems because RAS analyzed. Plants can introduce their own microbial flora of animals like birds [29].
Research on aquaponic fields has to the system, thus making the study of the changes on micro- been carried out recently in order to ascertain microbial bial diversity very interesting.
Ammonia Oxidizing Bacteria safety of its by-products [5, 51]. The microbial profile of AOB Nitrosomonas communis introduced in rhizoplane lettuce produced under soil-free aquaponics versus in-soil of aquaponic plants has been isolated and identified [48]. Less well-studied is the heterotrophic count. Aquaponics had significantly lower concentration of nitrification carried out by fungi. These organisms have coliform no detectable E. These 3.
Other works evaluated microbial water quality related 4. Metagenomics for Microbial Diversity Description. PCR to food safety in aquaponic system. This report analyzed amplification of genes has allowed the study of microbial plant and fish tissue, water, and supplement aquaponic input diversity.
Throughout all the research done in this field samples that can be a contamination vector from 11 different the conclusion is that majority of prokaryotic diversity still farms in Hawaii for approximately one year. Methodology remains unknown, mainly because these cells cannot be used for food safety determination was the traditional micro- grown under laboratory conditions [58, 59].
Several works bial isolation of E. The results PCR-based molecular techniques for study of microbial showed very low levels of E. These tools has allowed to have a look of general scene water. Plant and fish tissue analyzed and supplement inputs of microbial diversity in environmental samples. However, were shown to have very low levels of generic E. However microbial The amplification of 16S rRNA gene technique is based on determination was carried out with conventional methods for amplification of hypervariable regions of the gene anchoring microbial detection.
This can be likely conducted to analyze to conserved sequences. There are nine 9 hypervariable a short range of microbial pathogens, because fish and plants regions named V1—V9 that spanned between 50 and bp pathogens were not considered in the study. For a deep in length depending on region. Hypervariable regions are microbial profile the use of modern metagenomic approaches the key for universal microbial identification.
Primers have is necessary. Some strains of Bacillus sp. The information of this technique sp. Other pathogens sample [62].
Species prokaryotic cells without cultivation by applying fluorescence of Vibrio have been isolated from freshwater, estuarine, and in situ hybridization FISH with ribosomal RNA rRNA seawater environments, although most of them are probably targeted oligonucleotide probes. These oligonucleotides have saprophytic [28]. After Biosafety of aquaponic RAS will depend on correct man- stringent washing, specifically stained cells are detected via agement and control of opportunist microbial proliferation epifluorescence microscopy or flow cytometry [63].
Quanti- in the system [22]. Metagenomic and metatranscriptomic tative analyses of the composition and dynamics of micro- profile can be a powerful tool for determining the diversity of bial communities are an integral component of microbial pathogens and functional activity that can help to understand ecology. These techniques in combination with 16S rRNA their relationship with other microbes and possibly its regula- have allowed real progress in some cases, especially in very tion in the system.
Metagenomics approaches allow the meta- simple ecosystems such as endosymbionts or extreme envi- analysis of diversity in microorganisms of the aquaponic ronments. The contribution of these techniques to a better environment [53—56].
Omic Tools for Future Analysis of On the other hand, NGS technologies have more throughput the System because they have times more capacity of sequencing than Sanger method.
These technologies sequenced DNA The development of sequencing and high-throughput meth- molecules massively in parallel in a flow cell. The sequencing ods for cloning microbial genes directly from environ- is carried out in two forms, in a continuous real time or in ment has opened the possibilities for ecological microbiol- a stepwise iterative process. In both types of processes each ogy, mostly considering that microbes possess the highest clonal template or single DNA molecule is sequenced and potential of producing bioactive metabolites, enzymes, and can be quantified among the total sequences generated [26].
Moreover, these modern technologies focus on sequencing The study of larger fragments of environmental DNA of of large fragments of DNA as entire genomes or plasmids whole community is known as environmental genomics, instead of gene s or operons.
For this process is necessary ecogenomics, or metagenomics [57]. On the other hand, proteomics is the analysis of pro- After this step further bioinformatical analysis is necessary teome, the full complement of proteins expressed by an in which these fragments are assembled in linear sequences organism.
The number of proteins in the proteome organism that conform part of genome or total genome [65, 66]. The exceeds by far the number of genes [74]. Every fragment of assembling overlaps the different fragments and thus rebuilds DNA is biochemically similar to one another.
However, every complete linear sequences of the genome, known as contigs. The challenge technologies because to define its own identity, quantity, of this strategy lies on computational effort that requires fur- structure, and functionality of complete complements of thermore huge analysis and computational capacity [65, 67]. The former analysis focuses on metagenomic study regulatory processes that can be chemically transformed by single targets amplified with PCR and, then, the products during metabolism and provide a functional state of cellular are sequenced.
On the other hand, shotgun metagenomics biochemistry. The level of these chemical entities can be is targeted in total DNA isolated from an environmental regarded as the ultimate response of biological systems to sample and then sequenced, resulting in a profile of all genes genetic posttranslational modifications or environmental within the community. The basic definition of metagenomics changes epigenetic regulation. Metabolites serve as direct is the analysis of genomic DNA from a whole community; signatures of biochemical activity and therefore they are easy this separates it from genomics, which is the analysis of to correlate with phenotype making it a powerful tool in genomic DNA from an individual organism or cell [68, order to explode in different fields of science.
In parallel 69]. This can be defined on all levels of com- this topic because metagenomics allow microbial analysis on plexity, such as organisms, tissue, cells, or cell compartments. In metabolome analysis the most functional characteriza- 4. Metatranscriptomics, Proteomics, and Metabolomics for tions of genes involved in a metabolism are not based upon Microbial Functionality Description.
Metatranscriptomics, rigid biochemical testing. Many of putative function assign- proteomics, and metabolomics can provide information of ments of proteins do not describe biochemical function or functional analyses in microbial community at different biological role. It can be the result of gene duplication that is levels, gene expression, protein translation, and more recently responsible for many enzyme isoforms and exhibits different the metabolite network, respectively.
Recirculating Aquaculture, 3rd Edition 3rd Edition there is a trend to rear higher value species in recirculating aquaculture systems. More about The Recirculating Aquaculture, 4th Edition Book: This is the 4th edition of the book that has become known in the industry as the Big Yellow book. This hardcover textbook is widely regarded as the fundamental, and highly technical, reference for everything related to Recirculation Aquaculture Systems or RAS for short.
A complete reference book on recirculating aquaculture systems. Condition: Neu. Neuware - This is the first English book to Recirculating aquaculture systems book the current development of closed recirculating aquaculture systems cRASs in Japan, and its implications for industry in the near future.
It offers an introduction to the topic and discusses the industrial application of. Complete e-book full of useful figures, calculations, tables, and appendices. Includes step by step design instructions for building recirculating aquaculture systems.
Also includes descriptions of all relevant water treatment processes and the associated equipment needed. A thorough guide on how to plan and design a recirculating aquaculture system for profit or pleasure.
Learn the crucial planning steps and business decisions that go into designing an efficient recirculating aquaculture system. To ensure good water purification, recirculating systems consist of a number of components with specific functions. See detailed explanation on RAS technology below. Advantages of Recirculating Aquaculture System. The advantages of farming in RAS are.
Click Download or Read Online button to get recirculating aquaculture systems book now. This site is like a library, Use search box in the widget to get ebook that you want. This is the 4th edition of the book that has become known in the industry as the Yellow book. It addresses the subject of recirculating aquaculture systems RAS. Recirculating Aquaculture, 4th edition. Book June Recirculating systems for holding and growing fish have been used by fisheries researchers for nearly three decades.
Attempts to ad. The 2nd edition has added a 40 page chapter on aquaponics. The International Journal of Recirculating Aquaculture is a peer-reviewed journal dedicated to the consolidation of research and applications expertise in the area of recirculation systems. The journal provides a forum for the open exchange of reliable information on the subject of recirculating covers all aspects of recirculating aquaculture, including water.
Recirculating Aquaculture Systems. James M. Search for more papers by this author.
0コメント