scholarly journals Bacterial Relationships in Aquaponics: New Research Directions

2019 ◽  
pp. 145-161 ◽  
Author(s):  
Alyssa Joyce ◽  
Mike Timmons ◽  
Simon Goddek ◽  
Timea Pentz
Keyword(s):  
Microbial Communities ◽  
Plant Production ◽  
Microbial Decomposition ◽  
Recirculating Aquaculture ◽  
Recirculating Aquaculture Systems ◽  
Wide Range ◽  
Technical Specifications ◽  
New Research ◽  
System 1

AbstractThe growth rates and welfare of fish and the quality of plant production in aquaponics system rely on the composition and health of the system’s microbiota. The overall productivity depends on technical specifications for water quality and its movement amongst components of the system, including a wide range of parameters  including factors such as pH and flow rates which ensure that microbial components can act effectively in nitrification and remineralization processes. In this chapter, we explore current research examining the role of microbial communities in three units of an aquaponics system: (1) the recirculating aquaculture system (RAS) for fish production which includes biofiltration systems for denitrification; (2) the hydroponics units for plant production; and (3) biofilters and bioreactors, including sludge digester systems (SDS) involved in microbial decomposition and recovery/remineralization of solid wastes. In the various sub-disciplines related to each of these components, there is existing literature about microbial communities and their importance within each system (e.g. recirculating aquaculture systems (RAS), hydroponics, biofilters and digesters), but there is currently limited work examining interactions between these components in aquaponics system, thus making it an important area for further research.

scholarly journals Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Hannes Petruschke ◽  
Christian Schori ◽  
Sebastian Canzler ◽  
Sarah Riesbeck ◽  
Anja Poehlein ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Intestinal Microbiota ◽  
De Novo ◽  
Bacterial Species ◽  
Intestinal Microbiome ◽  
Single Strain ◽  
Small Proteins ◽  
Human Intestinal Microbiota ◽  
Wide Range

Abstract Background The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. Results We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. Conclusions We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract.

The Sacred Home in Renaissance Italy

2018 ◽  
Author(s):  
Abigail Brundin ◽  
Deborah Howard ◽  
Mary Laven
Keyword(s):  
Religious Experiences ◽  
Traditional Research ◽  
Gender And Age ◽  
Wide Range ◽  
Devotional Life ◽  
Renaissance Italy ◽  
New Research ◽  
The City ◽  
The Church

The Sacred Home in Renaissance Italy explores private devotional life in the Italian Renaissance home between 1400 and 1600, and suggests that piety was not confined to the Church and the convent but infused daily life within the household. Books, buildings, objects, spaces, images, and archival sources help to cast light on the practice of religion in the home. Acts of devotion, from routine prayers to extraordinary religious experiences such as miracles and visions, frequently took place at home amid the joys and trials of domestic life—childbirth, marriage, infertility, sickness, accidents, poverty, and death. The book moves beyond traditional research on the Renaissance in important ways. First, it breaks free from the usual focus on Venice, Florence, and Rome to investigate practices of piety across the Italian peninsula. In particular, new research into the city of Naples, the Marche, and the Venetian mainland offers fresh insights into the devotional life of the laity. Moreover, it goes beyond the study of elites to include artisanal and lower-status households, and points to the role of gender and age in shaping religious experience. Drawing on a wide range of textual, material, and visual sources, this book recovers a host of lost voices and compelling narratives at the intersection between the divine and the everyday. Its multidisciplinary approach enables unprecedented glimpses through the keyhole into the spiritual lives of Renaissance Italians.

Preliminary investigation of an idiopathic muscle disease in farmed burbot Lota lota

2020 ◽  
Vol 140 ◽  
pp. 179-186
Author(s):  
C Pietsch ◽  
F Tschudi ◽  
S Baumann ◽  
H Schmidt-Posthaus
Keyword(s):  
Preliminary Investigation ◽  
Granulomatous Inflammation ◽  
Muscle Disease ◽  
Health Issues ◽  
Lota Lota ◽  
Recirculating Aquaculture ◽  
Recirculating Aquaculture Systems ◽  
Causative Agents ◽  
Biological Methods

The rearing of less established fish species in recirculating aquaculture systems (RASs) is increasing, but may require adaptations of the rearing facilities if health impairments occur. We observed several health issues in burbot Lota lota reared for up to 2 yr in a RAS and used microbiological, histological and molecular-biological methods to identify the causative agents. Minor skin trauma led to the development of ulcers. In addition, several fillets of burbot showed pronounced granulomatous inflammation and calcification with signs of muscle fiber degeneration which resembled a condition called ‘sandy flesh disease’ in North American walleye. Several infectious agents were able to be excluded as a cause for the disease. Carnobacterium maltaromaticum was isolated in high numbers in some of the affected muscle tissue. However, the role of this bacterium or other causative agents or husbandry conditions remains to be elucidated.

A new research method to test auditory preferences in young listeners: Results from a consonance versus dissonance perception study

2016 ◽  
Vol 45 (5) ◽  
pp. 699-712 ◽  
Author(s):  
Nicola Di Stefano ◽  
Valentina Focaroli ◽  
Alessandro Giuliani ◽  
Domenico Formica ◽  
Fabrizio Taffoni ◽  
...  
Keyword(s):  
Young Children ◽  
Research Method ◽  
Perception And Action ◽  
Mutual Interaction ◽  
Experimental Session ◽  
Sound Emission ◽  
Wide Range ◽  
New Research ◽  
Further Development

To date, behavioural procedures adopted to assess sound preferences in young children have evaluated the responses of participants while listening to the stimuli administered by the experimenter. Due to the difficulties which may arise in the interpretation of the results, recent studies have suggested some limitations to these procedures, stimulating the further development of behavioural methods. Here, we introduce a new method for testing sound preferences in children, in which participants actively produce the stimuli during the experimental session. The apparatus consists of a musical lever which emits different sounds depending on its rotation around a hinge. The device was programmed to emit consonant and dissonant harmonic intervals. The procedure has been tested with 22 participants from 19 to 40 months of age. Results show that: (a) sound emission strongly stimulates toy manipulation; (b) the examined participants distinguished the two types of sounds, showing a preference for producing consonant over dissonant stimuli. This method could be used to study a wide range of sound qualities in young listeners, such as rhythm or pitch. Grounded in the mutual interaction between perception and action, this procedure is in line with recent research highlighting the role of embodiment in the perception of music.

scholarly journals Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Blanca M. Gonzalez-Silva ◽  
Kjell Rune Jonassen ◽  
Ingrid Bakke ◽  
Kjetill Østgaard ◽  
Olav Vadstein
Keyword(s):  
Microbial Communities ◽  
Rrna Gene ◽  
Physiological Plasticity ◽  
Oxidation Rates ◽  
Salinity Changes ◽  
Recirculating Aquaculture ◽  
Seawater Salinity ◽  
Recirculating Aquaculture Systems ◽  
Before And After

AbstractIn this study, nitrification before and after abrupt cross-transfer in salinity was investigated in two moving bed biofilm reactors inoculated with nitrifying cultures that had adaptation to freshwater (FR) and seawater salinities (SR). FR and SR MBRRs were exposed to short and long term cross-transfer in salinity, and the functional capacity of nitrifying microbial communities was quantified by the estimation of ammonia and nitrite oxidation rates. Salinity induced successions were evaluated before and after salinity change by deep sequencing of 16S rRNA gene amplicons and statistical analysis. The bacterial community structure was characterized and Venn diagrams were included. The results indicated that after salinity cross-transfer, the FR was not significantly recovered at seawater salinity whereas SR showed high resistance to stress caused by low-salt. Succession and physiological plasticity were the main mechanisms of the long-term adaption of the nitrifying communities exposed to abrupt salinity changes. Independently of salinity, some nitrifiers presented high physiological plasticity towards salinity and were very successful at both zero and full seawater salinity. SR culture is robust and suitable inoculum for ammonium removal from recirculating aquaculture systems and industrial wastewaters with variable and fast salinity changes. Our findings contradict the current perspective of the significance of salinity on the structure of nitrifying communities.

scholarly journals Not by transmission alone – the role of invention in cultural evolution

2020 ◽  
Author(s):  
Susan Perry ◽  
Alecia Carter ◽  
Marco Smolla ◽  
Erol Akcay ◽  
Sabine Nöbel ◽  
...  
Keyword(s):  
Social Learning ◽  
Data Set ◽  
Process Understanding ◽  
Wide Range ◽  
New Ideas ◽  
Four Levels ◽  
New Research ◽  
Creativity And Innovation ◽  
Nonhuman Species

Invention and social learning have together empowered our species to inhabit virtually every part of the world. For the past fifty years, however, social learning has been regarded as the fundamental driver for the emergence of tradition and culture. As a result, innovation has been relatively understudied, outside the human lineage. This has left basic questions unanswered, such as: What factors promote the creation of new ideas and practices? And what affects whether they are spread or lost? We review the existing literature, focusing on the following four levels of investigation: traits (what sorts of behaviours are easiest to invent?), individuals (what intrinsic and contextual factors make some individuals more likely to invent new things?), populations (what features of social relationships and societies promote the rise and spread of new inventions?), and ecological contexts. We aim to inspire new research agendas by summarizing what is known and highlighting theoretical and empirical gaps in our understanding of the innovative process. Understanding the origin of humans’ noteworthy levels of creativity requires a well-developed theory of creativity and innovation as well as a large comparative data set investigating these processes in nonhuman species from a wide range of taxa.

scholarly journals A Temporally Dynamic Gut Microbiome in Atlantic Salmon During Freshwater Recirculating Aquaculture System (RAS) Production and Post-seawater Transfer

2021 ◽  
Vol 8 ◽  
Author(s):  
Marlene Lorgen-Ritchie ◽  
Michael Clarkson ◽  
Lynn Chalmers ◽  
John F. Taylor ◽  
Herve Migaud ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Microbial Communities ◽  
16S Rrna Gene Sequencing ◽  
Fish Growth ◽  
Organic Load ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Recirculating Aquaculture ◽  
Recirculating Aquaculture Systems ◽  
Rrna Gene Sequencing

Atlantic salmon aquaculture is undergoing an expansion of land-based recirculating aquaculture systems (RAS), especially for freshwater (FW) stages of production. Juvenile salmon undergo parr-smolt transformation, also known as smoltification and become pre-adapted to tolerate seawater (SW). One aspect requiring study is the development of microbial communities during this time, especially in RAS systems. Here we analyzed temporal changes in microbiome associated with the intestine in Atlantic salmon during smolt production in a commercial RAS production facility and followed the same cohort of fish post-seawater transfer (SWT), using 16S rRNA gene sequencing. Microbial diversity and richness showed an increase over time across FW production, but declined sharply and significantly 1-week post-SWT before re-establishing itself with a completely different community structure after 4 weeks. Core microbial taxa could be assigned to three distinct categories; (1) omnipresent, (2) salinity specific, or (3) transient. By including diet and water samples in the analyses, we classified true core taxa associated with the host, those associated with the diet, and transient cores associated with microbial communities in tank water. The rising trend observed in microbial richness in the water may be a consequence of a temporal increase in organic load while dominance of Vibrionaceae may be attributed to the higher temperatures maintained during RAS production and above average natural water temperatures post-SWT. Functional analysis suggests modulation of metabolic pathways post-SWT, but downstream impacts on fish growth and health in a commercial setting remain to be elucidated. A deeper understanding of the interplay between microbial composition and functionality can play a role in optimizing fish performance in tightly regulated RAS production.

scholarly journals Enriched Microbial Communities for Ammonium and Nitrite Removal from Recirculating Aquaculture Systems

2021 ◽  
Author(s):  
Alireza Neissi ◽  
Gholamreza Rafiee ◽  
Shadi Rahimi ◽  
Hamid Farahmand ◽  
Santosh Pandit ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Performance ◽  
Pathogenic Bacteria ◽  
Environmental Water ◽  
Recirculating Aquaculture ◽  
Expression Of Genes ◽  
Recirculating Aquaculture Systems ◽  
Nitrite Oxidizing Bacteria ◽  
Nitrite Removal ◽  
Aquaculture Water

Abstract Background: The aim of this study was the enrichment of high-performance microbial communities in biofilters for removal of ammonium and nitrite from aquaculture water. Methods: Ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) were enriched from different environmental water samples. The microbial communities with higher ammonium and nitrite removal activity were selected and adapted to different temperatures [9 ºC, 15 ºC, room temperature (25 ºC), and 30 ºC]. The expression of genes involved in nitrification including ammonia monooxygenase (AMO) and nitrite oxidoreductase (NXR) were measured in temperature-adapted AOB and NOB microbiomes. The microbial species present in the selected microbiomes were identified via 16s rRNA sequencing. Results: The microbial communities containing Nitrosomonas oligotropha and Nitrobacter winogradskyi showed the highest ammonium and nitrite removal activity at all temperatures used for adaptation. Furthermore, the microbial communities do not contain any pathogenic bacteria. They also exhibited the highest expression of AMO and NXR genes. Using the enriched microbial communities, we achieved a 288% and 181% improvement in ammonium and nitrite removal over the commonly used communities in biofilters at 9 °C, respectively. Conclusions: These results suggest that the selected microbiomes allowed for a significant improvement of water quality in a recirculating aquaculture system (RAS).

scholarly journals Component Microenvironments and System Biogeography Structure Microorganism Distributions in Recirculating Aquaculture and Aquaponic Systems

mSphere ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Ryan P. Bartelme ◽  
Matthew C. Smith ◽  
Osvaldo J. Sepulveda-Villet ◽  
Ryan J. Newton
Keyword(s):  
Microbial Community ◽  
Waste Management ◽  
System Design ◽  
Management Practices ◽  
System Optimization ◽  
Plant Production ◽  
Rrna Gene ◽  
Edible Plant ◽  
Recirculating Aquaculture ◽  
Recirculating Aquaculture Systems

ABSTRACTFlowthrough and pond aquaculture system microbiome management practices aim to mitigate fish disease and stress. However, the operational success of recirculating aquaculture systems (RAS) depends directly on system microbial community activities. In RAS, each component environment is engineered for a specific microbial niche for waste management, as the water continuously flowing through the system must be processed before returning to the rearing tank. In this study, we compared waste management component microbiomes (rearing tank water, pH correction tank, solid-waste clarifier, biofilter, and degassing tower) within a commercial-scale freshwater RAS by high-throughput 16S rRNA gene sequencing. To assess consistency among freshwater RAS microbiomes, we also compared the microbial community compositions of six aquaculture and aquaponic farms. Community assemblages reflected site and source water relationships, and the presence of a hydroponic subsystem was a major community determinant. In contrast to the facility-specific community composition, some sequence variants, mainly classified intoFlavobacterium,Cetobacterium, the familySphingomonadaceae, and nitrifying guilds of ammonia-oxidizing archaea andNitrospira, were common across all facilities. The findings of this study suggest that, independently of system design, core taxa exist across RAS rearing similar fish species but that system design informs the individual aquatic microbiome assemblages. Future RAS design would benefit from understanding the roles of these core taxa and then capitalizing on their activities to further reduce system waste/added operational controls.IMPORTANCERecirculating aquaculture systems (RAS) are agroecosystems for intensive on-land cultivation of products of fisheries. Practitioners that incorporate edible plant production into RAS refer to these facilities as aquaponic systems (AP). RAS have the potential to offset declining production levels of wild global fisheries while reducing waste and product distance to market, but system optimization is needed to reduce costs. Both RAS and AP rely on microbial consortia for maintaining water quality and promoting fish/plant health, but little is known about the microorganisms actually present. This lack of knowledge prevents optimization of designs and operational controls to target the growth of beneficial microbial species or consortia. The significance of our research is in identifying the common microorganisms that inhabit production RAS and AP and the operational factors that influence which microorganisms colonize and become abundant. Identifying these organisms is a first step toward advanced control of microbial activities that improve reproducibility and reduce costs.

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