scholarly journals The Growth of Leaf Lettuce and Bacterial Communities in a Closed Aquaponics System with Catfish

Horticulturae ◽  
2021 ◽  
Vol 7 (8) ◽  
pp. 222
Author(s):  
Kenji Yamane ◽  
Yuuki Kimura ◽  
Keita Takahashi ◽  
Isamu Maeda ◽  
Masayuki Iigo ◽  
...  
Keyword(s):  
Plant Growth ◽  
Early Stage ◽  
Amplicon Sequencing ◽  
Small Scale ◽  
Rrna Gene ◽  
Culture Solution ◽  
Beneficial Effects ◽  
Sustainable Cultivation ◽  
Microbial Groups ◽  
Production Period

Aquaponics is a circulating and sustainable system that combines aquaculture and hydroponics and forms a symbiotic relationship between fish, plants, and microorganisms. We hypothesized that feed alone could support plant growth, but the symbiosis with fish adds some beneficial effects on plant growth in aquaponics. In this study, we created three closed culture systems, namely, aquaponics, hydroponics without nitrogen (N) and phosphorus (P), and aquaculture, and added the same amount of feed containing N and P to all the treatments in order to test the hypothesis. Accumulation of NO3− and PO43− was alleviated in aquaponics and hydroponics as a result of plant uptake. Lettuce plants grown in aquaponics grew vigorously until 2 weeks and contained a constant level of N in plants throughout the production period, whereas those in hydroponics grew slowly in the early stage and then vigorously after 2 weeks with a late increment of N concentration. These results suggest that catfish help with the faster decomposition of the feed, but, in hydroponics, feed can be slowly dissolved and decomposed owing to the absence of the fish. The bacterial community structures of the culture solution were investigated using 16S rRNA gene amplicon sequencing. At the class level, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were the major microbial groups in the solutions. Aquaponics prevented the pollution of tank solution and maintained a higher water quality compared with hydroponics and aquaculture, suggesting that aquaponics is a more sustainable cultivation system even in a small-scale system.

Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill

2022 ◽  
Author(s):  
Yiqi Cao ◽  
Baiyu Zhang ◽  
Charles W. Greer ◽  
Kenneth Lee ◽  
Qinhong Cai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Late Stage ◽  
Large Scale ◽  
Community Dynamics ◽  
Early Stage ◽  
Small Scale ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Microcosm Studies ◽  
Over Time

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.

scholarly journals Insights into the Potential of the Atlantic Cod Gut Microbiome as Biomarker of Oil Contamination in the Marine Environment

2019 ◽  
Vol 7 (7) ◽  
pp. 209 ◽  
Author(s):  
Juline M. Walter ◽  
Andrea Bagi ◽  
Daniela M. Pampanin
Keyword(s):  
Gut Microbiota ◽  
Marine Environment ◽  
Gut Microbiome ◽  
Atlantic Cod ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Comparison Results ◽  
Southern Norway ◽  
Microbial Groups

Background: Microorganisms are widespread in all environments, including in and on animal bodies. The gut microbiome has an essential influence on fish health, and is affected by several persistent and harmful organic and inorganic contaminants. Considering the shifts in gut microbiota composition observed in those studies, we hypothesized that certain microbial groups in the gut can serve as indicators of pollution. To test this hypothesis, we explored the possibility of identifying key microbial players that indicate environmental contamination. Methods: Published 16S rRNA gene amplicon sequencing data generated from the gut microbiota of Atlantic cod caught in geographically different Norwegian waters were used for bacterial diversity comparison. Results: Different microbiomes were identified between the northern Norway and southern Norway samples. Several bacterial genera previously identified as polycyclic aromatic hydrocarbon degraders were present only in the samples collected in the southern Norway area, suggesting fish contamination with oil-related compounds. Conclusions: The results contribute to the identification of bacterial taxa present in the Atlantic cod gut that indicate fish exposure to contaminants in the marine environment.

scholarly journals Contribution of Maternal and Paternal Transmission to Bacterial Colonization in Nematostella vectensis

2021 ◽  
Vol 12 ◽  
Author(s):  
Laura Baldassarre ◽  
Shani Levy ◽  
Rinat Bar-Shalom ◽  
Laura Steindler ◽  
Tamar Lotan ◽  
...  
Keyword(s):  
Vertical Transmission ◽  
Bacterial Communities ◽  
Bacterial Colonization ◽  
Surrounding Medium ◽  
Model Organism ◽  
Amplicon Sequencing ◽  
Nematostella Vectensis ◽  
Rrna Gene ◽  
Surrounding Water ◽  
Beneficial Effects

Microbial communities confer multiple beneficial effects to their multicellular hosts. To evaluate the evolutionary and ecological implications of the animal-microbe interactions, it is essential to understand how bacterial colonization is secured and maintained during the transition from one generation to the next. However, the mechanisms of symbiont transmission are poorly studied for many species, especially in marine environments, where the surrounding water constitutes an additional source of microbes. Nematostella vectensis, an estuarine cnidarian, has recently emerged as model organism for studies on host-microbes interactions. Here, we use this model organism to study the transmission of bacterial colonizers, evaluating the contribution of parental and environmental transmission to the establishment of bacterial communities of the offspring. We induced spawning in adult male and female polyps of N. vectensis and used their gametes for five individual fertilization experiments. While embryos developed into primary polyps, we sampled each developmental stage and its corresponding medium samples. By analyzing the microbial community compositions of all samples through 16S rRNA gene amplicon sequencing, we showed that all host tissues harbor microbiota significantly different from the surrounding medium. Interestingly, oocytes and sperms are associated with distinct bacterial communities, indicating the specific vertical transmission of bacterial colonizers by the gametes. These differences were consistent among all the five families analyzed. By overlapping the identified bacterial ASVs associated with gametes, offspring and parents, we identified specific bacterial ASVs that are well supported candidates for vertical transmission via mothers and fathers. This is the first study investigating bacteria transmission in N. vectensis, and among few on marine spawners that do not brood larvae. Our results shed light on the consistent yet distinct maternal and paternal transfer of bacterial symbionts along the different life stages and generations of an aquatic invertebrate.

scholarly journals Bacterial Diversity in a Dynamic and Extreme Sub-Arctic Watercourse (Pasvik River, Norwegian Arctic)

Water ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3098
Author(s):  
Maria Papale ◽  
Alessandro Ciro Rappazzo ◽  
Anu Mikkonen ◽  
Carmen Rizzo ◽  
Federica Moscheo ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Algal Blooms ◽  
Heavy Metal Contamination ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
The Arctic ◽  
Rrna Gene ◽  
Environmental Perturbations ◽  
Water And Sediment ◽  
Microbial Groups

Microbial communities promptly respond to the environmental perturbations, especially in the Arctic and sub-Arctic systems that are highly impacted by climate change, and fluctuations in the diversity level of microbial assemblages could give insights on their expected response. 16S rRNA gene amplicon sequencing was applied to describe the bacterial community composition in water and sediment through the sub-Arctic Pasvik River. Our results showed that river water and sediment harbored distinct communities in terms of diversity and composition at genus level. The distribution of the bacterial communities was mainly affected by both salinity and temperature in sediment samples, and by oxygen in water samples. Glacial meltwaters and runoff waters from melting ice probably influenced the composition of the bacterial community at upper and middle river sites. Interestingly, marine-derived bacteria consistently accounted for a small proportion of the total sequences and were also more prominent in the inner part of the river. Results evidenced that particular conditions occurring at sampling sites (such as algal blooms, heavy metal contamination and anaerobiosis) may select species at local scale from a shared bacterial pool, thus favoring certain bacterial taxa. Conversely, the few phylotypes specifically detected in some sites are probably due to localized external inputs introducing allochthonous microbial groups.

scholarly journals Effect of Bacillus spp. on Lettuce Growth and Root Associated Bacterial Community in a Small-Scale Aquaponics System

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 947
Author(s):  
Nasser Kasozi ◽  
Horst Kaiser ◽  
Brendan Wilhelmi
Keyword(s):  
Water Quality ◽  
Control Systems ◽  
Deep Water ◽  
Bacterial Communities ◽  
Small Scale ◽  
Rrna Gene ◽  
Culture Solution ◽  
Water Culture ◽  
Lettuce Growth ◽  
The Mean

The integration of probiotics in aquaponics systems is a strategy for mitigating environmental impacts and for promoting sustainable agriculture. In order to understand the role of probiotics, we investigated the effect of a commercial probiotic mixture of Bacillus subtilis and B. licheniformis on the growth of lettuce (Lactuca sativa L.) under deep-water culture integrated with Mozambique tilapia (Oreochromis mossambicus). We determined plant growth, water quality parameters, and leaf mineral analysis, and assessed the influence of a probiotic mixture on the microbiota. Bacterial communities were analyzed by high-throughput 16S rRNA gene sequencing. Compared to the control systems, the addition of the probiotic Bacillus significantly increased the concentration of nitrate and phosphate in deep water culture solution, which contributed to improved lettuce growth. In both the growth trials, the Fv/Fm, the mean shoot dry weight, and the mean fresh weight of the harvested shoots from the Bacillus treatment were significantly higher than those observed for the control plants. Higher concentrations of phosphorus, potassium, and zinc in the lettuce leaves were found in systems that received the Bacillus. Although differences were observed at the phylum level, Proteobacteria and Bacteroidetes were predominant in both the Bacillus-treatment and the control systems. At the genus level, however, the communities present in the two types of systems were heterogeneous with Bacillus-treated systems, containing significantly higher numbers of Chryseobacterium, Bacillus, Nitrospira, Polynucleobacter, and Thermomonas. The results indicate that Bacillus supplementation can effectively alleviate nutrient deficiencies, improve water quality, and modify the composition of bacterial communities in aquaponics systems.

scholarly journals Fecal Microbiota Dynamics Reveal the Feasibility of Early Weaning of Yak Calves under Conventional Grazing System

Biology ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 31
Author(s):  
Jianbo Zhang ◽  
Peng Wang ◽  
Renqing Dingkao ◽  
Mei Du ◽  
Anum Ali Ahmad ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Early Stage ◽  
Amplicon Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Early Weaning ◽  
Glucose And Lipid Metabolism ◽  
Blood Biochemical ◽  
Bacterial Microbiota ◽  
Significant Difference

Background: The gut microbiota plays an important role in the health and production of animals. However, little information is available on the dynamic variations and comparison of intestinal microbiota in post-weaning yak calves living on the QTP. Methods: We explored the fecal bacterial microbiota succession of yak calves at different months after early weaning (60 d) compared with cattle calves by 16S rRNA gene amplicon sequencing and functional composition prediction. Results: We found no significant difference in blood biochemical parameters related to glucose and lipid metabolism between yaks and calves in different months after weaning. The core fecal bacterial microbiota from both species of calves was dominated by Ruminococcaceae, Rikenellaceae, and Bacteroidaceae. The fecal microbial community has a great alteration within the time after weaning in both cattle and yak calves, but cattle showed a larger change. After five months, the microbiota achieves a stable and concentrated state. This is also similar to the functional profile. Conclusions: Based on the exploration of dynamic changes in the fecal microbiota at an early stage of life, our results illustrated that there were no negative effects of intestinal microbiota succession on yak calves when early weaning was employed.

scholarly journals Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert C. Kaplan ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
Martha L. Daviglus ◽  
...  
Keyword(s):  
Community Health ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Health Study ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Hispanic Community ◽  
The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

scholarly journals Gluconacetobacter diazotrophicus Pal5 Enhances Plant Robustness Status under the Combination of Moderate Drought and Low Nitrogen Stress in Zea mays L.

2021 ◽  
Vol 9 (4) ◽  
pp. 870
Author(s):  
Muhammad Aammar Tufail ◽  
María Touceda-González ◽  
Ilaria Pertot ◽  
Ralf-Udo Ehlers
Keyword(s):  
Zea Mays ◽  
Plant Growth ◽  
Zea Mays L ◽  
Growth Promotion ◽  
Nitrogen Stress ◽  
Rrna Gene ◽  
N Fixation ◽  
Gluconacetobacter Diazotrophicus ◽  
Maize Plants ◽  
Low Nitrogen

Plant growth promoting endophytic bacteria, which can fix nitrogen, plays a vital role in plant growth promotion. Previous authors have evaluated the effect of Gluconacetobacter diazotrophicus Pal5 inoculation on plants subjected to different sources of abiotic stress on an individual basis. The present study aimed to appraise the effect of G. diazotrophicus inoculation on the amelioration of the individual and combined effects of drought and nitrogen stress in maize plants (Zea mays L.). A pot experiment was conducted whereby treatments consisted of maize plants cultivated under drought stress, in soil with a low nitrogen concentration and these two stress sources combined, with and without G. diazotrophicus seed inoculation. The inoculated plants showed increased plant biomass, chlorophyll content, plant nitrogen uptake, and water use efficiency. A general increase in copy numbers of G. diazotrophicus, based on 16S rRNA gene quantification, was detected under combined moderate stress, in addition to an increase in the abundance of genes involved in N fixation (nifH). Endophytic colonization of bacteria was negatively affected by severe stress treatments. Overall, G. diazotrophicus Pal5 can be considered as an effective tool to increase maize crop production under drought conditions with low application of nitrogen fertilizer.

scholarly journals Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Janis R. Bedarf ◽  
Naiara Beraza ◽  
Hassan Khazneh ◽  
Ezgi Özkurt ◽  
David Baker ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
False Positive ◽  
Gene Sequencing ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

scholarly journals Retinitis pigmentosa is associated with shifts in the gut microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Oksana Kutsyr ◽  
Lucía Maestre-Carballa ◽  
Mónica Lluesma-Gomez ◽  
Manuel Martinez-Garcia ◽  
Nicolás Cuenca ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Gut Microbiome ◽  
Functional Decline ◽  
Retinal Disease ◽  
Photoreceptor Cells ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Alpha And Beta Diversity ◽  
Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

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