scholarly journals Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Daniela Rosado ◽  
Raquel Xavier ◽  
Jo Cable ◽  
Ricardo Severino ◽  
Pedro Tarroso ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Diversity ◽  
Water Temperature ◽  
Abiotic Factors ◽  
Seasonal Effect ◽  
Microbial Composition ◽  
Surrounding Water ◽  
European Seabass ◽  
And Function ◽  
The Impact

AbstractFish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

scholarly journals Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiome of Sorghum bicolor

2020 ◽  
Author(s):  
Heidi M.-L. Wipf ◽  
Ling Xu ◽  
Cheng Gao ◽  
Hannah B. Spinner ◽  
John Taylor ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Soil Health ◽  
Soil Management ◽  
Soil Microbiome ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Cover Cropping ◽  
And Function ◽  
The Impact ◽  
Plant Microbiome

Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California’s San Joaquin Valley that is under long-term cultivation with 1) standard (ST) or no tilling (NT) and 2) cover-cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal communities, versus bacterial. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. Additionally, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome and inform future efforts to configure trait-associated microbiomes in crops. Importance While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, there is very little work published on how the corresponding crop plant microbiome is impacted. With bacteria and fungi known to critically affect soil health and plant growth, we concurrently compared how the practices of no and standard tillage, in combination with either cover-cropping or fallow fields, shape soil and plant-associated microbiomes between the two classifications. In determining not only the response to treatment in microbial diversity and composition, but for activity as well, this work demonstrates the significance of agronomic practice in modulating plant-microbe interactions, as well as encourages future work on the mechanisms involved in community assemblages supporting similar crop outcomes.

Study on the Impact of Water Environmental Factors on Dominant Species of Phytoplankton around the Power Plant in Xiangshan Bay

2012 ◽  
Vol 610-613 ◽  
pp. 3371-3374 ◽  
Author(s):  
Hong Yang ◽  
Ying Zhao ◽  
Hui Rong Zhang ◽  
Gui Xiang Dai ◽  
Jun Ding ◽  
...  
Keyword(s):  
Power Plant ◽  
Environmental Factors ◽  
Statistical Model ◽  
Water Temperature ◽  
Temperature Increase ◽  
Dominant Species ◽  
Thermal Discharge ◽  
Xiangshan Bay ◽  
The Impact ◽  
Growth And Reproduction

The SPSS19.0 software was used to analyse the data of enclosure experiments last for 7 days in summer of 2011. Water temperature increase as a factor to establish the statistical model, and the response relation of thermal discharge warming and Coscinodiscus Jonesianus biomass was analyzed quantitatively. The results showed that, it would promote Coscinodiscus Jonesianus growth and reproduction with the water warming at 0.2°C to 0.79°C , which would be restrained at the water warming at 0.8°C to 2.0°C. When the water temperature increase 0.1°C, 0.4°C and 0.7°Cwill respectively result in Coscinodiscus Jonesianus biomass grow 216.12%, 72.87% and 15.05%. While the water temperature increase 1.0°C, 1.5°C and 2.0°C will respectively result in Coscinodiscus Jonesianus biomass reduce 6.38%, 17.95% and 26.17%.

scholarly journals The Destruction of the Anaerobic Environment Caused by Rumen Fistula Surgery Leads to Differences in the Rumen Microbial Diversity and Function of Sheep

2021 ◽  
Vol 8 ◽  
Author(s):  
Yurong Cao ◽  
Baozhen Zhu ◽  
Fei Li ◽  
Duihong Zhang ◽  
Tongqing Guo ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Relative Abundance ◽  
Neutral Detergent Fiber ◽  
Apparent Digestibility ◽  
Acid Detergent Fiber ◽  
Male Adult ◽  
Fistula Surgery ◽  
And Function ◽  
The Impact ◽  
Anaerobic Environment

This experiment was to study the impact of rumen fistula surgery on the rumen microbios in sheep. Six male adult Hu sheep (48.8 ± 0.23 kg, 0.5 years) were fed at 0700 and 1,800 with ad libitum access to water. The rumen fistula was installed in the same batch from 0600 to 0900. Monitoring the dry mater intake and the output of dry mater faces 1, 2, 4, 6, 8, 10, 12, 14 days after fistulated surgery. The collection of rumen fluid was arranged at 1d during rumen surgery (DRS1), 3d after rumen surgery (ARS3), and 14d after rumen surgery (ARS14) for volatile fatty acid (VFA) and DNA extraction for sequencing and bioinformatics analysis. There was no difference in DMI, the pH apparent digestibility of dry matter, organic matter, neutral detergent fiber, acid detergent fiber both before and 14 days after surgery. Increases were observed in the acetate and total VFA at ARS3. There was no difference in digestion of dry material, organic material, neutral detergent fiber, and acid detergent fiber before and after surgery. The relative abundance of Bacteroides decreased from 61.96% at DRS1 to 28.85% at ARS3. In comparison with the DRS1 and ARS3, the relative abundance of Firmicutes in the ARS14 increased to 44.58% (P < 0.01). Proteobacteria increased from 11.33% at DRS1 to 51.66% at ARS3 and then decreased to 11.39% at ARS14. Prevotella decreased form 61.06% at DRS1 to 28.04% in the ARS3. Succinivibrio increased from 8.32% at DRS1 to 48.58% at ARS3, but decreased to 10.43% in the ARS14. Compared with DRS1 and ARS3, the ARS14 was higher in the Simpson and Shannon index. As for the BugBase function prediction, rumen fistula surgery increased the microorganism abundance of aerobic and facultative anaerobic phenotype, and anaerobic phenotype was decreased in the ARS3. There was higher microorganism abundance of aerobic phenotype in the ARS14 than before fistula installation. In conclusion, the rumen fistula surgery destroys the anaerobic environment of rumen, leading to differences in rumen microbial diversity and function, but the apparent digestibility and total VFA were not affected.

scholarly journals Long term exposure of human gut microbiota with high and low emulsifier sensitivity to soy lecithin in M-SHIME model.

2021 ◽  
Author(s):  
Lisa Miclotte ◽  
Ellen De Paepe ◽  
Qiqiong Li ◽  
Andreja Rajkovic ◽  
John Van Camp ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Day Treatment ◽  
Treatment Phase ◽  
Microbial Composition ◽  
Soy Lecithin ◽  
Potential Health ◽  
And Function ◽  
The Impact

In the context of the potential health hazards related to food processing, dietary emulsifiers have been shown to alter the structure and function of the gut microbial community, both in vivo and in vitro. In mouse models, these emulsifier exposed gut microbiota were shown to contribute to gut inflammation. Several knowledge gaps remain to be addressed though. As such, the impact from a longer timeframe of exposure on the gut microbiota is not known and interindividual variability in microbiome response needs to be measured. To answer these research questions, in this study the faecal microbiota from two individuals, previously selected for high and low emulsifier sensitivity, were exposed to two concentrations of soy lecithin during a 7 day treatment phase in the dynamic mucosal simulator of the human intestinal microbial ecosystem (M-SHIME). The results showed mild effects from soy lecithin on the composition and functionality of these microbial communities, which depended on the original microbial composition. The effects also mostly levelled off after 3 days of exposure. The emulsifier sensitivity for which the microbiota were selected, was preserved. Some potentially concerning effects were also registered: butyrate levels, positively correlating with Faecalibacterium abundance, were lowered by soy lecithin. Also the abundance of the beneficial Bifidobacterium genus was lowered, while the abundance of the notorious unclassified Enterobacteriaceae was increased. Within the family of the unclassified Lachnospiraceae, several genera were either suppressed or stimulated. The effects that these microbial alterations would have on a living host is not yet certain, especially given the fact that large fractions of soy lecithins constituents can be absorbed. Nevertheless, choline and phosphatidylcholine, both primary and absorbable constituents of soy lecithin, have recently been linked to cardiovascular disease via the generation of TMA by the gut microbiota. Further studies that validate our findings and link them to potential health outcomes are thus justified.

scholarly journals Large-scale spatial heterogeneity of macrozooplankton in Lake of Geneva

1999 ◽  
Vol 56 (8) ◽  
pp. 1437-1451 ◽  
Author(s):  
Bernadette Pinel-Alloul ◽  
Catherine Guay ◽  
Nadine Angeli ◽  
Pierre Legendre ◽  
Pierre Dutilleul ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Water Temperature ◽  
Chlorophyll A ◽  
Large Scale ◽  
Abiotic Factors ◽  
Distribution Patterns ◽  
Small Scale ◽  
Lake Basin ◽  
Fish Biomass ◽  
Trophic Groups

Spatial distribution of macrozooplankton was studied during spring in Lake of Geneva to evaluate the influence of abiotic (water temperature and stability, nutrients) and biotic (bacteria, chlorophyll a, fish biomass) factors on macrozooplankton distribution. Mapping and spatial analyses revealed that abiotic factors, as well as crustacean abundances, were structured along a gradient in the great lake basin. Chlorophyll a biomass, bacteria density, cyclopoid abundance, and fish biomass showed more patchy or inshore-offshore distribution patterns. Using canonical analyses, we determined the relative contribution of the spatial and environmental factors to the distribution of macrozooplankton species and of trophic groups based on herbivory and omnivory/carnivory. The distribution of macrozooplankton can be explained by small-scale variations and lake gradients in abiotic and biotic factors, with a dominant contribution of the abiotic factors. Water temperature and stability, as well as ammonium, are the main factors related to macrozooplankton distribution in Lake of Geneva during spring. Chlorophyll a biomass was also related to the distribution of cyclopoids. The canonical models explained 35-72% of the variance in the distribution of total crustaceans, species, and trophic groups. However, 28-65% of the macrozooplankton variance remained unexplained, which may be due to fine-scale variations in other environmental factors.

scholarly journals The Upper Airway Microbiota, Environmental Exposures, Inflammation, and Disease

Medicina ◽  
2021 ◽  
Vol 57 (8) ◽  
pp. 823
Author(s):  
Ziyad Elgamal ◽  
Pratyush Singh ◽  
Patrick Geraghty
Keyword(s):  
Upper Airway ◽  
Environmental Exposures ◽  
Microbial Composition ◽  
Upper Airways ◽  
Airborne Pollutants ◽  
Host Interactions ◽  
Microbial Profile ◽  
And Function ◽  
Community Segregation ◽  
The Impact

Along with playing vital roles in pathogen exclusion and immune system priming, the upper airways (UAs) and their microbiota are essential for myriad physiological functions such as conditioning and transferring inhaled air. Dysbiosis, a microbial imbalance, is linked with various diseases and significantly impedes the quality of one’s life. Daily inhaled exposures and/or underlying conditions contribute to adverse changes to the UA microbiota. Such variations in the microbial community exacerbate UA and pulmonary disorders via modulating inflammatory and immune pathways. Hence, exploring the UA microbiota’s role in maintaining homeostasis is imperative. The microbial composition and subsequent relationship with airborne exposures, inflammation, and disease are crucial for strategizing innovating UA diagnostics and therapeutics. The development of a healthy UA microbiota early in life contributes to normal respiratory development and function in the succeeding years. Although different UA cavities present a unique microbial profile, geriatrics have similar microbes across their UAs. This lost community segregation may contribute to inflammation and disease, as it stimulates disadvantageous microbial–microbial and microbial–host interactions. Varying inflammatory profiles are associated with specific microbial compositions, while the same is true for many disease conditions and environmental exposures. A shift in the microbial composition is also detected upon the administration of numerous therapeutics, highlighting other beneficial and adverse side effects. This review examines the role of the UA microbiota in achieving homeostasis, and the impact on the UAs of environmental airborne pollutants, inflammation, and disease.

scholarly journals Evolution of fungal community associated with ready-to-eat pineapple during storage under different temperature conditions

2020 ◽  
Author(s):  
Evanthia Manthou ◽  
Gwendoline Coeuret ◽  
Stephane Chaillou ◽  
George-John E. Nychas
Keyword(s):  
Environmental Factors ◽  
Fungal Community ◽  
Large Scale ◽  
Influencing Factor ◽  
Amplicon Sequencing ◽  
Fungal Species ◽  
Its2 Region ◽  
Microbial Composition ◽  
Fresh Cut ◽  
The Impact

AbstractThe international market of fresh-cut products has witnessed dramatic growth in recent years, stimulated by consumer’s demand for healthy, nutritious and convenient foods. One of the main challenging issues for the quality and safety of these products is the potential microbial spoilage that can significantly reduce their shelf-life. The complete identification of fresh-cut product microbiota together with the evaluation of environmental factors impact on microbial composition is of primary importance. We therefore assessed the fungal communities associated with the spoilage of ready-to-eat (RTE) pineapple using a metagenetic amplicon sequencing approach, based on the ITS2 region. Our results revealed a significant variability on fungal species composition between the different batches of RTE pineapple. The initial microbiota composition was the main influencing factor and determined the progress of spoilage. Temperature and storage time were the secondary factors influencing spoilage and their impact was depending on the initial prevalent fungal species, which showed different responses to the various modifications. Our results strongly suggest that further large-scale sampling of RTE pineapple production should be conducted in order to assess the full biodiversity range of fungal community involved in the spoilage process and for unravelling the impact of important environmental factors shaping the initial microbiota.

scholarly journals Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

2021 ◽  
Vol 12 ◽  
Author(s):  
Ludek Sehnal ◽  
Elizabeth Brammer-Robbins ◽  
Alexis M. Wormington ◽  
Ludek Blaha ◽  
Joe Bisesi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Aquatic Ecosystems ◽  
Marine Mammals ◽  
Integrative Approach ◽  
Aquatic Animal ◽  
Gastrointestinal Microbiota ◽  
Microbial Composition ◽  
Aquatic Vertebrates ◽  
And Function ◽  
The Impact

Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.

Analysis of Colon Microbial Diversity of African Ostriches at Different Ages

2020 ◽  
Author(s):  
Peng Li ◽  
Yan Zhang ◽  
Jie Yang ◽  
Xiaoting Zhang ◽  
Lixun Ye ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Intestinal Tract ◽  
Microbial Population ◽  
Middle Part ◽  
Sequencing Technology ◽  
Microbial Composition ◽  
Different Ages ◽  
And Function ◽  
Dominant Bacteria ◽  
Richness Index

Abstract Background:The colon is the unique digestive organ of the African ostrich. It has a large microbial population, which plays an important role in the digestive process of the African ostriches. Methods: In order to understand the diversity of colon microbes in African ostriches, this study used metagenomics sequencing technology to sequence and analyze the colonic microbes of African ostriches at the age of 7, 30, 60 and 180 days. Results: The results showed that with the increase of age, the microbial richness index first increased and then decreased, the highest at 60 days of age (ACE 271.5, Chao1 274.097), while the microbial diversity gradually reduced with the increase of age, the highest at 7 days ( Shannon 3.203, Simpson 0.104). At the phylum level, the dominant bacteria phylum at 7 days of age is Firmicutes, while at 30 days of age, the phyla Firmicutes and Tenericutes are dominant phyla, and the abundance of Proteobacteria is highest at 60 days of age and 180 days of age. At the genus level, the dominant bacteria in the colon at 7 and 30 days are Anaeroplasma and Bacteroides. Acinetobacter is the dominant genus at 60 days, and the dominant genus at 180 days is Pseudomonas. PCA analysis showed that the microbial composition in the 180-day-old colon was very different from other days. The microbial composition in the anterior and middle part of the colon at 7-day-old was similar to that of 30-day-old, while the microbial composition in the latter part was similar to that of 60-day-old. Results of LEfSe analysis showed that there were 34, 37, and 36 differential flora in the colon at 7, 30, and 60 days, respectively, while there was only one differential flora at 180 days of age. Conclusion: The results of the study showed that the composition of the microbial community in the colon of African ostriches of different ages is different and there are different flora, but the microbes in the colon are still mainly concentrated in the phylum Firmicutes, Tenericutes, and Proteobacteria, which gives the intestinal tract and function of the African ostrich further research provides a theoretical basis.

scholarly journals Experimental warming reduces the diversity and functional potential of theSphagnummicrobiome

2017 ◽  
Author(s):  
Alyssa A. Carrell ◽  
Max Kolton ◽  
Melissa J. Warren ◽  
Dale A. Pelletier ◽  
Jennifer B. Glass ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Structure And Function ◽  
Peat Moss ◽  
Experimental Warming ◽  
Ecosystem Productivity ◽  
Functional Potential ◽  
Nitrogen Fixation Activity ◽  
Reduction Assay ◽  
And Function ◽  
The Impact

AbstractClimate change may reduce biodiversity leading to a reduction in ecosystem productivity. Despite numerous reports of a strong correlation of microbial diversity and ecosystem productivity, little is known about the warming effects on plant associated microbes. Here we explore the impact of experimental warming on the microbial and nitrogen-fixing (diazotroph) community associated with the widespread and ecologically relevantSphagnumgenus in a field warming experiment. To quantify changes in the abundance, diversity, and community composition ofSphagnummicrobiomes with warming we utilized qPCR and Illumina sequencing of the 16S SSU rRNA andnifHgene. Microbial and diazotroph community richness and Shannon diversity decreased with warming (p<0.05). The diazotroph communities shifted from diverse communities to domination by primarilyNostocaceae(25% in control samples to 99% in elevated temperature samples). In addition, the nitrogen fixation activity measured with the acetylene reduction assay (ARA) decreased with warming treatment. This suggests the negative correlation of temperature and microbial diversity corresponds to a reduction in functional potential within the diazotroph community. The results indicate that climate warming may alter the community structure and function in peat moss microbiomes, with implications for impacts to host fitness and ecosystem productivity, and carbon uptake potential of peatlands.

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