scholarly journals Aquaculture Water Quality Improvement by Mixed Bacillus and Its Effects on Microbial Community Structure

2021 ◽  
Author(s):  
Xue Li ◽  
Tianie Wang ◽  
Baorong Fu ◽  
Xiyan Mu
Keyword(s):  
Water Quality ◽  
Community Structure ◽  
Microbial Community ◽  
Relative Abundance ◽  
Bacillus Megaterium ◽  
Microbial Community Structure ◽  
Pathogenic Bacteria ◽  
Phosphorus Compounds ◽  
Nitrogen And Phosphorus ◽  
Aquaculture Water

Abstract Nutrients nitrogen and phosphorus pollution in aquaculture is one of the greatest challenges threatening the survival of aquatic organisms, which requires efficient and sustainable remediation approach. Microbial remediation, especially the application of probiotics, has recently gained popularity in improving the water quality and maintaining the health condition of aquatic animals. In the present study, two groups of mixed Bacillus (Bacillus megaterium and Bacillus subtilis (A0+BS) and Bacillus megaterium and Bacillus coagulans (A0+BC)) were applied to aquaculture system of Crucian carp to improve the treatment of nitrogenous and phosphorus compounds. The effects of mixed Bacillus on water quality, and the structure and function of microbial communities in aquaculture water were investigated. Our results showed that the improvement effect of mixed Bacillus A0+BS on water quality was better than that of A0+BC, and the NH4+-N, NO2--N, NO3--N and total phosphorus (TP) concentrations were reduced by 46.3%, 76.3%, 35.6%, and 80.3%, respectively. In addition, both groups of mixed Bacillus increased the diversity of bacterial community and decreased the diversity of fungal community. Microbial community analysis showed that mixed Bacillus A0+BS increased the relative abundance of bacteria related with nitrogen and phosphorus removal, e.g., Proteobacteria, Actinobacteria, Comamonas, and Stenotrophomonas, but decreased the relative abundance of pathogenic bacteria (Acinetobacter and Pseudomonas) and fungi (Epicoccum and Fusarium). The redundancy analysis showed that NH4+-N, NO2--N, and TP were primary environmental factors affecting the microbial community in aquaculture water. PICRUST analysis indicated that all functional pathways in the treatment groups were up-regulated, and all pathways in A0+BS group were richer than those in other groups. These results indicated that mixed Bacillus A0+BS addition produced good results in reducing nitrogenous and phosphorus compounds and shaped a favorable microbial community structure to further improve water quality.

scholarly journals Effects of tobacco–peanut relay intercropping on soil bacteria community structure

2019 ◽  
Vol 69 (13) ◽  
pp. 1531-1536 ◽  
Author(s):  
Lin Gao ◽  
Xin-min Liu ◽  
Yong-mei Du ◽  
Hao Zong ◽  
Guo-ming Shen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Soil Bacteria ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Continuous Cropping ◽  
Soil Microbial ◽  
Relay Intercropping ◽  
Bacteria Community Structure

Abstract Purpose A reasonable cultivation pattern is beneficial to maintain soil microbial activity and optimize the structure of the soil microbial community. To determine the effect of tobacco−peanut (Nicotiana tabacum−Arachis hypogaea) relay intercropping on the microbial community structure in soil, we compared the effects of relay intercropping and continuous cropping on the soil bacteria community structure. Methods We collected soil samples from three different cropping patterns and analyzed microbial community structure and diversity using high-throughput sequencing technology. Result The number of operational taxonomic units (OTU) for bacterial species in the soil was maximal under continuous peanut cropping. At the phylum level, the main bacteria identified in soil were Proteobacteria, Actinobacteria, and Acidobacteria, which accounted for approximately 70% of the total. The proportions of Actinobacteria and Firmicutes increased, whereas the proportion of Proteobacteria decreased in soil with tobacco–peanut relay intercropping. Moreover, the proportions of Firmicutes and Proteobacteria among the soil bacteria further shifted over time with tobacco–peanut relay intercropping. At the genus level, the proportions of Bacillus and Lactococcus increased in soil with tobacco–peanut relay intercropping. Conclusion The community structure of soil bacteria differed considerably with tobacco–peanut relay intercropping from that detected under peanut continuous cropping, and the proportions of beneficial bacteria (the phyla Actinobacteria and Firmicutes, and the genera Bacillus and Lactococcus) increased while the proportion of potentially pathogenic bacteria (the genera Variibacter and Burkholderia) decreased. These results provide a basis for adopting tobacco–peanut relay intercropping to improve soil ecology and microorganisms, while making better use of limited cultivable land.

scholarly journals Simulation-based approaches to characterize metagenome coverage as a function of sequencing effort and microbial community structure

2018 ◽  
Author(s):  
Taylor Royalty ◽  
Andrew D. Steen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Genome Size ◽  
Relative Abundance ◽  
Microbial Community Structure ◽  
Software Tool ◽  
Individual Genome ◽  
Base Pairs ◽  
Simulation Based ◽  
Sequencing Experiment

AbstractWe applied simulation-based approaches to characterize how microbial community structure influences the amount of sequencing effort to reconstruct metagenomes that are assembled from short read sequences. An initial analysis evaluated the quantity, completion, and contamination of complete-metagenome-assembled genome (complete-MAG) equivalents, a bioinformatic-pipeline normalized metric for MAG quantity, as a function of sequencing effort, on four preexisting sequence read datasets taken from a maize soil, an estuarine sediment, the surface ocean, and the human gut. These datasets were subsampled to varying degrees of completeness in order to simulate the effect of sequencing effort on MAG retrieval. Modeling suggested that sequencing efforts beyond what is typical in published experiments (1 to 10 Gbp) would generate diminishing returns in terms of MAG binning. A second analysis explored the theoretical relationship between sequencing effort and the proportion of available metagenomic DNA sequenced during a sequencing experiment as a function of community richness, evenness, and genome size. Simulations from this analysis demonstrated that while community richness and evenness influenced the amount of sequencing required to sequence a community metagenome to exhaustion, the effort necessary to sequence an individual genome to a target fraction of exhaustion was only dependent on the relative abundance of the corresponding organism and its genome size. A software tool, GRASE, was created to assist investigators further explore this relationship. Re-evaluation of the relationship between sequencing effort and binning success in the context of the relative abundance of genomes, as opposed to base pairs, provides a framework to design sequencing experiments based on the relative abundance of microbes in an environment rather than arbitrary levels of sequencing effort.

scholarly journals Water Quality and Microbial Community Changes in an Urban River after Micro-Nano Bubble Technology in Situ Treatment

Water ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 66 ◽  
Author(s):  
Yifei Wu ◽  
Hui Lin ◽  
Weizhao Yin ◽  
Sicheng Shao ◽  
Sihao Lv ◽  
...  
Keyword(s):  
Water Quality ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Oxygen Demand ◽  
Ammonia Nitrogen ◽  
Oxidation Reduction ◽  
Oxidation Reduction Potential ◽  
Dominant Bacteria

Currently, black-odor river has received great attention in China. In this study, the micro-nano bubble technology (MBT) was used to mitigate the water pollution rapidly and continuously by increasing the concentration of dissolved oxygen (DO) in water. During treatment, the concentration of DO increased from 0.60 mg/L to over 5.00 mg/L, and the oxidation reduction potential (ORP) also changed from a negative value to over 100.00 mV after only five days aeration. High throughput pyrosequencing technology was employed to identify the microbial community structure. At genus level, the dominant bacteria were anaerobic and nutrient-loving microbes (e.g., Arcobacter sp., Azonexus sp., and Citrobacter sp.) before, and the relative abundances of aerobic and functional microbes (e.g., Perlucidibaca sp., Pseudarcicella sp., Rhodoluna sp., and Sediminibacterium sp.) were increased after treatment. Meanwhile, the water quality was significantly improved with about 50% removal ratios of chemical oxygen demand (CODCr) and ammonia nitrogen (NH4+-N). Canonical correspondence analysis (CCA) results showed that microbial community structure shaped by COD, DO, NH4+-N, and TP, CCA1 and CCA2 explained 41.94% and 24.56% of total variances, respectively. Overall, the MBT could improve the water quality of urban black-odor river by raising the DO and activate the aerobic microbes.

Altered microbial community structure and metabolism in cow’s milk allergic mice treated with oral immunotherapy and fructo-oligosaccharides

2020 ◽  
Vol 11 (1) ◽  
pp. 19-32
Author(s):  
M.M. Vonk ◽  
P.A. Engen ◽  
A. Naqib ◽  
S.J. Green ◽  
A. Keshavarzian ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Propionic Acid ◽  
Butyric Acid ◽  
Relative Abundance ◽  
Microbial Community Structure ◽  
Oral Immunotherapy ◽  
Cow’S Milk ◽  
Microbiota Composition ◽  
Faecal Samples

Previously, we showed enhanced efficacy of oral immunotherapy (OIT) using fructo-oligosaccharides (FOS, prebiotics) added to the diet of cow’s milk allergic mice indicated by a reduction in clinical symptoms and mast cell degranulation. Prebiotics are fermented by gut bacteria, affecting both bacterial composition and availability of metabolites (i.e. short-chain fatty acids (SCFA)). It is thus far unknown which microbial alterations are involved in successful outcomes of OIT with prebiotic supplementation for the treatment of food allergy. To explore potential changes in the microbiota composition and availability of SCFA induced by OIT+FOS. C3H/HeOuJ mice were sensitised and received OIT with or without a FOS supplemented diet. After three weeks, faecal samples were collected to analyse gut microbiota composition using 16S rRNA sequencing. SCFA concentrations were determined in cecum content. FOS supplementation in sensitised mice changed the overall microbial community structure in faecal samples compared to sensitised mice fed the control diet (P=0.03). In contrast, a high level of resemblance in bacterial community structure was observed between the non-sensitised control mice and the OIT+FOS treated mice. OIT mice showed an increased relative abundance of the dysbiosis-associated phylum Proteobacteria compared to the OIT+FOS mice. FOS supplementation increased the relative abundance of genus Allobaculum (Firmicutes), putative butyrate-producing bacteria. OIT+FOS reduced the abundances of the genera’s unclassified Rikenellaceae (Bacteroidetes, putative pro-inflammatory bacteria) and unclassified Clostridiales (Firmicutes) compared to sensitised controls and increased the abundance of Lactobacillus (Firmicutes, putative beneficial bacteria) compared to FOS. OIT+FOS mice had increased butyric acid and propionic acid concentrations. OIT+FOS induced a microbial profile closely linked to non-allergic mice and increased concentrations of butyric acid and propionic acid. Future research should confirm whether there is a causal relationship between microbial modulation and the reduction in acute allergic symptoms induced by OIT+FOS.

scholarly journals Water quality and microbial community structure in juvenile Atlantic cod (Gadus morhua L.) cultures

Aquaculture ◽  
2011 ◽  
Vol 316 (1-4) ◽  
pp. 111-120 ◽  
Author(s):  
Terje van der Meeren ◽  
Laila Brunvold ◽  
Ruth-Anne Sandaa ◽  
Øivind Bergh ◽  
Tonje Castberg ◽  
...  
Keyword(s):  
Water Quality ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Gadus Morhua ◽  
Atlantic Cod

scholarly journals Effect of Elevated Salt Concentrations on the Aerobic Granular Sludge Process: Linking Microbial Activity with Microbial Community Structure

2011 ◽  
Vol 77 (22) ◽  
pp. 7942-7953 ◽  
Author(s):  
J. P. Bassin ◽  
M. Pronk ◽  
G. Muyzer ◽  
R. Kleerebezem ◽  
M. Dezotti ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Phosphorus Removal ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Granular Sludge ◽  
Phosphate Removal ◽  
Aerobic Granular Sludge ◽  
Nitrogen And Phosphorus ◽  
Content Type

ABSTRACTThe long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA andamoAgenes. PCR products obtained from genomic DNA and from rRNA after reverse transcription were compared to determine the presence of bacteria as well as the metabolically active fraction of bacteria. Fluorescencein situhybridization (FISH) was used to validate the PCR-based results and to quantify the dominant bacterial populations. The results demonstrated that ammonium removal efficiency was not affected by salt concentrations up to 33 g/liter NaCl. Conversely, a high accumulation of nitrite was observed above 22 g/liter NaCl, which coincided with the disappearance ofNitrospirasp. Phosphorus removal was severely affected by gradual salt increase. No P release or uptake was observed at steady-state operation at 33 g/liter NaCl, exactly when the polyphosphate-accumulating organisms (PAOs), “CandidatusAccumulibacter phosphatis” bacteria, were no longer detected by PCR-DGGE or FISH. Batch experiments confirmed that P removal still could occur at 30 g/liter NaCl, but the long exposure of the biomass to this salinity level was detrimental for PAOs, which were outcompeted by glycogen-accumulating organisms (GAOs) in the bioreactor. GAOs became the dominant microorganisms at increasing salt concentrations, especially at 33 g/liter NaCl. In the comparative analysis of the diversity (DNA-derived pattern) and the activity (cDNA-derived pattern) of the microbial population, the highly metabolically active microorganisms were observed to be those related to ammonia (Nitrosomonassp.) and phosphate removal (“CandidatusAccumulibacter”).

scholarly journals Impacts of Zostera eelgrasses on microbial community structure in San Diego coastal waters

Elem Sci Anth ◽  
2019 ◽  
Vol 7 ◽  
Author(s):  
Sahra J. Webb ◽  
Tia Rabsatt ◽  
Natalia Erazo ◽  
Jeff S. Bowman
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
San Diego ◽  
Pathogenic Bacteria ◽  
Marine Ecosystem ◽  
Rrna Gene ◽  
Microbial Composition ◽  
San Diego Bay ◽  
The Impact

Marine eelgrasses are influential to their surrounding environments through their many ecosystem services, ranging from the provisioning of food and shelter for marine life to serving as a natural defense against pollution and pathogenic bacteria. In the marine waters of San Diego, CA, USA, eelgrass beds comprised of Zostera spp. are an integral part of the coastal ecosystem. To evaluate the impact of eelgrass on bacterial and archaeal community structure we collected water samples in San Diego Bay and sequenced the 16S rRNA gene from paired eelgrass-present and eelgrass-absent sites. To test the hypothesis that microbial community structure is influenced by the presence of eelgrass we applied mixed effects models to these data and to bacterial abundance data derived by flow cytometry. This approach allowed us to identify specific microbial taxa that were differentially present at eelgrass-present and eelgrass-absent sites. Principal coordinate analysis organized the samples by location (inner vs. outer bay) along the first axis, where the first two axes accounted for a 90.8% of the variance in microbial community structure among the samples. Differentially present bacterial taxa included members of the order Rickettsiales, family Flavobacteriaceae, genus Tenacibaculum and members of the order Pseudomonadales. These findings constitute a unique look into the microbial composition of San Diego Bay and examine how eelgrasses contribute to marine ecosystem health, e.g., by supporting specific microbial communities and by filtering and trapping potentially harmful bacteria to the benefit of marine organisms.

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