Effect of Copper Ion Sterilization on Bacterial Community in a Freshwater Recirculating Aquaculture System

AbstractThe study aimed to evaluate the safety of copper ion sterilization based on copper ion residues in zebrafish (Brachydanio rerio), as well as bacterial community structure and diversity in recirculating aquaculture systems (RASs). The copper ion content was determined using national food safety standard GB 5009.13-2017. Bacterial community structures and alpha and beta diversity indexes were examined using the 16S rRNA gene sequences produced by Illumina HiSeq sequencing. The results revealed no significant copper ion enrichment in B. rerio when the copper ion concentration was 0.15 mg/L. The relative abundances of Erythrobacter, nitrite bacteria, and Flavanobacteria were clearly higher in the treatment group than in the control and differences in bacterial species richness and diversity were obvious. In addition, there was no sharp decrease in the microflora at the outflow of the copper ion generator. In conjunction with the changes in ammonia nitrogen, nitrate, and nitrite concentrations during the experiment, the results indicated that there were no significant effects on the purification efficacy of the biological filter, but the abundances of beneficial bacteria increased significantly. This is of great relevance in order to understand the response of bacterial communities affected by changing environmental conditions, such as copper ion sterilization.

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Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

Journal of Burn Care & Research ◽

10.1093/jbcr/irab244 ◽

2022 ◽

Author(s):

Chen Zheng-li ◽

Peng Yu ◽

Wu Guo-sheng ◽

Hong Xu-Dong ◽

Fan Hao ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Community Structure ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Sprague Dawley ◽

Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

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Effect of Bacillus mesonae H20-5 Treatment on Rhizospheric Bacterial Community of Tomato Plants under Salinity Stress

The Plant Pathology Journal ◽

10.5423/ppj.ft.10.2021.0156 ◽

2021 ◽

Vol 37 (6) ◽

pp. 662-672

Author(s):

Shin Ae Lee ◽

Hyeon Su Kim ◽

Mee Kyung Sang ◽

Jaekyeong Song ◽

Hang-Yeon Weon

Keyword(s):

Bacterial Community ◽

Plant Growth ◽

Soil Salinity ◽

Bacterial Communities ◽

Bacterial Species ◽

Rrna Gene ◽

Plant Growth Promoting Bacteria ◽

Tomato Plants ◽

Rhizosphere Soils ◽

Salinity Levels

Plant growth-promoting bacteria improve plant growth under abiotic stress conditions. However, their effects on microbial succession in the rhizosphere are poorly understood. In this study, the inoculants of Bacillus mesonae strain H20-5 were administered to tomato plants grown in soils with different salinity levels (EC of 2, 4, and 6 dS/m). The bacterial communities in the bulk and rhizosphere soils were examined 14 days after H20-5 treatment using Illumina MiSeq sequencing of the bacterial 16S rRNA gene. Although the abundance of H20-5 rapidly decreased in the bulk and rhizosphere soils, a shift in the bacterial community was observed following H20-5 treatment. The variation in bacterial communities due to H20-5 treatment was higher in the rhizosphere than in the bulk soils. Additionally, the bacterial species richness and diversity were greater in the H20-5 treated rhizosphere than in the control. The composition and structure of the bacterial communities varied with soil salinity levels, and those in the H20-5 treated rhizosphere soil were clustered. The members of Actinobacteria genera, including Kineosporia, Virgisporangium, Actinoplanes, Gaiella, Blastococcus, and Solirubrobacter, were enriched in the H20-5 treated rhizosphere soils. The microbial co-occurrence network of the bacterial community in the H20-5 treated rhizosphere soils had more modules and keystone taxa compared to the control. These findings revealed that the strain H20-5 induced systemic tolerance in tomato plants and influenced the diversity, composition, structure, and network of bacterial communities. The bacterial community in the H20-5 treated rhizosphere soils also appeared to be relatively stable to soil salinity changes.

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Uterine and vaginal bacterial community diversity prior to artificial insemination between pregnant and nonpregnant postpartum cows1

Journal of Animal Science ◽

10.1093/jas/skz210 ◽

2019 ◽

Vol 97 (10) ◽

pp. 4298-4304 ◽

Cited By ~ 4

Author(s):

Taylor B Ault ◽

Brooke A Clemmons ◽

Sydney T Reese ◽

Felipe G Dantas ◽

Gessica A Franco ◽

...

Keyword(s):

Bacterial Community ◽

Artificial Insemination ◽

Bacterial Communities ◽

Bacterial Species ◽

Beef Cows ◽

Community Diversity ◽

Rrna Gene ◽

Bacterial Community Diversity ◽

Hypervariable Regions ◽

Time Of Breeding

Abstract The present study evaluated the bovine vaginal and uterine bacterial community diversity and its relationship to fertility. Postpartum beef cows (n = 68) were synchronized beginning on day −21 and ending with timed artificial insemination (TAI) on day 0. Pregnancy was diagnosed 30 d after TAI. Uterine and vaginal flushes were collected on day −21, −9, and −2 for bacterial DNA extraction to sequence the V1 to V3 hypervariable regions of the 16S rRNA gene. Results indicated a decrease in the number of bacterial species over time in the uterus of resulting pregnant and nonpregnant beef cows (P < 0.0001). Principal coordinate analyses (PCoA) depicted clustering of samples, indicating closely related bacterial communities, by day in the uterus and vagina (P < 0.0001). At day −2, uterine samples from nonpregnant and pregnant animals clustered separately (P < 0.0001), with nonpregnant animal samples clustering tightly together. Overall, the current study suggests the shift in the reproductive bacterial communities’ diversity and phylogenetic relationship leading up to the time of breeding may contribute to successful pregnancy establishment.

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Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China

Annals of Microbiology ◽

10.1007/s13213-019-01529-9 ◽

2019 ◽

Vol 69 (13) ◽

pp. 1461-1473 ◽

Cited By ~ 3

Author(s):

Cheng-yu Wang ◽

Xue Zhou ◽

Dan Guo ◽

Jiang-hua Zhao ◽

Li Yan ◽

...

Keyword(s):

Bacterial Community ◽

Soil Ph ◽

Bacterial Communities ◽

Nitrifying Bacteria ◽

Rrna Gene ◽

Ecological Functions ◽

Illumina Hiseq ◽

Α Diversity ◽

Farmland Soils ◽

Soil Bacterial

Abstract Purpose To understand which environmental factors influence the distribution and ecological functions of bacteria in agricultural soil. Method A broad range of farmland soils was sampled from 206 locations in Jilin province, China. We used 16S rRNA gene-based Illumina HiSeq sequencing to estimated soil bacterial community structure and functions. Result The dominant taxa in terms of abundance were found to be, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, and Proteobacteria. Bacterial communities were dominantly affected by soil pH, whereas soil organic carbon did not have a significant influence on bacterial communities. Soil pH was significantly positively correlated with bacterial operational taxonomic unit abundance and soil bacterial α-diversity (P<0.05) spatially rather than with soil nutrients. Bacterial functions were estimated using FAPROTAX, and the relative abundance of anaerobic and aerobic chemoheterotrophs, and nitrifying bacteria was 27.66%, 26.14%, and 6.87%, respectively, of the total bacterial community. Generally, the results indicate that soil pH is more important than nutrients in shaping bacterial communities in agricultural soils, including their ecological functions and biogeographic distribution.

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Determination of stocking density limits for Crassostrea gigas larvae reared in flow-through and recirculating aquaculture systems and interaction between larval density and biofilm formation

Aquatic Living Resources ◽

10.1051/alr/2017023 ◽

2017 ◽

Vol 30 ◽

pp. 29 ◽

Cited By ~ 4

Author(s):

Katia Asmani ◽

Bruno Petton ◽

Jacqueline Le Grand ◽

Jérôme Mounier ◽

René Robert ◽

...

Keyword(s):

Crassostrea Gigas ◽

Biofilm Formation ◽

Larval Density ◽

Stocking Density ◽

Rrna Gene ◽

Larval Rearing ◽

Filamentous Bacteria ◽

Recirculating Aquaculture ◽

Recirculating Aquaculture Systems ◽

Flow Through

The first aim of this study was to determine the stocking density limits for Pacific oyster Crassostrea gigas larvae reared in flow-through system (FTS) and recirculating aquaculture systems (RAS). The second aim was to examine biofilm formation on the larval tank wall and its interaction with larvae growth. Three larvae concentrations were tested: 50, 150, and 300 mL−1. Chemical parameters and larvae performance were measured. The biofilm was observed by scanning electron microscopy, and its bacterial composition was investigated by pyrosequencing analysis of part of the 16S rRNA gene. The highest growth (13 µm day–1), survival (87%) and metamorphosis (50%) rates were observed in FTS at 50 larvae mL–1, while lower and similar performances occurred at 150 larvae mL–1 in both systems. At 300 larvae mL−1, performances dropped with occurrence of mortality. Biofilm thickness increased with larval density. The pioneer bacteria were coccobacilli followed by filamentous bacteria. The latter constituted abundant braids at the end of rearing at high larval concentrations. The first colonizers were mainly Rhodobacteraceae (α-Proteobacteria). The filamentous bacteria were Saprospirae (Bacteroidetes) and Anaerolineae (Chloroflexi). The biofilm was also made up of other minor groups, including Actinobacteria, Planctomycetes, δ-, γ-Proteobacteria, and Flavobacteriales. The biofilm's composition was more similar to that found in a sewage reactor than in open-sea collectors, which might negatively influence larval rearing due to potential metabolites. This first study on biofilms provides insights into the interaction between rearing density and larvae performance.

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Differences in Gut Bacterial Communities of Ips typographus (Coleoptera: Curculionidae) Induced by Enantiomer-Specific α-Pinene

Environmental Entomology ◽

10.1093/ee/nvaa098 ◽

2020 ◽

Vol 49 (5) ◽

pp. 1198-1205

Author(s):

Jia-Xing Fang ◽

Su-Fang Zhang ◽

Fu Liu ◽

Xun Zhang ◽

Feng-Bin Zhang ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Species ◽

Bacterial Community Composition ◽

Specific Effect ◽

Ips Typographus ◽

Gut Bacteria ◽

Rrna Gene ◽

Life Stages ◽

Relative Abundances ◽

The Relationship

Abstract The spruce bark beetle (Ips typographus L.) is a destructive pest of Eurasian spruce forests. Although the gut bacteria of this insect are considered to play important roles in its lifecycle, the relationship between I. typographus and its gut bacterial community is poorly characterized. In this study, 16S rRNA gene sequencing was used to determine gut bacterial community composition across successive I. typographus life stages. Responses of the gut bacteria to α-pinene enantiomers were also explored. Ips typographus gut bacterial populations were dominated by the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, and the relative abundance of these phyla varied across different developmental stages of the beetle. Bacterial species diversity and richness indices increased with developmental stage progression. Relative abundances of the dominant genera, Erwinia (Enterobacteriales: Enterobacteriaceae), Pseudoxanthomonas (Xanthomonadales: Xanthomonadaceae), Serratia (Enterobacteriales: Enterobacteriaceae), and Romboutsia (Clostridiales: Peptostreptococcaceae), also varied across successive I. typographus life stages. Large disparities in the gut bacterial community of male adults were observed when the beetles were treated with S-(–)-α-pinene and R-(+)-α-pinene. The relative abundances of Lactococcus (Lactobacillales: Streptococcaceae) and Lelliottia (Enterobacteriales: Enterobacteriaceae) increased drastically with R-(+)-α-pinene and S-(–)-α-pinene treatment, respectively. This indicated a distinct enantiomer-specific effect of α-pinene on the I. typographus gut bacteria. This study demonstrated the plasticity of gut bacteria during I. typographus development, when α-pinene host monoterpenes are encountered. This study provides new insights into the relationship between ‘I. typographus–gut bacteria’ symbionts and host trees.

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Characterizing the structural diversity of a bacterial community associated with filter materials in recirculating aquaculture systems of Scortum barcoo

Canadian Journal of Microbiology ◽

10.1139/w11-130 ◽

2012 ◽

Vol 58 (3) ◽

pp. 303-310 ◽

Cited By ~ 3

Author(s):

Peng Zhu ◽

Yangfang Ye ◽

Fangfang Pei ◽

Kaihong Lu

Keyword(s):

Water Quality ◽

Bacterial Community ◽

Clone Library ◽

Stable Operation ◽

Recirculating Aquaculture System ◽

Operation Condition ◽

Recirculating Aquaculture ◽

Filter Materials ◽

Aquaculture System ◽

Recirculating Aquaculture Systems

The bacterial community structure associated with filter materials in the recirculating aquaculture system of Scortum barcoo was investigated using the 16S rRNA gene clone library method. Preliminary results showed that the clone library constructed from the initial operation condition was characterized by 31 taxa of bacteria belonging to eight phyla including Proteobacteria, Acidobacteria, Firmicutes, Fusobacteria, Sphingobacteria, Bacteroidetes, Verrucomicrobiae, and Actinobacteria. There were 14 taxa of bacteria belonging to four phyla including Proteobacteria, Acidobacteria, Planctomycetacia, and Nitrospirae from the stable operation condition where the water quality was well maintained. Nitrospirae was only found under the stable operation condition in this study. Our results further indicated that Nitrospira was dominated by members of the Nitrospira sp. lineages, with a minor fraction related to Nitrospira moscoviensis and an unknown Nitrospira cluster. These great differences of both diversity and composition between two operation conditions suggested that the composition of the microbial community varied with the degree of water quality in the recirculating aquaculture system of S. barcoo.

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Retrofitting Sea Cucumber Nursery Tanks to Recirculating Aquaculture Systems for Highly Intensive Litopenaeus vannamei Aquaculture

Applied Sciences ◽

10.3390/app11209478 ◽

2021 ◽

Vol 11 (20) ◽

pp. 9478

Author(s):

Yishuai Du ◽

Jianping Xu ◽

Li Zhou ◽

Fudi Chen ◽

Tianlong Qiu ◽

...

Keyword(s):

Litopenaeus Vannamei ◽

Sea Cucumber ◽

Stocking Density ◽

Ammonia Nitrogen ◽

Average Weight ◽

Recirculating Aquaculture ◽

Nitrite Nitrogen ◽

Innovative Methodology ◽

Recirculating Aquaculture Systems ◽

Total Ammonia

Designing good recirculating aquaculture systems (RASs) is challenging in shrimp aquaculture. In this study, two sets of RASs were constructed using sea cucumber nursery tanks for rearing Litopenaeus vannamei. Recirculating aquaculture was supported by key technologies such as sewage collection and aeration systems adapted to the rectangular tanks and technologies for the removal of sewage, shrimp shells, and dead individuals. Six-hundred and eighty-five thousand juveniles were selected for rearing in the newly constructed RASs, where the average stocking density was 1013 shrimp/m3. During the recirculating aquaculture period of 53 days, the water temperature of the tanks was 24–31 °C, the salinity was 25–32‰, the pH was 6.4–8.2, the DO was ≥ 4.9 mg/L, the concentration of total ammonia nitrogen (TAN) was maintained between 0.17 and 4.9 mg/L, the concentration of nitrite nitrogen (NO2-N) was between 0.12 and 4.7 mg/L, and the total number of Vibrio bacteria remained between 330 and 9700 cfu/mL. At the end of the experiment, the final average weight of individual shrimp was 13.43 g, and the average yield reached 12.92 kg/m3. The great improvement in growth performance marks a breakthrough in RAS technology of shrimp, and it supports the use of an innovative methodology for the retrofitting and utilization of idle sea cucumber nursery tanks.

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Worldwide exploration of the microbiome harbored by the cnidarian model, Exaiptasia pallida indicates a lack of bacterial association specificity at a lower taxonomic rank

10.7287/peerj.preprints.2338v1 ◽

2016 ◽

Author(s):

Tanya Brown ◽

Christopher Otero ◽

Alejandro Grajales ◽

Estefania Rodriguez ◽

Mauricio Rodriguez-Lanetty

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Bacterial Species ◽

Sea Anemone ◽

Microbial Consortia ◽

Rrna Gene ◽

Core Microbiome ◽

Wide Range ◽

Exaiptasia Pallida

Examination of host-microbe interactions in basal metazoans, such as cnidarians is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemone Exaiptasia pallida shows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1-V4 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated with E. pallida are broadly conserved across geographic space with samples, containing largely Proteobacteria and Bacteroides. However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. These results contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. Instead, our findings suggest that environmental settings, not host specificity seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone model E. pallida is the first global-scale study of its kind.

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Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing

PeerJ ◽

10.7717/peerj.9122 ◽

2020 ◽

Vol 8 ◽

pp. e9122

Author(s):

Li Chen ◽

Yuzhu Li ◽

Lei Jin ◽

Li He ◽

Xiaolin Ao ◽

...

Keyword(s):

Bacterial Community ◽

High Throughput ◽

Relative Abundance ◽

High Throughput Sequencing ◽

Middle Layer ◽

Ammonia Nitrogen ◽

Western China ◽

Rrna Gene ◽

Linear Discriminant ◽

Pit Mud

“Yibin Baijiu” (YB) is a special Chinese strong-aroma Baijiu (CSAB) that originated in Yibin, a city in western China. YB is fermented in cellars lined with pit mud (PM), the microbiota in which may affect YB quality. In this study, high throughput sequencing of the 16S rRNA gene was used to demonstrate the bacterial community structure and diversity in PM of YB. In addition, the physicochemical characteristics of PM were also analyzed, including moisture content, pH, and available phosphorous, ammonia nitrogen, and humic acid levels. Results showed that Firmicutes was the dominant phylum in all PM samples with abundance > 70.0%, followed by Euryarchaeota (11.3%), Bacteroidetes (6.5%), Synergistetes (3.0%), Actinobacteria (1.4%), and Proteobacteria (1.2%). Furthermore, 14 different genera with average relative abundance of > 1% were detected. The Chao1 and Shannon indexes did not vary significantly between the sub-layer and middle-layer PM (P > 0.05). However, Linear discriminant analysis Effect Size (LEfSe) analysis showed that the relative abundance of Lactobacillus in the sub-layer PM was significantly higher than in middle-layer PM. pH differed significantly (P < 0.05) between the two groups. Canonical correspondence analysis revealed that bacterial community in PM correlated significantly with available phosphorous content and pH. Our study provides basic data for further elucidating the diversity of microbiota in the PM of YB and the potential mechanism of Baijiu production.

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