scholarly journals Exploring Bacterial Communities in Aquaponic Systems

Water ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 260 ◽  
Author(s):  
Mathilde Eck ◽  
Abdoul Sare ◽  
Sébastien Massart ◽  
Zala Schmautz ◽  
Ranka Junge ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Dynamic Equilibrium ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
The Core ◽  
Diverse Communities ◽  
Sampled Systems ◽  
Tripartite Relationship ◽  
Decoupled Systems

Aquaponics is a production system based on the dynamic equilibrium between fish, plants, and microorganisms. In order to better understand the role of microorganisms in this tripartite relationship, we studied the bacterial communities hosted in eight aquaponic and aquaculture systems. The bacterial communities were analyzed by 16S rRNA gene deep sequencing. At the phylum level, the bacterial communities from all systems were relatively similar with a predominance of Proteobacteria and Bacteroidetes. At the genus level, however, the communities present in the sampled systems were more heterogeneous. The biofilter samples harbored more diverse communities than the corresponding sump samples. The core microbiomes from the coupled and decoupled systems shared more common operational taxonomic units than with the aquaculture systems. Eventually, some of the taxa identified in the systems could have beneficial functions for plant growth and health, but a deeper analysis would be required to identify the precise functions involved in aquaponics.

scholarly journals The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

2017 ◽  
Vol 1 (3) ◽  
pp. 158-168 ◽  
Author(s):  
Kristi Gdanetz ◽  
Frances Trail
Keyword(s):  
Bacterial Communities ◽  
Management Strategy ◽  
Crop Yields ◽  
Management Strategies ◽  
Growing Season ◽  
Amplicon Sequencing ◽  
Antagonistic Activity ◽  
Rrna Gene ◽  
Operational Taxonomic Units ◽  
Plant Organ

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.

Variation in the microbiome of the spider mite Tetranychus truncatus with sex, instar and endosymbiont infection

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Yu-Xi Zhu ◽  
Zhang-Rong Song ◽  
Shi-Mei Huo ◽  
Kun Yang ◽  
Xiao-Yue Hong
Keyword(s):  
Spider Mite ◽  
Potential Role ◽  
Developmental Stages ◽  
Spider Mites ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Operational Taxonomic Units ◽  
Dominant Bacteria ◽  
The 16S Rrna Gene

ABSTRACT Most arthropod-associated bacterial communities play a crucial role in host functional traits, whose structure could be dominated by endosymbionts. The spider mite Tetranychus truncatus is a notorious agricultural pest harboring various endosymbionts, yet the effects of endosymbionts on spider mite microbiota remain largely unknown. Here, using deep sequencing of the 16S rRNA gene, we characterized the microbiota of male and female T. truncatus with different endosymbionts (Wolbachia and Spiroplasma) across different developmental stages. Although the spider mite microbiota composition varied across the different developmental stages, Proteobacteria were the most dominant bacteria harbored in all samples. Positive relationships among related operational taxonomic units dominated the significant coassociation networks among bacteria. Moreover, the spider mites coinfected with Wolbachia and Spiroplasma had a significantly higher daily fecundity and juvenile survival rate than the singly infected or uninfected spider mites. The possible function of spider-mite associated bacteria was discussed. Our results highlight the dynamics of spider mite microbiotas across different life stages, and the potential role of endosymbionts in shaping the microbiota of spider mites and improving host fitness.

scholarly journals The Oral Microbiome of Healthy Japanese People at the Age of 90

2020 ◽  
Vol 10 (18) ◽  
pp. 6450 ◽  
Author(s):  
Yoshiaki Nomura ◽  
Erika Kakuta ◽  
Noboru Kaneko ◽  
Kaname Nohno ◽  
Akihiro Yoshihara ◽  
...  
Keyword(s):  
Human Microbiome ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Operational Taxonomic Units ◽  
The Core ◽  
Hypervariable Regions ◽  
Study Population ◽  
Granulicatella Adiacens

For a healthy oral cavity, maintaining a healthy microbiome is essential. However, data on healthy microbiomes are not sufficient. To determine the nature of the core microbiome, the oral-microbiome structure was analyzed using pyrosequencing data. Saliva samples were obtained from healthy 90-year-old participants who attended the 20-year follow-up Niigata cohort study. A total of 85 people participated in the health checkups. The study population consisted of 40 male and 45 female participants. Stimulated saliva samples were obtained by chewing paraffin wax for 5 min. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene were amplified by PCR. Pyrosequencing was performed using MiSeq. Operational taxonomic units (OTUs) were assigned on the basis of a 97% identity search in the EzTaxon-e database. Using the threshold of 100% detection on the species level, 13 species were detected: Streptococcus sinensis, Streptococcus pneumoniae, Streptococcus salivarius, KV831974_s, Streptococcus parasanguinis, Veillonella dispar, Granulicatella adiacens, Streptococcus_uc, Streptococcus peroris, KE952139_s, Veillonella parvula, Atopobium parvulum, and AFQU_vs. These species represent potential candidates for the core make-up of the human microbiome.

scholarly journals Culex pipiens and Culex restuans egg rafts harbor diverse bacterial communities compared to their midgut tissues

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Elijah O. Juma ◽  
Chang-Hyun Kim ◽  
Christopher Dunlap ◽  
Brian F. Allan ◽  
Chris M. Stone
Keyword(s):  
Bacterial Communities ◽  
Culex Pipiens ◽  
Mosquito Species ◽  
Gravid Female ◽  
Distance Matrix ◽  
Rrna Gene ◽  
Culex Restuans ◽  
Host Tissues

Abstract Background The bacterial communities associated with mosquito eggs are an essential component of the mosquito microbiota, yet there are few studies characterizing and comparing the microbiota of mosquito eggs to other host tissues. Methods We sampled gravid female Culex pipiens L. and Culex restuans Theobald from the field, allowed them to oviposit in the laboratory, and characterized the bacterial communities associated with their egg rafts and midguts for comparison through MiSeq sequencing of the 16S rRNA gene. Results Bacterial richness was higher in egg rafts than in midguts for both species, and higher in Cx pipiens than Cx. restuans. The midgut samples of Cx. pipiens and Cx. restuans were dominated by Providencia. Culex pipiens and Cx. restuans egg rafts samples were dominated by Ralstonia and Novosphingobium, respectively. NMDS ordination based on Bray-Curtis distance matrix revealed that egg-raft samples, or midgut tissues harbored similar bacterial communities regardless of the mosquito species. Within each mosquito species, there was a distinct clustering of bacterial communities between egg raft and midgut tissues. Conclusion These findings expand the list of described bacterial communities associated with Cx. pipiens and Cx. restuans and the additional characterization of the egg raft bacterial communities facilitates comparative analysis of mosquito host tissues, providing a basis for future studies seeking to understand any functional role of the bacterial communities in mosquito biology.

scholarly journals Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures

2004 ◽  
Vol 70 (2) ◽  
pp. 804-813 ◽  
Author(s):  
Christian Winter ◽  
Arjan Smit ◽  
Gerhard J. Herndl ◽  
Markus G. Weinbauer
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Tropical Atlantic ◽  
Viral Lysis ◽  
Batch Cultures ◽  
Operational Taxonomic Units ◽  
The Impact

ABSTRACT During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.

scholarly journals Culex pipiens L. and Culex restuans egg rafts harbor diverse bacterial communities compared to their midgut tissues

2020 ◽  
Author(s):  
Elijah O. Juma ◽  
Chang-Hyun Kim ◽  
Christopher Dunlap ◽  
Brian F. Allan ◽  
Chris M. Stone
Keyword(s):  
Bacterial Communities ◽  
Culex Pipiens ◽  
Mosquito Species ◽  
Gravid Female ◽  
Distance Matrix ◽  
Rrna Gene ◽  
Culex Restuans ◽  
Host Tissues

AbstractBackgroundThe bacterial communities associated with mosquito eggs are an essential component of the mosquito microbiota, yet there are few studies characterizing and comparing the microbiota of mosquito eggs to other host tissues.MethodsWe sampled gravid female Culex pipiens and Culex restuans from the field, allowed them to oviposit in the laboratory, and characterized the microbiota associated with their egg rafts and midguts for comparison through MiSeq sequencing of the 16S rRNA gene.ResultsBacterial richness was higher in egg rafts than in midguts for both species, and higher in Cx pipiens L. than Cx. restuans. The midgut samples of Cx. pipiens and Cx. restuans were dominated by Providencia. Culex pipiens L. and Cx. restuans egg rafts samples were dominated by Ralstonia and Novosphingobium, respectively. NMDS ordination based on Bray-Curtis distance matrix revealed that egg raft samples, or midgut tissues harbored similar bacterial communities regardless of the mosquito species. Within each mosquito species, there were distinct clustering of bacterial communities between egg raft and midgut tissues.ConclusionThese findings expand the list of described bacterial communities associated with Cx. pipiens L. and Cx. restuans and the additional characterization of the egg raft bacterial communities facilitates comparative analysis of mosquito host tissues, providing a basis for future studies seeking to understand any functional role of microbiota in mosquito biology.

scholarly journals Bacterial Communities Associated with the Cycling of Non-Starch Polysaccharides and Phytate in Aquaponics Systems

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 631
Author(s):  
Daniel Menezes-Blackburn ◽  
Nahad Al-Mahrouqi ◽  
Buthaina Al-Siyabi ◽  
Adhari Al-Kalbani ◽  
Ralf Greiner ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Pcr Amplification ◽  
Aquatic Organisms ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Culture Techniques ◽  
Operational Taxonomic Units ◽  
Catalytic Mechanisms ◽  
Rrna Gene Sequencing

Aquaponics are efficient systems that associate aquatic organisms’ production and plants by recirculating water and nutrients between aquaculture and hydroponic tanks. In this study, we characterised the bacterial communities in the freshwater aquaponics system that can mineralise polysaccharides and phytate by producing carbohydrate-degrading enzymes and phytases, by 16S rRNA gene sequencing and in vitro culture techniques. Around 20% of the operational taxonomic units (zOTUs) identified were previously reported to carry fibre-degrading enzyme putative genes, namely β-glucanase (1%), xylanase (5%), or cellulases (17%). Ten % of the zOTUs were previously reported to carry putative genes of phytases with different catalytic mechanisms, namely β-propeller (6%), histidine acid phytases (3%), and protein tyrosine phytase (<1%). Thirty-eight morphologically different bacteria were isolated from biofilms accumulated in fish and plant compartments, and identified to belong to the Bacilli class. Among these, 7 could produce xylanase, 8 produced β-glucanase, 14 produced cellulase, and 11 isolates could secrete amylases. In addition, Staphylococcus sp. and Rossellomorea sp. could produce consistent extracellular phytate-degrading activity. The PCR amplification of β-propeller genes both in environmental samples and in the isolates obtained showed that this is the most ecologically relevant phytase type in the aquaponics systems used. In summary, the aquaponics system is abundant with bacteria carrying enzymes responsible for plant-nutrient mineralisation.

scholarly journals Environmental characteristics and changes of bacterial communities in the meltwater runoff of glacier in Ny-Alesund, Arctic

2021 ◽  
Author(s):  
Lidong Lin ◽  
Nengfei Wang ◽  
Wenbing Han ◽  
Botao Zhang ◽  
Jiaye Zang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Operational Taxonomic Units ◽  
The Core ◽  
Meltwater Runoff ◽  
Glacial Runoff ◽  
Weighted Correlation

Abstract The present study assessed the diversity and composition of bacterial communities in glacial runoff and glacial soils in the Midre Lovénbreen glacier region of Svalbard. A total of 6,593 operational taxonomic units were identified by high-throughput sequencing. The results showed differences in bacterial community composition between the upper and lower reaches of glacial runoff. The abundance of Actinobacteria, Firmicutes, Betaproteobacteria and Gammaproteobacteria in the upper reaches of glacial runoff was higher than that in the lower reaches. In contrast, the the abundance of Cyanobacteria and Alphaproteobacteria in the downstream of glacial runoff was higher than that in the upstream. In addition, we compared bacterial diversity and composition between glacial runoff areas and soils. The chart analysis showed that bacterial diversity in glacial soil was higher than that in the glacial runoff. Some typical bacteria in the soil, such as Actinobacteria, entered glacial runoff through contact between them. The abundance of Acidobacteria, Sphingobacterium and Flavobacterium was higher in glacial soil. Weighted correlation network analysis showed that the core bacteria in glacial runoff and glacial soil were typical bacteria in different habitats. Distance-based redundancy analysis revealed that NO 2 - -N was the most significant factor affecting the distribution of soil bacterial community, while NO 3 - -N was the most significant factor affecting the distribution of glacial runoff bacterial community.

scholarly journals Termites Are Associated with External Species-Specific Bacterial Communities

2020 ◽  
Vol 87 (2) ◽  
Author(s):  
Patrik Soukup ◽  
Tomáš Větrovský ◽  
Petr Stiblik ◽  
Kateřina Votýpková ◽  
Amrita Chakraborty ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Negative Effects ◽  
Termite Species ◽  
Positive Effects ◽  
Operational Taxonomic Units ◽  
Wide Range ◽  
Species Specific ◽  
And Control

ABSTRACT All termites have established a wide range of associations with symbiotic microbes in their guts. Some termite species are also associated with microbes that grow in their nests, but the prevalence of these associations remains largely unknown. Here, we studied the bacterial communities associated with the termites and galleries of three wood-feeding termite species by using 16S rRNA gene amplicon sequencing. We found that the compositions of bacterial communities among termite bodies, termite galleries, and control wood fragments devoid of termite activities differ in a species-specific manner. Termite galleries were enriched in bacterial operational taxonomic units (OTUs) belonging to Rhizobiales and Actinobacteria, which were often shared by several termite species. The abundance of several bacterial OTUs, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus, was reduced in termite galleries. Our results demonstrate that both termite guts and termite galleries harbor unique bacterial communities. IMPORTANCE As is the case for all ecosystem engineers, termites impact their habitat by their activities, potentially affecting bacterial communities. Here, we studied three wood-feeding termite species and found that they influence the composition of the bacterial communities in their surrounding environment. Termite activities have positive effects on Rhizobiales and Actinobacteria abundance and negative effects on the abundance of several ubiquitous genera, such as Bacillus, Clostridium, Corynebacterium, and Staphylococcus. Our results demonstrate that termite galleries harbor unique bacterial communities.

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