scholarly journals Reproductive System Symbiotic Bacteria Are Conserved between Two Distinct Populations ofEuprymna scolopesfrom Oahu, Hawaii

mSphere ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Allison H. Kerwin ◽  
Spencer V. Nyholm
Keyword(s):  
Local Adaptation ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Model Organism ◽  
Amplicon Sequencing ◽  
Host Population ◽  
Euprymna Scolopes ◽  
Isolated Populations ◽  
Content Type ◽  
Kaneohe Bay

ABSTRACTFemale Hawaiian bobtail squid,Euprymna scolopes, harbor a symbiotic bacterial community in a reproductive organ, the accessory nidamental gland (ANG). This community is known to be stable over several generations of wild-caught bobtail squid but has, to date, been examined for only one population in Maunalua Bay, Oahu, HI. This study assessed the ANG and corresponding egg jelly coat (JC) bacterial communities for another genetically isolated host population from Kaneohe Bay, Oahu, HI, using 16S amplicon sequencing. The bacterial communities from the ANGs and JCs of the two populations were found to be similar in richness, evenness, phylogenetic diversity, and overall community composition. However, the Kaneohe Bay samples formed their own subset within the Maunalua Bay ANG/JC community. AnAlteromonadaceaegenus, BD2-13, was significantly higher in relative abundance in the Kaneohe Bay population, and severalAlphaproteobacteriataxa also shifted in relative abundance between the two groups. This variation could be due to local adaptation to differing environmental challenges, to localized variability, or to functional redundancy among the ANG taxa. The overall stability of the community between the populations further supports a crucial functional role that has been hypothesized for this symbiosis.IMPORTANCEIn this study, we examined the reproductive ANG symbiosis found in two genetically isolated populations of the Hawaiian bobtail squid,Euprymna scolopes. The stability of the community reported here provides support for the hypothesis that this symbiosis is under strong selective pressure, while the observed differences suggest that some level of local adaptation may have occurred. These two host populations are frequently used interchangeably as source populations for research.Euprymna scolopesis an important model organism and offers the opportunity to examine the interplay between a binary and a consortial symbiosis in a single model host. Understanding the inherent natural variability of this association will aid in our understanding of the conservation, function, transmission, and development of the ANG symbiosis.

scholarly journals Importance of Micromonospora spp. as Colonizers of Cellulose in Freshwater Lakes as Demonstrated by Quantitative Reverse Transcriptase PCR of 16S rRNA

2012 ◽  
Vol 78 (9) ◽  
pp. 3495-3499 ◽  
Author(s):  
Alexandre B. de Menezes ◽  
James E. McDonald ◽  
Heather E. Allison ◽  
Alan J. McCarthy
Keyword(s):  
16S Rrna ◽  
Reverse Transcriptase ◽  
Quantitative Pcr ◽  
Lake Sediment ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Bacterial Population ◽  
Freshwater Lakes ◽  
Content Type ◽  
Water Columns

ABSTRACTThe relative abundance of micromonosporas in the bacterial communities inhabiting cellulose baits, water columns, and sediments of two freshwater lakes was determined by quantitative PCR (qPCR) of reverse-transcribed 16S rRNA.Micromonosporaspp. were shown to be significant members of the active bacterial population colonizing cellulosic substrates in the lake sediment, and their increased prevalence with greater depth was confirmed by enumeration of CFU.

scholarly journals Indoor-Biofilter Growth and Exposure to Airborne Chemicals Drive Similar Changes in Plant Root Bacterial Communities

2014 ◽  
Vol 80 (16) ◽  
pp. 4805-4813 ◽  
Author(s):  
Jacob A. Russell ◽  
Yi Hu ◽  
Linh Chau ◽  
Margarita Pauliushchyk ◽  
Ioannis Anastopoulos ◽  
...  
Keyword(s):  
Indoor Air ◽  
Bacterial Communities ◽  
Plant Root ◽  
Amplicon Sequencing ◽  
Biomass Energy ◽  
Plant Roots ◽  
Content Type ◽  
16S Rrna Amplicon Sequencing ◽  
Wide Range ◽  
Different Strains

ABSTRACTDue to the long durations spent inside by many humans, indoor air quality has become a growing concern. Biofiltration has emerged as a potential mechanism to clean indoor air of harmful volatile organic compounds (VOCs), which are typically found at concentrations higher indoors than outdoors. Root-associated microbes are thought to drive the functioning of plant-based biofilters, or biowalls, converting VOCs into biomass, energy, and carbon dioxide, but little is known about the root microbial communities of such artificially grown plants, how or whether they differ from those of plants grown in soil, and whether any changes in composition are driven by VOCs. In this study, we investigated how bacterial communities on biofilter plant roots change over time and in response to VOC exposure. Through 16S rRNA amplicon sequencing, we compared root bacterial communities from soil-grown plants with those from two biowalls, while also comparing communities from roots exposed to clean versus VOC-laden air in a laboratory biofiltration system. The results showed differences in bacterial communities between soil-grown and biowall-grown plants and between bacterial communities from plant roots exposed to clean air and those from VOC-exposed plant roots. Both biowall-grown and VOC-exposed roots harbored enriched levels of bacteria from the genusHyphomicrobium. Given their known capacities to break down aromatic and halogenated compounds, we hypothesize that these bacteria are important VOC degraders. While different strains ofHyphomicrobiumproliferated in the two studied biowalls and our lab experiment, strains were shared across plant species, suggesting that a wide range of ornamental houseplants harbor similar microbes of potential use in living biofilters.

scholarly journals Characterization of Geographically Distinct Bacterial Communities Associated with Coral Mucus Produced by Acropora spp. and Porites spp.

2012 ◽  
Vol 78 (15) ◽  
pp. 5229-5237 ◽  
Author(s):  
B. A. McKew ◽  
A. J. Dumbrell ◽  
S. D. Daud ◽  
L. Hepburn ◽  
E. Thorpe ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
Coral Host ◽  
Coral Mucus ◽  
Content Type ◽  
First Report ◽  
Mexican Caribbean ◽  
The Caribbean

ABSTRACTAcroporaandPoritescorals are important reef builders in the Indo-Pacific and Caribbean. Bacteria associated with mucus produced byPoritesspp. andAcroporaspp. from Caribbean (Punta Maroma, Mexico) and Indo-Pacific (Hoga and Sampela, Indonesia) reefs were determined. Analysis of pyrosequencing libraries showed that bacterial communities from Caribbean corals were significantly more diverse (H′, 3.18 to 4.25) than their Indonesian counterparts (H′, 2.54 to 3.25). Dominant taxa wereGammaproteobacteria,Alphaproteobacteria,Firmicutes, andCyanobacteria, which varied in relative abundance between coral genera and region. Distinct coral host-specific communities were also found; for example,Clostridialeswere dominant onAcroporaspp. (at Hoga and the Mexican Caribbean) compared toPoritesspp. and seawater. Within theGammproteobacteria,Halomonasspp. dominated sequence libraries fromPoritesspp. (49%) andAcroporaspp. (5.6%) from the Mexican Caribbean, compared to the corresponding Indonesian coral libraries (<2%). Interestingly, with the exception ofPoritesspp. from the Mexican Caribbean, there was also a ubiquity ofPsychrobacterspp., which dominatedAcroporaandPoriteslibraries from Indonesia andAcroporalibraries from the Caribbean. In conclusion, there was a dominance ofHalomonasspp. (associated withAcroporaandPorites[Mexican Caribbean]),Firmicutes(associated withAcropora[Mexican Caribbean] and withAcroporaandPorites[Hoga]), andCyanobacteria(associated withAcroporaandPorites[Hoga] andPorites[Sampela]). This is also the first report describing geographically distinctPsychrobacterspp. associated with coral mucus. In addition, the predominance ofClostridialesassociated withAcroporaspp. provided additional evidence for coral host-specific microorganisms.

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 Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems

2015 ◽  
Vol 81 (18) ◽  
pp. 6463-6473 ◽  
Author(s):  
Jennifer L. A. Shaw ◽  
Paul Monis ◽  
Laura S. Weyrich ◽  
Emma Sawade ◽  
Mary Drikas ◽  
...  
Keyword(s):  
Water Quality ◽  
Drinking Water ◽  
Water Treatment ◽  
Bacterial Communities ◽  
Distribution Systems ◽  
Water Distribution ◽  
Amplicon Sequencing ◽  
Content Type ◽  
Drinking Water Distribution Systems ◽  
Drinking Water Distribution

ABSTRACTDrinking water assessments use a variety of microbial, physical, and chemical indicators to evaluate water treatment efficiency and product water quality. However, these indicators do not allow the complex biological communities, which can adversely impact the performance of drinking water distribution systems (DWDSs), to be characterized. Entire bacterial communities can be studied quickly and inexpensively using targeted metagenomic amplicon sequencing. Here, amplicon sequencing of the 16S rRNA gene region was performed alongside traditional water quality measures to assess the health, quality, and efficiency of two distinct, full-scale DWDSs: (i) a linear DWDS supplied with unfiltered water subjected to basic disinfection before distribution and (ii) a complex, branching DWDS treated by a four-stage water treatment plant (WTP) prior to disinfection and distribution. In both DWDSs bacterial communities differed significantly after disinfection, demonstrating the effectiveness of both treatment regimes. However, bacterial repopulation occurred further along in the DWDSs, and some end-user samples were more similar to the source water than to the postdisinfection water. Three sample locations appeared to be nitrified, displaying elevated nitrate levels and decreased ammonia levels, and nitrifying bacterial species, such asNitrospira, were detected.Burkholderialeswere abundant in samples containing large amounts of monochloramine, indicating resistance to disinfection. Genera known to contain pathogenic and fecal-associated species were also identified in several locations. From this study, we conclude that metagenomic amplicon sequencing is an informative method to support current compliance-based methods and can be used to reveal bacterial community interactions with the chemical and physical properties of DWDSs.

scholarly journals Selective Bacterial Community Enrichment between the Pitcher Plants Sarracenia minor and Sarracenia flava

2021 ◽  
Author(s):  
Scott M. Yourstone ◽  
Ilon Weinstein ◽  
Elizabeth Ademski ◽  
Elizabeth A. Shank ◽  
Nikolas M. Stasulli
Keyword(s):  
Bacterial Community ◽  
Comparative Studies ◽  
Bacterial Communities ◽  
Environmental Samples ◽  
Environmental Variables ◽  
Geographic Location ◽  
Amplicon Sequencing ◽  
Pitcher Plants ◽  
Content Type

This study uses amplicon sequencing to compare the bacterial communities of environmental samples from the detritus of the leaf cavities of Sarracenia minor and Sarracenia flava pitcher plants. We sampled the detritus at the same time and in the same geographic location, eliminating many environmental variables present in other comparative studies.

scholarly journals A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1658
Author(s):  
Jan C. Plaizier ◽  
Anne-Mette Danscher ◽  
Paula A. Azevedo ◽  
Hooman Derakhshani ◽  
Pia H. Andersen ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Control Diet ◽  
Rrna Gene ◽  
Ruminal Acidosis ◽  
Clustering Patterns ◽  
The 16S Rrna Gene ◽  
Distal Jejunum

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Conventional myelosuppressive chemotherapy for non-haematological malignancy disrupts the intestinal microbiome

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lito E. Papanicolas ◽  
Sarah K. Sims ◽  
Steven L. Taylor ◽  
Sophie J. Miller ◽  
Christos S. Karapetis ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Haematological Malignancy ◽  
Amplicon Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Conventional Chemotherapy ◽  
Myelosuppressive Chemotherapy ◽  
Gram Positive Bacteria ◽  
Faecal Samples

Abstract Background The gut microbiota influences many aspects of host physiology, including immune regulation, and is predictive of outcomes in cancer patients. However, whether conventional myelosuppressive chemotherapy affects the gut microbiota in humans with non-haematological malignancy, independent of antibiotic exposure, is unknown. Methods Faecal samples from 19 participants with non-haematological malignancy, who were receiving conventional chemotherapy regimens but not antibiotics, were examined prior to chemotherapy, 7–12 days after chemotherapy, and at the end of the first cycle of treatment. Gut microbiota diversity and composition was determined by 16S rRNA gene amplicon sequencing. Results Compared to pre-chemotherapy samples, samples collected 7–12 days following chemotherapy exhibited increased richness (mean 120 observed species ± SD 38 vs 134 ± 40; p = 0.007) and diversity (Shannon diversity: mean 6.4 ± 0.43 vs 6.6 ± 0.41; p = 0.02). Composition was significantly altered, with a significant decrease in the relative abundance of gram-positive bacteria in the phylum Firmicutes (pre-chemotherapy median relative abundance [IQR] 0.78 [0.11] vs 0.75 [0.11]; p = 0.003), and an increase in the relative abundance of gram-negative bacteria (Bacteroidetes: median [IQR] 0.16 [0.13] vs 0.21 [0.13]; p = 0.01 and Proteobacteria: 0.015 [0.018] vs 0.03 [0.03]; p = 0.02). Differences in microbiota characteristics from baseline were no longer significant at the end of the chemotherapy cycle. Conclusions Conventional chemotherapy results in significant changes in gut microbiota characteristics during the period of predicted myelosuppression post-chemotherapy. Further study is indicated to link microbiome changes during chemotherapy to clinical outcomes.

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