scholarly journals Intergenerational microbial transmission in the little skate (Leucoraja erinacea)

2020 ◽  
Author(s):  
Katelyn Mika ◽  
Alexander S. Okamoto ◽  
Neil H. Shubin ◽  
David B. Mark Welch
Keyword(s):  
Bacterial Communities ◽  
Internal Surface ◽  
Amplicon Sequencing ◽  
Site Specific ◽  
Bacterial Phyla ◽  
16S Rrna Amplicon Sequencing ◽  
Primary Mechanism ◽  
Bacterial Transmission ◽  
Embryonic Skin ◽  
Egg Capsule

AbstractMicrobial transmission from parent to offspring is hypothesized to be universal in vertebrates. However, evidence for this is limited as many clades remain unexamined. Chondrichthyes, as one of the earliest–branching vertebrate lineages, provide an opportunity to investigate the phylogenetic breadth of this hypothesis. To assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, Leucoraja erinacea, at six points during ontogeny. We identify site-specific microbiomes dominated by the bacterial phyla Proteobacteria and Bacteroidetes, a composition similar to, but distinct from, that of other chondrichthyans. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop. Our study is the first exploration of the chondrichthyan microbiome throughout ontogeny and provides the first evidence of vertical transmission in this group, which may be the primary mechanism for the signature of phylosymbiosis previously observed in elasmobranchs.

scholarly journals Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea)

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Katelyn Mika ◽  
Alexander S. Okamoto ◽  
Neil H. Shubin ◽  
David B. Mark Welch
Keyword(s):  
Bacterial Community ◽  
Embryonic Development ◽  
Community Dynamics ◽  
Internal Surface ◽  
Amplicon Sequencing ◽  
Phylogenetic Position ◽  
Published Data ◽  
Bacterial Phyla ◽  
Bacterial Community Dynamics ◽  
Egg Capsule

Abstract Background Microbial transmission from parent to offspring is hypothesized to be widespread in vertebrates. However, evidence for this is limited as many evolutionarily important clades remain unexamined. There is currently no data on the microbiota associated with any Chondrichthyan species during embryonic development, despite the global distribution, ecological importance, and phylogenetic position of this clade. In this study, we take the first steps towards filling this gap by investigating the microbiota associated with embryonic development in the little skate, Leucoraja erinacea, a common North Atlantic species and popular system for chondrichthyan biology. Methods To assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, at six points during ontogeny. Community composition was analyzed using the QIIME2 pipeline and microbial continuity between stages was tracked using FEAST. Results We identify site-specific and stage-specific microbiota dominated by the bacterial phyla Proteobacteria and Bacteroidetes. This composition is similar to, but distinct from, that of previously published data on the adult microbiota of other chondrichthyan species. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop. Conclusions Our study is the first exploration of the chondrichthyan microbiota throughout ontogeny and provides the first evidence of vertical transmission in this group.

scholarly journals From the Andes to the desert: First overview of the bacterial community in the Rimac river, the main source of water for Lima, Peru

2020 ◽  
Author(s):  
Pedro E. Romero ◽  
Erika Calla-Quispe ◽  
Camila Castillo-Vilcahuaman ◽  
Mateo Yokoo ◽  
Hammerly Lino Fuentes-Rivera ◽  
...  
Keyword(s):  
Metropolitan Area ◽  
Bacterial Communities ◽  
Geographical Location ◽  
Microbiological Quality ◽  
Amplicon Sequencing ◽  
Urban Sewage ◽  
16S Rrna Amplicon Sequencing ◽  
The Andes ◽  
Metabolic Functions ◽  
Quality Assessments

AbstractBackgroundThe Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. We aim to produce the first characterization of bacterial communities in the Rimac river using a 16S rRNA amplicon sequencing approach which would be useful to identify bacterial diversity and potential understudied pathogens.ResultsWe report a higher diversity in bacterial communities from the Upper and, especially, Middle Rimac compared to the Lower Rimac (Metropolitan zone). Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility, quorum sensing and xenobiotics metabolism. Additional metabolomic analyses showed the presence natural flavonoids and antibiotics in the Upper Rimac, and herbicides in the Lower Rimac.ConclusionsThe dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, but that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.

scholarly journals Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Michele Pittol ◽  
Erin Scully ◽  
Daniel Miller ◽  
Lisa Durso ◽  
Lidia Mariana Fiuza ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Developmental Stages ◽  
Amplicon Sequencing ◽  
Fertilizer Application ◽  
Rice Fields ◽  
Reproductive Stage ◽  
Vegetative Stage ◽  
Bacterial Phyla ◽  
16S Amplicon Sequencing ◽  
South Of Brazil

In agricultural systems, interactions between plants and microorganisms are important to maintaining production and profitability. In this study, bacterial communities in floodwaters of rice fields were monitored during the vegetative and reproductive stages of rice plant development using 16S amplicon sequencing. The study was conducted in the south of Brazil, during the crop years 2011/12 and 2012/13. Comparative analyses showed strong differences between the communities of floodwaters associated with the two developmental stages. During the vegetative stage, 1551 operational taxonomic units (OTUs) were detected, while less than half that number (603) were identified in the reproductive stage. The higher bacterial richness observed in floodwater collected during the vegetative stage may have been favored by the higher concentration of nutrients, such as potassium, due to rhizodeposition and fertilizer application. Eighteen bacterial phyla were identified in both samples. Both communities were dominated by Gammaproteobacteria. In the vegetative stage, Alphaproteobacteria and Betaproteobacteria were more abundant and, in contrast, Bacilli and Clostridia were the more dominant classes in the reproductive stage. The major bacterial taxa identified have been previously identified as important colonizers of rice fields. The richness and composition of bacterial communities over cultivation time may contribute to the sustainability of the crop.

scholarly journals Localization of bacterial communities within gut compartments across Cephalotes turtle ants

2021 ◽  
Author(s):  
Peter J. Flynn ◽  
Catherine L. D’Amelio ◽  
Jon G. Sanders ◽  
Jacob A. Russell ◽  
Corrie S. Moreau
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Digestive Tract ◽  
Bacterial Communities ◽  
Evolutionary History ◽  
Amplicon Sequencing ◽  
Caste Differentiation ◽  
Animal Group ◽  
16S Rrna Amplicon Sequencing ◽  
Host Phylogeny

Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes. We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion. IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.

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 Two Distinct Soil Disinfestations Differently Modify the Bacterial Communities in a Tomato Field

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1375
Author(s):  
Masaru Nakayasu ◽  
Kyoko Ikeda ◽  
Shinichi Yamazaki ◽  
Yuichi Aoki ◽  
Kazufumi Yazaki ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Bacterial Communities ◽  
Quantitative Polymerase Chain Reaction ◽  
Amplicon Sequencing ◽  
Growth And Yield ◽  
16S Rrna Amplicon Sequencing ◽  
Tomato Field ◽  
Pathogen Suppression ◽  
Polymerase Chain ◽  
Soil Environmental Factors

Reductive soil disinfestation (RSD) and soil solarization (SS) were evaluated based on environmental factors, microbiome, and suppression of Fusarium oxysporum in a tomato field soil. Soil environmental factors (moisture content, electric conductivity, pH, and redox potential (RP)) were measured during soil disinfestations. All factors were more strongly influenced by RSD than SS. 16S rRNA amplicon sequencing of RSD- and SS-treated soils was performed. The bacterial communities were taxonomically and functionally distinct depending on treatment methods and periods and significantly correlated with pH and RP. Fifty-four pathways predicted by PICRUSt2 (third level in MetaCyc hierarchy) were significantly different between RSD and SS. Quantitative polymerase chain reaction demonstrated that both treatments equally suppressed F. oxysporum. The growth and yield of tomato cultivated after treatments were similar between RSD and SS. RSD and SS shaped different soil bacterial communities, although the effects on pathogen suppression and tomato plant growth were comparable between treatments. The existence of pathogen-suppressive microbes, other than Clostridia previously reported to have an effect, was suggested. Comparison between RSD and SS provides new aspects of unknown disinfestation patterns and the usefulness of SS as an alternative to RSD.

scholarly journals Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10302
Author(s):  
Li Song ◽  
Zhenzhi Pan ◽  
Yi Dai ◽  
Lin Chen ◽  
Li Zhang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
Cadmium Concentration ◽  
Normal Growth ◽  
Amplicon Sequencing ◽  
Negative Influence ◽  
Cadmium Pollution ◽  
16S Rrna Amplicon Sequencing ◽  
The Impact

Cadmium pollution is becoming a serious problem due to its nondegradability and substantial negative influence on the normal growth of crops, thereby harming human health through the food chain. Rhizospheric bacteria play important roles in crop tolerance. However, there is little experimental evidence which demonstrates how various cadmium concentrations affect the bacterial community in wheat fields including rhizosphere microorganisms and nonrhizosphere (bulk) microorganisms. In this study, 16S rRNA amplicon sequencing technology was used to investigate bacterial communities in rhizosphere and bulk soils under different levels of pollution in terms of cadmium concentration. Both the richness and diversity of the rhizosphere microorganism community were higher under nonpolluted soil and very mild and mild cadmium-contaminated soils than compared with bulk soil, with a shift in community profile observed under severe cadmium pollution. Moreover, cadmium at various concentrations had greater influence on bacterial composition than for the nonpolluted site. In addition, redundancy analysis (RDA) and Spearman’s analysis elucidated the impact of exchangeable Cd and total Cd on bacterial community abundance and composition. This study suggests that cadmium imposes a distinct effect on bacterial community, both in bulk and rhizosphere soils of wheat fields. This study increases our understanding of how bacterial communities in wheat fields shaped under different concentrations of cadmium.

scholarly journals Analysis of Mountain Chickadee (Poecile gambeli) associated bacterial communities across urban and rural habitats

2021 ◽  
Author(s):  
Colton Robert Alexander Stephens ◽  
Breanne M McAmmond ◽  
Jonathan Douglas Van Hamme ◽  
Ken A Otter ◽  
Matthew W Reudink ◽  
...  
Keyword(s):  
Success Rate ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Urban Environments ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Poecile Gambeli ◽  
Rural Environments ◽  
Potential Pathogen ◽  
Mountain Chickadee

Host associated microbial communities play important roles in wildlife health, but these dynamics can be influenced by environmental factors. Urbanization has numerous consequences on wildlife; however, the degree to which wildlife associated bacterial communities and potential bacterial pathogens vary across urban to rural/native habitat gradients remains largely unknown. We used 16S rRNA gene amplicon sequencing to examine bacterial communities found on mountain chickadee (Poecile gambeli) feathers and nests in urban and rural habitats. Feathers and nests in urban and rural sites had similar abundances of major bacterial phyla and dominant genera with pathogenic members. However, richness of bacterial communities and potential pathogens on birds were higher in urban habitats, and potential pathogens accounted for some of the differences in bacterial occurrence between urban and rural environments. We predicted habitat using potential pathogen occurrence with a 90% success rate for feather bacteria, and a 72.2% success rate for nest bacteria, suggesting an influence of urban environments on potential pathogen presence. We additionally observed similarities in bacterial communities between nests and their occupants, suggesting bacterial transmission between them. These findings improve our understanding of the bacterial communities associated with urban wildlife and suggest that urbanization may impact wildlife associated bacterial community compositions.

scholarly journals Stingless Bee Honey: Evaluating Its Antibacterial Activity and Bacterial Diversity

Insects ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 500 ◽  
Author(s):  
Farah Nadiah Rosli ◽  
Mohd Hafiz Fikri Hazemi ◽  
Muhamad Afiq Akbar ◽  
Syazwani Basir ◽  
Hakimi Kassim ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Health Benefit ◽  
Amplicon Sequencing ◽  
Alcaligenes Faecalis ◽  
Stingless Bee ◽  
Bacterial Phyla ◽  
16S Rrna Amplicon Sequencing ◽  
Characterization Study ◽  
Medicinal Properties ◽  
Dominant Bacteria

Stingless bee honey (SBH) is an astounding ‘miracle liquid’ with countless medicinal properties for various diseases such as gastroenteritis, cataracts, as well as for wound-healing. However, knowledge regarding it is still rather scarce. Henceforth, it is intriguing for us to contemplate on the less-studied stingless bee and its honey in particular. First and foremost, the antimicrobial ability of honey from eight different stingless bee species was tested to further proven its health benefit. Homotrigona fimbriata honey showed the highest antimicrobial activity with inhibition against five bacteria; Serratia marcescens, Escherichia coli, Bacillus subtilis, Alcaligenes faecalis and Staphylococcus aureus. The next aim of our study is to characterize their honey bacterial community via the use of 16S rRNA amplicon sequencing technology. A total of eight bacterial phyla, 71 families, 155 genera and 70 species were identified from our study and two of the stingless bee species honey were determined to have the highest bacterial diversity compared to other six stingless bee species, namely Heterotrigona erythrogastra and Tetrigona melanoleuca. Furthermost, Lactobacillus malefermentans was thought to be the native dominant bacteria of SBH due to its predominant presence throughout all studied species. The aforementioned SBH’s antimicrobial results and characterization study of its bacterial diversity are hoped to carve the pathway towards extending its probiotic ability into our everyday lives.

scholarly journals Land Use Effects on Airborne Bacterial Communities Are Evident in Both Near-Surface and Higher-Altitude Air

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 85
Author(s):  
Allison M. Spring ◽  
Kenneth D. Domingue ◽  
Thomas V. Kerber ◽  
Margaret M. Mooney ◽  
Rebecca L. Hale ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Small Scale ◽  
Dispersal Patterns ◽  
Near Surface ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Surface Samples ◽  
Land Use Effects

Land use influences the composition of near-surface airborne bacterial communities, and bacteria can be transported through the atmosphere at global scales. The atmosphere mixes vertically, but rigorously assessing whether the effects of land use on atmospheric communities extends to higher altitudes requires examining communities from multiple altitudes collected at a stable location and timeframe. In this study, we collected near-surface (<2 m) and higher-altitude (150 m) air samples from three sites in an agricultural/developed location and a forested/undeveloped location. We used bacterial 16S rRNA amplicon sequencing to compare communities and predict functionality by altitude. Higher-altitude and near-surface communities did not differ in composition within each location. Communities collected above the undeveloped location were equally variable at both altitudes; higher-altitude samples from the developed location predominantly contained Firmicutes and were less variable than near-surface samples. We also compared airborne taxa to those present in soil and snow. Communities from higher-altitude samples above the developed location contained fewer overlapping taxa with soil and snow sources, and overlapping Operational Taxonomic Units (OTUs) among the three sources differed by location. Our results suggest that land use affects the composition of both near-surface and higher-altitude airborne bacterial communities and, therefore, may influence broad bacterial dispersal patterns. This small-scale pilot study provides a framework for simultaneously examining local and regional airborne microbial communities that can be applied to larger studies or studies using different types of samplers.

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