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 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 The Biocontrol Agent and Insect Pathogen Photorhabdus luminescens Interacts with Plant Roots

2020 ◽  
Vol 86 (17) ◽  
Author(s):  
Alice Regaiolo ◽  
Nazzareno Dominelli ◽  
Karsten Andresen ◽  
Ralf Heermann
Keyword(s):  
Biological Control ◽  
Pest Management ◽  
Root Exudates ◽  
Biological Control Agent ◽  
Plant Root ◽  
Specific Interaction ◽  
Plant Roots ◽  
Photorhabdus Luminescens ◽  
Content Type ◽  
Root Interactions

ABSTRACT The number of sustainable agriculture techniques to improve pest management and environmental safety is rising, as biological control agents are used to enhance disease resistance and abiotic stress tolerance in crops. Here, we investigated the capacity of the Photorhabdus luminescens secondary variant to react to plant root exudates and their behavior toward microorganisms in the rhizosphere. P. luminescens is known to live in symbiosis with entomopathogenic nematodes (EPNs) and to be highly pathogenic toward insects. The P. luminescens-EPN relationship has been widely studied, and this combination has been used as a biological control agent; however, not much attention has been paid to the putative lifestyle of P. luminescens in the rhizosphere. We performed transcriptome analysis to show how P. luminescens responds to plant root exudates. The analysis highlighted genes involved in chitin degradation, biofilm regulation, formation of flagella, and type VI secretion system. Furthermore, we provide evidence that P. luminescens can inhibit growth of phytopathogenic fungi. Finally, we demonstrated a specific interaction of P. luminescens with plant roots. Understanding the role and the function of this bacterium in the rhizosphere might accelerate the progress in biocontrol manipulation and elucidate the peculiar mechanisms adopted by plant growth-promoting rhizobacteria in plant root interactions. IMPORTANCE Insect-pathogenic Photorhabdus luminescens bacteria are widely used in biocontrol strategies against pests. Very little is known about the life of these bacteria in the rhizosphere. Here, we show that P. luminescens can specifically react to and interact with plant roots. Understanding the adaptation of P. luminescens in the rhizosphere is highly important for the biotechnological application of entomopathogenic bacteria and could improve future sustainable pest management in agriculture.

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 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 MISIRoot: A Robotic Minimum Invasion in Situ Imaging System for Plant Root Phenotyping

2020 ◽  
Author(s):  
Zhihang Song ◽  
Wei Qiu ◽  
Jian Jin
Keyword(s):  
Plant Protection ◽  
Plant Root ◽  
Low Cost ◽  
3D Structure ◽  
Color Images ◽  
Plant Roots ◽  
Natural Soil ◽  
Wide Range ◽  
Root Phenotyping

Abstract Background: Plant root phenotyping technologies play an important role in breeding, plant protection, and other plant science research projects. The root phenotyping customers urgently need technologies that are low-cost, in situ, non-destructive to the roots, and suitable for the natural soil environment. Many recently developed root phenotyping methods such as minirhizotron, X-CT, and MRI scanners have their unique advantages in observing plant roots, but they also have disadvantages and cannot meet all the critical requirements simultaneously. Results: The study in this paper focuses on the development of a new plant root phenotyping robot that is minimally invasive to plants and working in situ inside natural soil, called “MISIRoot”. The MISIRoot system mainly consists of an industrial-level robotic arm, a mini-size camera with lighting set, a plant pot holding platform, and the image processing software for root recognition and feature extraction. MISIRoot can take high-resolution color images of the roots in soil with minimal disturbance to the root and reconstruct the plant roots’ three-dimensional (3D) structure at an accuracy of 0.1 mm. In a test assay, well-watered and drought-stressed groups of corn plants were measured by MISIRoot at V3, V4, and V5 stages. The system successfully acquired the RGB color images of the roots and extracted the 3D points cloud data containing the locations of the detected roots. The plants measured by MISIRoot and plants not measured (control) were carefully compared with the results from the Hyperspectral Imaging Facility (reference). No significant differences were found between the two groups of plants at different growth stages. Conclusion: The MISIRoot system recently developed at Purdue University has been proved effective in root phenotyping with multiple advantages: With a comparatively low cost and minimal invasion to the plant, this system can automatically measure the root’s 3D structure and take color images of the roots in ordinary soil media, and in situ. This system provides a new option for root phenotyping researchers and has a potential to be applied in a wide range of research topics such as breeding, plant protection and so on.

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 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 Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics

mSystems ◽  
2021 ◽  
Author(s):  
Vittorio Tracanna ◽  
Adam Ossowicki ◽  
Marloes L. C. Petrus ◽  
Sam Overduin ◽  
Barbara R. Terlouw ◽  
...  
Keyword(s):  
Fungal Pathogens ◽  
Pathogenic Fungi ◽  
Amplicon Sequencing ◽  
Plant Pathogenic Fungi ◽  
Content Type ◽  
Major Threat ◽  
Wide Range

Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops.

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 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.

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