Contribution of Maternal and Paternal Transmission to Bacterial Colonization in Nematostella vectensis

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.

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The Growth of Leaf Lettuce and Bacterial Communities in a Closed Aquaponics System with Catfish

Horticulturae ◽

10.3390/horticulturae7080222 ◽

2021 ◽

Vol 7 (8) ◽

pp. 222

Author(s):

Kenji Yamane ◽

Yuuki Kimura ◽

Keita Takahashi ◽

Isamu Maeda ◽

Masayuki Iigo ◽

...

Keyword(s):

Plant Growth ◽

Early Stage ◽

Amplicon Sequencing ◽

Small Scale ◽

Rrna Gene ◽

Culture Solution ◽

Beneficial Effects ◽

Sustainable Cultivation ◽

Microbial Groups ◽

Production Period

Aquaponics is a circulating and sustainable system that combines aquaculture and hydroponics and forms a symbiotic relationship between fish, plants, and microorganisms. We hypothesized that feed alone could support plant growth, but the symbiosis with fish adds some beneficial effects on plant growth in aquaponics. In this study, we created three closed culture systems, namely, aquaponics, hydroponics without nitrogen (N) and phosphorus (P), and aquaculture, and added the same amount of feed containing N and P to all the treatments in order to test the hypothesis. Accumulation of NO3− and PO43− was alleviated in aquaponics and hydroponics as a result of plant uptake. Lettuce plants grown in aquaponics grew vigorously until 2 weeks and contained a constant level of N in plants throughout the production period, whereas those in hydroponics grew slowly in the early stage and then vigorously after 2 weeks with a late increment of N concentration. These results suggest that catfish help with the faster decomposition of the feed, but, in hydroponics, feed can be slowly dissolved and decomposed owing to the absence of the fish. The bacterial community structures of the culture solution were investigated using 16S rRNA gene amplicon sequencing. At the class level, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were the major microbial groups in the solutions. Aquaponics prevented the pollution of tank solution and maintained a higher water quality compared with hydroponics and aquaculture, suggesting that aquaponics is a more sustainable cultivation system even in a small-scale system.

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Forfeiting the founder effect: turnover defines biofilm community succession

10.1101/282574 ◽

2018 ◽

Cited By ~ 2

Author(s):

Colin J. Brislawn ◽

Emily B. Graham ◽

Karl Dana ◽

Peter Ihardt ◽

Sarah J. Fansler ◽

...

Keyword(s):

Bacterial Colonization ◽

Amplicon Sequencing ◽

18S Rrna Gene ◽

Rrna Gene ◽

Community Succession ◽

Ecological Processes ◽

Functional Capabilities ◽

Resolution Imaging ◽

Successional Stages ◽

Almost All

ABSTRACTMicrobial community succession is a fundamental process that effects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are poorly understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the roles of founder species? We performed a succession experiment within a hypersaline microbial mat ecosystem to investigate how ecological processes contributed to the turnover of founder species. Bacterial and micro-eukaryotic founder species were identified from primary succession and tracked through a defined maturation period using 16S and 18S rRNA gene amplicon sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate basic functional capabilities. The majority of the founder species did not maintain high relative abundances in later stages of succession. Turnover (versus nestedness) was the dominant process shaping the final community structure. We also asked if different ecological processes acted on bacteria versus eukaryotes during successional stages and found that deterministic and stochastic forces corresponded more with eukaryote and bacterial colonization, respectively. Our results show that taxa from different kingdoms, that share habitat in the tight spatial confines of a biofilm, were influenced by different ecological forces and time scales of succession.

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Gut microbiota composition is associated with narcolepsy type 1

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000000896 ◽

2020 ◽

Vol 7 (6) ◽

pp. e896

Author(s):

Alexandre Lecomte ◽

Lucie Barateau ◽

Pedro Pereira ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Bacterial Communities ◽

Beta Diversity ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Differential Abundance ◽

Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

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

Phytobiomes Journal ◽

10.1094/pbiomes-05-17-0023-r ◽

2017 ◽

Vol 1 (3) ◽

pp. 158-168 ◽

Cited By ~ 51

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.

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Temporal variation in soil bacterial communities can be confounded with spatial variation

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa192 ◽

2020 ◽

Vol 96 (12) ◽

Author(s):

Syrie M Hermans ◽

Hannah L Buckley ◽

Fiona Curran-Cournane ◽

Matthew Taylor ◽

Gavin Lear

Keyword(s):

Temporal Variation ◽

Bacterial Communities ◽

Amplicon Sequencing ◽

Spatial Distance ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Causal Processes ◽

Fundamental Understanding ◽

Soil Bacterial ◽

Indigenous Forest

ABSTRACT Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13–24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.

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Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz179 ◽

2019 ◽

Author(s):

Lara Parata ◽

Shaun Nielsen ◽

Xing Xing ◽

Torsten Thomas ◽

Suhelen Egan ◽

...

Keyword(s):

Coral Reef ◽

Gastrointestinal Tract ◽

Bacterial Community ◽

Gut Microbiota ◽

Bacterial Communities ◽

Food Source ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Bacterial Symbionts ◽

Adult Fish

Abstract Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.

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Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

10.21203/rs.3.rs-384378/v1 ◽

2021 ◽

Author(s):

Nicole E Adams ◽

Madeleine A Becker ◽

Suzanne Edmands

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Captive Breeding ◽

Interdisciplinary Approach ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sample Collection ◽

Channel Island ◽

Island Fox ◽

Urocyon Littoralis

Abstract Background With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and look at the effects of geography and captivity on the variation in bacterial communities. Results Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Conclusions Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

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Press xenobiotic disturbance favors deterministic assembly with a shift in function and structure of bacterial communities in sludge bioreactors

10.1101/2020.10.15.341966 ◽

2020 ◽

Author(s):

Ezequiel Santillan ◽

Hari Seshan ◽

Stefan Wuertz

Keyword(s):

Community Structure ◽

Bacterial Communities ◽

Temporal Dynamics ◽

Treatment Plant ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Batch Reactors ◽

Function Structure ◽

Community Function ◽

And Function

AbstractDisturbance is thought to affect community assembly mechanisms, which in turn shape community structure and the overall function of the ecosystem. Here, we tested the effect of a continuous (press) xenobiotic disturbance on the function, structure, and assembly of bacterial communities within a wastewater treatment system. Two sets of four-liter sequencing batch reactors were operated in triplicate with and without the addition of 3-chloroaniline for a period of 132 days, following 58 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of bacterial community structure were derived from 16S rRNA gene amplicon sequencing. Community function, structure and assembly differed between press disturbed and undisturbed reactors. Temporal partitioning of assembly mechanisms via phylogenetic and non-phylogenetic null modelling analysis revealed that deterministic assembly prevailed for disturbed bioreactors, while the role of stochastic assembly was stronger for undisturbed reactors. Our findings are relevant because research spanning various disturbance types, environments and spatiotemporal scales is needed for a comprehensive understanding of the effects of press disturbances on assembly mechanisms, structure, and function of microbial communities.Graphical abstract

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Homogenization of Rhizosphere Bacterial Communities by Pea (Pisum sativum L.) Cultivated under Different Conservation Agricultural Practices in the Eastern Himalayas

10.1101/662775 ◽

2019 ◽

Author(s):

Diptaraj Chaudhari ◽

Krishnappa Rangappa ◽

Anup Das ◽

Jayanta Layek ◽

Savita Basavaraju ◽

...

Keyword(s):

Bacterial Communities ◽

Management Practices ◽

Soil Health ◽

Agricultural Practices ◽

Amplicon Sequencing ◽

Soil Samples ◽

Residue Management ◽

Bulk Soil ◽

Rrna Gene ◽

North East

AbstractConservation agriculture offers a suitable system to harmonize agriculture with the environment, especially in fragile ecosystems of North-East India. Soil microbes play pivotal roles in ecosystem functioning and act as indispensable indicators of overall fitness of crop plant and soil health. Here we demonstrated that altercations in residue management and tillage practices lead to the development of differential bacterial communities forcing the pea plants to recruit special groups of bacteria leading to highly homogenous rhizosphere communities. Pea rhizosphere and bulk soil samples were collected, and bacterial community structure was estimated by 16S rRNA gene amplicon sequencing and predictive functional analysis was performed using Tax4Fun. The effect on pea plants was evident in the bacterial communities as the overall diversity of rhizosphere samples was significantly higher to that of bulk soil samples. Bacillus, Staphylococcus, Planomicrobium, Enterobacter, Arthrobacter, Nitrobacter, Geobacter, and Sphingomonas were noticed as the most abundant genera in the rhizosphere and bulk soil samples. The abundance of Firmicutes and Proteobacteria altered significantly in the rhizosphere and bulk samples, which was further validated by qPCR. Selection of specific taxa by pea plant was indicated by the higher values of mean proportion of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter and Sphingomonas in rhizosphere samples, and Massilia, Paenibacillus and Planomicrobium in bulk soil samples. Tillage and residue management treatments did not significantly alter the bacterial diversity, while their influence was observed on the abundance of few genera. Recorded results revealed that pea plant selects specific taxa into its rhizosphere plausibly to meet its requirements for nutrient uptake and stress amelioration under the different tillage and residue management practices.

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

mSphere ◽

10.1128/msphere.00531-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 4

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.

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