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 Unveiling Endophytic Bacterial Community Structures of Different Rice Cultivars Grown in a Cadmium-Contaminated Paddy Field

2021 ◽  
Vol 12 ◽  
Author(s):  
Chaoqun Chu ◽  
Meiyu Fan ◽  
Chongyang Song ◽  
Ni Li ◽  
Chao Zhang ◽  
...  
Keyword(s):  
Paddy Field ◽  
Bacterial Communities ◽  
Endophytic Bacteria ◽  
Reproductive Stage ◽  
Vegetative Stage ◽  
Rrna Gene ◽  
Rice Cultivars ◽  
Cd Stress ◽  
Bacterial Phyla ◽  
Rice Roots

Endophytic bacteria play potentially important roles in the processes of plant adaptation to the environment. Understanding the composition and dynamics of endophytic bacterial communities under heavy metal (HM) stress can reveal their impacts on host development and stress tolerance. In this study, we investigated root endophytic bacterial communities of different rice cultivars grown in a cadmium (Cd)-contaminated paddy field. These rice cultivars are classified into low (RBQ, 728B, and NX1B) and high (BB and S95B) levels of Cd-accumulating capacity. Our metagenomic analysis targeting 16S rRNA gene sequence data reveals that Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes, and Spirochaetes are predominant root endophytic bacterial phyla of the five rice cultivars that we studied. Principal coordinate analysis shows that the developmental stage of rice governs a larger source of variation in the bacterial communities compared to that of any specific rice cultivar or of the root Cd content. Endophytic bacterial communities during the reproductive stage of rice form a more highly interconnected network and exhibit higher operational taxonomic unit numbers, diversities, and abundance than those during the vegetative stage. Forty-five genera are significantly correlated with Cd content in rice root, notably including positive-correlating Geobacter and Haliangium; and negative-correlating Pseudomonas and Streptacidiphilus. Furthermore, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis shows that functional pathways, such as biosynthesis of siderophore and type II polyketide products, are significantly enhanced during the reproductive stage compared to those during the vegetative stage under Cd stress. The isolated endophytic bacteria from the Cd-contaminated rice roots display high Cd resistance and multiple traits that may promote plant growth, suggesting their potential application in alleviating HM stress on plants. This study describes in detail for the first time the assemblage of the bacterial endophytomes of rice roots under Cd stress and may provide insights into the interactions among endophytes, plants, and HM contamination.

scholarly journals Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

2017 ◽  
Author(s):  
Benjamin E. Rubin ◽  
Jon G. Sanders ◽  
Kyle M. Turner ◽  
Naomi E. Pierce ◽  
Sarah D. Kocher
Keyword(s):  
Social Interactions ◽  
Bacterial Communities ◽  
Bacterial Abundance ◽  
De Novo ◽  
Amplicon Sequencing ◽  
Social Forms ◽  
Phylogenetic Reconstructions ◽  
16S Amplicon Sequencing ◽  
Species Specific ◽  
Genome Assemblies

AbstractSocial interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviors and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both social and solitary bee species within the behaviorally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms, and most halictid species appear to share similar gut bacterial communities. However, several strains of Sodalis, a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between social and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate that Sodalis has independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting that Sodalis strains compete for access to hosts. De novo genome assemblies indicate that these three lineages are subject to widespread relaxed selection and that Sodalis is undergoing genome degeneration during the colonization of these hosts.

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 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 Social behaviour in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

2018 ◽  
Vol 5 (7) ◽  
pp. 180369 ◽  
Author(s):  
Benjamin E. R. Rubin ◽  
Jon G. Sanders ◽  
Kyle M. Turner ◽  
Naomi E. Pierce ◽  
Sarah D. Kocher
Keyword(s):  
Social Interactions ◽  
Bacterial Communities ◽  
Bacterial Abundance ◽  
Social Groups ◽  
Amplicon Sequencing ◽  
Solitary Bee ◽  
Social Forms ◽  
Phylogenetic Reconstructions ◽  
16S Amplicon Sequencing ◽  
Species Specific

Social interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviours and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both eusocial and solitary bee species within the behaviourally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms; most halictid species appear to share similar gut bacterial communities. However, several strains of Sodalis, a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between eusocial and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate that Sodalis has independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting that Sodalis strains compete for access to hosts. The symbiosis between halictids and Sodalis therefore appears to be in its early stages.

scholarly journals Dietary and developmental shifts in butterfly-associated bacterial communities

2018 ◽  
Vol 5 (5) ◽  
pp. 171559 ◽  
Author(s):  
Kruttika Phalnikar ◽  
Krushnamegh Kunte ◽  
Deepa Agashe
Keyword(s):  
Bacterial Communities ◽  
Developmental Stages ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Butterfly Species ◽  
Active Selection ◽  
Key Factor ◽  
Taxonomic Groups ◽  
The Impact

Bacterial communities associated with insects can substantially influence host ecology, evolution and behaviour. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analysed bacterial communities of 12 butterfly species across different developmental stages, using amplicon sequencing of the 16S rRNA gene. Butterfly larvae typically consume leaves of a single host plant, whereas adults are more generalist nectar feeders. Thus, we expected bacterial communities to vary substantially across butterfly development. Surprisingly, only few species showed significant dietary and developmental transitions in bacterial communities, suggesting weak impacts of dietary transitions across butterfly development. On the other hand, bacterial communities were strongly influenced by butterfly species and family identity, potentially due to dietary and physiological variation across the host phylogeny. Larvae of most butterfly species largely mirrored bacterial community composition of their diets, suggesting passive acquisition rather than active selection. Overall, our results suggest that although butterflies harbour distinct microbiomes across taxonomic groups and dietary guilds, the dramatic dietary shifts that occur during development do not impose strong selection to maintain distinct bacterial communities across all butterfly hosts.

scholarly journals Secondary metabolites of Bacillus subtilis impact soil-derived semi-synthetic bacterial community assembly

2020 ◽  
Author(s):  
Heiko T. Kiesewalter ◽  
Carlos N. Lozano-Andrade ◽  
Mikael L. Strube ◽  
Ákos T. Kovács
Keyword(s):  
Bacillus Subtilis ◽  
Secondary Metabolites ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Ecological Role ◽  
16S Amplicon Sequencing ◽  
Bacterial Protein Synthesis ◽  
Mock Communities

AbstractSecondary metabolites provide Bacillus subtilis with increased competitiveness towards other microorganisms. In particular nonribosomal peptides (NRPs) have an enormous antimicrobial potential by causing cell lysis, perforation of fungal membranes, enzyme inhibition or disruption of bacterial protein synthesis. This knowledge was primarily acquired in vitro when B. subtilis was competing with other microbial monocultures. However, our understanding of the true ecological role of these small molecules is limited.In this study, we have established soil-derived semi-synthetic mock communities containing 13 main genera and supplemented them with B. subtilis P5_B1 WT, its NRP deficient strain sfp or single NRP mutants incapable of producing surfactin, plipastatin or bacillaene. 16S amplicon sequencing revealed that the invasion of NRP-producing B. subtilis strains had no major impact on the bacterial communities. Still, the abundances of the two genera Lysinibacillus and Viridibacillus were reduced. Interestingly, this effect was diminished in communities supplemented with the NRPs deficient strain. Growth profiling of Lysinibacillus fusiformis M5 exposed to either spent media of the B. subtilis strains or pure surfactin indicates the sensitivity of this strain towards the biosurfactant surfactin.Our study provides a more in-depth insight into the influence of B. subtilis NRPs on semi-synthetic bacterial communities and helps to understand their ecological role.

scholarly journals 16S amplicon sequencing of microbial communities in enriched and non-enriched sediments of non-volcanic hot spring with temperature gradients

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10995
Author(s):  
Muhammad Yasir ◽  
Arooj K. Qureshi ◽  
Esam I. Azhar
Keyword(s):  
Microbial Diversity ◽  
Hot Springs ◽  
Hot Spring ◽  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Microbial Composition ◽  
Sediment Samples ◽  
Bacterial Phyla ◽  
16S Amplicon Sequencing ◽  
Culture Dependent

Microorganisms in geothermal springs can offer insights into the fundamental and applied study of extremophiles. However, low microbial abundance and culturing requirements limit the ability to analyze microbial diversity in these ecosystems. In this study, culture-dependent and culture-independent techniques were used to analyze sediment samples from the non-volcanic Tatta Pani hot springs in district Poonch of Azad Kashmir. Microbial composition, temperature gradient, and enrichment effects on rare taxa were evaluated. In total, 31 distinct bacterial phyla and 725 genera were identified from the non-enriched Tatta Pani hot spring sediment samples, and 33 distinct bacterial phyla and 890 genera from the enriched sediment samples. Unique phyla specimens from the enriched samples included Candidatus Cloacimonetes, Caldiserica, and Korarchaeota archaea. The enriched samples yielded specific microbiota including 805 bacteria and 42 archaea operational taxonomic units with 97% similarity, though decreased thermophilic microbiota were observed in the enriched samples. Microbial diversity increased as temperature decreased. Candidate novel species were isolated from the culture-dependent screening, along with several genera that were not found in the 16S amplicon sequencing data. Overall, the enriched sediments showed high microbial diversity but with adverse changes in the composition of relatively dominant bacteria. Metagenomic analyses are needed to study the diversity, phylogeny, and functional investigation of hot spring microbiota.

scholarly journals Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

2020 ◽  
Vol 16 ◽  
pp. 2983-2998
Author(s):  
Heiko T Kiesewalter ◽  
Carlos N Lozano-Andrade ◽  
Mikael L Strube ◽  
Ákos T Kovács
Keyword(s):  
Bacillus Subtilis ◽  
Secondary Metabolites ◽  
Bacterial Communities ◽  
Amplicon Sequencing ◽  
Ecological Role ◽  
16S Amplicon Sequencing ◽  
Bacterial Protein Synthesis ◽  
Mock Communities

Secondary metabolites provide Bacillus subtilis with increased competitiveness towards other microorganisms. In particular, nonribosomal peptides (NRPs) have an enormous antimicrobial potential by causing cell lysis, perforation of fungal membranes, enzyme inhibition, or disruption of bacterial protein synthesis. This knowledge was primarily acquired in vitro when B. subtilis was competing with other microbial monocultures. However, our understanding of the true ecological role of these small molecules is limited. In this study, we have established soil-derived semisynthetic mock communities containing 13 main genera and supplemented them with B. subtilis P5_B1 WT, the NRP-deficient strain sfp, or single-NRP mutants incapable of producing surfactin, plipastatin, or bacillaene. Through 16S amplicon sequencing, it was revealed that the invasion of NRP-producing B. subtilis strains had no major impact on the bacterial communities. Still, the abundance of the two genera Lysinibacillus and Viridibacillus was reduced. Interestingly, this effect was diminished in communities supplemented with the NRP-deficient strain. Growth profiling of Lysinibacillus fusiformis M5 exposed to either spent media of the B. subtilis strains or pure surfactin indicated the sensitivity of this strain towards the biosurfactant surfactin. Our study provides a more in-depth insight into the influence of B. subtilis NRPs on semisynthetic bacterial communities and helps to understand their ecological role.

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