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 Dietary and Developmental Shifts in Butterfly-Associated Bacterial Communities

2017 ◽  
Author(s):  
Kruttika Phalnikar ◽  
Krushnamegh Kunte ◽  
Deepa Agashe
Keyword(s):  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Butterfly Species ◽  
Species Identity ◽  
Active Selection ◽  
Key Factor ◽  
Host Diet ◽  
Taxonomic Groups ◽  
The Impact

ABSTRACTBacterial communities associated with insects can substantially influence host ecology, evolution and behavior. Host diet is a key factor that shapes bacterial communities, but the impact of dietary transitions across insect development is poorly understood. We analyzed bacterial communities of 12 butterfly species across different development stages, using 16S rDNA amplicon sequencing. 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, very few species showed significant 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 identity and dietary variation across species. 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 harbor 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.

scholarly journals Groundwater bacterial communities evolve over time, exhibiting oscillating similarity patterns in response to recharge

2021 ◽  
Author(s):  
Lijuan Yan ◽  
Syrie Hermans ◽  
Kai Uwe Totsche ◽  
Robert Lehmann ◽  
Martina Herrmann ◽  
...  
Keyword(s):  
Groundwater Recharge ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
High Temporal Resolution ◽  
Aquatic Environments ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Environmental Selection ◽  
The Impact ◽  
Over Time

Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in groundwater bacterial communities of shallow fractured bedrock community, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n=230) along a hillslope recharge area. We show that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and showed oscillating dissimilarity patterns which corresponded to periods of groundwater recharge; the impact of recharge events on the groundwater microbiome was linked to the recharge strength and local environmental selection strength. Sampling period was able to explain up to 29.5% of the variability in bacterial community composition. We observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The majority of groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, groundwater microbiomes vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the complex dynamics of bacterial communities in groundwater and demonstrated that successive shocks disturb the bacterial communities, leading to decreased similarity to the initial state over time.

scholarly journals Wine Terroir and the Soil Bacteria: An Amplicon Sequencing–Based Assessment of the Barossa Valley and Its Sub-Regions

2021 ◽  
Vol 11 ◽  
Author(s):  
Jia Zhou ◽  
Timothy R. Cavagnaro ◽  
Roberta De Bei ◽  
Tiffanie M. Nelson ◽  
John R. Stephen ◽  
...  
Keyword(s):  
Soil Bacteria ◽  
Bacterial Community Composition ◽  
Geographic Distance ◽  
Hypervariable Region ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Factors Affecting ◽  
Growing Conditions ◽  
Community Dissimilarity ◽  
The Impact

A wines’ terroir, represented as wine traits with regional distinctiveness, is a reflection of both the biophysical and human-driven conditions in which the grapes were grown and wine made. Soil is an important factor contributing to the uniqueness of a wine produced by vines grown in specific conditions. Here, we evaluated the impact of environmental variables on the soil bacteria of 22 Barossa Valley vineyard sites based on the 16S rRNA gene hypervariable region 4. In this study, we report that both dispersal isolation by geographic distance and environmental heterogeneity (soil plant-available P content, elevation, rainfall, temperature, spacing between row and spacing between vine) contribute to microbial community dissimilarity between vineyards. Vineyards located in cooler and wetter regions showed lower beta diversity and a higher ratio of dominant taxa. Differences in soil bacterial community composition were significantly associated with differences in fruit and wine composition. Our results suggest that environmental factors affecting wine terroir, may be mediated by changes in microbial structure, thus providing a basic understanding of how growing conditions affect interactions between plants and their soil bacteria.

scholarly journals Susceptibility of Red Mason Bee Larvae to Bacterial Threats Due to Microbiome Exchange with Imported Pollen Provisions

Insects ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 373 ◽  
Author(s):  
Anna Voulgari-Kokota ◽  
Ingolf Steffan-Dewenter ◽  
Alexander Keller
Keyword(s):  
Ribosomal Rna ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Solitary Bees ◽  
Rrna Gene ◽  
Bacillus Sp ◽  
Population Declines ◽  
Paenibacillus Sp ◽  
Inoculation Treatment ◽  
The Impact

Solitary bees are subject to a variety of pressures that cause severe population declines. Currently, habitat loss, temperature shifts, agrochemical exposure, and new parasites are identified as major threats. However, knowledge about detrimental bacteria is scarce, although they may disturb natural microbiomes, disturb nest environments, or harm the larvae directly. To address this gap, we investigated 12 Osmia bicornis nests with deceased larvae and 31 nests with healthy larvae from the same localities in a 16S ribosomal RNA (rRNA) gene metabarcoding study. We sampled larvae, pollen provisions, and nest material and then contrasted bacterial community composition and diversity in healthy and deceased nests. Microbiomes of pollen provisions and larvae showed similarities for healthy larvae, whilst this was not the case for deceased individuals. We identified three bacterial taxa assigned to Paenibacillus sp. (closely related to P. pabuli/amylolyticus/xylanexedens), Sporosarcina sp., and Bacillus sp. as indicative for bacterial communities of deceased larvae, as well as Lactobacillus for corresponding pollen provisions. Furthermore, we performed a provisioning experiment, where we fed larvae with untreated and sterilized pollens, as well as sterilized pollens inoculated with a Bacillus sp. isolate from a deceased larva. Untreated larval microbiomes were consistent with that of the pollen provided. Sterilized pollen alone did not lead to acute mortality, while no microbiome was recoverable from the larvae. In the inoculation treatment, we observed that larval microbiomes were dominated by the seeded bacterium, which resulted in enhanced mortality. These results support that larval microbiomes are strongly determined by the pollen provisions. Further, they underline the need for further investigation of the impact of detrimental bacterial acquired via pollens and potential buffering by a diverse pollen provision microbiome in solitary bees.

scholarly journals Selection for Cu-Tolerant Bacterial Communities with Altered Composition, but Unaltered Richness, via Long-Term Cu Exposure

2012 ◽  
Vol 78 (20) ◽  
pp. 7438-7446 ◽  
Author(s):  
Jeanette Berg ◽  
Kristian K. Brandt ◽  
Waleed A. Al-Soud ◽  
Peter E. Holm ◽  
Lars H. Hansen ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Metal Tolerance ◽  
Bacterial Community Composition ◽  
Community Response ◽  
Leucine Incorporation ◽  
Rrna Gene ◽  
Sequence Information ◽  
Content Type ◽  
Relative Abundances ◽  
The Impact

ABSTRACTToxic metal pollution affects the composition and metal tolerance of soil bacterial communities. However, there is virtually no knowledge concerning the responses of members of specific bacterial taxa (e.g., phyla or classes) to metal toxicity, and contradictory results have been obtained regarding the impact of metals on operational taxonomic unit (OTU) richness. We used tag-coded pyrosequencing of the 16S rRNA gene to elucidate the impacts of copper (Cu) on bacterial community composition and diversity within a well-described Cu gradient (20 to 3,537 μg g−1) stemming from industrial contamination with CuSO4more than 85 years ago. DNA sequence information was linked to analysis of pollution-induced community tolerance (PICT) to Cu, as determined by the [3H]leucine incorporation technique, and to chemical characterization of the soil. PICT was significantly correlated to bioavailable Cu, as determined by the results seen with a Cu-specific bioluminescent biosensor strain, demonstrating a specific community response to Cu. The relative abundances of members of several phyla or candidate phyla, including theProteobacteria,Bacteroidetes,Verrumicrobia,Chloroflexi,WS3, andPlanctomycetes, decreased with increasing bioavailable Cu, while members of the dominant phylum, theActinobacteria, showed no response and members of theAcidobacteriashowed a marked increase in abundance. Interestingly, changes in the relative abundances of classes frequently deviated from the responses of the phyla to which they belong. Despite the apparent Cu impacts on Cu resistance and community structure, bioavailable Cu levels did not show any correlation to bacterial OTU richness (97% similarity level). Our report highlights several bacterial taxa responding to Cu and thereby provides new guidelines for future studies aiming to explore the bacterial domain for members of metal-responding taxa.

scholarly journals 16S rRNA Amplicon Sequencing of Sediment Bacterial Communities in an Oyster Farm in Rhode Island

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Joshua T. E. Stevens ◽  
Robinson W. Fulweiler ◽  
Priyanka Roy Chowdhury
Keyword(s):  
16S Rrna ◽  
Rhode Island ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
16S Rrna Amplicon Sequencing ◽  
Oyster Farm ◽  
Rrna Gene Sequencing ◽  
The Impact

Little is known about the impact of oyster farming on sediment microbial communities. Here, we use 16S rRNA gene sequencing to identify bacterial communities in 24 sediment samples collected from an oyster farm in Ninigret Pond, RI. A total of 13,147 unique operational taxonomic units (OTUs) were assigned, with Proteobacteria being the dominant phyla across all samples.

scholarly journals Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR

2021 ◽  
Author(s):  
Annemarie Siebert ◽  
Katharina Hofmann ◽  
Lena Staib ◽  
Etienne V. Doll ◽  
Siegfried Scherer ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Dna Extraction ◽  
Raw Milk ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Microbiome Analysis ◽  
Eukaryotic Dna ◽  
Selective Lysis ◽  
The Impact

Abstract The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. Key points • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.

scholarly journals SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Clarisse Marotz ◽  
Pedro Belda-Ferre ◽  
Farhana Ali ◽  
Promi Das ◽  
Shi Huang ◽  
...  
Keyword(s):  
Health Care Providers ◽  
Rna Virus ◽  
Bacterial Community Composition ◽  
Hospital Setting ◽  
Amplicon Sequencing ◽  
Hospital Environment ◽  
Rrna Gene ◽  
Sequence Variant ◽  
Care Providers ◽  
Single Amplicon

Abstract Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. Methods We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. Results Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. Conclusions These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment.

scholarly journals Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Sonia Ciccazzo ◽  
Alfonso Esposito ◽  
Eleonora Rolli ◽  
Stefan Zerbe ◽  
Daniele Daffonchio ◽  
...  
Keyword(s):  
High Altitude ◽  
Developmental Stage ◽  
Bacterial Communities ◽  
Developmental Stages ◽  
Gene Diversity ◽  
Intergenic Spacer ◽  
Intermediate Stage ◽  
Plant Colonization ◽  
Early Developmental Stage ◽  
Rrna Gene

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05) on 16S rRNA gene diversity revealed significant differences (P<0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

scholarly journals Shaping of the Present-Day Deep Biosphere at Chicxulub by the Impact Catastrophe That Ended the Cretaceous

2021 ◽  
Vol 12 ◽  
Author(s):  
Charles S. Cockell ◽  
Bettina Schaefer ◽  
Cornelia Wuchter ◽  
Marco J. L. Coolen ◽  
Kliti Grice ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Granitic Rocks ◽  
Rrna Gene ◽  
Deep Biosphere ◽  
Deep Subsurface ◽  
Cell Biomass ◽  
Colonization Potential ◽  
The Impact

We report on the effect of the end-Cretaceous impact event on the present-day deep microbial biosphere at the impact site. IODP-ICDP Expedition 364 drilled into the peak ring of the Chicxulub crater, México, allowing us to investigate the microbial communities within this structure. Increased cell biomass was found in the impact suevite, which was deposited within the first few hours of the Cenozoic, demonstrating that the impact produced a new lithological horizon that caused a long-term improvement in deep subsurface colonization potential. In the biologically impoverished granitic rocks, we observed increased cell abundances at impact-induced geological interfaces, that can be attributed to the nutritionally diverse substrates and/or elevated fluid flow. 16S rRNA gene amplicon sequencing revealed taxonomically distinct microbial communities in each crater lithology. These observations show that the impact caused geological deformation that continues to shape the deep subsurface biosphere at Chicxulub in the present day.

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