scholarly journals Dietary specialization in mutualistic acacia-ants affects relative abundance but not identity of host-associated bacteria

2018 ◽  
Vol 28 (4) ◽  
pp. 900-916 ◽  
Author(s):  
Benjamin E. R. Rubin ◽  
Stefanie Kautz ◽  
Brian D. Wray ◽  
Corrie S. Moreau
Keyword(s):  
Relative Abundance ◽  
Dietary Specialization ◽  
Associated Bacteria ◽  
Acacia Ants

scholarly journals Autoregulation of Nodulation Interferes with Impacts of Nitrogen Fertilization Levels on the Leaf-Associated Bacterial Community in Soybeans

2011 ◽  
Vol 77 (6) ◽  
pp. 1973-1980 ◽  
Author(s):  
Seishi Ikeda ◽  
Mizue Anda ◽  
Shoko Inaba ◽  
Shima Eda ◽  
Shusei Sato ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Relative Abundance ◽  
Nitrogen Fertilization ◽  
Arbuscular Mycorrhizal ◽  
Rrna Gene ◽  
Wild Type ◽  
Associated Bacteria ◽  
Autoregulation Of Nodulation ◽  
Soybean Leaves ◽  
The Impact

ABSTRACTThe diversities leaf-associated bacteria on nonnodulated (Nod−), wild-type nodulated (Nod+), and hypernodulated (Nod++) soybeans were evaluated by clone library analyses of the 16S rRNA gene. To analyze the impact of nitrogen fertilization on the bacterial leaf community, soybeans were treated with standard nitrogen (SN) (15 kg N ha−1) or heavy nitrogen (HN) (615 kg N ha−1) fertilization. Under SN fertilization, the relative abundance ofAlphaproteobacteriawas significantly higher in Nod−and Nod++soybeans (82% to 96%) than in Nod+soybeans (54%). The community structure of leaf-associated bacteria in Nod+soybeans was almost unaffected by the levels of nitrogen fertilization. However, differences were visible in Nod−and Nod++soybeans. HN fertilization drastically decreased the relative abundance ofAlphaproteobacteriain Nod−and Nod++soybeans (46% to 76%) and, conversely, increased those ofGammaproteobacteriaandFirmicutesin these mutant soybeans. In theAlphaproteobacteria, cluster analyses identified two operational taxonomic units (OTUs) (Aurantimonassp. andMethylobacteriumsp.) that were especially sensitive to nodulation phenotypes under SN fertilization and to nitrogen fertilization levels. Arbuscular mycorrhizal infection was not observed on the root tissues examined, presumably due to the rotation of paddy and upland fields. These results suggest that a subpopulation of leaf-associated bacteria in wild-type Nod+soybeans is controlled in similar ways through the systemic regulation of autoregulation of nodulation, which interferes with the impacts of N levels on the bacterial community of soybean leaves.

scholarly journals Dysfunction of the histone demethylase IBM1 in Arabidopsis reshapes the root-associated bacteria community

2020 ◽  
Author(s):  
Suhui Lv ◽  
Yu Yang ◽  
Li Peng ◽  
Kai Tang ◽  
Richa Kaushal ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Epigenetic Regulation ◽  
16S Rrna Gene Sequencing ◽  
Histone Demethylase ◽  
Rrna Gene ◽  
Biological Processes ◽  
Community Members ◽  
Associated Bacteria ◽  
Rrna Gene Sequencing ◽  
Root Microbiota

AbstractRoot-associated bacteria communities are influential to plant growth and stress tolerance. Epigenetic regulation plays important roles in many plant biological processes, but its potential impacts on the assembly of root microbiota remain unclear. Here we report that dysfunction of the histone demethylase IBM1 in Arabidopsis substantially alters root-associated soil bacteria community. We compared two alleles of ibm1 mutant (ibm1-1 and ibm1-4) with wild type Arabidopsis regarding the root-associated bacteria community by 16S rRNA gene sequencing. The constrained principal coordinate analysis (PCoA) showed that the ibm1 mutants are both clearly separated from Col-0 along the major coordinates. Among the 29 families which have a relative abundance more than 0.5% in at least one sample, 10 and 11 families were commonly affected by ibm1-1 and ibm1-4 alleles in the rhizosphere and the endosphere compartment, respectively. Notably, the ACMs (Abundant Community members) belonging Pseudomonadaceae showed increased relative abundance in the ibm1 mutant alleles compared to Col-0 in both the rhizosphere and the endosphere compartments. The ACMs belonging to Oxalobacteraceae mostly showed decreased relative abundance in ibm1 mutants compared to Col-0 in endosphere compartment. These findings demonstrate an influential function of IBM1-mediated epigenetic regulation in shaping the root-associated microbiota.

scholarly journals Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome

2019 ◽  
Author(s):  
Florencia Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Vaginosis ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Associated Bacteria

Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentration of individual species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We analyzed 1320 samples from 20 women with a history of frequent bacterial vaginosis, who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and total bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, p<2.2e-16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacterial vaginosis-associated bacteria associated with larger errors. 92% of errors >0.5 log10 occurred when relative abundance was <10%. Many errors occurred during early bacterial expansion or late contraction. When relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR. However, targeted qPCR is required to capture bacteria at low relative abundance, particularly with BV-associated bacteria during the early onset of bacterial vaginosis.

scholarly journals Bacterial Associates of Two Caribbean Coral Species Reveal Species-Specific Distribution and Geographic Variability

2012 ◽  
Vol 78 (18) ◽  
pp. 6438-6449 ◽  
Author(s):  
Kathleen M. Morrow ◽  
Anthony G. Moss ◽  
Nanette E. Chadwick ◽  
Mark R. Liles
Keyword(s):  
Relative Abundance ◽  
Coral Species ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Spatial Scales ◽  
Life History Strategies ◽  
Coral Host ◽  
Associated Bacteria ◽  
Content Type ◽  
Specific Distribution ◽  
Bacterial Assemblages

ABSTRACTScleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean,Montastraea faveolataandPorites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here thatM. faveolataandP. astreoidesharbor distinct, host-specific bacteria but that specificity varies by species and site.P. astreoidesgenerally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus,Endozoicomonas, within the orderOceanospirillales. The bacterial assemblages associated withM. faveolataare significantly more diverse and exhibit higher specificity at the family level thanP. astreoidesassemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude that the two coral species studied harbor distinct bacterial assemblages within the SML, but the degree to which each species maintains specific microbial associations varies both within each site and across large spatial scales. The taxonomic scale (i.e., phylum versus genus) at which scientists examine coral-microbe associations, in addition to host-elicited factors and environmental fluctuations, must be considered carefully in future studies of the coral holobiont.

scholarly journals Relative abundance of Bacillus spp., surfactant-associated bacterium present in a natural sea slick observed by satellite SAR imagery over the Gulf of Mexico

Elem Sci Anth ◽  
2018 ◽  
Vol 6 ◽  
Author(s):  
Kathryn Lynn Howe ◽  
Cayla Whitney Dean ◽  
John Kluge ◽  
Alexander Victor Soloviev ◽  
Aurelien Tartar ◽  
...  
Keyword(s):  
Gulf Of Mexico ◽  
Relative Abundance ◽  
Dna Analysis ◽  
Capillary Waves ◽  
Sea Surface ◽  
Subsurface Water ◽  
Surface Microlayer ◽  
Associated Bacteria ◽  
Sea Surface Microlayer ◽  
Bacillus Spp

The damping of short gravity-capillary waves (Bragg waves) due to surfactant accumulation under low wind speed conditions results in the formation of natural sea slicks. These slicks are detectable visually and in synthetic aperture radar satellite imagery. Surfactants are produced by natural life processes of many marine organisms, including bacteria, phytoplankton, seaweed, and zooplankton. In this work, samples were collected in the Gulf of Mexico during a research cruise on the R/V F.G. Walton Smith to evaluate the relative abundance of Bacillus spp., surfactant-associated bacteria, in the sea surface microlayer compared to the subsurface water at 0.2 m depth. A method to reduce potential contamination of microlayer samples during their collection on polycarbonate filters was implemented and advanced, including increasing the number of successive samples per location and changing sample storage procedures. By using DNA analysis (real-time polymerase chain reaction) to target Bacillus spp., we found that in the slick areas, these surfactant-associated bacteria tended to reside mostly in subsurface waters, lending support to the concept that the surfactants they may produce move to the surface where they accumulate under calm conditions and enrich the sea surface microlayer.

scholarly journals Mutualistic acacia-ants show that specialized bacteria are not required for the evolution of herbivory

2017 ◽  
Author(s):  
Benjamin E.R. Rubin ◽  
Stefanie Kautz ◽  
Brian D. Wray ◽  
Corrie S. Moreau
Keyword(s):  
Bacterial Communities ◽  
Trophic Position ◽  
Isotope Analysis ◽  
Acetic Acid Bacteria ◽  
Animal Nutrition ◽  
Metagenomic Sequencing ◽  
Nitrogen Recycling ◽  
Associated Bacteria ◽  
Bacterial Endosymbionts ◽  
Acacia Ants

AbstractAcacia-ant mutualists in the genus Pseudomyrmex nest obligately in acacia plants and, through stable isotope analysis, we show that they are among the strictest of herbivores, feeding exclusively from their hosts. The diets of herbivorous insects such as these are often enriched by obligate bacterial endosymbionts through nitrogen recycling and even gaseous di-nitrogen fixation. We, therefore, examine the bacterial communities associated with mutualistic acacia-ants, comparing them with related non-mutualists in order to determine whether they host bacterial partners likely to contribute to the enrichment of their diets. However, despite their low trophic position, we find no evidence for bacteria-assisted nutrition in either adults or larvae. These acacia-ants do not host any species- or clade-specific bacteria, though several lineages of acetic acid bacteria present across social insects do differ in abundance between mutualists and non-mutualists, likely in response to the sugar-rich diets of their hosts. In addition, two novel lineages of Actinomycetales inhabit both mutualistic and non-mutualistic Pseudomyrmex and differ in abundance between the juveniles of these groups, potentially serving as defensive symbionts. Metagenomic sequencing of these taxa reveal substantial capacity for the production of defensive chemicals. Overall, we find little evidence for nutrition-associated bacteria in these strictly herbivorous ants, showing that bacteria are not as essential to animal nutrition as is often hypothesized.

scholarly journals Regulation of the Coral-Associated Bacteria and Symbiodiniaceae in Acropora valida Under Ocean Acidification

2021 ◽  
Vol 12 ◽  
Author(s):  
Ruiqi Ge ◽  
Jiayuan Liang ◽  
Kefu Yu ◽  
Biao Chen ◽  
Xiaopeng Yu ◽  
...  
Keyword(s):  
Ocean Acidification ◽  
Real Time ◽  
Community Composition ◽  
Relative Abundance ◽  
Coral Host ◽  
Ph Gradients ◽  
Associated Bacteria ◽  
The Real ◽  
The Stability ◽  
Acropora Valida

Ocean acidification is one of many stressors that coral reef ecosystems are currently contending with. Thus, understanding the response of key symbiotic microbes to ocean acidification is of great significance for understanding the adaptation mechanism and development trend of coral holobionts. Here, high-throughput sequencing technology was employed to investigate the coral-associated bacteria and Symbiodiniaceae of the ecologically important coral Acropora valida exposed to different pH gradients. After 30 days of acclimatization, we set four acidification gradients (pH 8.2, 7.8, 7.4, and 7.2, respectively), and each pH condition was applied for 10 days, with the whole experiment lasting for 70 days. Although the Symbiodiniaceae density decreased significantly, the coral did not appear to be bleached, and the real-time photosynthetic rate did not change significantly, indicating that A. valida has strong tolerance to acidification. Moreover, the Symbiodiniaceae community composition was hardly affected by ocean acidification, with the C1 subclade (Cladocopium goreaui) being dominant among the Symbiodiniaceae dominant types. The relative abundance of the Symbiodiniaceae background types was significantly higher at pH 7.2, indicating that ocean acidification might increase the stability of the community composition by regulating the Symbiodiniaceae rare biosphere. Furthermore, the stable symbiosis between the C1 subclade and coral host may contribute to the stability of the real-time photosynthetic efficiency. Finally, concerning the coral-associated bacteria, the stable symbiosis between Endozoicomonas and coral host is likely to help them adapt to ocean acidification. The significant increase in the relative abundance of Cyanobacteria at pH 7.2 may also compensate for the photosynthesis efficiency of a coral holobiont. In summary, this study suggests that the combined response of key symbiotic microbes helps the whole coral host resist the threats of ocean acidification.

Warming temperatures alter the relative abundance and distribution of two co-occurring foundational seagrasses in Chesapeake Bay, USA

2018 ◽  
Vol 599 ◽  
pp. 65-74 ◽  
Author(s):  
JP Richardson ◽  
JS Lefcheck ◽  
RJ Orth
Keyword(s):  
Chesapeake Bay ◽  
Relative Abundance ◽  
Abundance And Distribution

Environmental correlates of relative abundance of potentially dangerous sharks in nearshore areas, southeastern Australia

2018 ◽  
Vol 599 ◽  
pp. 157-179 ◽  
Author(s):  
KA Lee ◽  
M Roughan ◽  
RG Harcourt ◽  
VM Peddemors
Keyword(s):  
Relative Abundance ◽  
Environmental Correlates ◽  
Southeastern Australia
Sign in / Sign up

Export Citation Format

Share Document