scholarly journals Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

2016 ◽  
Vol 13 (2) ◽  
pp. 252 ◽  
Author(s):  
P. R. Frade ◽  
V. Schwaninger ◽  
B. Glasl ◽  
E. Sintes ◽  
R. W. Hill ◽  
...  
Keyword(s):  
Host Species ◽  
Community Dynamics ◽  
Sulfur Compound ◽  
Quantitative Polymerase Chain Reaction ◽  
Sulfur Compounds ◽  
Microbial Processes ◽  
Coral Host ◽  
Gene Abundance ◽  
Coral Surface ◽  
Degrading Bacteria

Environmental context Corals produce copious amounts of dimethylsulfoniopropionate (DMSP), a sulfur compound implicated in climate regulation. We studied DMSP concentrations inside corals and unveiled the linkage between DMSP availability and the abundance of DMSP-degrading bacterial groups inhabiting the corals’ surface. Our findings suggest that DMSP mediates the interplay between corals and microbes, highlighting the importance of sulfur compounds for microbial processes in corals and for the resilience of coral reef ecosystems. Abstract Corals produce copious amounts of dimethylsulfoniopropionate (DMSP), a sulfur compound thought to play a role in structuring coral-associated bacterial communities. We tested the hypothesis that a linkage exists between DMSP availability in coral tissues and the community dynamics of bacteria in coral surface mucus. We determined DMSP concentrations in three coral species (Meandrina meandrites, Porites astreoides and Siderastrea siderea) at two sampling depths (5 and 25m) and times of day (dawn and noon) at Curaçao, Southern Caribbean. DMSP concentration (4–409nmolcm–2 coral surface) varied with host species-specific traits such as Symbiodinium cell abundance, but not with depth or time of sampling. Exposure of corals to air caused a doubling of their DMSP concentration. The phylogenetic affiliation of mucus-associated bacteria was examined by clone libraries targeting three main subclades of the bacterial DMSP demethylase gene (dmdA). dmdA gene abundance was determined by quantitative Polymerase Chain Reaction (qPCR) against a reference housekeeping gene (recA). Overall, a higher availability of DMSP corresponded to a lower relative abundance of the dmdA gene, but this pattern was not uniform across all host species or bacterial dmdA subclades, suggesting the existence of distinct DMSP microbial niches or varying dmdA DMSP affinities. This is the first study quantifying dmdA gene abundance in corals and linking related changes in the community dynamics of DMSP-degrading bacteria to DMSP availability. Our study suggests that DMSP mediates the regulation of microbes by the coral host and highlights the significance of sulfur compounds for microbial processes in coral reefs.

scholarly journals Ecological Response in the Integrated Process of Biostimulation and Bioaugmentation of Diesel-Contaminated Soil

2021 ◽  
Vol 11 (14) ◽  
pp. 6305
Author(s):  
Xiaosen Li ◽  
Yakui Chen ◽  
Xianyuan Du ◽  
Jin Zheng ◽  
Diannan Lu ◽  
...  
Keyword(s):  
Nitrogen Cycle ◽  
Contaminated Soil ◽  
Quantitative Polymerase Chain Reaction ◽  
Chemical Properties ◽  
Gas Chromatography Mass Spectrometry ◽  
Functional Genes ◽  
Alkane Degradation ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic ◽  
Amine Compounds

The study applied microbial molecular biological techniques to show that 2.5% to 3.0% (w/w) of diesel in the soil reduced the types and number of bacteria in the soil and destroyed the microbial communities responsible for the nitrogen cycle. In the meantime, the alkane degradation gene alkB and polycyclic aromatic hydrocarbons (PAHs) degradation gene nah evolved in the contaminated soil. We evaluated four different remediation procedures, in which the biostimulation-bioaugmentation joint process reached the highest degradation rate of diesel, 59.6 ± 0.25% in 27 days. Miseq sequencing and quantitative polymerase chain reaction (qPCR) showed that compared with uncontaminated soil, repaired soil provides abundant functional genes related to soil nitrogen cycle, and the most significant lifting effect on diesel degrading bacteria γ-proteobacteria. Quantitative analysis of degrading functional genes shows that degrading bacteria can be colonized in the soil. Gas chromatography-mass spectrometry (GC-MS) results show that the components remaining in the soil after diesel degradation are alcohol, lipids and a small amount of fatty amine compounds, which have very low toxicity to plants. In an on-site remediation experiment, the diesel content decreased from 2.7% ± 0.3 to 1.12% ± 0.1 after one month of treatment. The soil physical and chemical properties returned to normal levels, confirming the practicability of the biosimulation-bioaugmentation jointed remediation process.

scholarly journals Links between mouse and vole social networks and their gut microbiomes support predictions from metacommunity theory

2020 ◽  
Author(s):  
Joël W. Jameson ◽  
Steven W. Kembel ◽  
Denis Réale
Keyword(s):  
Social Networks ◽  
Host Species ◽  
Community Dynamics ◽  
Peromyscus Maniculatus ◽  
Interspecific Interactions ◽  
Host Community ◽  
Social Proximity ◽  
Strongly Connected ◽  
Bacterial Transmission

ABSTRACTMetacommunity theory predicts that strongly connected individuals will harbour similar gut microbiomes (GMs) and affiliating with more individuals should increase GM diversity. Additionally, cross-species bacterial transmission may play a role in how interspecific interactions affect host community dynamics. We tracked sympatric mice (Peromyscus maniculatus) and voles (Myodes gapperi) and constructed social networks for each species and both species together. We tested whether: 1) similarity in GM composition between individuals correlates with their social proximity within and across species; 2) GM diversity correlates with a host’s number of conspecific or heterospecific neighbours. We could not differentiate associations between GM composition and mouse social proximity or habitat. In voles, social proximity explained part of the GM composition. GM composition associated with interspecific social proximity, and mouse GM diversity correlated with number of vole neighbours. Contributions of host-host bacterial transmission to the GM partly follow metacommunity theory but depend on host species.

Biological processes in modelling soil functions – a balancing act between too complex and too simple

2021 ◽  
Author(s):  
Sara König ◽  
Ulrich Weller ◽  
Thomas Reitz ◽  
Bibiana Betancur-Corredor ◽  
Birgit Lang ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Microbial Activity ◽  
Community Dynamics ◽  
Spatial Scales ◽  
Simulation Models ◽  
Microbial Processes ◽  
Biological Processes ◽  
Soil Functions ◽  
Management Options ◽  
The Impact

<p>Mechanistic simulation models are an essential tool for predicting soil functions such as nutrient cycling, water filtering and storage, productivity and carbon storage as well as the complex interactions between these functions. Most soil functions are driven or affected by soil organisms. Yet, biological processes are often neglected in soil function models or implicitly described by rate parameters. This can be explained by the high complexity of the soil ecosystem with its dynamic and heterogeneous environment, and by the range of temporal and spatial scales these processes are taking place at. On the other hand, the technical capabilities to explore microbial activity and communities in soil has greatly improved, resulting in new possibilities to understand soil microbial processes on various scales.</p><p>However, to integrate such biological processes in soil modelling, we need to find the right level of detail. Here, we present a systemic soil model approach to simulate the impact of different management options and changing climate on soil functions integrating biological activity on the profile scale. We use stoichiometric considerations to simulate microbial processes involved in different soil functions without explicitly describing community dynamics or functional groups. With this approach we are able to mechanistically describe microbial activity and its impact on the turnover of organic matter and nutrient cycling as driven by agricultural soil management.</p><p>Further, we discuss general challenges and ongoing developments to additionally consider, e.g., microbe-fauna-interactions or microbial feedback with soil structure dynamics.</p>

scholarly journals Reduction of Sulfur Compounds through Genetic Improvement of Native Saccharomyces cerevisiae Useful for Organic and Sulfite-Free Wine

Foods ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 658 ◽  
Author(s):  
Alice Agarbati ◽  
Laura Canonico ◽  
Francesca Comitini ◽  
Maurizio Ciani
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Improvement ◽  
Sulfur Compound ◽  
Malolactic Fermentation ◽  
Sulfur Compounds ◽  
Wine Production ◽  
Yeast Strains ◽  
Specific Strain ◽  
Mass Mating ◽  
Strain Variability

Sulfites and sulfides are produced by yeasts in different amounts depending on different factors, including growth medium and specific strain variability. In natural must, some strains can produce an excess of sulfur compounds that confer unpleasant smells, inhibit malolactic fermentation and lead to health concerns for consumers. In organic wines and in sulfite-free wines the necessity to limit or avoid the presence of sulfide and sulfite requires the use of selected yeast strains that are low producers of sulfur compounds, with good fermentative and aromatic aptitudes. In the present study, exploiting the sexual mass-mating spores’ recombination of a native Saccharomyces cerevisiae strain previously isolated from grape, three new S. cerevisiae strains were selected. They were characterized by low sulfide and sulfite production and favorable aromatic imprinting. This approach, that occurs spontaneously also in nature, allowed us to obtain new native S. cerevisiae strains with desired characteristics that could be proposed as new starters for organic and sulfite-free wine production, able to control sulfur compound production and to valorize specific wine types.

scholarly journals Helminth Community Dynamics in Populations of Blue-Winged Teal (Anas discors) Using Two Distinct Migratory Corridors

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Jason M. Garvon ◽  
Alan M. Fedynich ◽  
Markus J. Peterson ◽  
Danny B. Pence
Keyword(s):  
Species Richness ◽  
Host Species ◽  
Community Dynamics ◽  
Helminth Species ◽  
Avian Host ◽  
Helminth Community ◽  
Intermediate Species ◽  
Anas Discors ◽  
Isolating Mechanisms ◽  
Migratory Corridor

The influence of spatially distinct host subpopulations on helminth community structure and pattern was examined in a migratory avian host species. Forty helminth species represented by 24,082 individuals were collected from 184 blue-winged teal (Anas discors; BWT) from 2 primary migratory corridors in Florida (eastern migratory corridor; EMC) and Louisiana and Texas (western migratory corridor; WMC). Mean species richness was greater in BWT from the WMC (x¯±S.E=10.2 ± 0.3species) than the EMC (8.6 ± 0.2). The helminth community from the WMC had higher abundances of 6 common/intermediate species. Corridor helminth communities were similar in species composition but less similar when incorporating abundances of those species. Overlapping distributions of phylogenetically related host species that share generalist helminth species across ecologically similar habitats seem to mitigate the isolating mechanisms that are necessary for the distinct coevolutionary pathways to develop between adjacent corridors.

scholarly journals Microbial insights from Antarctic and Mediterranean shallow-water bone-eating worms

Polar Biology ◽  
2020 ◽  
Vol 43 (10) ◽  
pp. 1605-1621 ◽  
Author(s):  
Olivia H. Hewitt ◽  
Cristina Díez-Vives ◽  
Sergi Taboada
Keyword(s):  
16S Rrna ◽  
Shallow Water ◽  
Host Species ◽  
Heterotrophic Bacteria ◽  
Amplicon Sequencing ◽  
Body Tissue ◽  
16S Rrna Amplicon Sequencing ◽  
Degrading Bacteria ◽  
Contrasting Habitats ◽  
Root Tissues

Abstract Bone-eating worms of the genus Osedax (Annelida, Siboglinidae) form unique holobionts (functional entity comprising host and associated microbiota), highly adapted to inhabit bone tissue of marine vertebrates. These gutless worms have developed nutritional symbioses housing intracellular, horizontally acquired, heterotrophic bacteria hypothesised to harness nutrients from organic compounds, sequestered within the bone. Despite previous efforts, critical mechanisms mediating activity and acquisition of diverse bacterial assemblages remain unclear. Using 16S rRNA amplicon sequencing, we performed detailed taxonomic and predicted functional analyses shedding light on the microbial communities of two shallow-water Osedax species (Osedax deceptionensis and Osedax ‘mediterranea’) from contrasting habitats (Antarctic and Mediterranean Sea), in two tissue types (roots and palps). Comparative assessments between host species revealed distinct microbial assemblages whilst, within host species and body tissue, relative symbiont frequencies retained high variability. We reported relatively high abundances of microbes previously classified as primary endosymbionts, Ribotype 1 (order Oceanospirillales), and diverse likely secondary epibionts warranting further exploration as recurrent Osedax associates. Surprisingly, O. ‘mediterranea’ exhibited relatively low abundance of Oceanospirillales, but increased abundance of other potentially hydrocarbon degrading bacteria from the family Alteromonadaceae. We hypothesise the presence of functionally similar, non-Oceanospirillales primary endosymbionts within O. ‘mediterranea’. Functional metagenomic profiling (using 16S rRNA sequences) predicted broad metabolic capabilities, encompassing relatively large abundances of genes associated with amino acid metabolism. Comparative analyses between host body tissue communities highlighted several genes potentially providing critical functions to the Osedax host or that confer adaptations for intracellular life, housed within bone embedded host root tissues.

scholarly journals DNA from lake sediments reveals the long-term dynamics and diversity of <i>Synechococcus</i> assemblages

2013 ◽  
Vol 10 (6) ◽  
pp. 3817-3838 ◽  
Author(s):  
I. Domaizon ◽  
O. Savichtcheva ◽  
D. Debroas ◽  
F. Arnaud ◽  
C. Villar ◽  
...  
Keyword(s):  
16S Rrna ◽  
Environmental Conditions ◽  
Trophic Status ◽  
Community Dynamics ◽  
Environmental Changes ◽  
Quantitative Polymerase Chain Reaction ◽  
Additive Models ◽  
Phosphorus Concentration ◽  
Rrna Gene

Abstract. While picocyanobacteria (PC) are important actors in carbon and nutrient cycles in aquatic systems, factors controlling their interannual dynamics and diversity are poorly known due to the general lack of long-term monitoring surveys. This study intended to fill this gap by applying a DNA-based paleolimnological approach to sediment records from a deep subalpine lake that has experienced dramatic changes in environmental conditions during the last century (eutrophication, re-oligotrophication and large-scale climate changes). In particular, we investigated the long-term (100 yr) diversity and dynamics of Synechococcus,, PC that have presumably been affected by both the lake trophic status changes and global warming. The lake's morphological and environmental conditions provided the ideal conditions for DNA preservation in the sediment archives. Generalised additive models applied to quantitative PCR (qPCR; quantitative Polymerase Chain Reaction) results highlighted that an increase in summer temperature could have a significant positive impact on the relative abundance of Synechococcus, (fraction of Synechococcus, in total cyanobacteria). The diversity of Synechococcus, in Lake Bourget was studied by phylogenetic analyses of the 16S rRNA gene and the following internally transcribed spacer (ITS). Up to 23 different OTUs (based on 16S rRNA), which fell into various cosmopolitan or endemic clusters, were identified in samples from the past 100 yr. Moreover, the study of ITS revealed a higher diversity within the major 16S rRNA-defined OTUs. Changes in PC diversity were related to the lake's trophic status. Overall, qPCR and sequencing results showed that environmental changes (in temperature and phosphorus concentration) affected Synechococcus, community dynamics and structure, translating into changes in genotype composition. These results also helped to re-evaluate the geographical distribution of some Synechococcus, clusters. Providing such novel insights into the long-term history of an important group of primary producers, this study illustrates the promising approach that consists in coupling molecular tools and paleolimnology to reconstruct a lake's biodiversity history.

scholarly journals Seasonal and Sexual Differences in the Microbiota of the Hoopoe Uropygial Secretion

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 407 ◽  
Author(s):  
Sonia Rodríguez-Ruano ◽  
Manuel Martín-Vivaldi ◽  
Juan Peralta-Sánchez ◽  
Ana García-Martín ◽  
Ángela Martínez-García ◽  
...  
Keyword(s):  
Breeding Season ◽  
Community Dynamics ◽  
Quantitative Polymerase Chain Reaction ◽  
Infection Risk ◽  
Uropygial Gland ◽  
Molecular Fingerprinting ◽  
Microbial Community Dynamics ◽  
High Infection ◽  
Uropygial Secretion

The uropygial gland of hoopoe nestlings and nesting females hosts bacterial symbionts that cause changes in the characteristics of its secretion, including an increase of its antimicrobial activity. These changes occur only in nesting individuals during the breeding season, possibly associated with the high infection risk experienced during the stay in the hole-nests. However, the knowledge on hoopoes uropygial gland microbial community dynamics is quite limited and based so far on culture-dependent and molecular fingerprinting studies. In this work, we sampled wild and captive hoopoes of different sex, age, and reproductive status, and studied their microbiota using quantitative polymerase chain reaction (qPCR), fluorescence in situ hybridization (FISH) and pyrosequencing. Surprisingly, we found a complex bacterial community in all individuals (including non-nesting ones) during the breeding season. Nevertheless, dark secretions from nesting hoopoes harbored significantly higher bacterial density than white secretions from breeding males and both sexes in winter. We hypothesize that bacterial proliferation may be host-regulated in phases of high infection risk (i.e., nesting). We also highlight the importance of specific antimicrobial-producing bacteria present only in dark secretions that may be key in this defensive symbiosis. Finally, we discuss the possible role of environmental conditions in shaping the uropygial microbiota, based on differences found between wild and captive hoopoes.

scholarly journals Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

2013 ◽  
Vol 80 (1) ◽  
pp. 408-419 ◽  
Author(s):  
Yanling Zheng ◽  
Lijun Hou ◽  
Silvia Newell ◽  
Min Liu ◽  
Junliang Zhou ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Yangtze Estuary ◽  
Estuarine Sediments ◽  
Ammonia Oxidizing Bacteria ◽  
Intertidal Sediments ◽  
The Yangtze Estuary ◽  
Α Subunit ◽  
Unifrac Distance ◽  
Gene Abundance ◽  
Potential Nitrification

ABSTRACTDiversity, abundance, and activity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using the ammonia monooxygenase α subunit (amoA) in the intertidal sediments of the Yangtze Estuary. Generally, AOB had a lower diversity ofamoAgenes than did AOA in this study. Clone library analysis revealed great spatial variations in both AOB and AOA communities along the estuary. The UniFrac distance matrix showed that all the AOB communities and 6 out of 7 AOA communities in the Yangtze Estuary were statistically indistinguishable between summer and winter. The studied AOB and AOA community structures were observed to correlate with environmental parameters, of which salinity, pH, ammonium, total phosphorus, and organic carbon had significant correlations with the composition and distribution of both communities. Also, the AOA communities were significantly correlated with sediment clay content. Quantitative PCR (qPCR) results indicated that the abundance of AOBamoAgenes was greater than that of AOAamoAgenes in 10 of the 14 samples analyzed in this study. Potential nitrification rates were significantly greater in summer than in winter and had a significant negative correlation with salinity. In addition, potential nitrification rates were correlated strongly only with archaealamoAgene abundance and not with bacterialamoAgene abundance. However, no significant differences were observed between rates measured with and without ampicillin (AOB inhibitor). These results implied that archaea might play a more important role in mediating the oxidation of ammonia to nitrite in the Yangtze estuarine sediments.

Sign in / Sign up

Export Citation Format

Share Document