scholarly journals Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene

2021 ◽  
Vol 9 (2) ◽  
pp. 355
Author(s):  
Eric Capo ◽  
Sofia Ninnes ◽  
Isabelle Domaizon ◽  
Stefan Bertilsson ◽  
Christian Bigler ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Mountain Lakes ◽  
Species Sorting ◽  
Eukaryotic Diversity ◽  
Holocene Sediment ◽  
Lake Formation ◽  
Sediment Records ◽  
Sediment Profiles ◽  
Diverse Microbial Community

On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co-located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock-dominated lakes—where the oldest DNA samples are dated to only a few hundred years after the lake formation—certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.

Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

2014 ◽  
Vol 1051 ◽  
pp. 311-316 ◽  
Author(s):  
Xi Mei Luo ◽  
Zhi Lei Gao ◽  
Hui Min Zhang ◽  
An Jun Li ◽  
Hong Kui He ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Real Time Quantitative Pcr ◽  
Sequencing Technologies ◽  
Specific Pcr ◽  
Pit Mud ◽  
Almost All ◽  
Polymerase Chain Reaction Primers

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

scholarly journals Stressor interactions under differential exogenous microbial exposure in Daphnia magna

2021 ◽  
Author(s):  
Shira Houwenhuyse ◽  
Lore Bulteel ◽  
Naina Goel ◽  
Isabel Vanoverberghe ◽  
Ellen Decaestecker
Keyword(s):  
Body Size ◽  
Microbial Communities ◽  
Daphnia Magna ◽  
Stress Responses ◽  
Multiple Stressors ◽  
Natural Environments ◽  
Laboratory Setting ◽  
Natural Conditions ◽  
Aspergillus Aculeatus ◽  
Diverse Microbial Community

Studies on stressor responses are often performed in controlled laboratory settings. The microbial communities in laboratory setting often differ from the natural environment, which could ultimately be reflected in different stress responses. In this study, we investigated how stressor responses differed between laboratory and natural conditions in Daphnia magna when exposed to single or multiple stressors. Daphnia individuals were exposed to the toxic cyanobacterium Microcystis aeruginosa and a fungal infection, Aspergillus aculeatus like type. Three genotypes were included to investigate genotype-specific responses. Survival, reproduction and body size were monitored for three weeks and gut microbial communities were sampled and characterized at the end of the experiment. Our study shows that natural environments have a more diverse microbial community compared with laboratory conditions, which was ultimately reflected in the gut microbiomes after inoculation. Stressor responses in Daphnia were affected by their bacterial environment for survival, but not for fecundity and body size. Fecuntiy and body size did show a main stressor effect, which could possibly be linked with stessor-specific microbiomes (for Microcystis and the combined stressor treatment). In addition, genotype-specific responses were detected for survival and fecundity, which could be linked with the selective capabilities of the Daphnia genotypes to select beneficial or neutral microbial stains from the environment.

scholarly journals High-throughput amplicon sequencing reveals the spatiotemporal effects, abiotic and biotic shaping factors for the microbial communities in tropical mangrove sediments in Sanya, China

2020 ◽  
Author(s):  
Wu Qu ◽  
Boliang Gao ◽  
Jie Wu ◽  
Min Jin ◽  
Jianxin Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Amplicon Sequencing ◽  
Biotic Factors ◽  
Community Structures ◽  
Mangrove Sediments ◽  
Element Cycling ◽  
Microbial Community Structures

Abstract Background Microbial roles in element cycling and nutrient providing are crucial for mangrove ecosystems and serve as important regulators for climate change in Earth ecosystem. However, some key information about the spatiotemporal influences and abiotic and biotic shaping factors for the microbial communities in mangrove sediments remains lacking. Methods In this work, 22 sediment samples were collected from multiple spatiotemporal dimensions, including three locations, two depths, and four seasons, and the bacterial, archaeal, and fungal community structures in these samples were studied using amplicon sequencing. Results The microbial community structures were varied in the samples from different depths and locations based on the results of LDA effect size analysis, principal coordinate analysis, the analysis of similarities, and permutational multivariate ANOVA. However, these microbial community structures were stable among the seasonal samples. Linear fitting models and Mantel test showed that among the 13 environmental factors measured in this study, the sediment particle size (PS) was the key abiotic shaping factor for the bacterial, archaeal, or fungal community structure. Besides PS, salinity and humidity were also significant impact factors according to the canonical correlation analysis (p ≤ 0.05). Co-occurrence networks demonstrated that the bacteria assigned into phyla Ignavibacteriae, Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria were the key biotic factors for shaping the bacterial community in mangrove sediments. Conclusions This work showed the variability on spatial dimensions and the stability on temporal dimension for the bacterial, archaeal, or fungal microbial community structure, indicating that the tropical mangrove sediments are versatile but stable environments. PS served as the key abiotic factor could indirectly participate in material circulation in mangroves by influencing microbial community structures, along with salinity and humidity. The bacteria as key biotic factors were found with the abilities of photosynthesis, polysaccharide degradation, or nitrogen fixation, which were potential indicators for monitoring mangrove health, as well as crucial participants in the storage of mangrove blue carbons and mitigation of climate warming. This study expanded the knowledge of mangroves for the spatiotemporal variation, distribution, and regulation of the microbial community structures, thus further elucidating the microbial roles in mangrove management and climate regulation.

scholarly journals Agricultural Pollution Risks Influence Microbial Ecology in Honghu Lake

2018 ◽  
Author(s):  
Maozhen Han ◽  
Melissa Dsouza ◽  
Chunyu Zhou ◽  
Hongjun Li ◽  
Junqian Zhang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Physicochemical Properties ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Agricultural Pollution ◽  
Agricultural Activities ◽  
Sediment Samples ◽  
Water And Sediment ◽  
Honghu Lake

AbstractBackgroundAgricultural activities, such as stock-farming, planting industry, and fish aquaculture, can influence the physicochemistry and biology of freshwater lakes. However, the extent to which these agricultural activities, especially those that result in eutrophication and antibiotic pollution, effect water and sediment-associated microbial ecology, remains unclear.MethodsWe performed a geospatial analysis of water and sediment associated microbial community structure, as well as physicochemical parameters and antibiotic pollution, across 18 sites in Honghu lake, which range from impacted to less-impacted by agricultural pollution. Furthermore, the co-occurrence network of water and sediment were built and compared accorded to the agricultural activities.ResultsPhysicochemical properties including TN, TP, NO3--N, and NO2--N were correlated with microbial compositional differences in water samples. Likewise, in sediment samples, Sed-OM and Sed-TN correlated with microbial diversity. Oxytetracycline and tetracycline concentration described the majority of the variance in taxonomic and predicted functional diversity between impacted and less-impacted sites in water and sediment samples, respectively. Finally, the structure of microbial co-associations was influenced by the eutrophication and antibiotic pollution.ConclusionThese analyses of the composition and structure of water and sediment microbial communities in anthropologically-impacted lakes are imperative for effective environmental pollution monitoring. Likewise, the exploration of the associations between environmental variables (e.g. physicochemical properties, and antibiotics) and community structure is important in the assessment of lake water quality and its ability to sustain agriculture. These results show agricultural practices can negatively influence not only the physicochemical properties, but also the biodiversity of microbial communities associated with the Honghu lake ecosystem. And these results provide compelling evidence that the microbial community can be used as a sentinel of eutrophication and antibiotics pollution risk associated with agricultural activity; and that proper monitoring of this environment is vital to maintain a sustainable environment in Honghu lake.

scholarly journals Intercropping with Potato-Onion Enhanced the Soil Microbial Diversity of Tomato

2020 ◽  
Vol 8 (6) ◽  
pp. 834
Author(s):  
Naihui Li ◽  
Danmei Gao ◽  
Xingang Zhou ◽  
Shaocan Chen ◽  
Chunxia Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Organic Carbon ◽  
Bacterial Community ◽  
Soil Organic Carbon ◽  
Microbial Communities ◽  
Fungal Community ◽  
Soil Microbial Communities ◽  
Tomato Seedling ◽  
Soil Microbial ◽  
Potato Onion

Intercropping can achieve sustainable agricultural development by increasing plant diversity. In this study, we investigated the effects of tomato monoculture and tomato/potato-onion intercropping systems on tomato seedling growth and changes of soil microbial communities in greenhouse conditions. Results showed that the intercropping with potato-onion increased tomato seedling biomass. Compared with monoculture system, the alpha diversity of soil bacterial and fungal communities, beta diversity and abundance of bacterial community were increased in the intercropping system. Nevertheless, the beta-diversity and abundance of fungal community had no difference between the intercropping and monoculture systems. The relative abundances of some taxa (i.e., Acidobacteria-Subgroup-6, Arthrobacter, Bacillus, Pseudomonas) and several OTUs with the potential to promote plant growth were increased, while the relative abundances of some potential plant pathogens (i.e., Cladosporium) were decreased in the intercropping system. Redundancy analysis indicated that bacterial community structure was significantly influenced by soil organic carbon and pH, the fungal community structure was related to changes in soil organic carbon and available phosphorus. Overall, our results suggested that the tomato/potato-onion intercropping system altered soil microbial communities and improved the soil environment, which may be the main factor in promoting tomato growth.

scholarly journals Plumage iridescence is associated with distinct feather microbiota in a tropical passerine

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Veronika Gvoždíková Javůrková ◽  
Erik D. Enbody ◽  
Jakub Kreisinger ◽  
Kryštof Chmel ◽  
Jakub Mrázek ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Community Structure ◽  
Microbial Communities ◽  
Plumage Coloration ◽  
Microbial Load ◽  
Sexual Dichromatism ◽  
Physiological Processes ◽  
Fitness Consequences ◽  
Future Work

Abstract Birds present a stunning diversity of plumage colors that have long fascinated evolutionary ecologists. Although plumage coloration is often linked to sexual selection, it may impact a number of physiological processes, including microbial resistance. At present, the degree to which differences between pigment-based vs. structural plumage coloration may affect the feather microbiota remains unanswered. Using quantitative PCR and DGGE profiling, we investigated feather microbial load, diversity and community structure among two allopatric subspecies of White-shouldered Fairywren, Malurus alboscapulatus that vary in expression of melanin-based vs. structural plumage coloration. We found that microbial load tended to be lower and feather microbial diversity was significantly higher in the plumage of black iridescent males, compared to black matte females and brown individuals. Moreover, black iridescent males had distinct feather microbial communities compared to black matte females and brown individuals. We suggest that distinctive nanostructure properties of iridescent male feathers or different investment in preening influence feather microbiota community composition and load. This study is the first to point to structural plumage coloration as a factor that may significantly regulate feather microbiota. Future work might explore fitness consequences and the role of microorganisms in the evolution of avian sexual dichromatism, with particular reference to iridescence.

scholarly journals Late quaternary Nupela taxa of Retezat Mts (S. Carpathians), with description of Nupela pocsii sp. nov. (Bacillariophyceae)

2013 ◽  
Vol 58 (2) ◽  
pp. 427-436 ◽  
Author(s):  
Krisztina Buczkó ◽  
Agata Z. Wojtal ◽  
Enikő K. Magyari
Keyword(s):  
New Species ◽  
Late Quaternary ◽  
First Record ◽  
Mountain Lakes ◽  
Correct Identification ◽  
Holocene Sediment ◽  
Characteristic Features ◽  
High Asymmetry ◽  
A New Species ◽  
High Diversity

Abstract Nupela pocsii Buczkó & Wojtal, sp. nov., a new species from the Retezat Mountains (S. Carpathians), is described. High asymmetry (along apical and transapical axes and in raphe pattern) and small dimensions are the most characteristic features of this taxon. Nupela pocsii was found during paleolimnological research in early Holocene sediment of Lake Brazi. Seven other representatives of the genus Nupela were detected in high-resolution diatom analyses of three lake sediment sequences of the Retezat Mts: Nupela fennica (Hustedt) Lange-Bertalot, N. imperfecta (Schimanski) Lange-Bertalot, N. impexiformis (Lange-Bertalot) Lange-Bertalot, N. lapidosa (Krasske) Lange-Bertalot, N. paludigena (R. P. Scherer) Lange-Bertalot, N. vitiosa (Schimanski) Siver & Hamilton and an unidentified Nupela Vyverman & Compere species. Our results suggest high diversity of oligotraphenic species in these mountain lakes during their ontogeny, which began 17,000-15,000 years ago. In addition to the newly described species this is also the first record of N. paludigena in European lakes, although its occurrence was previously documented by SEM and LM from Lake Saint Anna without correct identification.

A quantitative comparison of microbial community structure of estuarine sediments from microcosms and the field

1986 ◽  
Vol 32 (4) ◽  
pp. 319-325 ◽  
Author(s):  
Thomas W. Federle ◽  
Robert J. Livingston ◽  
Loretta E. Wolfe ◽  
David C. White
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Ecological Factors ◽  
Estuarine Sediments ◽  
Physical Factors ◽  
Multivariate Statistical ◽  
Apalachicola Bay ◽  
Sound Experiment

Estuarine soft-bottom sediments in microcosms and the field were compared with regard to microbial community structure. Community structure was determined by analyzing the fatty acids derived from the microbial lipids in the sediments. Fatty acid profiles were compared using a multivariate statistical approach. Experiments were performed using sediments from St. George Sound and Apalachicola Bay, Florida. The community structure of St. George Sound sediments was apparently controlled by epibenthic predators. In Apalachicola Bay, the dominant influences were physical factors related to the flow of the Apalachicola River. In the St. George Sound experiment, microbial communities in the microcosms differed from those in the field after only 2 weeks, and the degree of this difference increased substantially as time progressed. In the Apalachicola Bay experiment, although microbial communities in the microcosms were detectably different from those in the field, the degree of this difference was not large nor did it increase with time. This differential behavior of sediment communities from different sites may be related to the different ecological factors regulating community composition at these sites.

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