scholarly journals Chemical and microbiological characterization of primary biological aerosol particles at the boreal forest

2020 ◽  
Author(s):  
Jose Ruiz-Jimenez ◽  
Magdalena Okuljar ◽  
Outi-Maaria Sietiö ◽  
Giorgia Demaria ◽  
Thanaporn Liangsupree ◽  
...  
Keyword(s):  
Amino Acids ◽  
Particle Size ◽  
Size Distribution ◽  
Aerosol Particles ◽  
Gene Copy ◽  
Particle Size Fractions ◽  
Copy Numbers ◽  
Phase Chemistry ◽  
Gene Copy Numbers ◽  
Biological Aerosol Particles

Abstract. Primary biological aerosol particles (PBAPs) play an important role in the interaction between biosphere, atmosphere and climate, affecting cloud and precipitation formation processes. The contribution of pollen, plant fragments, spores, bacteria, algae and viruses to PBAPs is well known. In order to explore the complex interrelationships between airborne and particulate chemical traces (amino acids, saccharides), gene copy numbers, gas phase chemistry and the particle size distribution, 84 size-segregated aerosol samples from four particle size fractions ( 10 µm) were collected at SMEAR II station, Finland in autumn 2017. The gene copy numbers and size distribution of bacteria, Pseudomonas and fungi in PBAPs were determined by DNA extraction and amplification. In addition, free amino acids (19) and saccharides (8) were analyzed in aerosol samples by hydrophilic interaction liquid chromatography -mass spectrometry (HILIC-MS). Different machine learning (ML) approaches, such as cluster analysis, discriminant analysis, neural network and multiple linear regression (MLR) were used for the clarification of several aspects related to the PBAPs composition. Clear variations were observed for the composition of PBAPs as a function of the particle size. In most cases, the highest concentration values, gene copy numbers in the case of microbes, were observed for 2.5–10 µm particles followed by > 10 µm, 1–2.5 µm and

scholarly journals Determination of free amino acids, saccharides, and selected microbes in biogenic atmospheric aerosols – seasonal variations, particle size distribution, chemical and microbial relations

2021 ◽  
Vol 21 (11) ◽  
pp. 8775-8790
Author(s):  
Jose Ruiz-Jimenez ◽  
Magdalena Okuljar ◽  
Outi-Maaria Sietiö ◽  
Giorgia Demaria ◽  
Thanaporn Liangsupree ◽  
...  
Keyword(s):  
Amino Acids ◽  
Particle Size ◽  
Particle Size Distribution ◽  
Gas Phase ◽  
Free Amino Acids ◽  
Free Amino ◽  
Gene Copy ◽  
Copy Numbers ◽  
Biogenic Aerosols ◽  
Gene Copy Numbers

Abstract. Primary biological aerosol particles (PBAPs) play an important role in the interaction between biosphere, atmosphere, and climate, affecting cloud and precipitation formation processes. The presence of pollen, plant fragments, spores, bacteria, algae, and viruses in PBAPs is well known. In order to explore the complex interrelationships between airborne and particulate chemical tracers (amino acids, saccharides), gene copy numbers (16S and 18S for bacteria and fungi, respectively), gas phase chemistry, and the particle size distribution, 84 size-segregated aerosol samples from four particle size fractions (< 1.0, 1.0–2.5, 2.5–10, and > 10 µm) were collected at the SMEAR II station, Finland, in autumn 2017. The gene copy numbers and size distributions of bacteria, Pseudomonas, and fungi in biogenic aerosols were determined by DNA extraction and amplification. In addition, free amino acids (19) and saccharides (8) were analysed in aerosol samples by hydrophilic interaction liquid chromatography–mass spectrometry (HILIC-MS). Different machine learning (ML) approaches, such as cluster analysis, discriminant analysis, neural network analysis, and multiple linear regression (MLR), were used for the clarification of several aspects related to the composition of biogenic aerosols. Clear variations in composition as a function of the particle size were observed. In most cases, the highest concentration values and gene copy numbers (in the case of microbes) were observed for 2.5–10 µm particles, followed by > 10, 1–2.5, and < 1.0 µm particles. In addition, different variables related to the air and soil temperature, the UV radiation, and the amount of water in the soil affected the composition of biogenic aerosols. In terms of interpreting the results, MLR provided the greatest improvement over classical statistical approaches such as Pearson correlation among the ML approaches considered. In all cases, the explained variance was over 91 %. The great variability of the samples hindered the clarification of common patterns when evaluating the relation between the presence of microbes and the chemical composition of biogenic aerosols. Finally, positive correlations were observed between gas-phase VOCs (such as acetone, toluene, methanol, and 2-methyl-3-buten-2-ol) and the gene copy numbers of microbes in biogenic aerosols.

Predominance of ammonia-oxidizing archaea andnirK-gene-bearing denitrifiers among ammonia-oxidizing and denitrifying populations in sediments of a large urban eutrophic lake (Lake Donghu)

2013 ◽  
Vol 59 (7) ◽  
pp. 456-464 ◽  
Author(s):  
Jie Hou ◽  
Xiuyun Cao ◽  
Chunlei Song ◽  
Yiyong Zhou
Keyword(s):  
Amoa Gene ◽  
Eutrophic Lake ◽  
Gene Copy ◽  
Nirs Gene ◽  
Bacterial Amoa Gene ◽  
Archaeal Amoa Gene ◽  
Copy Numbers ◽  
Significant Difference ◽  
Nirk Gene ◽  
Gene Copy Numbers

The coupled nitrification–denitrification process plays a pivotal role in cycling and removal of nitrogen in aquatic ecosystems. In the present study, the communities of ammonia oxidizers and denitrifiers in the sediments of 2 basins (Guozhenghu Basin and Tuanhu Basin) of a large urban eutrophic lake (Lake Donghu) were determined using the ammonia monooxygenase subunit A (amoA) gene and the nitrite reductase gene. At all sites of this study, the archaeal amoA gene predominated over the bacterial amoA gene, whereas the functional gene for denitrification nirK gene far outnumbered the nirS gene. Spatially, compared with the Tuanhu Basin, the Guozhenghu Basin showed a significantly greater abundance of the archaeal amoA gene but less abundance of the nirK and nirS genes, while there was no significant difference of bacterial amoA gene copy numbers between the 2 basins. Unlike the archaeal amoA gene, the nirK gene showed a significant difference in community structure between the 2 basins. Archaeal amoA diversity was limited to the water–sediment cluster of Crenarchaeota, in sharp contrast with nirK for which 22 distinct operational taxonomic units were found. Accumulation of organic substances were found to be positively related to nirK and nirS gene copy numbers but negatively related to archaeal amoA gene copy numbers, whereas the abundance of the bacterial amoA gene was related to ammonia concentration.

scholarly journals Evolution of dosage compensation does not depend on genomic background

2020 ◽  
Author(s):  
Michail Rovatsos ◽  
Lukáš Kratochvíl
Keyword(s):  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Genomic Region ◽  
Gene Copy ◽  
Gene Dose ◽  
Copy Numbers ◽  
Compensation Mechanisms ◽  
Gene Copy Numbers ◽  
Softshell Turtles

AbstractOrganisms evolved various mechanisms to cope with the differences in the gene copy numbers between sexes caused by degeneration of Y and W sex chromosomes. Complete dosage compensation or at least expression balance between sexes was reported predominantly in XX/XY, but rarely in ZZ/ZW systems. However, this often-reported pattern is based on comparisons of lineages where sex chromosomes evolved from non-homologous genomic regions, potentially differing in sensitivity to differences in gene copy numbers. Here we document that two reptilian lineages (XX/XY iguanas and ZZ/ZW softshell turtles), which independently co-opted the same ancestral genomic region for the function of sex chromosomes, evolved different gene dose regulatory mechanisms. The independent co-option of the same genomic region for the role of sex chromosome as in the iguanas and the softshell turtles offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and for gene identity. We showed that the parallel loss of functional genes from the Y chromosome of the green anole and the W chromosome of the Florida softshell turtle led to different dosage compensation mechanisms. Our approach controlling for genetic background thus does not support that the variability in the regulation of the gene dose differences is a consequence of ancestral autosomal gene content.

scholarly journals Expanding an expanded genome: long-read sequencing ofTrypanosoma cruzi

2018 ◽  
Author(s):  
Luisa Berná ◽  
Matías Rodríguez ◽  
María Laura Chiribao ◽  
Adriana Parodi-Talice ◽  
Sebastián Pita ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Gc Content ◽  
Gene Copy ◽  
Accurate Estimation ◽  
Sequencing Technologies ◽  
Copy Numbers ◽  
Long Reads ◽  
Long Read ◽  
Large Clusters ◽  
Gene Copy Numbers

Although the genome ofTrypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degree of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated withT. cruzi´sgenome since they permit directly determining the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, allows not only accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of twoT. cruziclones: the hybrid TCC (DTU TcVI) and the non-hybrid Dm28c (DTU TcI), determined by PacBio SMRT technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome ofT. cruziis composed of a "core compartment" and a "disruptive compartment" which exhibit opposite gene and GC content composition. New tandem and disperse repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families MUC and trans-sialidases allows now a better overview of these complex groups of genes.

scholarly journals Growth of sedimentaryBathyarchaeotaon lignin as an energy source

2018 ◽  
Vol 115 (23) ◽  
pp. 6022-6027 ◽  
Author(s):  
Tiantian Yu ◽  
Weichao Wu ◽  
Wenyue Liang ◽  
Mark Alexander Lever ◽  
Kai-Uwe Hinrichs ◽  
...  
Keyword(s):  
Energy Source ◽  
Estuarine Sediments ◽  
Gene Copy ◽  
Organic Substrates ◽  
Metabolic Functions ◽  
Copy Numbers ◽  
Tetraether Lipids ◽  
Archaeal Lipids ◽  
Gene Copy Numbers ◽  
Direct Confirmation

Members of the archaeal phylumBathyarchaeotaare among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth ofBathyarchaeotain the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth ofBathyarchaeotasubgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth ofBathyarchaeota. Meanwhile, putative bathyarchaeotal tetraether lipids incorporated13C from13C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth’s most abundant biopolymers in anoxic marine sediment.

Collecting amino acids in the Enceladus plume

2018 ◽  
Vol 18 (1) ◽  
pp. 47-59 ◽  
Author(s):  
Melissa Guzman ◽  
Ralph Lorenz ◽  
Dana Hurley ◽  
William Farrell ◽  
John Spencer ◽  
...  
Keyword(s):  
Amino Acids ◽  
Particle Size ◽  
Particle Size Distribution ◽  
Size Distribution ◽  
Free Amino Acids ◽  
Free Amino ◽  
Deep Ocean ◽  
Mass Rate ◽  
Bubble Bursting ◽  
Deep Ocean Water

AbstractWe numerically model the dynamics of the Enceladus plume ice grains and define our nominal plume model as having a particle size distributionn(R) ~R−qwithq= 4 and a total particulate mass rate of 16 kg s−1. This mass rate is based on average plume brightness observed by Cassini across a range of orbital positions. The model predicts sample volumes of ~1600 µg for a 1 m2collector on a spacecraft making flybys at 20–60 km altitudes above the Enceladus surface. We develop two scenarios to predict the concentration of amino acids in the plume based on these assumed sample volumes. We specifically consider Glycine, Serine, α-Alanine, α-Aminoisobutyric acid and Isovaline. The first ‘abiotic’ model assumes that Enceladus has the composition of a comet and finds abundances between 2 × 10−6to 0.003 µg for dissolved free amino acids and 2 × 10−5to 0.3 µg for particulate amino acids. The second ‘biotic’ model assumes that the water of Enceladus's ocean has the same amino acid composition as the deep ocean water on Earth. We compute the expected captured mass of amino acids such as Glycine, Serine, and α-Alanine in the ‘biotic’ model to be between 1 × 10−5to 2 × 10−5µg for dissolved free amino acids and dissolved combined amino acids and about 0.0002 µg for particulate amino acids. Both models consider enhancements due to bubble bursting. Expected captured mass of amino acids is calculated for a 1 m2collector on a spacecraft making flybys with a closest approach of 20 km during mean plume activity for the given nominal particle size distribution.

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