Exploring Microbial Resource of Different Rhizocompartments of Dominant Plants Along the Salinity Gradient Around the Hypersaline Lake Ejinur

Lake littoral zones can also be regarded as another extremely hypersaline environment due to hypersaline properties of salt lakes. In this study, high-throughput sequencing technique was used to analyze bacteria and fungi from different rhizocompartments (rhizosphere and endosphere) of four dominant plants along the salinity gradient in the littoral zones of Ejinur Salt Lake. The study found that microbial α-diversity did not increase with the decrease of salinity, indicating that salinity was not the main factor on the effect of microbial diversity. Distance-based redundancy analysis and regression analysis were used to further reveal the relationship between microorganisms from different rhizocompartments and plant species and soil physicochemical properties. Bacteria and fungi in the rhizosphere and endosphere were the most significantly affected by SO42–, SOC, HCO3–, and SOC, respectively. Correlation network analysis revealed the potential role of microorganisms in different root compartments on the regulation of salt stress through synergistic and antagonistic interactions. LEfSe analysis further indicated that dominant microbial taxa in different rhizocompartments had a positive response to plants, such as Marinobacter, Palleronia, Arthrobacter, and Penicillium. This study was of great significance and practical value for understanding salt environments around salt lakes to excavate the potential microbial resources.

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Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes

Frontiers in Microbiology ◽

10.3389/fmicb.2021.737616 ◽

2021 ◽

Vol 12 ◽

Author(s):

David Johnston-Monje ◽

Janneth P. Gutiérrez ◽

Luis Augusto Becerra Lopez-Lavalle

Keyword(s):

High Throughput Sequencing ◽

Brachypodium Distachyon ◽

Brachiaria Decumbens ◽

Operational Taxonomic Units ◽

Bacterial Microbiome ◽

Fungal Populations ◽

To Come ◽

Bacteria And Fungi ◽

Plant Life Cycle

Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.

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Microbial community structure and diversity within hypersaline Keke Salt Lake environments

Canadian Journal of Microbiology ◽

10.1139/cjm-2016-0773 ◽

2017 ◽

Vol 63 (11) ◽

pp. 895-908 ◽

Cited By ~ 18

Author(s):

Rui Han ◽

Xin Zhang ◽

Jing Liu ◽

Qifu Long ◽

Laisheng Chen ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

High Throughput Sequencing ◽

Salt Lake ◽

16S Rrna Genes ◽

Rrna Genes ◽

Tibet Plateau ◽

Hypersaline Lake ◽

Hypersaline Lakes

Keke Salt Lake is located in the Qaidamu Basin of China. It is a unique magnesium sulfate-subtype hypersaline lake that exhibits a halite domain ecosystem, yet its microbial diversity has remained unstudied. Here, the microbial community structure and diversity was investigated via high-throughput sequencing of the V3–V5 regions of 16S rRNA genes. A high diversity of operational taxonomic units was detected for Bacteria and Archaea (734 and 747, respectively), comprising 21 phyla, 43 classes, and 201 genera of Bacteria and 4 phyla, 4 classes, and 39 genera of Archaea. Salt-saturated samples were dominated by the bacterial genera Bacillus (51.52%–58.35% relative abundance), Lactococcus (9.52%–10.51%), and Oceanobacillus (8.82%–9.88%) within the Firmicutes phylum (74.81%–80.99%), contrasting with other hypersaline lakes. The dominant Archaea belonged to the Halobacteriaceae family, and in particular, the genera (with an abundance of >10% of communities) Halonotius, Halorubellus, Halapricum, Halorubrum, and Natronomonas. Additionally, we report the presence of Nanohaloarchaeota and Woesearchaeota in Qinghai–Tibet Plateau lakes, which has not been previously documented. Total salinity (especially Mg2+, Cl–, Na+, and K+) mostly correlated with taxonomic distribution across samples. These results expand our understanding of microbial resource utilization within hypersaline lakes and the potential adaptations of dominant microorganisms that allow them to inhabit such environments.

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Bioinformatics Analysis and Validation of Differentially Expressed MicroRNAs with Their Target Genes Involved in GLP-1RA Facilitated Osteogenesis

Current Bioinformatics ◽

10.2174/1574893615999200508091615 ◽

2020 ◽

Vol 15 ◽

Author(s):

Na Wang ◽

Yukun Li ◽

Sijing Liu ◽

Liu Gao ◽

Chang Liu ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Bioinformatics Analysis ◽

Differentially Expressed ◽

Functional Study ◽

Regulation Network ◽

Glucagon Like Peptide 1 ◽

G Protein Coupled ◽

Lower Expression

Background: Recent studies revealed that the hypoglycemic hormone, glucagon-like peptide-1 (GLP-1), acted as an important modulator in osteogenesis of bone marrow derived mesenchymal stem cells (BMSCs). Objectives: The aim of this study was to identify the specific microRNA (miRNA) using bioinformatics analysis and validate the presence of differentially expressed microRNAs with their target genes after GLP-1 receptor agonist (GLP-1RA) administration involved in ostogenesis of BMSCs. Methods: MiRNAs were extracted from BMSCs after 5 days’ treatment and sent for high-throughput sequencing for differentially expressed (DE) miRNAs analyses. Then the expression of the DE miRNAs verified by the real-time RT-PCR analyses. Target genes were predicted, and highly enriched GOs and KEGG pathway analysis were conducted using bioinformatics analysis. For the functional study, two of the target genes, SRY (sex determining region Y)-box 5 (SOX5) and G protein-coupled receptor 84 (GPR84), were identified. Results: A total of 5 miRNAs (miRNA-509-5p, miRNA-547-3p, miRNA-201-3p, miRNA-201-5p, and miRNA-novel-272-mature) were identified differentially expressed among groups. The expression of miRNA-novel-272-mature were decreased during the osteogenic differentiation of BMSCs, and GLP-1RA further decreased its expression. MiRNA-novel-272-mature might interact with its target mRNAs to enhance osteogenesis. The lower expression of miRNA-novel-272-mature led to an increase in SOX5 and a decrease in GPR84 mRNA expression, respectively. Conclusions: Taken together, these results provide further insights to the pharmacological properties of GLP-1RA and expand our knowledge on the role of miRNAs-mRNAs regulation network in BMSCs’ differentiation.

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DOM degradation by light and microbes along the Yukon River-coastal ocean continuum

Scientific Reports ◽

10.1038/s41598-021-89327-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Brice K. Grunert ◽

Maria Tzortziou ◽

Patrick Neale ◽

Alana Menendez ◽

Peter Hernes

Keyword(s):

Organic Matter ◽

Dissolved Organic Matter ◽

Salinity Gradient ◽

Coastal Ocean ◽

Interactive Effects ◽

The Arctic ◽

Yukon River ◽

Spring Freshet ◽

Dom Composition

AbstractThe Arctic is experiencing rapid warming, resulting in fundamental shifts in hydrologic connectivity and carbon cycling. Dissolved organic matter (DOM) is a significant component of the Arctic and global carbon cycle, and significant perturbations to DOM cycling are expected with Arctic warming. The impact of photochemical and microbial degradation, and their interactive effects, on DOM composition and remineralization have been documented in Arctic soils and rivers. However, the role of microbes, sunlight and their interactions on Arctic DOM alteration and remineralization in the coastal ocean has not been considered, particularly during the spring freshet when DOM loads are high, photoexposure can be quite limited and residence time within river networks is low. Here, we collected DOM samples along a salinity gradient in the Yukon River delta, plume and coastal ocean during peak river discharge immediately after spring freshet and explored the role of UV exposure, microbial transformations and interactive effects on DOM quantity and composition. Our results show: (1) photochemical alteration of DOM significantly shifts processing pathways of terrestrial DOM, including increasing relative humification of DOM by microbes by > 10%; (2) microbes produce humic-like material that is not optically distinguishable from terrestrial humics; and (3) size-fractionation of the microbial community indicates a size-dependent role for DOM remineralization and humification of DOM observed through modeled PARAFAC components of fluorescent DOM, either through direct or community effects. Field observations indicate apparent conservative mixing along the salinity gradient; however, changing photochemical and microbial alteration of DOM with increasing salinity indicate changing DOM composition likely due to microbial activity. Finally, our findings show potential for rapid transformation of DOM in the coastal ocean from photochemical and microbial alteration, with microbes responsible for the majority of dissolved organic matter remineralization.

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Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Atmosphere ◽

10.3390/atmos12070809 ◽

2021 ◽

Vol 12 (7) ◽

pp. 809

Author(s):

Sen Wang ◽

Wanyu Liu ◽

Jun Li ◽

Haotian Sun ◽

Yali Qian ◽

...

Keyword(s):

Seasonal Variation ◽

Relative Abundance ◽

Pathogenic Bacteria ◽

High Throughput Sequencing ◽

Fine Particulate Matter ◽

Ecological Functions ◽

Factors Affecting ◽

Bacterial Phyla ◽

Variation Characteristics ◽

Bacteria And Fungi

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

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16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽

10.1007/s00300-021-02843-2 ◽

2021 ◽

Author(s):

Eleanor E. Jackson ◽

Ian Hawes ◽

Anne D. Jungblut

Keyword(s):

16S Rrna ◽

18S Rrna ◽

High Throughput Sequencing ◽

Microbial Mats ◽

Gene Diversity ◽

Salinity Gradient ◽

18S Rrna Gene ◽

Rrna Gene ◽

Ice Shelf ◽

The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

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Discovery of MicroRNAs and Their Target Genes Related to Drought in Paulownia “Yuza 1” by High-Throughput Sequencing

International Journal of Genomics ◽

10.1155/2017/3674682 ◽

2017 ◽

Vol 2017 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Minjie Deng ◽

Yabing Cao ◽

Zhenli Zhao ◽

Lu Yang ◽

Yanfang Zhang ◽

...

Keyword(s):

Drought Stress ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Plant Hormone ◽

Target Genes ◽

Reference Data ◽

Relevant Information ◽

Putative Target

Understanding the role of miRNAs in regulating the molecular mechanisms responsive to drought stress was studied in Paulownia “yuza 1.” Two small RNA libraries and two degradome libraries were, respectively, constructed and sequenced in order to detect miRNAs and their target genes associated with drought stress. A total of 107 miRNAs and 42 putative target genes were identified in this study. Among them, 77 miRNAs were differentially expressed between drought-treated Paulownia “yuza 1” and the control (60 downregulated and 17 upregulated). The predicted target genes were annotated using the GO, KEGG, and Nr databases. According to the functional classification of the target genes, Paulownia “yuza 1” may respond to drought stress via plant hormone signal transduction, photosynthesis, and osmotic adjustment. Furthermore, the expression levels of seven miRNAs (ptf-miR157b, ptf-miR159b, ptf-miR398a, ptf-miR9726a, ptf-M2153, ptf-M2218, and ptf-M24a) and their corresponding target genes were validated by quantitative real-time PCR. The results provide relevant information for understanding the molecular mechanism of Paulownia resistance to drought and reference data for researching drought resistance of other trees.

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Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans

BMC Genomics ◽

10.1186/s12864-021-07439-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yong Shi ◽

Heng Xia ◽

Xiaoting Cheng ◽

Libin Zhang

Keyword(s):

Secondary Metabolites ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Flavonoid Biosynthesis ◽

Integrated Network ◽

Osmanthus Fragrans ◽

Flavonoid Synthesis ◽

Genome Wide

AbstractBackgroundOsmanthus fragransis an important economical plant containing multiple secondary metabolites including flavonoids and anthocyanins. During the past years, the roles of miRNAs in regulating the biosynthesis of secondary metabolites in plants have been widely investigated. However, few studies on miRNA expression profiles and the potential roles in regulating flavonoid biosynthesis have been reported inO. fragrans.ResultsIn this study, we used high-throughput sequencing technology to analyze the expression profiles of miRNAs in leaf and flower tissues ofO. fragrans. As a result, 106 conserved miRNAs distributed in 47 families and 88 novel miRNAs were identified. Further analysis showed there were 133 miRNAs differentially expressed in leaves and flowers. Additionally, the potential target genes of miRNAs as well as the related metabolic pathways were predicted. In the end, flavonoid content was measured in flower and leaf tissues and potential role of miR858 in regulating flavonoid synthesis was illustrated inO. fragrans.ConclusionsThis study not only provided the genome-wide miRNA profiles in the flower and leaf tissue ofO. fragrans, but also investigated the potential regulatory role of miR858a in flavonoid synthesis inO. fragrans. The results specifically indicated the connection of miRNAs to the regulation of secondary metabolite biosynthesis in non-model economical plant.

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Salsolaius gen. nov. a new genus of Apalochrini (Coleoptera, Melyridae, Malachiinae) from the salt Lake Way of Western Australia

Zootaxa ◽

10.11646/zootaxa.5082.4.7 ◽

2021 ◽

Vol 5082 (4) ◽

pp. 393-400

Author(s):

ZHENHUA LIU ◽

ADAM ŚLIPIŃSKI ◽

HONG PANG

Keyword(s):

Western Australia ◽

Type Species ◽

New Genus ◽

Salt Lake ◽

Salt Lakes ◽

Male And Female ◽

Male Specific

Apalochrini comprises nearly half of the genera of Australian Melyridae, which are all recognized by male specific characters, and are commonly found on grasses, flowers and riverside or seashore rocks. Here we describe a new genus Salsolaius gen. nov. from Lake Way of Western Australia, representing the first known genus of Australian Melyridae inhabitating in salt lakes. The new genus can be easily distinguished by asymmetrically biserrate antennae and exposed apical abdomen from above in both male and female, the former characters is firstly found in Melyridae. Consequently, Salsolaius biserratus sp. nov. was described as the type species of this genus. An updated key to genera of Australian Apalochrini is provided.

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Chlorinated metabolites from Streptomyces sp. highlight the role of biosynthetic mosaics and superclusters in the evolution of chemical diversity

Organic & Biomolecular Chemistry ◽

10.1039/d1ob00600b ◽

2021 ◽

Author(s):

Mahmud Tareq Morshed ◽

Ernest Lacey ◽

Daniel Vuong ◽

Alastair E Lacey ◽

Soo-sum Lean ◽

...

Keyword(s):

Chemical Diversity ◽

Streptomyces Sp ◽

Bacteria And Fungi

LCMS-guided screening of a library of biosynthetically talented bacteria and fungi identified Streptomyces sp. MST-144321 as a prolific producer of chlorinated metabolites. We isolated and characterised six new and nine...

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