scholarly journals Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Wenjun Li ◽  
Xiaofang Li
Keyword(s):  
Community Structure ◽  
Mine Tailings ◽  
Fluorescent In Situ Hybridization ◽  
High Throughput Sequencing ◽  
Microbial Consortia ◽  
Metabolic Reconstruction ◽  
Metal Release ◽  
Community Members ◽  
Oxidative Stresses

Abstract Background Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community structure in acidic tailings environments. We still know little about the microbial metabolic capacities of alkaline sulphidic environment where microbial processes are critically important for the revegetation. Microbial communities therein may not only provide soil functions, but also ameliorate the environment stresses for plants’ survival. Results In this study, we detected a considerable amount of viable bacterial and archaeal cells using fluorescent in situ hybridization in alkaline sulphidic tailings from Mt Isa, Queensland. By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings. Assembly of 10 metagenome-assembled genomes (MAGs), with 5 nearly complete, was achieved. From this, detailed insights into the community metabolic capabilities was derived. Dominant microbial species were seen to possess powerful resistance systems for osmotic, metal and oxidative stresses. Additionally, these community members had metabolic capabilities for sulphide oxidation, for causing increased salinity and metal release, and for leading to N depletion. Conclusions Here our results show that a considerable amount of microbial cells inhabit the mine tailings, who possess a variety of genes for stress response. Metabolic reconstruction infers that the microbial consortia may actively accelerate the sulphide weathering and N depletion therein.

scholarly journals Regulation of community functional composition across taxonomic variation by resource-consumer dynamics

2019 ◽  
Author(s):  
Lee Worden
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
High Throughput Sequencing ◽  
Taxonomic Composition ◽  
Functional Composition ◽  
Vital Rates ◽  
Community Members ◽  
Functional Responses ◽  
Functional Community ◽  
Consumer Model

AbstractHigh-throughput sequencing techniques such as metagenomic and metatranscriptomic technologies allow cataloging of functional characteristics of microbial community members as well as their taxonomic identity. Such studies have found that a community’s composition in terms of ecologically relevant functional traits or guilds can be conserved more strictly across varying settings than taxonomic composition is. I use a standard ecological resource-consumer model to examine the dynamics of traits relevant to resource consumption, and analyze determinants of functional composition. This model demonstrates that interaction with essential resources can regulate the community-wide abundance of ecologically relevant traits, keeping them at consistent levels despite large changes in the abundances of the species housing those traits in response to changes in the environment, and across variation between communities in species composition. Functional composition is shown to be able to track differences in environmental conditions faithfully across differences in community composition. Mathematical conditions on consumers’ vital rates and functional responses sufficient to produce conservation of functional community structure across taxonomic differences are presented.

scholarly journals Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Manuel Kleiner
Keyword(s):  
Gene Expression ◽  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Large Scale ◽  
Molecular Level ◽  
Carbon Sources ◽  
Community Members ◽  
Insight Into

ABSTRACT Metaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members. However, recently developed metaproteomic tools allow quantification of per-species biomass to determine community structure, in situ carbon sources of community members, and the uptake of labeled substrates by community members. In this perspective, I provide a brief overview of the questions that we can currently address, as well as new metaproteomics-based approaches that we and others are developing to address even more questions in the study of microbial communities and plant and animal microbiota. I also highlight some areas and technologies where I anticipate developments and potentially major breakthroughs in the next 5 years and beyond.

1796: Analysis of Chromosomal Aneuploidy in Patients with Oligoasthenoteratozoospermia(OAT) Using Fluorescent in-situ Hybridization

2007 ◽  
Vol 177 (4S) ◽  
pp. 596-597
Author(s):  
Joseph P. Alukal ◽  
Bobby B. Najari ◽  
Wilson Chuang ◽  
Lata Murthy ◽  
Monica Lopez-Perdomo ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescent In Situ Hybridization ◽  
Chromosomal Aneuploidy

scholarly journals Simultaneous genotypic and immunophenotypic analysis of interphase cells using dual-color fluorescence: a demonstration of lineage involvement in polycythemia vera

Blood ◽  
1992 ◽  
Vol 80 (4) ◽  
pp. 1033-1038 ◽  
Author(s):  
CM Price ◽  
EJ Kanfer ◽  
SM Colman ◽  
N Westwood ◽  
AJ Barrett ◽  
...  
Keyword(s):  
Polycythemia Vera ◽  
Fluorescent In Situ Hybridization ◽  
Chromosomal Abnormalities ◽  
Myeloproliferative Disorders ◽  
Chromosome 8 ◽  
Dual Fluorescence ◽  
Interphase Cell ◽  
Molecular Alterations ◽  
Interphase Cells

Abstract Fluorescent in situ hybridization has become a useful technique by which chromosomal abnormalities may be shown in interphase cells. We present a dual-fluorescence method whereby a chromosomal and immunophenotypic marker can be visualized simultaneously in the same interphase cell. Two patients with the myeloproliferative disorder polycythemia vera and trisomy for chromosome 8 have been studied using this technique and selective involvement of the myeloid and erythrocyte lineages has been shown by the detection of the trisomy in immunophenotyped cells. Simultaneous analysis of genotype and immunophenotype in individual cells from patients with myeloproliferative disorders or leukemia may help identify the developmental and lineage status of cells in which molecular alterations have resulted in clonal advantage.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

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