Potential bacterial resources for bioremediation of organochlorine pesticides and flame retardants recognized from forest soil across China.

Microbe-mediated remediation becomes a desire method for removal of persistent organic pollutants (POPs) due to its eco-friendly and sustainable nature. The improvement of practical feasibility requires constructing comprehensive species pool, while it is still limited by the rapid recognition of potential bacterial resources from environment. Here, based on the relative abundances of bacterial OTUs and pollutant concentrations, we established indexes to assess their tolerance to organochlorine pesticides (OCPs) and flame retardants (FRs) that are atmospheric transported and naturally accumulated in forest soil via forest filter effect.

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota.

Research on the microbial community and function of the anammox process for environmentally friendly wastewater treatment has achieved certain success, which may mean more universal insights are needed. However, the comprehensive understanding of the anammox process is constrained by the limited taxonomic assignment and functional characterization of anammox microbiota, primarily due to the scarcity of high-quality genomes for most organisms. This study reported a global genome catalog of anammox microbiotas based on numerous metagenomes obtained from both lab- and full-scale systems.

Cancer cell-derived exosomes promote NSCLC progression via the miR-199b-5p/HIF1AN axis.

Background: Exosomes are mediators of intercellular communication. Cancer cell-secreted exosomes allow exosome donor cells to promote cancer growth, as well as metastasis.

Methods: Here, exosomes were isolated from the serum of non-small cell lung cancer (NSCLC) patients and characterized by transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA) and western blot analysis.

Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations.

It has been extensively studied that the gut microbiome provides animals flexibility to adapt to food variability. Yet, how gut phageome responds to diet variation of wild animals remains unexplored. Here, we analyze the eco-evolutionary dynamics of gut phageome in six wild gibbons (Hoolock tianxing) by collecting individually-resolved fresh fecal samples and parallel feeding behavior data for 15 consecutive months.

Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons.

Wild animals may encounter multiple challenges especially food shortage and altered diet composition in their suboptimal ranges. Yet, how the gut microbiome responds to dietary changes remains poorly understood. Prior studies on wild animal microbiomes have typically leaned upon relatively coarse dietary records and individually unresolved fecal samples.

Increased Leaf Bacterial Network Complexity along the Native Plant Diversity Gradient Facilitates Plant Invasion?

Understanding the mechanisms of biological invasion is critical to biodiversity protection. Previous studies have produced inconsistent relationships between native species richness and invasibility, referred to as the invasion paradox. Although facilitative interactions among species have been proposed to explain the non-negative diversity-invasibility relationship, little is known about the facilitation of plant-associated microbes in invasions.

Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings.

Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties.

Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China.

Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment.

Unraveling microbe-mediated degradation of lignin and lignin-derived aromatic fragments in the Pearl River Estuary sediments.

Estuaries are one of the most crucial areas for the transformation and burial of terrestrial organic carbon (TerrOC), playing an important role in the global carbon cycle. While the transformation and degradation of TerrOC are mainly driven by microorganisms, the specific taxa and degradation processes involved remain largely unknown in estuaries. We collected surface sediments from 14 stations along the longitudinal section of the Pearl River Estuary (PRE), P.

Sabulicella rubraurantiaca gen. nov., sp. nov., a new member of the family Acetobacteraceae, isolated from desert soil.

Strain SYSU D01096 was isolated from a sandy soil sample collected from Gurbantunggut Desert in Xinjiang, PR China. Phylogenetic analysis of the nearly full-length 16S rRNA gene sequence revealed that strain SYSU D01096 belonged to the family Acetobacteraceae and was closest to Rubritepida flocculans DSM 14296 (96.0% similarity).

Scaling of energy gaps in phosphorene nanoflakes.

Electronic structure of phosphorene nanoflakes which consist of hundreds of phosphorus atoms are studied in the framework of unrestricted Hartree-Fock approach. On the base of Pariser-Parr-Pople model for electron-electron interactions, a simplified Bethe-Salpeter formalism is established for the calculation of excitation states of the system. Taking into account the electron-hole interaction in various dielectric environments, the optical gap of a triangular phosphorene nanoflake is shown to increase as the screening effect becomes stronger while its graphene counterpart exhibits just the opposite dependence.

Microbial diversity in extreme environments.

A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions.

Genomic Insights into the Ecological Role and Evolution of a Novel Order, " Sysuiplasmatales".

Recent omics studies have provided invaluable insights into the metabolic potential, adaptation, and evolution of novel archaeal lineages from a variety of extreme environments. We utilized a genome-resolved metagenomic approach to recover eight medium- to high-quality metagenome-assembled genomes (MAGs) that likely represent a new order (" Sysuiplasmatales") in the class from mine tailings and acid mine drainage (AMD) sediments sampled from two copper mines in South China. 16S rRNA gene-based analyses revealed a narrow habitat range for these uncultured archaea limited to AMD and hot spring-related environments.

Rhizosphere bacterial community composition affects cadmium and arsenic accumulation in rice (Oryza sativa L.).

Cadmium (Cd) and arsenic (As) contamination in paddy soils poses serious health risks to humans. The accumulation of Cd and As in rice (Oryza sativa L.) depends on their bioavailability, which is affected by soil physicochemical properties and soil microbial activities.

Metagenomic Assembly: Reconstructing Genomes from Metagenomes.

Assembly of metagenomic sequence data into microbial genomes is of critical importance for disentangling community complexity and unraveling the functional capacity of microorganisms. The rapid development of sequencing technology and novel assembly algorithms have made it possible to reliably reconstruct hundreds to thousands of microbial genomes from raw sequencing reads through metagenomic assembly. In this chapter, we introduce a routinely used metagenomic assembly workflow including read quality filtering, assembly, contig/scaffold binning, and postassembly check for genome completeness and contamination.

Diversity and Genomic Characterization of a Novel Parvarchaeota Family in Acid Mine Drainage Sediments.

Recent genome-resolved metagenomic analyses of microbial communities from diverse environments have led to the discovery of many novel lineages that significantly expand the phylogenetic breadth of Archaea. Here, we report the genomic characterization of a new archaeal family based on five metagenome-assembled genomes retrieved from acid mine drainage sediments. Phylogenomic analyses placed these uncultivated archaea at the root of the candidate phylum Parvarchaeota, which expand this lesser-known phylum into two family levels.

Metal-Resistance in Bacteria: Why Care?

Heavy metal resistance is more than the tolerance one has towards a particular music genera [...

Unraveling bacteria-mediated degradation of lignin-derived aromatic compounds in a freshwater environment.

Terrestrial organic carbon-lignin plays a crucial role in the global carbon balance. However, limited studies presented the functional and ecological traits of lignin decomposers population in natural aquatic ecosystem. In this study, we performed a multi-omics analysis by deploying amplicon, metagenomic, and metatranscriptomic approaches to identify the key potential degraders and pathways involved lignin-derived aromatic compounds in the later stage of lignin degradation.

Dynamic games for secure and resilient control system design.

Modern control systems are featured by their hierarchical structure composed of cyber, physical and human layers. The intricate dependencies among multiple layers and units of modern control systems require an integrated framework to address cross-layer design issues related to security and resilience challenges. To this end, game theory provides a bottom-up modeling paradigm to capture the strategic interactions among multiple components of the complex system and enables a holistic view to understand and design cyber-physical-human control systems.

Depth-related variability in viral communities in highly stratified sulfidic mine tailings.

Background: Recent studies have significantly expanded our knowledge of viral diversity and functions in the environment. Exploring the ecological relationships between viruses, hosts, and the environment is a crucial first step towards a deeper understanding of the complex and dynamic interplays among them.

Results: Here, we obtained extensive 16S rRNA gene amplicon, metagenomics sequencing, and geochemical datasets from different depths of two highly stratified sulfidic mine tailings cores with steep geochemical gradients especially pH, and explored how variations in viral community composition and functions were coupled to the co-existing prokaryotic assemblages and the varying environmental conditions.

Abnormal scaling of excitons in phosphorene quantum dots.

Excitonic states of a many-electron system in phosphorene quantum dots (PQDs) are investigated theoretically by using a configuration interaction approach. For a triangular PQD in various dielectric environments, its exciton is found to obey two distinct scaling rules. When there is a strong screening effect present in the nanodot, the exciton binding energy (Δex) is shown to be around -150 meV as the long-range Coulomb interactions are totally suppressed and it increases to about 100 meV when the effective dielectric constant (εr) decreases to 12.