Soil biofilms:microbial interactions,challenges,and advanced techniques for ex-situ characterization

Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival.Biofilms enable intensive inter-and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins.Here,we first discuss organization,dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome.Social interactions among bacteria,such as cooperation and competition,are discussed.We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms.Microfluidic platforms,which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with highthroughput screening and novel measurements,are also highlighted.This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.

Graphene quantum dots rescue protein dysregulation of pancreatic β-cells exposed to human islet amyloid polypeptide

The amyloid aggregation of peptides and proteins is a hallmark of neurological disorders and type 2 diabetes.Human islet amyloid polypeptide(IAPP),co-secreted with insulin by pancreaticβ-cells,plays dual roles in both glycemic control and the pathology of type 2 diabetes.While IAPP can activate the NLRP3 inflammasome and modulate cellular autophagy,apoptosis and extracellular matrix metabolism,no data is available concerning intracellular protein expression upon exposure to the polypeptide.More surprisingly,how intracellular protein expression is modulated by nanoparticle inhibitors of protein aggregation remains entirely unknown.In this study,we first examined the changing proteomes ofβTC6,a pancreaticβ-cell line,upon exposure to monomeric,oligomeric and fibrillar IAPP,and detailed cellular protein expression rescued by graphene quantum dots(GQDs),an IAPP inhibitor.We found that 29 proteins were significantly dysregulated by the IAPP species,while majority of these proteins were nucleotide-binding proteins.Collectively,our liquid chromatography tandem-mass spectrometry,fluorescence quenching,helium ion microscopy,cytotoxicity and discreet molecular dynamics simulations data revealed a remarkable capacity of GQDs in regulating aberrant protein expression through H-bonding and hydrophobic interactions,pointing to nanomedicine as a new frontier against human amyloid diseases.

Zooming in to acquire micro-reaction:Application of microfluidics on soil microbiome

Microfluidics confers unique advantages in microbiological studies as these devices can accurately replicate the micro-and even nano-scale structures of soil to simulate the habitats of bacteria.It not only helps us understand the spatial distribution of bacterial communities(such as biofilms),but also provides mechanistic insights into microbial behaviors including chemotaxis and horizontal gene transfer(HGT).Microfluidics provides a feasible means for real-time,in situ studies and enables indepth exploration of the mechanisms of interactions in the soil microbiome.This review aims to introduce the basic principles of microfluidic technology and summarize the recent progress in microfluidic devices to study bacterial spatial distribution and functions,as well as biological processes,such bacterial chemotaxis,biofilm streamers(BS),quorum sensing(QS),and HGT.The challenges in and future development of microfluidics for soil microbiological studies are also discussed.