Microfluidic hotspots in bacteria research:A review of soil and related advances

Soil science is an inherently diverse and multidisciplinary subject that cannot develop further without the continuous introduction and promotion of emerging technologies.One such technology that is widely used in biomedicine and similar research fields,microfluidics,poses significant benefits for soil research;however,this technology is still underutilized in the field.Microfluidics offers unparalleled opportunities in soil bacterial cultivation,observation,and manipulation when compared to conventional approaches to these tasks.This review focuses on the use of microfluidics for bacteria research and,where possible,pulls from examples in the literature where the technologies were used for soil related research.The review also provides commentary on the use of microfluidics for soil bacteria research and discusses the key challenges researchers face when implementing this technology.We believe that microfluidic chips and their associated auxiliary technologies provide a prime inroad into the future of soil science research.

Soil Biogeochemical Cycle Couplings Inferred from a Function-Taxon Network

Soil biogeochemical cycles and their interconnections play a critical role in regulating functions and services of environmental systems.However,the coupling of soil biogeochemical processes with their mediating microbes remains poorly understood.Here,we identified key microbial taxa regulating soil biogeochemical processes by exploring biomarker genes and taxa of contigs assembled from metagenomes of forest soils collected along a latitudinal transect(18°N to 48°N)in eastern China.Among environmental and soil factors,soil pH was a sensitive indicator for functional gene composition and diversity.A function-taxon bipartite network inferred from metagenomic contigs identified the microbial taxa regulating coupled biogeochemical cycles between carbon and phosphorus,nitrogen and sulfur,and nitrogen and iron.Our results provide novel evidence for the coupling of soil biogeochemical cycles,identify key regulating microbes,and demonstrate the efficacy of a new approach to investigate the processes and microbial taxa regulating soil ecosystem functions.

FACS-iChip:a high-efficiency iChip system for microbial‘dark matter’mining

The isolation chip method(iChip)provides a novel approach for culturing previously uncultivable microorganisms;this method is currently limited by the user being unable to ensure single-cell loading within individual wells.To address this limitation,we integrated flow cytometry-based fluorescence-activated cell sorting with a modified iChip(FACS-iChip)to effectively mine microbial dark matter in soils.This method was used for paddy soils with the aim of mining uncultivable microorganisms and making preliminary comparisons between the cultured microorganisms and the bulk soil via 16S rRNA gene sequencing.Results showed that the FACS-iChip achieved a culture recovery rate of almost 40%and a culture retrieval rate of 25%.Although nearly 500 strains were cultured from 19 genera with 8 FACS-iChip plates,only six genera could be identified via 16S rRNA gene amplification.This result suggests that the FACS-iChip is capable of detecting strains in the currently dead spaces of PCR-based sequencing technology.We,therefore,conclude that the FACS-iChip system provides a highly efficient and readily available approach for microbial‘dark matter’mining.

Correction to:FACS-iChip:a high-efficiency iChip system for microbial‘dark matter’mining

The original version of this article unfortunately contained a mistake.The presentation of Table 2 was incorrect.The corrected Table 2 is given below.The original article has been corrected.