Isolation and characterisation of Methylocystis spp. for poly-3-hydroxybutyrate production using waste methane feedstocks

Two-tiered mutualism improves survival and competitiveness of cross-feeding soil bacteria

Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms that underlie these interactions and their association with metal/metalloid biogeochemistry, however, remain poorly understood. Here, we identified two soil bacteria, Bacillus sp. BP-3 and Delftia sp. DT-2, that engage in a two-tiered mutualism. Strain BP-3 has low utilization ability of pyruvic acid while strain DT-2 lacks hexokinase, lacks a phosphotransferase system, and is defective in glucose utilization. When strain BP-3 is grown in isolation with glucose, it releases pyruvic acid to the environment resulting in acidification and eventual self-killing. However, when strain BP-3 is grown together with strain DT-2, strain DT-2 utilizes the released pyruvic acid to meet its energy requirements, consequently rescuing strain BP-3 from pyruvic acid-induced growth inhibition. The two bacteria further enhance their collective competitiveness against other microbes by using arsenic as a weapon. Strain DT-2 reduces relatively non-toxic methylarsenate [MAs(V)] to highly toxic methylarsenite [MAs(III)], which kills or suppresses competitors, while strain BP-3 detoxifies MAs(III) by methylation to non-toxic dimethylarsenate [DMAs(V)]. These two arsenic transformations are enhanced when strains DT-2 and BP-3 are grown together. The two strains, along with their close relatives, widely co-occur in soils and their abundances increase with the soil arsenic concentration. Our results reveal that these bacterial types employ a two-tiered mutualism to ensure their collective metabolic activity and maintain their ecological competitive against other soil microbes. These findings shed light on the intricateness of bacterial interactions and their roles in ecosystem functioning.

Microbial community structure and diversity in fish-flower (mint) symbiosis

The fish-flower symbiosis model is an eco-friendly sustainable farming technology combining plants, fish and microorganisms in a recirculating aquaculture system. However, there are few studies on the structure and diversity of microbial communities in fish intestines, culture water and plant roots during fish-flower symbiosis. Here, we cultured carp (Cyprinus carpio), crucian carp (Carassius auratus) and grass carp (Ctenopharyngodon idella) with mint (Mentha spicala L.) and extracted total genomic DNA from intestinal microorganisms, culture-water microorganisms and root microorganisms for each fish species for high-throughput sequencing of 16S rRNA genes. Analysis of microbial community structure and diversity revealed changes in abundance of microbial genera in the intestines and culture water of each fish species, including changes in the dominant taxa. Pirellula, Truepera, Aquincola, Cetobacterium and Luteolibacter were widespread in the fish intestine, culture water and mint root system. This study revealed the effects of mint feeding on the structure and diversity of microbial communities of fish, water bodies and the mint root system during fish-flower symbiosis, providing a theoretical reference for the promotion and application of fish-flower (mint) symbiosis technology and healthy fish culture technology.

In Vivo Genome Editing in Type I and II Methanotrophs Using a CRISPR/Cas9 System

Methanotrophic bacteria are Gram-negative, aerobic organisms that use methane as their sole source of carbon and energy. In this study, we constructed and exemplified a CRISPR/Cas9 genome editing system and used it to successfully make gene deletions and insertions in the type I methanotroph Methylococcus capsulatus Bath and the type II methanotroph Methylocystis parvus OBBP. High frequencies of gene deletions and insertions were achieved in combination with homology-directed repair. In M. parvus OBBP, we also investigated the impact of several parameters on the CRISPR/Cas9 genome editing, where the ligD gene was targeted with various PAM sequences and guide RNA spacer sequences, homology arms of variable length, differences in the duration of mating during conjugation, and exploiting promoters of different strengths to control the expression of cas9 and sgRNA. Although not the first attempt to develop a CRISPR/Cas system in methanotrophs, this work demonstrated for the first time an efficient CRISPR/Cas9 system generating scarless clean gene deletions and insertions in methanotroph genomes.