Estuarine salt marshes are highly productive ecosystems subjected to regular disturbances by hydrodynamic exchange. However, little is known about how distinct assembly processes and co-occurrence of taxa influence the structure of the abundant and rare bacterial biospheres in these soil systems. This study aims at unravelling these intricacies by studying a typical estuarine salt marsh located in Hangzhou Bay, China. Our study provides important pieces of evidence on the diverse distribution of rare and abundant bacterial biospheres. We show that a few abundant taxa are central nodes in species co-occurrence, potentially playing important roles as keystone species in the system. In addition, we highlight a dynamic interplay of assembly processes structuring these two subcommunities.

Increasing evidence has emerged supporting a tight link between gut bacterial community and shrimp health. However, the knowledge about the variation of gut bacterial community, especially with different disease onset time, remains elusive. Here, healthy and diseased shrimps were collected at 3 disease-outbreak times (day 70, 80 and 85) to investigate the variation of gut bacterial community and its underlying ecological process with 16S rRNA gene amplicon sequencing. The gut bacterial community of diseased shrimp was distinct from the healthy one and temporally less stable, characterized by decreased alpha-diversity and dispersive structure. And its dominant ecological process experienced a transition with disease onset time, although deterministic process mainly governed the healthy gut bacterial assembly. In addition, the core microbiota of healthy shrimp gut harbored more diverse bacterial taxa with more cooperative interactions, while the diseased core microbiota showed opposite pattern with significantly higher abundance of opportunistic pathogens as well. These findings indicate that shrimp heath is highly relevant to the homeostasis of its gut bacterial community. Preservation and restoration of the bacterial community equilibrium could represent an effective strategy for shrimp disease prevention.

As microplastic pollution continues to increase, an emerging threat is the potential for microplastics to act as novel substrates and/or carriers for pathogens. This is of particular concern for aquatic product safety given the growing evidence of microplastic ingestion by aquaculture species. However, the potential risks of pathogens associated with microplastics in mariculture remain poorly understood. Here, an in situ incubation experiment involving three typical microplastics including polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) was conducted during the summer–autumn period in a mariculture cage. The identification of potential pathogens based on the 16S rRNA gene amplicon sequencing and a custom-made database for pathogenic bacteria involved in aquatic environments, was performed to assess the risks of different microplastics attaching potential pathogens. The enrichment of pathogens was not observed in microplastic-associated communities when compared with free-living and particle-attached communities in surrounding seawater. Despite the lower relative abundance, pathogens showed different preferences for three microplastic substrates, of which PET was the most favored by pathogens, especially potentially pathogenic members of Vibrio, Tenacibaculum, and Escherichia. Moreover, the colonization of these pathogens on microplastics was strongly affected by environmental factors (e.g., temperature, nitrite). Our results provide insights into the ecological risks of microplastics in mariculture industry.

Anthropogenic disturbances and global climate change are causing large-scale biodiversity loss and threatening ecosystem functions. However, due to the lack of knowledge on microbial species loss, our understanding on how functional profiles of soil microbes respond to diversity decline is still limited. Here, we evaluated the biotic homogenization of global soil metagenomic data to examine whether microbial functional structure is resilient to significant diversity reduction. Our results showed that although biodiversity loss caused a decrease in taxonomic species by 72%, the changes in the relative abundance of diverse functional categories were limited. The stability of functional structures associated with microbial species richness decline in terrestrial systems suggests a decoupling of taxonomy and function. The changes in functional profile with biodiversity loss were function-specific, with broad-scale metabolism functions decreasing and typical nutrient-cycling functions increasing. Our results imply high levels of microbial physiological versatility in the face of significant biodiversity decline, which, however, does not necessarily mean that a loss in total functional abundance, such as microbial activity, can be overlooked in the background of unprecedented species extinction.