Strigolactones shape the assembly of root-associated microbiota in response to phosphorus availability.

Plants rely on strigolactones (SLs) to regulate their development and form symbiotic relationships with microbes as part of the adaptive phosphorus (P) efficiency strategies. However, the impact of SLs on root-associated microbial communities in response to P availability remains unknown. Here, root microbiota of SL biosynthesis (max3-11) and perception (d14-1) were compared to wild-type Col-0 plants under different P concentrations. Using high-throughput sequencing, the relationship between SLs, P concentrations, and the root-associated microbiota was investigated to reveal the variation in microbial diversity, composition, and interaction. Plant genotypes and P availability played important but different roles in shaping the root-associated microbial community. Importantly, SLs were found to attract Acinetobacter in low P conditions, which included an isolated CP-2 (Acinetobacter soli) that could promote plant growth in cocultivation experiments. Moreover, SLs could change the topologic structure within co-occurrence networks and increase the number of keystone taxa (e.g., Rhizobiaceae and Acidobacteriaceae) to enhance microbial community stability. This study reveals the key role of SLs in mediating root-associated microbiota interactions.IMPORTANCEStrigolactones (SLs) play a crucial role in plant development and their symbiotic relationships with microbes, particularly in adapting to phosphorus levels. Using high-throughput sequencing, we compared the root microbiota of plants with SL biosynthesis and perception mutants to wild-type plants under different phosphorus concentrations. These results found that SLs can attract beneficial microbes in low phosphorus conditions to enhance plant growth. Additionally, SLs affect microbial network structures, increasing the stability of microbial communities. This study highlights the key role of SLs in shaping root-associated microbial interactions, especially in response to phosphorus availability.

Extracellular proteins of Desulfovibrio vulgaris as adsorbents and redox shuttles promote biomineralization of antimony.

Biomineralization is the key process governing the biogeochemical cycling of multivalent metals in the environment. Although some sulfate-reducing bacteria (SRB) are recently recognized to respire metal ions, the role of their extracellular proteins in the immobilization and redox transformation of antimony (Sb) remains elusive. Here, a model strain Desulfovibrio vulgaris Hildenborough (DvH) was used to study microbial extracellular proteins of functions and possible mechanisms in Sb(V) biomineralization. We found that the functional groups (N-H, CO, O-CO, NH2-R and RCOH/RCNH2) of extracellular proteins could adsorb and fix Sb(V) through electrostatic attraction and chelation. DvH could rapidly reduce Sb(V) adsorbed on the cell surface and form amorphous nanometer-sized stibnite and/or antimony trioxide, respectively with sulfur and oxygen. Proteomic analysis indicated that some extracellular proteins involved in electron transfer increased significantly (p < 0.05) at 1.8 mM Sb(V). The upregulated flavoproteins could serve as a redox shuttle to transfer electrons from c-type cytochrome networks to reduce Sb(V). Also, the upregulated extracellular proteins involved in sulfur reduction, amino acid transport and protein synthesis processes, and the downregulated flagellar proteins would contribute to a better adaption under 1.8 mM Sb(V). This study advances our understanding of how microbial extracellular proteins promote Sb biomineralization in DvH.

Interactions and Stability of Gut Microbiota in Zebrafish Increase with Host Development.

Understanding interactions within the gut microbiome and its stability are of critical importance for deciphering ecological issues within the gut ecosystem. Recent studies indicate that long-term instability of gut microbiota is associated with human diseases, and recovery of stability is helpful in the return to health. However, much less is known about such topics in fish, which encompass nearly half of all vertebrate diversity. Here, we examined the assembly and succession of gut microbiota in more than 550 zebrafish, and evaluated the variations of microbial interactions and stability across fish development from larva to adult using molecular ecological network analysis. We found that microbial interactions and stability in the fish gut ecosystem generally increased with host development. This could be attributed to the development of the zebrafish immune system, the increasing amount of space available for microbial colonization within the gut, and the greater stability of nutrients available for the colonized microbiota in adult zebrafish. Moreover, the potential keystone taxa, even those with relatively low abundances, played important roles in affecting the microbial interactions and stability. These findings indicate that regulating rare keystone taxa in adult fish may have great potential in gut microbial management to maintain gut ecosystem stability, which could also provide references for managing gut microbiota in humans and other animals. IMPORTANCE Understanding gut microbial stability and the underlying mechanisms is an important but largely ignored ecological issue in vertebrate fish. Here, using a zebrafish model and network analysis of the gut microbiota we found that microbial interactions and stability in the gut ecosystem increase with fish development. This finding has important implications for microbial management to maintain gut homeostasis and provide better gut ecosystem services for the host. First, future studies should always consider using fish of different age groups to gain a full understanding of gut microbial networks. Second, management of the keystone taxa, even those that are only present at a low abundance, during the adult stage may be a viable pathway to maintain gut ecosystem stability. This study greatly expands our current knowledge regarding gut ecosystem stability in terms of ecological networks affected by fish development, and also highlights potential directions for gut microbial management in humans and other animals.

Environmental effects of nanoparticles on the ecological succession of gut microbiota across zebrafish development.

The environmental stresses could significantly affect the structure and functions of microbial communities colonized in the gut ecosystem. However, little is known about how engineered nanoparticles (ENPs), which have recently become a common pollutant in the environment, affect the gut microbiota across fish development. Based on the high-throughput sequencing of the 16S rRNA gene amplicon, we explored the ecological succession of gut microbiota in zebrafish exposed to nanoparticles for three months. The nanoparticles used herein including titanium dioxide nanoparticles (nTiO2, 100 µg/L), zinc oxide nanoparticles (nZnO, 100 µg/L), and selenium nanoparticles (nSe, 100 µg/L). Our results showed that nanoparticles exposure reduced the alpha diversity of gut microbiota at 73-90 days post-hatching (dph), but showed no significant effects at 14-36 dph. Moreover, nTiO2 significantly (p < 0.05) altered the composition of the gut microbial communities at 73-90 dph (e.g., decreasing abundance of Cetobacterium and Vibrio). Moreover, we found that homogeneous selection was the major process (16.6-57.8%) governing the community succession of gut microbiota. Also, nanoparticles exposure caused topological alterations to microbial networks and led to increased positive interactions to destabilize the gut microbial community. This study reveals the environmental effects of nanoparticles on the ecological succession of gut microbiota across zebrafish development, which provides novel insights to understand the gut microbial responses to ENPs over the development of aquatic animals.

Resistance and Resilience of Fish Gut Microbiota to Silver Nanoparticles.

Understanding mechanisms governing the resistance and resilience of microbial communities is essential for predicting their ecological responses to environmental disturbances. Although we have a good understanding of such issues for soil and lake ecosystems, how ecological resistance and resilience regulate the microbiota in the fish gut ecosystem remains unclear. Using the zebrafish model, we clarified the potential mechanisms governing the gut microbiota after exposure to silver nanoparticles (AgNPs). Here, we explored the ecological resistance and resilience of gut microbiota in zebrafish exposed to different concentrations of AgNPs (i.e., 10, 33 and 100 µg/liter) for 15, 45, 75 days. The high-throughput sequencing analysis of the 16S rRNA gene showed that AgNP exposure significantly reduced the α-diversity of gut microbiota and resulted in obvious dynamics of community composition and structure. However, the rebound of zebrafish gut microbiota was pushed toward an alternative state after 15 days of AgNP exposure. We found that homogeneous selection was a more prevalent contributor in driving gut community recovery after AgNP exposure. The resilience and resistance of gut microbiota responses to AgNP disturbance might be mainly determined by the predominant keystone taxa such as Acinetobacter and Gemmata. This study not only expanded our understanding of fish gut microbiota's responses to pollutants but also provided new insights into maintaining host-microbiome stability during environmental perturbations. IMPORTANCE Understanding the ecological mechanisms governing the resistance and resilience of microbial communities is a key issue to predict their responses to environmental disturbances. Using the zebrafish model, we wanted to clarify the potential mechanisms governing the resistance and resilience of gut microbiota after exposure to silver nanoparticles (AgNPs). We found that AgNP contamination significantly reduced the α-diversity of gut microbiota and resulted in obvious changes in community composition. The resilience and resistance of gut microbiota to AgNPs might be associated with the predominant keystone taxa (e.g., Acinetobacter and Gemmata). This study greatly expanded our understanding of how fish gut microbiota responds to environmental perturbations and maintains stability.

Synergistic effects of antimony and arsenic contaminations on bacterial, archaeal and fungal communities in the rhizosphere of Miscanthus sinensis: Insights for nitrification and carbon mineralization.

The impacts of metal(loids) on soil microbial communities are research focuses to understand nutrient cycling in heavy metal-contaminated environments. However, how antimony (Sb) and arsenic (As) contaminations synergistically affect microbially-driven ecological processes in the rhizosphere of plants is poorly understood. Here we examined the synergistic effects of Sb and As contaminations on bacterial, archaeal and fungal communities in the rhizosphere of a pioneer plant (Miscanthus sinensis) by focusing on soil carbon and nitrogen cycle. High contamination (HC) soils showed significantly lower levels of soil enzymatic activities, carbon mineralization and nitrification potential than low contamination (LC) environments. Multivariate analysis indicated that Sb and As fractions, pH and available phosphorus (AP) were the main factors affecting the structure and assembly of microbial communities, while Sb and As contaminations reduced the microbial alpha-diversity and interspecific interactions. Random forest analysis showed that microbial keystone taxa provided better predictions for soil carbon mineralization and nitrification under Sb and As contaminations. Partial least squares path modeling indicated that Sb and As contaminations could reduce the carbon mineralization and nitrification by influencing the microbial biomass, alpha-diversity and soil enzyme activities. This study enhances our understanding of microbial carbon and nitrogen cycling affected by Sb and As contaminations.

Fish growth enhances microbial sulfur cycling in aquaculture pond sediments.

Microbial sulfate reduction and sulfur oxidation are vital processes to enhance organic matter degradation in sediments. However, the diversity and composition of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) and their environmental driving factors are still poorly understood in aquaculture ponds, which received mounting of organic matter. In this study, bacterial communities, SRB and SOB from sediments of aquaculture ponds with different sizes of grass carp (Ctenopharyngodon idellus) were analysed using high-throughput sequencing and quantitative real-time PCR (qPCR). The results indicated that microbial communities in aquaculture pond sediments of large juvenile fish showed the highest richness and abundance of SRB and SOB, potentially further enhancing microbial sulfur cycling. Specifically, SRB were dominated by Desulfobulbus and Desulfovibrio, whereas SOB were dominated by Dechloromonas and Leptothrix. Although large juvenile fish ponds had relatively lower concentrations of sulfur compounds (i.e. total sulfur, acid-volatile sulfide and elemental sulfur) than those of larval fish ponds, more abundant SRB and SOB were found in the large juvenile fish ponds. Further redundancy analysis (RDA) and linear regression indicated that sulfur compounds and sediment suspension are the major environmental factors shaping the abundance and community structure of SRB and SOB in aquaculture pond sediments. Findings of this study expand our current understanding of microbial driving sulfur cycling in aquaculture ecosystems and also provide novel insights for ecological and green aquaculture managements.