Qian Zhang

Although millions of plant growth–promoting bacteria (PGPBs) are currently used in agriculture and soil health restoration, their potential environmental threats have largely been ignored. Here, rhizosphere soils from Chilean temperate rainforests (CTR) were collected and studied as an attractive, novel source of potentially safer PGPBs. A total of 847 isolates was assembled, and representative PGPB phenotypes and biocontrol (BC) activities were screened. Forty isolates that exhibited most of the tested PGPB phenotypes and BC activities were selected, and their antibiotic resistance (AR) and presumptive virulence factors were assayed. Of these, the 4 rhizosphere isolates with the lowest AR and virulence values were selected, designated ‘potentially safer PGPBs’ and inoculated into tomato seeds. Our results showed that between 86 and 100% of the rhizosphere-collection isolates exhibited at least one of the tested PGPB phenotypes, while 26.9 to 40.7% showed in vitro antagonistic activity against at least one of the tested plant pathogens. Low percentages of AR (Ochrobactrum , Brucella , Microbacterium and Bacillus resulted in significantly ( p ≤ 0.05) greater tomato ( Solanum lycopersicum ) seedling growth compared with uninoculated controls. These results of our study were obtained in a short–term in vitro seedling screening assay and indicate that CTR rhizosphere soils merit further evaluation as a source of potentially safer PGPB candidates showing a low in vitro risk profile, in line with the ‘Food Security’ and ‘One Health’ approaches.

When a harmful algal bloom collapses, does the coastal water quality recover? We addressed this question using the natural bloom of the haptophyte Phaeocystis globosa in coastal waters around Xiamen Island, China. Bacterial and microeukaryotic communities in the water samples ( n = 105) monthly collected from five sites from September 2023 to March 2024 were analyzed using 16S and 18S rRNA amplicon sequencing, genotype-specific qPCR, iCAMP-based assembly inference, partial least squares path modeling, bloom stage-specific co-occurrence networks, and amplicon-based functional prediction. Bloom development drove coordinated physicochemical change. Both bacterial and microeukaryotic communities were displaced from their pre-bloom state but did not return to the original state within the 7-month series. However, their patterns of succession were different. Bacterial communities underwent coherent system-wide succession. They diverged spatially during the bloom. Their assembly shifted toward stochasticity, with the deterministic contribution falling from 46.3% pre-bloom to 27.8% during the bloom and recovering only to 30.3% post-bloom. Their co-occurrence network was most complex during the bloom period. In contrast, microeukaryotic communities retained stronger site-specific structure throughout succession, and their network connectivity peaked after the bloom collapsed. Water quality variables explained 45.9% of bacterial but only 13.1% of microeukaryotic community variation. Predicted functional profiles also showed stage-associated changes. The same bloom thus pushed bacterial and microeukaryotic communities toward different post-disturbance configurations on different timescales. We therefore propose a cross-domain monitoring framework that integrates stage-specific taxa, a community state index, and network complexity. This framework can diagnose bloom onset, collapse, and genuine post-bloom recovery in eutrophic coastal waters. IMPORTANCE: Harmful algal blooms disturb coastal waters well beyond the period when the causative alga is abundant. This study shows that the effects of a Phaeocystis globosa bloom on the coastal microbiome lasted after the bloom itself ended and that bacteria and microeukaryotes recovered along different paths and on different timescales. Algal counts or nutrient concentrations alone therefore cannot adequately capture the recovery of coastal water quality. We suggest an alternative monitoring framework that combines stage-specific indicator taxa, a community state index, and network topology, so that coastal water quality can be assessed more reliably.

To evaluate the association between respiratory tract microorganisms at birth and the subsequent development and severity of bronchopulmonary dysplasia (BPD) in preterm infants. This prospective cohort study enrolled 98 preterm infants (gestational age < 32 weeks, birth weight < 2,000 g). Tracheal aspirate samples were collected through endotracheal intubation within 2 h after birth. Using 16S rRNA sequencing, we characterized the airway microbiome and performed co-occurrence network analysis with compositionally robust methods. Among 98 preterm infants analyzed, the incidence of BPD was 68.4%, comprising 31 grade I, 20 grade II, and 16 grade III cases. Airway microbiota in infants with BPD exhibited distinct severity-stage patterns: Escherichia-Shigella and Streptococcus were significantly enriched in grade I, while Chryseobacterium increased markedly in grade III, accompanied by a significant reduction in Streptococcus . Microbial co-occurrence network analysis yielded three key insights. (i) Network complexity declined sharply with BPD severity, being sparsest in grade III. (ii) Distinct keystone taxa were identified across different groups: Acinetobacter and Fusobacterium in the non-BPD group; Brevundimonas and Fusobacterium in grade I; Fusobacterium and Acinetobacter at grade II and grade III. (iii) In a multivariable model adjusted for key clinical confounders, a higher microbial network density at birth was independently associated with a substantially reduced risk (OR = 0.12, P < 0.05). The ecological architecture of the neonatal airway microbiome at birth, defined by network complexity and keystone taxa, is associated with BPD severity. This highlights microbial network stability as a novel factor and ecological interactions as a target for future research. IMPORTANCE: Bronchopulmonary dysplasia (BPD) remains the most common chronic lung disease in preterm infants. While its pathogenesis is incompletely understood, the role of the early respiratory microbe is increasingly recognized. Previous studies have largely focused on individual pathogenic taxa, overlooking the complex ecological interactions within microbial communities. Our analysis reveals that the architecture of microbial co-occurrence networks in the neonatal airway varies significantly with BPD severity. Notably, network complexity decreased markedly as BPD severity increased. We identified specific keystone taxa uniquely associated with disease outcomes, suggesting that microbial ecosystem stability rather than individual species may be a critical factor in BPD pathogenesis. These findings shift the focus from single microbes to the stability of the microbial ecosystem as a novel risk factor for severe BPD, offering new avenues for risk stratification and early intervention.

Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 10⁴ to 10⁸ copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal–Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.