Paul G. Dennis

Plant-associated microbiomes vary between environments, making it challenging to identify microorganisms that consistently associate with crop hosts. Here, we characterised bacterial communities associated with banana (Musa ABB ’Pisang Awak’) plants grown in soils collected from three banana-producing regions of Daerah Istimewa Yogyakarta, Indonesia. Bacterial communities from bulk soil and ectorhizosphere compartments were characterised using 16S rRNA gene amplicon sequencing. Bacterial diversity and community composition differed significantly among soils, with Site explaining substantially more variation than Compartment. Despite this variation, an abundance-occupancy approach identified 20 bacterial operational taxonomic units (OTUs) that occurred consistently across all three soils and were therefore designated as members of the Indonesian core microbiome. Although these taxa represented only 0.38% of the 5,269 OTUs detected, they collectively accounted for approximately 26% of bacterial relative abundance. Comparison with previously defined banana core microbiomes revealed substantial overlap, with 13 of the 20 Indonesian core OTUs matching taxa previously identified within Australian and/or internationally distributed banana core microbiomes. Furthermore, 63 of 74 internationally distributed core taxa and 27 of 36 Australian core taxa were recovered in Indonesian soils. These findings support the existence of a conserved banana-associated bacterial microbiome that persists across distinct production systems and soils with contrasting edaphic characteristics.

Biodegradable polymers (BPs) are often seen as sustainable alternatives to conventional plastics. However, their actual degradability in soils, a major sink for plastic pollution, varies considerably. Moreover, their breakdown can influence soil microbial communities, with potential consequences for ecosystem function. Here, we compared the impacts of four major BP types: (1) poly(3-hydroxybutyrate- co -3-hydroxyvalerate) (PHBV), (2) poly(butylene adipate- co -terephthalate) (PBAT), (3) poly(butylene succinate) (PBS), and (4) poly(lactic acid) (PLA), on soil and plastisphere microbial communities. Standardised BP samples were buried in soil for 117 days, after which bacterial and fungal biomass load and diversity were assessed in the BPs and surrounding soils using quantitative PCR and metabarcoding. X-ray micro-computed tomography (µXCT) and gel permeation chromatography (GPC) were also used to compare signs of degradation. PLA exhibited negligible signs of degradation, no evidence of microbial colonisation, and minimal impacts on microbial diversity relative to bulk soil. In contrast, PHBV, PBAT, and PBS underwent marked degradation and supported distinct microbial assemblages with elevated biomass but reduced diversity, indicating selective enrichment of specific taxa. These findings demonstrate that BPs differ markedly in their environmental degradability and influence on soil microbial communities, providing insights to support polymer selection for more sustainable plastic use.

Citrate-based plasticizers are often marketed as eco-friendly alternatives to phthalates like dibutyl phthalate (DBP). Here, we investigated these assertions by examining the response of soil microbial communities to biopolymer samples plasticized with acetyl tributyl citrate (ATBC), triethyl citrate (TEC), DBP, or nothing (control). Samples were buried in soil for 14 weeks, after which the biomass and diversity of bacterial and fungal communities associated with the biopolymer, attached soil, and bulk soil were characterized using metabarcoding and quantitative PCR. Differences between buried (incubated) and nonincubated biopolymer samples were also analyzed using X-ray microcomputed tomography, gel permeation chromatography, and ¹H-nuclear magnetic resonance spectroscopy to assess biopolymer degradation and plasticizer migration. Surface degradation and plasticizer migration were observed for all treatments, with minor impacts of plasticizers on microbial biomass and alpha diversity. Critically, however, plastisphere bacterial communities formed two groups that were compositionally distinct. One group comprised the DBP samples while the other comprised the control, ATBC, and TEC samples. This indicates that DBP can impact soil bacterial community composition on release from biopolymer blends, while the effects of the citrate-based plasticizers were reduced─supporting their use as potentially less environmentally impactful alternatives to phthalates.

On commercial banana (Musa spp.) plantations, soils are often supplemented with phosphorus (P) fertiliser to optimise production. Such additions may influence the diversity and function of soil microbial communities, which play important roles in P cycling and affect plant fitness. Here, we characterised the effects of P addition on the diversity and function of banana-associated microbial communities. P addition was associated with significant increases in soil P and the activities of alpha-glucosidase, chitinase, arylsulphatase, and acid phosphatase, but not beta-glucosidase or xylosidase. P addition also expedited bunch emergence and harvest, but did not influence fruit yield, plant height, or foliar P. There were no significant effects of P addition on the alpha or beta diversity of bacterial, fungal, and nematode communities, including members of the core microbiome. The only exceptions to this was an increase in the relative abundance of a Fusarium population in roots. These results indicate that phosphorus application to banana soils may stimulate microbial enzyme activities with minor or negligible effects on microbial diversity.

Poor maternal diet during pregnancy predisposes to severe lower respiratory tract infections (sLRI) in infancy, which in turn, increases childhood asthma risk, however the underlying mechanisms remain poorly understood. Here, we show that the offspring of high fat diet (HFD)-fed mothers (‘HFD-reared pups’) developed a sLRI following pneumovirus inoculation in early-life and subsequent asthma in later-life upon allergen exposure. Prior to infection, HFD-reared pups developed microbial dysbiosis and low-grade systemic inflammation (LGSI), characterized by hyper-granulopoiesis in the liver and elevated inflammatory cytokine expression, most notably IL-17A, IL-6 and sIL-6R (indicative of IL-6 trans-signaling) in the circulation and multiple organs, but most prominently the liver. Inhibition of IL-6 trans-signaling, using sgp130Fc transgenic mice or via specific genetic deletion of IL-6Ra on neutrophils, conferred protection against both diseases. Taken together, our findings suggest that a maternal HFD induces neonatal LGSI that predisposes to sLRI and subsequent asthma via neutrophil-mediated IL-6 trans-signaling.

Objective: Chronic obstructive pulmonary disease (COPD) is a major cause of global illness and death, most commonly caused by cigarette smoke. The mechanisms of pathogenesis remain poorly understood, limiting the development of effective therapies. The gastrointestinal microbiome has been implicated in chronic lung diseases via the gut-lung axis, but its role is unclear. Design: Using an in vivo mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT), we characterised the faecal microbiota using metagenomics, proteomics and metabolomics. Findings were correlated with airway and systemic inflammation, lung and gut histopathology and lung function. Complex carbohydrates were assessed in mice using a high resistant starch diet, and in 16 patients with COPD using a randomised, double-blind, placebo-controlled pilot study of inulin supplementation. Results: FMT alleviated hallmark features of COPD (inflammation, alveolar destruction, impaired lung function), gastrointestinal pathology and systemic immune changes. Protective effects were additive to smoking cessation, and transfer of CS-associated microbiota after antibiotic-induced microbiome depletion was sufficient to increase lung inflammation while suppressing colonic immunity in the absence of CS exposure. Disease features correlated with the relative abundance of Muribaculaceae, Desulfovibrionaceae and Lachnospiraceae family members. Proteomics and metabolomics identified downregulation of glucose and starch metabolism in CS-associated microbiota, and supplementation of mice or human patients with complex carbohydrates improved disease outcomes. Conclusion: The gut microbiome contributes to COPD pathogenesis and can be targeted therapeutically.

The ability to sense and direct movement along chemical gradients is known as ‘chemotaxis’ and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change and may recruit symbionts that enhance host stress tolerance. Decoding this language of attraction could support the development of microbiome management strategies that would enhance agricultural production and sustainability. In this study, we employ a culture-independent bait-trap chemotaxis assay to capture microbial communities attracted to root exudates from phosphorus (P)-sufficient and P-deficient Arabidopsis thaliana Col-0 plants. The captured populations were then enumerated and characterised using flow cytometry and phylogenetic marker gene sequencing, respectively. Exudates attracted significantly more cells than the control but did not differ between P treatments. Relative to exudates from P-sufficient plants, those collected from P-deficient plants attracted a significantly less diverse bacterial community that was dominated by members of the Paenibacillus, which is a genus known to include powerful phosphate solubilisers and plant growth promoters. These results suggest that in response to P deficiency, Arabidopsis exudates attract organisms that could help to alleviate nutrient stress.