Biology subjects

Edlund, A.

Publications and source records attributed to Edlund, A..

7 recordsLinked to original sources

bioRxiv2026

Soil microbial inoculants augment fertilizer performance across contrasting cropping systems in Rwanda

Smallholder farming systems in sub-Saharan Africa are constrained by declining soil fertility, erosion, and rising fertilizer costs, creating an urgent need for scalable inputs that sustain yields while maintaining soil health. While there is some evidence that microbial inoculants may offer a promising complement to conventional fertility management, field-scale evidence in tropical cereal and tuber systems remains limited. Here, we evaluated a multi-species inoculant composed of 20-22 Bacillus and Streptomyces species on potato and maize across four sites in Rwanda over two growing seasons (2025A and 2025B). Treatments included the inoculant applied at two rates (150 and 250 g ha-1), both alone and in combination with standard fertilization (inorganic fertilizer plus manure), alongside untreated and fertilized controls. Co-application of the inoculant with standard fertilization increased yield and plant biomass beyond fertilization alone, with gains of 6-51% for maize and 3-58% for potato. However, while the inoculant applied alone outperformed untreated controls, it generally did not match standard fertilization. Responses were strongest and most consistent for large-grade potato tubers, and application rate interacted with crop type, whereby the lower dose maximized marketable tuber yield, while maize showed a positive dose-response for grain and biomass. Yield increases were not accompanied by reductions in crop nutrient density, which was instead governed by site-level differences. Altogether, these results indicate that multi-species microbial inoculants are an effective complement to existing fertility practices that may offer, pending further research, a potential pathway to partial fertilizer replacement while sustaining productivity and nutritional quality in smallholder tropical agriculture.

ecology↗

bioRxiv2026

Complex microbial consortia improve yield and physiological performance of leafy greens under deficit irrigation

O_LIWater scarcity is an increasing constraint on agricultural productivity, particularly for high-value vegetable crops. Deficit irrigation strategies can reduce water use but frequently compromise yield and crop physiological status. Scalable, biologically based tools are needed to sustain crop performance under reduced water input without reliance on additional agrochemical inputs. C_LIO_LIFive functionally diverse microbial consortia were assembled from taxa selected to support rhizosphere colonization, soil structural stabilization, and fungal-mediated nutrient and water foraging. Consortia were evaluated in greenhouse trials with lettuce (Lactuca sativa) and spinach (Spinacia oleracea) grown under full irrigation or a 30% deficit irrigation regime (70% of crop water requirement). Crop responses were assessed using yield, harvest delay, root length, wilting incidence, chlorophyll content, and Water Band Index. C_LIO_LIAcross both crops, microbial consortium treatments improved performance under deficit irrigation relative to untreated water-stressed controls. In lettuce, yield increased by 3-9%; in spinach, yield increased by 4-13%, with several treatments restoring performance to levels not significantly different from fully irrigated controls. C_LIO_LIMicrobial treatments reduced harvest delay by an average of three to four days, improved root length, lowered wilting incidence, and reduced WBI, indicating attenuation of plant water stress. In several cases, physiological responses under deficit irrigation approached those observed under full irrigation despite 30% lower water input. Higher application rates generally produced stronger responses, though this trend was not always statistically significant. C_LIO_LISynthesis and applications. Complex microbial consortia can buffer the physiological and yield penalties of deficit irrigation in leafy green crops. These findings demonstrate the potential of soil microbiome-based inoculants as scalable, biologically derived tools to improve agricultural water-use efficiency and resilience under increasing water scarcity. Practical adoption of such consortia could reduce irrigation demand in intensive vegetable production systems without proportional yield loss, supporting both economic and environmental sustainability goals in water-limited agricultural contexts. C_LI

microbiology↗

bioRxiv2022

mucG, mucH,and mucI modulate production of mutanocyclin and reutericyclins in Streptococcus mutans B04Sm5

Streptococcus mutans is considered a primary etiologic agent of dental caries, which is the most common chronic infectious disease worldwide. S. mutans B04Sm5 was recently shown to produce reutericyclins and mutanocyclin through the muc biosynthetic gene cluster, and to utilize reutericyclins to inhibit the growth of neighboring commensal Streptococci. In this study, examination of S. mutans and muc phylogeny suggested evolution of an ancestral S. mutans muc into three lineages within one S. mutans clade, and then horizontal transfer of muc to other S. mutans clades. The roles of the mucG and mucH transcriptional regulators, and the mucI transporter, were also examined. mucH was demonstrated to encode a transcriptional activator of muc. mucH deletion reduced production of mutanocyclin and reutericyclins, and eliminated the impaired growth and inhibition of neighboring Streptococci phenotypes which are associated with reutericyclin production. {Delta}mucG had increased mutanocyclin and reutericyclin production, which impaired growth and increased the ability to inhibit neighboring Streptococci. However, deletion of mucG also caused reduced expression of mucD, mucE, and mucI. Deletion of mucI reduced mutanocyclin and reutericylin production, but enhanced growth, suggesting that mucI may not transport reutericyclin as its homolog does in Limosilactobacillus reuteri. Further research is needed to determine the roles of mucG and mucI, and to identify any co-factors affecting the activity of the mucG and mucH regulators. Overall, this study provided pangenome and phylogenetic analysis that serves as a resource for S. mutans research, and began elucidation of the regulation of reutericyclins and mutanocyclin production in S. mutans. ImportanceS. mutans must be able to outcompete neighboring organisms in its ecological niche in order to cause dental caries. S. mutans B04Sm5 inhibited the growth of neighboring commensal Streptococci through production of reutericyclins via the muc biosynthetic gene cluster. In this study, carriage of muc was examined across S. mutans, which showed that 35 of 244 RefSeq S. mutans genomes encoded muc and provided a valuable update to the S. mutans pangenome and phylogeny. The roles of the mucG and mucH transcriptional regulators, and the mucI transporter, were also examined. All 3 genes impacted production of mutanocyclin and reutericyclins, which affected the growth rates, transcriptomes, and the ability of the S. mutans strains to inhibit the growth of neighboring commensals.

microbiology↗

bioRxiv2020

Commensal oral Rothia mucilaginosa produces enterobactin - a metal chelating siderophore

Next-generation sequencing studies of saliva and dental plaque from subjects in both healthy and diseased states have identified bacteria belonging to the Rothia genus as ubiquitous members of the oral microbiota. To gain a deeper understanding of molecular mechanisms underlying the chemical ecology of this unexplored group, we applied a genome mining approach that targets functionally important biosynthetic gene clusters (BGCs). All 45 genomes that were mined, representing Rothia mucilaginosa, R. dentocariosa and R. aeria, harbored a catechol-siderophore-like BGC. To explore siderophore production further we grew the previously characterized R. mucilaginosa ATCC 25296 in liquid cultures, amended with glycerol, which led to the identification of the archetype siderophore enterobactin by using tandem Liquid Chromatography Mass Spectrometry (LC/MS/MS), High Performance Liquid Chromatography (HPLC), and Nuclear Magnetic Resonance (NMR) spectroscopy. Normally attributed to pathogenic gut bacteria, R. mucilaginosa is the first commensal oral bacterium found to produce enterobactin. Co-cultivation studies including R. mucilaginosa or purified enterobactin revealed that enterobactin reduced growth of certain strains of cariogenic Streptococcus mutans and pathogenic strains of Staphylococcus aureus. Commensal oral bacteria were either unaffected by, reduced in growth, or induced to grow adjacent to enterobactin producing R. mucilaginosa or the pure compound. Taken together with Rothias known capacity to ferment a variety of carbohydrates and amino acids, our findings of enterobactin production adds an additional level of explanation to R. mucilaginosas colonization success of the oral cavity. Enterobactin is the strongest Fe(III)-binding siderophore known, and its role in oral health requires further investigation. ImportanceThe communication language of the human oral microbiota is vastly underexplored. However, a few studies have shown that specialized small molecules encoded by BGCs have critical roles such as in colonization resistance against pathogens and quorum sensing. Here, by using a genome mining approach in combination with compound screening of growth cultures, we identified that the commensal oral community member mucilaginosa harbors a catecholate-siderophore BGC, which is responsible for the biosynthesis of enterobactin. The iron-scavenging role of enterobactin is known to have positive effects on the hosts iron pool and negative effects on host immune function, however its role in oral health remains unexplored. R. mucilaginosa was previously identified as an abundant community member in cystic fibrosis, where bacterial iron cycling plays a major role in virulence development. With respect to irons broad biological importance, iron-chelating enterobactin may explain R. mucilaginosas colonization success in both health and disease.

microbiology↗

bioRxiv2019

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules

Dental caries is the most common chronic infectious disease globally. The microbial communities associated with caries have mainly been examined using relatively low-resolution 16S rRNA gene amplicon sequencing and/or using downstream analyses that are unsound for the compositional nature of the data provided by sequencing. Additionally, the relationship between caries, oral microbiome composition, and host immunological markers has not been explored. In this study, the oral microbiome and a panel of 38 host markers was analyzed across the saliva from 23 children with dentin caries and 24 children with healthy dentition. Metagenomic sequencing, followed by investigation using tools designed to be robust for compositional data, illustrated that several Prevotella spp. were prevalent in caries, while Rothia spp. were associated with the health. The contributional diversity (extent to which multiple taxa contribute to each pathway) of functional pathways present in the oral microbiome was decreased in the caries group. This decrease was especially noticeable in several pathways known to impede caries pathogenesis, including arginine and branched-chain amino acid biosynthesis. 10 host immunological markers were found to be significantly elevated in the saliva of the caries group, and microbe-metabolite co-occurrence analysis provided an atlas of relationships contributing to the bi-directional influence between the oral microbiome and the host immune system. Finally, 527 metagenome-assembled genomes were obtained from the metagenomics data, representing 151 species. 23 taxa were novel genera/species and a further 20 taxa were novel species. This study thus serves as a model analysis pipeline that will tremendously expand our knowledge of the oral microbiome and its relationship to dental caries once applied to large populations.

microbiology↗

bioRxiv2019

Cariogenic Streptococcus mutans produces strain-specific antibiotics that impair commensal colonization

Streptococcus mutans is a common constituent of dental plaque and an etiologic agent of dental caries (tooth decay). Here we elucidate a biosynthetic pathway, encoded by globally distributed strains of S. mutans, which produces a series of bioactive small molecules including reutericyclin and two N-acyl tetramic acid analogues active against oral commensal bacteria. This pathway may provide S. mutans with a competitive advantage, promoting dysbiosis and caries pathogenesis.

microbiology↗

bioRxiv2018

Identification of the bacterial biosynthetic gene clusters of the oral microbiome illuminates the unexplored social language of bacteria during health and disease

Small molecules are the primary communication media of the microbial world. Recent bioinformatics studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria, and their connection to health versus disease, in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for over 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals with either good oral health, dental caries, or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Co-abundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in health, but greatly reduced in dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the worlds most common chronic diseases.\n\nIMPORTANCEThe healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the worlds most common and costly chronic infectious diseases, and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities, and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome, and how it devolves in the case of two prominent diseases.

microbiology↗