Biology subjects

Maccario, L.

Publications and source records attributed to Maccario, L..

6 recordsLinked to original sources

bioRxiv2023

Fertilizer and cultivar affect the barley rhizobiome, while domestication age only affects growth at low nutrient levels

Modern plant breeding has provided barley cultivars that produce high yields when supplied with ample amounts of mineral fertilizer. This narrow selection criterion may have reduced key traits facilitating vital microbiome-plant interactions. Here, we investigated the performance of three old and four modern barley cultivars grown at different fertilizer regimes and assessed the root microbiome composition using 16s rRNA amplicon sequencing. The objectives were to investigate: i) nutrient availability effects on nutrient uptake and biomass production and, ii) how domestication age, cultivar, and fertilizer treatment affect the root microbiome. Without fertilizer, old cultivars outperformed modern ones in terms of biomass and had higher leaf concentration of nitrogen, potassium, sulphur, iron, zinc, and copper. This suggests that older barley cultivars retained the ability of their wild ancestor to collaborate with the soil microbiome resulting in improved nutrient acquisition in low-input systems. Interestingly, domestication age did not significantly affect the diversity of the rhizo-microbiome, which was instead dependent on individual cultivar and fertilizer treatment. HighlightOlder barley cultivars outperform the modern ones in terms of biomass at low nutrient availability. However, the rhizo-microbial diversity depended on the individual cultivar and fertilizer regime.

plant biology↗

bioRxiv2023

Evolution of genotypic and phenotypic diversity in multispecies biofilms

Bacterial fitness and adaptability in microbial communities are influenced by interspecies interactions and spatial organization. This study investigated how these factors shape the evolutionary dynamics of Bacillus thuringiensis. A distinct phenotypic variant of B. thuringiensis emerged consistently under both planktonic and biofilm conditions, as well as in monospecies and mixed-species settings, but was strongly selected in biofilms and during coexistence with Pseudomonas defluvii and/ or Pseudomonas brenneri. Compared to its ancestor, the variant exhibited shorter generation times, reduced sporulation, auto-aggregation, and lower biomass in mixed-species biofilms. Mutations in the spo0A regulator, which controls sporulation and biofilm matrix production, were identified in all variants. Proteomics revealed a reduction in TasA, a key matrix protein, in the variant but increased levels in co-culture with P. brenneri. These findings highlight how interspecies interactions drive B. thuringiensis diversification, promoting traits like reduced matrix production and species coexistence, with implications for microbial consortia applications in agriculture and biopesticides.

microbiology↗

bioRxiv2023

Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans

Type IV-A CRISPR-Cas systems are primarily encoded on plasmids and form multi-subunit ribonucleoprotein complexes with unknown biological functions. In contrast to other CRISPR-Cas types, they lack the archetypical CRISPR acquisition module and encode a DinG helicase instead of a nuclease component. Type IV-A3 systems are carried by large conjugative plasmids that often harbor multiple antibiotic-resistance genes. Although their CRISPR array contents suggest a role in inter-plasmid conflicts, this function and the underlying mechanisms have remained unexplored. Here, we demonstrate that a plasmid-encoded type IV-A3 CRISPR-Cas system co-opts the type I-E adaptation machinery from its clinical Klebsiella pneumoniae host to update its CRISPR array. Furthermore, we demonstrate that robust interference of conjugative plasmids and phages is elicited through CRISPR RNA-dependent transcriptional repression. By targeting plasmid core functions, type IV-A3 can prevent the uptake of incoming plasmids, limit their horizontal transfer, and destabilize co-residing plasmids, altogether supporting type IV-A3s involvement in plasmid competition. Collectively, our findings shed light on the molecular mechanisms and ecological function of type IV-A3 systems and have broad implications for understanding and countering the spread of antibiotic resistance in clinically relevant strains.

microbiology↗

bioRxiv2022

An easily modifiable conjugative plasmid for studying horizontal gene transfer

Horizontal gene transfer is an important mechanism in bacterial evolution and can occur at striking frequencies when mediated by mobile genetic elements. Conjugative plasmids are mobile genetic elements that are main drivers of horizontal transfer and a major facilitator in the spread of antibiotic resistance genes. However, conjugative plasmid models that readily can be genetically modified with the aim to study horizontal transfer are not currently available. The aim of this study was to develop a conjugative plasmid model where the insertion of gene cassettes such as reporter genes (e.g., fluorescent proteins) or antibiotic resistance genes would be efficient and convenient. For that, we introduced a single attTn7 site into the conjugative broad-host-range IncP-1 plasmid pKJK5 in a non-disruptive manner. Furthermore, a version with lower transfer rate and a non-conjugative version of pKJK5-attTn7 were also constructed. The advantage of having the attTn7 sites is that genes of interest can be introduced in a single step with very high success rate using the Tn7 transposition system. In addition, larger genetic fragments can be inserted. To illustrate the efficacy of the constructed pKJK5 plasmids, they were complimented with sfgfp in addition to seven different {beta}-lactamase genes representing the four known classes of {beta}-lactamases.

evolutionary biology↗

bioRxiv2020

Snow Microbiome Functional Analyses Reveal Novel Microbial Metabolism of Complex Organic Compounds

Microbes active in extremely cold environments are not as well explored as those of other extreme environments. Studies have revealed a substantial microbial diversity and identified cold-specific microbiome molecular functions. We analyzed the metagenomes and metatranscriptomes of twenty snow samples collected during early and late spring in Svalbard, Norway using our computational read-based microbiome function annotation tool, mi-faser. Our results revealed a more diverse microbiome functional capacity and activity in the early compared to in the late spring samples. The dissimilarity between the metagenomes and metatranscriptomes of the same samples was also significantly higher in the early spring. These findings suggest that early spring samples may contain a larger fraction of DNA of dormant organisms, while late spring samples reflect a new community that is metabolically active. We additionally showed that the abundance of the sequencing reads mapping to the fatty acid synthesis-related microbial pathways was significantly positively correlated with organic acid levels, in both our late spring metagenomes and metatranscriptomes. Moreover, the geraniol degradation pathway and the styrene degradation pathway read abundances correlated and inversely correlated, respectively, with the organic acid levels. These results suggest a possible nutrient switch. Our study thus highlights the activity of microbial degradation pathways of complex organic compounds previously unreported at low temperatures.

bioinformatics↗

bioRxiv2019

Transcriptomic responses to warming and cooling of an Arctic tundra soil microbiome

BackgroundArctic surface soils experience pronounced seasonal changes in temperature and chemistry. However, it is unclear how these changes affect microbial degradation of organic matter, nitrogen cycling and microbial stress responses. We combined measurements of microbiome transcriptional activity, CO2 production, and pools of carbon and nitrogen to investigate the microbial response to warming in the laboratory, from -10 {degrees}C to 2 {degrees}C, and subsequent cooling, from 2 {degrees}C to -10 {degrees}C, of a high Arctic tundra soil from Svalbard, Norway.\n\nResultsGene expression was unaffected by warming from -10 {degrees}C to -2 {degrees}C and by cooling from -2 {degrees}C to -10 {degrees}C, while upon freezing (2 {degrees}C to -2 {degrees}C) a defense response against oxidative stress was observed. Following modest transcriptional changes one day after soil thaw, a more pronounced response was observed after 17 days, involving numerous functions dominated by an upregulation of genes involved in transcription, translation and chaperone activity. Transcripts related to carbohydrate metabolism and degradation of complex polymers (e.g. cellulose, hemicellulose and chitin) were also enhanced following 17 days of soil thaw, which was accompanied by a four-fold increase in CO2 production. In addition, anaerobic ammonium oxidation and turnover of organic nitrogen were upregulated. In contrast, nitrification, denitrification and assimilatory nitrate reduction were downregulated leading to an increase in the concentration of soil inorganic nitrogen.\n\nConclusionthe microorganisms showed negligible response to changes in sub-zero temperatures and a delayed response to thaw, which after 17 days led to upregulation of soil organic matter degradation and enhanced CO2 production, as well as downregulation of key pathways in nitrogen cycling and a concomitant accumulation of inorganic nitrogen available for plants.

microbiology↗