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Biology subjects

Bonito, G.

Publications and source records attributed to Bonito, G..

3 recordsLinked to original sources

Biochar alters soil properties, microbial community diversity, and enzyme activities, while decreasing conifer performance

Biochars are porous charcoal-like materials that can enhance soil health and plant growth, but its use has not been adequately evaluated in woody cropping systems. We set up an experimental Christmas tree plantation on a Marlette series soil amended with two types of biochar and conducted two studies on the impacts of biochar on the agroecosystem over three years following establishment. The first study investigated the effects of biochar on plant performance, soil physicochemical properties and extracellular enzyme activities, while the second investigated the response of the root-associated fungal community. Both biochars stimulated five extracellular enzyme activities, with increases of between 67% and 446%. Structural equation modelling identified increases to dissolved organic carbon and soil moisture as potential mechanisms of biochars effects on enzyme activities. Tree growth and survival were negatively affected by biochar application, depending on the tree species and biochar applied, which may have been due to induced nitrogen limitation. High-throughput sequencing showed that biochar decreased the diversity of root-associated fungal communities, with the ectomycorrhizal species Wilcoxina mikolae reaching levels of hyper-dominance on balsam fir in response to one of the biochars. Further studies should investigate how biochar can be harnessed to remediate specific soil quality issues or restructure soil ecosystems in ways that improve crop performance.

ecology

Host genetic control of succession in the switchgrass leaf fungal microbiome

Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass (Panicum virgatum). We also sampled a replicated subset of genotypes across three additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association mapping and RNA-sequencing to show that three cysteine-rich receptor-like kinases were linked to a genetic locus associated with microbiome structure. These genes were more highly expressed in genotypes susceptible to fungal pathogens, which were central to microbial covariance networks, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome.

ecology

CONSTAX2: Improved taxonomic classification of environmental DNA markers

CONSTAX - the CONSensus TAXonomy classifier - was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicons and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 can be used to classify prokaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable, command line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases, new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability and ImplementationCONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/.

bioinformatics