Biology subjects

Picot, E.

Publications and source records attributed to Picot, E..

3 recordsLinked to original sources

bioRxiv2025

Rapid Assembly and Functional Differentiation of the Soil Surface Microbiome in Temperate Agricultural soil

The surface of dryland soils is typically covered by biological soil crusts (BSC) dominated by cyanobacteria, lichens or moss which contribute key ecosystem functions. However, while photosynthetic biota have been observed on the surface of temperate agricultural soils, understanding of the development, biodiversity and functional significance of these communities is extremely limited. We investigated the temporal development of the soil surface community following tillage and during subsequent growth of a wheat crop. Amplicon analysis showed that establishment of the soil surface microbiome was rapid over the winter period, with distinct communities of phototrophs, bacteria and protists detected 60 days after tillage. There was rapid succession with yellow-green algae (Xanthophyceae) dominating early stages of development, followed by Cyanobacteria and Charophytes and finally moss. Temporal dynamics of fungal and protist communities was influenced by eDNA deposition from plant pathogens inhabiting the crop canopy and wild animal parasites. For all groups, assembly processes in the surface soil became increasingly dominated by dispersal limitation over time while assembly of bulk soil communities became predominantly influenced by drift. Metagenome analysis showed that the soil surface had developed a distinct functional profile relative to bulk soil after 9 months, enriched in photosynthetic processes which were largely from eukaryotic algae rather than cyanobacteria. Additionally the 3-Hydroxypropionate bicycle and reductive TCA carbon fixation pathways were enriched in surface soil. The abundance of genes involved in heterotrophic carbon, nitrogen, phosphorus and sulphur cycling processes were also enriched in surface soil. This included reads of carbohydrate active enzymes, nitrification, denitrification and sulphate reduction genes, largely attributed to the enrichment of Actinobacteria, Bacteroidetes and Proteobacteria in the soil surface. Overall, we show overlap in dominant phototrophic taxa between temperate agricultural and BSC in arid soils, but with notable differences, including abundance of Xanthphycae and Charophytes. Furthermore, the functional signatures of the soil surface communities indicate that they may play an important role in the delivery of ecosystem functions in temperate agricultural systems.

microbiology↗

bioRxiv2021

The plant circadian clock gene LHY influences Medicago truncatula nodulation

Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which are factories of metabolic activity. We discovered that the circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY) affects nodulation in Medicago truncatula. By carrying out expression analysis of transcripts over time in nodules we found that the clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. Rhythmic transcripts in root nodules include a subset of Nodule-specific Cysteine Rich peptides (NCRs) that have the LHY-bound conserved Evening Element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis. HighlightsO_LIThe circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY) impacts on successful Medicago truncatula-rhizobial symbiosis C_LIO_LIThe plant clock coordinates rhythmic patterns of metabolic and regulatory activity in nodules and drives rhythmic expression of a subset of Nodule-specific Cysteine Rich (NCR) genes. C_LIO_LIRhythmic expression of NCRs may be important for temporal coordination of bacterial activity with plant host rhythms to ensure optimal symbiosis. C_LI

plant biology↗

bioRxiv2021

Tree phyllospheres are a habitat for diverse populations of CO-oxidising bacteria

BackgroundCarbon monoxide (CO) is a naturally occurring and ubiquitous trace gas in the atmosphere. As a product of combustion processes, it can reach concentrations in the mg/m3 range in urban areas, contributing to air pollution. Aerobic CO-degrading microorganisms have been identified previously and are thought to remove ~370 Tg of CO in soils and oceans per year. Based on the presence of genes encoding subunits of the enzyme carbon monoxide dehydrogenase in metagenomes, a large fraction of soil bacteria may have the potential for CO degradation. The activity and diversity of CO-degrading microorganisms in above ground habitats such as the phyllosphere has not been addressed, however, and their potential role in global CO cycling remains unknown. ResultsMonitoring of CO-degradation in leaf washes of two common British trees, Ilex aquifolium and Crataegus monogyna, demonstrated CO uptake in all samples investigated. Leaf washes of I. aquifolium had significantly higher CO oxidation rates than those of C. monogyna. A diverse range of bacterial taxa were identified as candidate CO-oxidising taxa based on high-throughput sequencing and multivariate statistical analysis of 16S rRNA amplicon data, as well as functional diversity analysis based on coxL, the gene encoding the large subunit of CO-dehydrogenase. Candidate CO-oxidising taxa included a range of Rhizobiales and Burkholderiales, of which the Burkholderiales OTUs were abundant colonisers of the phyllosphere at the time of sampling, as indicated by 16S rRNA gene sequencing. In addition, an estimated 12.4% of leaf OTUs in samples of this study contained coxL homologues, based on their predicted genomes. We also mined data of publicly available phyllosphere metagenomes for genes encoding subunits of CO-dehydrogenase which indicated that, on average, 25% of phyllosphere bacteria contained CO-dehydrogenase gene homologues. A CO-oxidising Phyllobacteriaceae strain was isolated from phyllosphere samples which contains genes encoding both CODH as well as a RuBisCO. ConclusionsThe phyllosphere, a vast microbial habitat, supports diverse and potentially abundant CO-oxidising bacteria. These findings identify tree phyllosphere bacteria as a potential sink for atmospheric CO and highlight the need for a more detailed assessment of phyllosphere microbial communities in the global cycle of CO.

microbiology↗