Biology subjects

Dunfield, K. E.

Publications and source records attributed to Dunfield, K. E..

3 recordsLinked to original sources

bioRxiv2024

Complex responses of soil prokaryotes, fungi and protists to prairie restoration on retired agricultural lands

Restoring native ecosystems on marginal croplands has many benefits but the impacts on belowground biodiversity are less clear, in part because the limiting factors regulating soil biota are complex and poorly described. Here, we studied how grassland prairie restoration of marginal croplands affected the diversity and composition of soil microbiota on 5 conventional farms from Ontario, Canada. Soil samples (0-15 cm) were collected from annually cultivated fields and adjacent planted perennial grassland where cultivation and chemical inputs had ceased several years previously. Following DNA extraction, we estimated bacterial and fungal abundance using quantitative PCR, and microbial diversity of prokaryotes, fungi and protists using amplicon high-throughput sequencing. Under both land uses, prokaryotic communities were dominated by Proteobacteria, Actinobacteria and Acidobacteria, fungal communities by Ascomycota, and protist communities by Rhizaria (TSAR), Evosea (Amoebozoa) and Chlorophyta (Archaeplastida). Prairie restoration did not have a consistent effect on soil microbial abundance, richness or evenness, which responses varied across farms. Microbial genetic and taxonomic community composition (i.e., sequence variant and genus level) were affected by land use, farm and the interaction between these two factors. Generally, prairie soils had higher relative abundance of Latescibacterota, Desulfobacterota, Acidobacteriota and Glomeromycota, and lower of Deinococcota, Chytridiomycota and Amoebozoa_X. In terms of differentially abundant fungal genera, prairies promoted more fungal plant symbionts, less saprotrophs and no plant pathogens. Interkingdom networks revealed changes in potential microbe-microbe associations with prairie restoration, with only 8 associations in common between land uses. The relationship between soil microbial diversity and physicochemical properties varied across microbial groups, diversity metrics and land uses. Our results evidence the complexity associated with restoring soils from agricultural land to natural ecosystems, with unspecified farm-specific factors (e.g., soil type, prairie species, management history) strongly modulating the response of different microbial groups and variables.

microbiology↗

bioRxiv2022

Dynamics of methane cycling microbiome during methane flux hot moments from riparian buffer systems

Riparian buffer systems (RBS) are a common agroforestry practice that consists of keeping a forested boundary adjacent to water bodies in agricultural landscapes, thus helping to protect aquatic ecosystems from adverse impacts. Nevertheless, despite the multiple benefits they provide, RBSs can be hotspots of methane emissions since abundant organic carbon and high-water tables are often found in these soils. In southern Ontario, Canada, the rehabilitation of Washington Creeks streambank occurred in 1985. In a recent study, methane (CH4) fluxes were measured biweekly for two years (2017-2018) in four different vegetative riparian areas alongside Washington creek: a rehabilitated tree buffer (RH), a grassed buffer (GRB), an undisturbed deciduous forest (UNF), an undisturbed coniferous forest (CF), and an adjacent agricultural field (AGR) for comparison. Based on methane fluxes in 2018 and hot moments identified, we selected two dates from summer (July 04 and August 15) and use soil sampling from those days to assess the CH4 cycling microbial communities in these RBS. We used qPCR and high-throughput sequencing from both DNA and cDNA to measure the diversity and activity of the methanogen and methanotroph communities. Methanogens were abundant in all riparian soils, including the archaeal genera Methanosaeta, Methanosarcina, Methanomassiliicoccus Methanoreggula, but they were mostly active in UNF soils. Among methanotrophs, Methylocystis was the most abundant taxon in all the riparian sites, except for AGR soils where the methanotrophs community mostly comprised members of rice paddy clusters (RPCs and RPC-1) and upland soil clusters (TUSC and USC). In summary, these results indicate that differences in CH4 fluxes between RBS at Washington creek are influenced by differences in the presence and activity of methanogens, which were higher in the deciduous forest (UNF) soils during hot moments CH4 flux, likely due to high water content in that soils. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/517857v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1dcde21org.highwire.dtl.DTLVardef@17b59e5org.highwire.dtl.DTLVardef@14adfb0org.highwire.dtl.DTLVardef@a3b411_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

The biological sink of atmospheric H2 is more sensitive to spatial variation of microbial diversity than N2O and CO2 emissions in an agroecosystem

The relationship between soil microbial diversity and agroecosystem functioning is controversial due to the elevated diversity level and the functional redundancy of microorganisms. A field trial was established to test the hypothesis that enhanced crop diversity with the integration of winter cover crops (WCC) in a conventional maize-soy rotation promotes microbial diversity and the biological sink of H2 in soil, while reducing N2O emissions to the atmosphere. Vicia villosa (hairy vetch), Avena sativa (oat), and Raphanus sativus (Daikon radish) were cultivated alone or in combinations and flux measurements were performed throughout two subsequent growing seasons. Soil acted as a net sink for H2 and as a net source for CO2 and N2O. CO2 flux was the most sensitive to WCC whereas a significant spatial variation was observed for H2 flux with soil uptake rates observed in the most productive area two-fold greater than the baseline level. Sequencing and quantification of taxonomic and functional genes were integrated to explain variation in trace gas fluxes with compositional changes in soil microbial communities. Fungal communities were the most sensitive to WCC, but neither community abundance nor beta diversity were found to be indicative of fluxes. The alpha diversity of taxonomic and functional genes, expressed as the number of effective species, was integrated into composite variables extracted from multivariate analyses. Only the composite variable computed with the inverse Simpsons concentration index displayed a reproducible pattern throughout both growing seasons, with functional genes and bacterial 16S rRNA gene defining the two most contrasting gradients. The composite variable was decoupled from WCC treatment and explained 19-20% spatial variation of H2 fluxes. Sensitivity of the trace gas exchange process to soil properties at the local scale was inconsistent among H2, N2O and CO2, with the former being the most related to microbial diversity distribution pattern.

ecology↗