The legacy effect of cover crops on soil fungal populations in a cereal rotation

Detheridge, Andrew; Brand, Graham; Fychan, Rhun; Crotty, Felicity; Sanderson, Ruth; Griffith, Gareth; Marley, Christina L.

doi:10.1016/j.agee.2016.04.022

Cited by 119 publications

(67 citation statements)

References 74 publications

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“…Community composition in every OTU grouping shifted between spring and summer sampling times, including groupings not affected by cover crop species identity (i.e., Insect Pathogens and Abundant OTUs). Strong effects of season and/or time on fungal communities, especially AM fungi, from cover crop treatments have been observed elsewhere [34][35][36][37] . The two main disturbances that occurred between the spring and summer sampling events were the addition of bedded dairy manure and tillage.…”

Section: Discussionmentioning

confidence: 75%

“…Identifying suitable cover crops for a particular context is highly dependent on the goals of the farm manager, and the use of cover crop mixtures can provide multiple ecosystem services in a single growing season [6][7][8][9]65 . Not all cover crops will have similar impacts on soil microbes, e.g., some cover crops have been associated with increased AM fungal biomass and hyphal densities 15,36 , while others support increases in non-AM fungi 17,35,36 .…”

Section: Discussionmentioning

confidence: 99%

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Fungal community shifts in soils with varied cover crop treatments and edaphic properties

Cloutier

Murrell

Barbercheck

et al. 2020

Sci Rep

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Cover cropping is proposed to enhance soil microbial diversity and activity, with cover crop type affecting microbial groups in different ways. We compared fungal community compositions of bulk soils differing by cover crop treatment, season, and edaphic properties in the third year of an organic, conventionally tilled rotation of corn-soybean-wheat planted with winter cover crops. We used Illumina amplicon sequencing fungal assemblages to evaluate effects of nine treatments, each replicated four times, consisting of six single winter cover crop species, a three-species mixture, a six-species mixture, and fallow. Alpha-diversity of fungal communities was not affected by cover crop species identity, function, or diversity. Sampling season influenced community composition as well as genus-level abundances of arbuscular mycorrhizal (AM) fungi. Cover crop mixtures, specifically the three-species mixture, had distinct AM fungal community compositions, while cereal rye and forage radish monocultures had unique Core OTU compositions. Soil texture, pH, permanganate oxidizable carbon, and chemical properties including Cu, and P were important variables in models of fungal OTU distributions across groupings. These results showed how fungal composition and potential functions were shaped by cover crop treatment as well as soil heterogeneity.Microbial diversity is an important aspect of soil health, as soil microbial communities mediate many biogeochemical processes and are sensitive to disturbances that can lead to long-lasting ecosystem effects 1 . Greater richness and evenness in the representation of bacteria and fungi in soils can help mitigate plant responses to environmental stressors 2 . With the advent of high-throughput DNA sequencing technologies that allow for more detailed genetic information, we can determine if and how microbial compositions shift in response to disturbance and edaphic differences and, to some degree, what those changes may mean for ecosystem processes.Cover cropping is the practice of growing ground-covering crops during the intervals between successive cash crops. Cover cropping imparts numerous benefits to soil, including the addition of organic carbon (C) from roots, root exudates, and aboveground residues and the improvement of soil structure and tilth 3-5 . Ecosystem services provided by cover crops include protection from soil erosion, enhanced soil water-holding capacity, reduced weed colonization and growth, plant resilience to pathogens and increased crop yield 5,6 . Legume cover crops provide biologically fixed nitrogen (N), while grasses take up excess soil inorganic N and improve N retention. A complete suite of ecosystem services is not deliverable by any one cover crop species. Thus, planting mixtures of cover crops has been proposed as a means to provide varied combinations of ecosystem services based on the functional traits of individual cover crop species 5,7-10 .Cover crops may alter microbial community diversity and function by varying the types and composition of exuded C...

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Section: Discussionmentioning

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Fungal community shifts in soils with varied cover crop treatments and edaphic properties

Cloutier

Murrell

Barbercheck

et al. 2020

Sci Rep

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“…Rumen bacteria, methanogenic archaea and fungal communities were analysed using NGS DNA metabarcoding as previously described (Belanche et al, 2016a,b;Detheridge et al, 2016). For bacterial and methanogen sequencing, the amplification of the V1-V2 and the V2-V3 hypervariable regions of the 16S rRNA was performed, respectively, while for the fungi, the D1 variable region of the large (28S) subunit (LSU) of the rRNA locus was amplified.…”

Section: Next-generation Sequencingmentioning

confidence: 99%

Maternal versus artificial rearing shapes the rumen microbiome having minor long‐term physiological implications

Belanche

Yáñez-Ruíz

Detheridge

et al. 2019

Environmental Microbiology

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Summary Increasing productivity is a key target in ruminant science which requires better understanding of the rumen microbiota. This study investigated how maternal versus artificial rearing shapes the rumen microbiota using 24 sets of triplet lambs. Lambs within each sibling set were randomly assigned to natural rearing on the ewe (NN); ewe colostrum for 24 h followed by artificial milk feeding (NA); and colostrum alternative and artificial milk feeding (AA). Maternal colostrum feeding enhanced VFA production at weaning but not thereafter. At weaning, lambs reared on milk replacer had no rumen protozoa and lower microbial diversity, whereas natural rearing accelerated the rumen microbial development and facilitated the transition to solid diet. Differences in the rumen prokaryotic communities disappear later in life when all lambs were grouped on the same pasture up to 23 weeks of age. However, NN animals retained higher fungal diversity and abundances of Piromyces, Feramyces and Diplodiniinae protozoa as well as higher feed digestibility (+4%) and animal growth (+6.5%) during the grazing period. Nevertheless, no correlations were found between rumen microbiota and productive outcomes. These findings suggest that the early life nutritional intervention determine the initial rumen microbial community, but the persistence of these effects later in life is weak.

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“…For this reason, we refer to these sequences as belonging to root-associated communities throughout. Indeed, all of the fungal and bacterial families we detected (see below) are well-known to be tightly associated with plant roots [44][45][46][47] and belong to diverse ecological guilds, from symbionts to saprotrophs.…”

Section: Reconstructing the Root-associated Meta-transcriptome From Hmentioning

confidence: 96%

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota

et al. 2019

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Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early "omics" experiments focused mainly on the species composition of microbial communities, new "meta-omics" approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research. Author Contributions: Conceptualization, M.C. and P.B.; methodology, M.C. and S.G.; formal analysis, M.C.; investigation, M.C. and M.N.; data curation, M.C.; writing-original draft preparation, M.C. and P.B.; writing-review and editing, M.C., P.B., S.G., M.N., W.N.H. and L.L.; visualization, M.C.; funding acquisition, P.B., W.N.H. and L.L. All authors have read and agreed to the published version of the manuscript.

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The legacy effect of cover crops on soil fungal populations in a cereal rotation

Cited by 119 publications

References 74 publications

Fungal community shifts in soils with varied cover crop treatments and edaphic properties

Fungal community shifts in soils with varied cover crop treatments and edaphic properties

Maternal versus artificial rearing shapes the rumen microbiome having minor long‐term physiological implications

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota

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