Toward more sustainable tropical agriculture with cover crops: Soil microbiome responses to nitrogen management

Cover crops are a potential pathway for ecological cultivation in agricultural systems. In tropical no-till agricultural systems, the maintenance of residues on the soil surface and the addition of nitrogen (N) benefit the growth and grain yield of cash crops as well as the chemical and physical properties of the soil. However, the effects of these management practices on the soil microbiota are largely unknown. Here, we evaluated the effects of the timing of N application as a pulse disturbance and the growth of different cover crop species before maize in rotation on soil properties, maize productivity, and soil bacterial and fungal community diversity and composition. N fertilizer was applied either on live cover crops (palisade grass or ruzigrass), on cover crop straw just before maize seeding or in the maize V4 growth stage. Soils previously cultivated with palisade grass established similar microbial communities regardless of N application timing, with increases in total bacteria, total archaea, nutrients, and the C:N ratio. The soil microbial alpha diversity in treatments with palisade grass did not vary with N application timing, whereas the bacterial and fungal diversities in the treatments with ruzigrass decreased when N was applied to live ruzigrass or maize in the V4 growth stage. We conclude that palisade grass is a more suitable cover crop than ruzigrass, as palisade grass enhanced soil microbial diversity and maize productivity regardless of N application timing. Ruzigrass could be used as an alternative to palisade grass when N is applied during the straw phase. However, considering the entire agricultural system (soil–plant–microbe), ruzigrass is not as efficient as palisade grass in tropical no-till cover crop–maize rotation systems. Palisade grass is a suitable cover crop alternative for enhancing maize productivity, soil chemical properties and nutrient cycling, regardless of the timing of N application. Additionally, this study demonstrates that a holistic approach is valuable for evaluating soil diversity and crop productivity in agricultural systems

Stem traits, compartments and tree species affect fungal communities on decaying wood

Dead wood quantity and quality is important for forest biodiversity, by determining wood-inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer- and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long-term carbon dynamics of dead trees

Rhizosphere microbiome response to host genetic variability: A trade-off between bacterial and fungal community assembly

Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae and Acidobacteriaceae, and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars

Responses of soil rare and abundant microorganisms to recurring biotic disturbances

Periodic inoculations of soil-beneficial microbes can increase their populations, but they also act as recurring biotic disturbances on the native microbial community. Soil rare and abundant microorganisms disproportionally shape the community diversity and stability. Uncovering their dynamic responses to recurring biotic disturbances and the underlying driving factors helps improve our understanding of the inoculation effects. Here, we imposed temporally recurring biotic disturbances by inoculating soils with phosphate-solubilizing bacteria, nitrogen-fixing bacteria, and the combination of both, with the overall aim of studying the successive responses of bacterial and fungal subcommunities along a rarity index. Our results showed that, in both bacterial and fungal communities, the relatively rare taxa exhibited higher diversity than the abundant taxa, and the relative abundance of rare taxa increased with recurring disturbances. However, the responses of rare and abundant taxa to inoculations were different between bacteria and fungi and were related to time and inoculation frequency. The rarer bacteria and the more abundant fungi explained most of the effects of inoculations on the resident microbial community. About 20 percent of the microbes changed their rarity categories over time, and most of the changes and interactions occurred within the rarer taxa during the first 45 days. Modeling analyses and co-occurrence networks indicated that microbial interactions, soil biochemical factors, and inoculation time drove the shifts of subcommunities. In summary, relatively rare bacteria and relatively abundant fungi play major roles in understanding the impacts of recurring biotic disturbances, while the conditionality of microbial rarity is dependent on both biotic and abiotic factors

Responses of soil rare and abundant microorganisms to recurring biotic disturbances

Periodic inoculations of soil-beneficial microbes can increase their populations, but they also act as recurring biotic disturbances on the native microbial community. Soil rare and abundant microorganisms disproportionally shape the community diversity and stability. Uncovering their dynamic responses to recurring biotic disturbances and the underlying driving factors helps improve our understanding of the inoculation effects. Here, we imposed temporally recurring biotic disturbances by inoculating soils with phosphate-solubilizing bacteria, nitrogen-fixing bacteria, and the combination of both, with the overall aim of studying the successive responses of bacterial and fungal subcommunities along a rarity index. Our results showed that, in both bacterial and fungal communities, the relatively rare taxa exhibited higher diversity than the abundant taxa, and the relative abundance of rare taxa increased with recurring disturbances. However, the responses of rare and abundant taxa to inoculations were different between bacteria and fungi and were related to time and inoculation frequency. The rarer bacteria and the more abundant fungi explained most of the effects of inoculations on the resident microbial community. About 20 percent of the microbes changed their rarity categories over time, and most of the changes and interactions occurred within the rarer taxa during the first 45 days. Modeling analyses and co-occurrence networks indicated that microbial interactions, soil biochemical factors, and inoculation time drove the shifts of subcommunities. In summary, relatively rare bacteria and relatively abundant fungi play major roles in understanding the impacts of recurring biotic disturbances, while the conditionality of microbial rarity is dependent on both biotic and abiotic factors

Forage Grasses Steer Soil Nitrogen Processes, Microbial Populations, and Microbiome Composition in A Long-term Tropical Agriculture System

Forage grasses used in cropping no-till systems in tropical regions alter soil chemical properties, but their long-term impact on soil microbial processes of the nitrogen (N) cycle and microbial community abundance, composition and structure are unknown. Here, microbial functions related to nitrogen fixation, nitrification and denitrification as well as bacterial, archaeal and fungal populations were evaluated in a long-term field experiment in which tropical forage grasses palisade grass (Urochloa brizantha (Hochst. Ex A. Rich.) R.D. Webster) and ruzigrass (U. ruziziensis (R. Germ. and C.M. Evrard) Crins) were cultivated with or without N fertilization. Uncultivated soil was used as a control. Forage grasses, especially palisade grass, increased soil bacterial and fungal abundances, whereas the archaeal population was highest in uncultivated soil. In soils cultivated with forage grasses, N fertilization favored N-cycle-related genes; however, cultivation of palisade grass increased the abundances of amoA bacteria (AOB) and amoA archaea (AOA) genes associated with soil nitrification and decreased the abundances of genes nirS, nirK and nosZ genes related to denitrification, compared to ruzigrass and control, regardless of N input. In addition, abundances of total bacteria and total fungi were associated with the N cycle and plant biomass in soils cultivated with forage grasses. Forage cultivation clearly benefitted the soil nutrient environment (S-SO42-, Mg2+, total-C and -N, N-NO3- and N-NH4+) and microbiome (bacteria and fungi) compared with uncultivated soil. In soil cultivated with palisade grass, the microbial community composition was unresponsive to N addition. The high N uptake by palisade grass supports the competitive advantage of this plant species over microorganisms for N sources. Our results suggest that palisade grass has advantages over ruzigrass for use in agriculture systems, regardless of N input

Rhizosphere microbiome response to host genetic variability: A trade-off between bacterial and fungal community assembly

Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae and Acidobacteriaceae, and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars

Extracting the GEMs: Genotype, Environment, and Microbiome Interactions Shaping Host Phenotypes

One of the fundamental tenets of biology is that the phenotype of an organism (Y) is determined by its genotype (G), the environment (E), and their interaction (GE). Quantitative phenotypes can then be modeled as Y = G + E + GE + e, where e is the biological variance. This simple and tractable model has long served as the basis for studies investigating the heritability of traits and decomposing the variability in fitness. The importance and contribution of microbe interactions to a given host phenotype is largely unclear, nor how this relates to the traditional GE model. Here we address this fundamental question and propose an expansion of the original model, referred to as GEM, which explicitly incorporates the contribution of the microbiome (M) to the host phenotype, while maintaining the simplicity and tractability of the original GE model. We show that by keeping host, environment, and microbiome as separate but interacting variables, the GEM model can capture the nuanced ecological interactions between these variables. Finally, we demonstrate with an in vitro experiment how the GEM model can be used to statistically disentangle the relative contributions of each component on specific host phenotypes.</p

Responses of soil rare and abundant microorganisms to recurring biotic disturbances

Periodic inoculations of soil-beneficial microbes can increase their populations, but they also act as recurring biotic disturbances on the native microbial community. Soil rare and abundant microorganisms disproportionally shape the community diversity and stability. Uncovering their dynamic responses to recurring biotic disturbances and the underlying driving factors helps improve our understanding of the inoculation effects. Here, we imposed temporally recurring biotic disturbances by inoculating soils with phosphate-solubilizing bacteria, nitrogen-fixing bacteria, and the combination of both, with the overall aim of studying the successive responses of bacterial and fungal subcommunities along a rarity index. Our results showed that, in both bacterial and fungal communities, the relatively rare taxa exhibited higher diversity than the abundant taxa, and the relative abundance of rare taxa increased with recurring disturbances. However, the responses of rare and abundant taxa to inoculations were different between bacteria and fungi and were related to time and inoculation frequency. The rarer bacteria and the more abundant fungi explained most of the effects of inoculations on the resident microbial community. About 20 percent of the microbes changed their rarity categories over time, and most of the changes and interactions occurred within the rarer taxa during the first 45 days. Modeling analyses and co-occurrence networks indicated that microbial interactions, soil biochemical factors, and inoculation time drove the shifts of subcommunities. In summary, relatively rare bacteria and relatively abundant fungi play major roles in understanding the impacts of recurring biotic disturbances, while the conditionality of microbial rarity is dependent on both biotic and abiotic factors