Microbial Functional Properties Research Articles

Microbial functioning in Mediterranean forest soils: Does land use legacy matter?

AbstractLand use is known to be one of the major factors driving soil microbial and physico‐chemical properties. Understanding its long‐term effect remains a major challenge in assessing current soil functioning. Here, soil microbial and physico‐chemical properties of recent and very recent forests (forests developed in 1958 vs. after 1958) were compared with those of ancient forests (present in 1860 and 1958) to assess the effect of Land Use Legacy (LUL). LUL effects were further analysed depending on contrasting (i) climate conditions (sub‐humid vs. humid Mediterranean climates) and (ii) seasons (winter and summer), to examine whether LUL modified microbial responses to different spatio‐temporal climate conditions. Microbial indicators (lignocellulolytic activities, basal respiration, and microbial biomass) and physico‐chemical properties (C and N contents, mineralogical analyses, pH and conductivity) were assessed. A strong effect of past agricultural practice (terrace cultivation) was observed in soils from very recent forests: reduced microbial biomass and activities as well as number of Quercus pubescens stems together with increased phosphorous content and pH. Interestingly, LUL effect did not affect microbial and physico‐chemical responses to seasonal contrasts (winter vs. summer). Microbial response to LUL was not influenced by climate while climate modified LUL effects on some physico‐chemical properties (CaCO3, Corg, and K content). Moreover, soil recovered “pristine” physico‐chemical and microbial functional properties after at least 60 years of reforestation.

Use of metagenomics and metabolomics to quantify changes in rhizosphere soil microbial function in response to mulching regimes

AbstractThe effects of distinct mulching regimes on the microbial functional properties and metabolic profiles of rhizosphere soil remain largely unknown. Here, we conducted metagenomic and metabolomic analyses to explore the microbial functional specificity and metabolic pathways under three mulching regimes, namely, traditional flat planting with non‐mulch (TP), ridge‐furrow plastic film mulching (RF), and plastic film mulching (PFM). Compared to TP treatment, RF and PFM treatments significantly improved the soil temperature and moisture content, stimulated the increase of five extracellular enzyme activities, thereby reducing soil nutrient content (soil pH, total N, soil organic carbon, NH4+‐N, and NO3−‐N) to meet crop demand for nutrients. In addition, RF treatment significantly decreased the relative abundance of nxrA, while increasing the relative abundance of nasA, thereby further decreasing NO3−‐N content. However, RF and PFM treatments had no significant effect on the relative abundance of nirB, nirD, nrfA, and nrfH. Meanwhile, PFM and RF treatment stimulated the increase of extracellular enzyme activities accelerated microbial metabolism, thereby promoting the synthesis of metabolites involved in carbohydrate metabolism, lipid metabolism, nucleotide metabolism, and amino acid metabolism. Metabolomics and network analyses revealed that RF and PFM treatments not only enriched organoheterocyclic compounds, organic acids and derivatives, lipids and lipid‐like molecules, and organic oxygen compounds but also increased their relative abundance in the major modules. Overall, this study provides deep insights into how mulching regimes alter soil microbial functional potential and metabolic profiles, which may have predictable impacts on the rhizosphere soil nutrient cycling of agroecosystems under mulching systems in semiarid regions.

Microbial community diversity in the soil of Barrientos Island estimated by RAPD and Biolog Ecoplate methods

The diversity of soil microbial communities at Barrientos Island with differents soil characteristics were evaluated using PCR-based method random amplified polymorphic DNA (RAPD) and community level physiological profiles (CLPP) of Biolog Ecoplate. The soils were selected from 17 different locations around Barrientos Island inhabited by different breeders. Shannon-Weaver index and multivariate analysis were performed to characterize variations of soil microbial communities. Both RAPD and CLPP methods exhibited that most soils with different type of rookery and characteristics could possibly affect the DNA sequence diversity and soil microbial diversity. The abandoned type of rookery had the highest Shannon-Weaver index as exhibited by soil sample 445 (3.4 for RAPD) and 450 (3.09 for CLPP). Higher coefficients of DNA sequence similarity were found in soil samples colonized by similar breeders, like soil 442 and 446 (both were active Chinstrap rookery) shared highest similarity in DNA sequences (73.53). The cluster analysis of RAPD profiles by UPGMA and principle component analysis (PCA) of Biolog Ecoplate exhibited similar influence of type of rookery and soil condition towards soil microbial community diversity. The results may suggest that the change in microbial community DNA composition is accompanied with the change in microbial functional properties.

Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire

Despite a well-documented effect of high dietary zinc oxide on the pig intestinal microbiota composition less is it yet known about changes in microbial functional properties or the effect of organic zinc sources. Forty weaning piglets in four groups were fed diets supplemented with 40 or 110 ppm zinc as zinc oxide, 110 ppm as Zn-Lysinate, or 2500 ppm as zinc oxide. Host zinc homeostasis, intestinal zinc fractions, and ileal nutrient digestibility were determined as main nutritional and physiological factors putatively driving colon microbial ecology. Metagenomic sequencing of colon microbiota revealed only clear differences at genus level for the group receiving 2500 ppm zinc oxide. However, a clear group differentiation according to dietary zinc concentration and source was observed at species level. Functional analysis revealed significant differences in genes related to stress response, mineral, and carbohydrate metabolism. Taxonomic and functional gene differences were accompanied with clear effects in microbial metabolite concentration. Finally, a selection of certain antibiotic resistance genes by dietary zinc was observed. This study sheds further light onto the consequences of concentration and chemical form of dietary zinc on microbial ecology measures and the resistome in the porcine colon.

Endophytic Microbial Community DNA Extraction from the Plant Phyllosphere.

The plant phyllosphere, which represents all plant parts that are above the ground, is considered one of the most extensive ecosystems to be colonized by microorganisms, both at the surface as epiphytes or as endophytes within the plant. These plant-associated microbial communities are reservoirs of microbial diversity and they can be important for plant health. The characterization of microbial communities in diverse plants, such as Espeletia plants that are endemic to the Paramo ecosystem in the Andes Mountains, can shed light regarding possible interactions among microorganisms and microbial functional properties. Obtaining DNA from plant endophytic microbial communities involves various steps to ensure that samples are free of contamination from microorganisms present on the plant surface (epiphytes). Plant leaves are first surface sterilized, cut into pieces, homogenized using glass beads, and then used for DNA extraction using a commercially available kit. DNA samples are then quantified and analyzed using Qubit® 2.0 for use in PCR amplification of 16S rRNA genes.

Relative contributions of plant traits and soil microbial properties to mountain grassland ecosystem services

SummaryPlant functional diversity and soil microbial community composition are tightly coupled. Changes in these interactions may influence ecosystem functioning. Links between plant functional diversity, soil microbial communities and ecosystem functioning have been demonstrated in experiments using plant monocultures and mixtures, using broad plant and microbial functional groups, but have not been examined in diverse natural plant communities.We quantified the relative effects of plant and microbial functional properties on key ecosystem functions. We measured plant functional diversity, soil microbial community composition and parameters associated with nitrogen (N) cycling and key nutrient cycling processes at three grassland sites in different parts of Europe. Because plant structure and function strongly influence soil microbial communities, we determined relationships between ecosystem properties, plant traits and soil community characteristics following a sequential approach in which plant traits were fitted first, followed by the additional effects of soil micro‐organisms.We identified a continuum from standing green biomass and standing litter, linked mostly with plant traits, to potentialNmineralization and potential leaching of soil inorganicN, linked mostly with microbial properties. Plant and microbial functional parameters were equally important in explaining % organic matter content in soil. A parallel continuum ran from plant height, linked with above‐ground biomass, to plant quality effects captured by the leaf economics spectrum, which were linked with the recycling of carbon (C) andN.More exploitative species (higher specific leaf area, leafNconcentrations and lower leaf dry matter content) and taller swards, along with soil microbial communities dominated by bacteria, with rapid microbial activities, were linked with greater fodder production, but poorCandNretention. Conversely, dominance by conservative species (with opposite traits) and soil microbial communities dominated by fungi, and bacteria with slow activities, were usually linked with low production, but greater soilCstorage andNretention.Synthesis– Grassland production,Csequestration and soilNretention are jointly related to plant and microbial functional traits. Managing grasslands for selected, or multiple, ecosystem services will thus require a consideration of the joint effects of plant and soil communities. Further understanding of the mechanisms that link plant and microbial functional traits is essential to achieve this.