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74 results for “soil microbe”
Assessing the role of soil microbes in the dynamics of P release from poorly soluble P forms
<p>Dataset and script used for the publication <em>Assessing the role of soil microbes in the dynamics of P release from poorly soluble P forms, </em>doi (to be determined).</p>
Nitrogen addition alters plant competition directly more than indirectly through soil microbes.
Eutrophication, the excessive addition of nutrients to ecosystems, is a pervasive component of global environmental change that can alter community dynamics. Although nitrogen addition experiments have widely documented important declines in plant diversity and shifts in plant species composition, the underlying causes of these outcomes are widely debated. Nitrogen inputs may directly affect plant competition for light or soil water or may influence plant species indirectly by altering the composition of soil microbes. In a 28-year field nitrogen addition experiment, we tested whether nitrogen-induced changes to soil microbes could indirectly alter the outcome of competition between codominant foundation plant species. In the field, long-term addition of inorganic nitrogen slowed the competitive take-over of blue grama grass (Bouteloua gracilis) by black grama grass (B. eriopoda) and thereby stabilized the ecotone between two grassland ecosystems in central New Mexico, USA.
Deschampsia biomass, soil microbes and endophyte root colonization for snowmelt and microbial innoculation transplant experiment in the Green Lakes Valley, 2015-2018
As organisms shift their geographic distributions in response to climate change, biotic interactions have emerged as an important factor driving the rate and success of range expansions. Plant-microbe interactions are an understudied but potentially important factor governing plant range shifts. We studied the distribution and function of microbes present in high-elevation unvegetated soils, areas that plants are colonizing as climate warms, snow melts earlier and the summer growing season lengthens. Using a manipulative snowpack and microbial inoculation transplant experiment, we tested the hypothesis that growing season length and microbial community composition interact to control plant elevational range shifts. We predicted that a lengthening growing season combined with dispersal to patches of soils with more mutualistic microbes and fewer pathogenic microbes would facilitate plant survival and growth in previously unvegetated areas. We identified negative effects on survival of the common alpine bunchgrass Deschampsia cespitosa in both short and long growing seasons, suggesting an optimal growing season length for plant survival in this system that balances time for growth with soil moisture levels. Importantly, growing season length and microbes interacted to affect plant survival and growth, such that microbial community composition increased in importance in suboptimal growing season lengths. Further, plants grown with microbes from unvegetated soils grew as well or better than plants grown with microbes from vegetated soils. These results suggest that the rate and spatial extent of plant colonization of unvegetated soils in mountainous areas experiencing climate change could depend on both growing season length and soil microbial community composition, with microbes potentially playing more important roles as growing seasons lengthen.
NEON Biorepository Soil Microbe Collection (Bulk Subsamples) (repackaging of occurrences published by the NEON Biorepository Data Portal)
This collection contains samples collected during periodic soil sampling and frozen at ultra-low temperatures in order to provide material for microbial sequencing or other microbial analyses (NEON sample classes: sls_soilCoreCollection_in.geneticArchiveSample1ID, sls_soilCoreCollection_in.geneticArchiveSample2ID, sls_soilCoreCollection_in.geneticArchiveSample3ID, sls_soilCoreCollection_in.geneticArchiveSample4ID, sls_soilCoreCollection_in.geneticArchiveSample5ID,sls_metagenomicsPooling_in.compositeSampleID). Archive samples are collected during each soil sampling bout and are promptly frozen. Three unique locations are sampled per plot, with ten plots per site. Bouts occur three times per year in order to capture the prevailing conditions at the site during different seasons, except in Alaska where only 1 bout is possible. Soil sampling is conducted to a maximum depth of 30 ± 1 cm, and when organic (O) and mineral (M) horizons are present within a single profile, they are separated prior to analysis and archiving. However, other sub-horizons are not separated. During the majority of bouts, only the top horizon (O if present, else M) is collected and archived. Soils are homogenized and non-soil material is removed by hand in the field, then subsamples are immediately frozen on dry ice. They are maintained in ultra-low temperature freezers until shipment to the Biorepository. See links below for NEON data products that provide physical, chemical, and biological measurements for these same soils (soil pH and moisture are always measured; chemical properties as well as microbial community composition and biomass are determined only for a subset of collection bouts). In addition, a more detailed characterization of the dominant soil types at each site, including taxonomy, texture, bulk density, and geochemical properties, occurred during the construction period of NEON through two projects. These data are available in NEON data products Soil physical and chemical
NEON Biorepository Soil Microbe Collection (DNA Extracts ) (repackaging of occurrences published by the NEON Biorepository Data Portal)
This collection contains genetic extracts from soil microbes collected during periodic soil sampling at NEON terrestrial sites (NEON sample class: mic_dnaExtraction_in.soilDnaSampleID). Three unique locations are sampled per plot with ten soil plots per site. Bouts occur three times per year in order to capture the prevailing conditions at the site during different seasons, except in Alaska where there only 1 bout is possible. However, the frequency of genetic analysis and thus DNA archiving varies by site type. Soil sampling is conducted to a maximum depth of 30 ± 1 cm, and when organic (O) and mineral (M) horizons are present within a single profile, they are separated prior to analysis and archiving. However, other sub-horizons are not separated. During the majority of bouts, only the top horizon (O if present, else M) is analyzed for genetic content. Soils are homogenized and non-soil material is removed by hand in the field, then subsamples are immediately frozen on dry ice. They are maintained in ultra-low temperature freezers until they are shipped to an analytical facility for DNA extraction, sample preparation and sequencing. During peak greenness bouts, subsamples from each of the 3 sampling locations per plot are combined to form a plot-level composite that is used for metagenomics analysis. Laboratory metadata are delivered to NEON for QC testing and acceptance, and then formatted for upload to public sequence repositories. Genetic extracts are shipped from the analytical facility in 96-well plates to the NEON Biorepository to be archived at -80 degrees Celsius. See links below for NEON data products that provide physical, chemical, and biological measurements for these same soils (soil pH, moisture, and microbial properties are always measured; chemical properties are determined only for a subset of collection bouts). The metabarcoding protocol used by Battelle Applied Genomics is available in the NEON document library (https://data.neonscience.org/docu
scmcclelland/joint-mediation-study: Data, Analysis, and Figure Scripts for "Soil organic carbon sequestration jointly-mediated by plants and microbes after compost application"
<p>This repository contains data, analysis, and figure scripts to create findings from the manuscript "Soil organic carbon sequestration jointly-mediated by plants and microbes after compost application" currently under minor revisions.</p> <p>This release includes updated code, primarily improvements to figures, and a new script for a supplementary map figure.</p>
Data from: Soil microbes influence the ecology and evolution of plant plasticity
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Data for Lynn et al. “Soil microbes that may accompany climate warming increase alpine plant production”; accepted at Oecologia
Climate change is causing species with non-overlapping ranges to come in contact, and a key challenge is to predict the consequences of such species re-shuffling. Experiments on plants have focused largely on novel competitive interactions; other species interactions, such as plant-microbe symbioses, while less studied, may also influence plant responses to climate change. In this greenhouse study, we evaluated interactions between soil microbes and alpine-restricted plant species, simulating a warming scenario in which low elevation microbes migrate upslope into the distribution of alpine plants. We examined three alpine grasses from the Rocky Mountains, CO, USA (Poa alpina, Festuca brachyphylla, Elymus scribneri). We used soil inocula from within (resident) or below (novel) the plants' current elevation range and examined responses in plant biomass, plant traits, and fungal colonization of roots. Resident soil inocula from the species' home range decreased biomass to a greater extent than novel soil inocula. The depressed growth in resident soils suggested these soils harbor more carbon-demanding microbes, as plant biomass generally declined with greater fungal colonization of roots, especially in resident soil inocula. Although plant traits did not respond to the provenance of soil inocula, specific leaf area declined and root:shoot ratio increased when soil inocula were sterilized, indicating microbial mediation of plant trait expression. Contrary to current predictions, our findings suggest that if upwardly migrating microbes were to displace current soil microbes, alpine plants may benefit from this warming-induced microbial re-shuffling.
Data from: Plant-soil microbe feedbacks depend on distance and ploidy in a mixed cytotype population of Larrea tridentata
<p><strong>Premise of the study</strong></p> <p>Theory predicts that mixed ploidy populations should be short-lived due to strong fitness disadvantages for the rare ploidy. However, mixed ploidy populations are common, suggesting that the fitness costs for rare ploidies are counterbalanced by ecological benefits that emerge when rare. We investigated whether differences in ecological interactions with soil microbes help to maintain a tetraploid-hexaploid population of <em>Larrea tridentata </em>(creosote bush) in the Sonoran Desert, California, USA, where prior work documented ploidy-specific root-associated microbes.</p> <p><strong>Methods</strong></p> <p>We used a plant-soil feedback (PSF) experiment to test whether host-specific soil microbes can alter the outcomes of intra-ploidy vs. inter-ploidy competition. Host-specific soil microbes can build up over time; thus, distance from a host plant can affect the fitness of nearby plants.</p> <p><strong>Key results</strong></p> <p>Seedlings grown in soils from near plants of a different ploidy produced greater biomass relative to seedlings grown in soils from near plants of the same ploidy. Moreover, seedlings grown in soils from near plants of a different ploidy produced greater biomass than those grown in soils from further away from plants of a different ploidy. This suggests the ecological consequences of PSF may facilitate the persistence of mixed ploidy populations.</p> <p><strong>Conclusions</strong></p> <p>This is the first evidence, to our knowledge, consistent with plant-soil microbe feedback as a viable mechanism to maintain the coexistence of multiple ploidy levels in a single population.</p>
Interactions between soil microbes and native species drive a diversity-invasibility relationship
<p>Soil microbes can affect both the invasiveness of exotic plants and the invasibility of native plant communities, but it still remains unclear whether soil microbes can influence the relationship between native plant species diversity and community invasibility. We constructed native plant communities with three levels of species richness (one, three, or six species) in un-sterilized or sterilized soil (i.e., with or without soil microbes) and let them not be invaded by exotic plant species or invaded by one of three exotic species (<em>Solidago canadensis</em>, <em>Erigeron canadensis</em> or <em>Symphyotrichum subulatum</em>) highly invasive in China. The soils conditioned by the native plant communities not invaded by the exotic species were used as soil microbe inocula to test whether richness-induced differences in soil microbes affect the growth of each of the three invasive species. Compared with the presence of soil microbes, the absence of soil microbes weakened the negative species richness-invasibility relationship, indicating that soil microbes can contribute to the higher invasion resistance of more diverse native plant communities. In the presence of soil microbes, the higher invasion resistance of more diverse communities was mainly ascribed to the complementarity effect. However, soil microbes from communities with a higher species richness did not have a stronger negative effect on the growth of any of the three invasive species. We conclude that soil microbes can alter the diversity-invasibility relationship through promoting the complementarity effect on the community invasion resistance. Our results highlight the importance to integrate the role of soil microbes in testing the diversity-invasibility hypothesis.</p>
Soil microbes respond to four-year warming and precipitation alteration
<p><span>The alpine grasslands of the Tibetan Plateau store 23.2 Pg soil organic carbon (SOC), which becomes susceptible to microbial degradation with climate warming. However, accurate prediction of how the soil carbon (C) stock changes under future climate warming is hampered by our limited understanding of below-ground complex microbial communities. Here, we show that 4 years of warming strongly stimulated methane (CH<sub>4</sub>) uptake by 93.8% and aerobic respiration (CO<sub>2</sub>) by % in the soils of alpine grassland ecosystem. Due to no significant effects of warming on net ecosystem CO<sub>2</sub> exchange (NEE), the warming-stimulated CH<sub>4</sub> uptake enlarged the carbon sink capacity of whole ecosystem. Furthermore, precipitation alternation didn't alter such warming effects, despite the significant effects of precipitation on NEE and soil CH<sub>4</sub> flux</span><span><span>es</span><span> were observed. Metagenomic sequencing revealed that </span></span><span>warming led to significant shifts in the overall microbial community structure and the abundances of functional genes, which contrasted to no detectable changes after 2 years of warming. Carbohydrate utilization genes were significantly increased by warming, corresponding with significant increases in soil aerobic respiration. Increased methanotrophic genes and decreased methanogenic genes were observed under warming, which significantly (<em>R<sup>2</sup> </em>= 0.59, <em>P</em> < 0.001) correlated with warming-enhanced CH<sub>4</sub> uptakes. Furthermore, 212 metagenome-assembled genomes (MAGs) were recovered, including many populations involved in the degradation of various organic matter and a highly-abundant methylotrophic population of the <em>Methyloceanibacter</em> genus. Collectively, our results provide compelling evidence that specific microbial functional traits for CH<sub>4 </sub>and CO<sub>2</sub> cycling processes respond to climate warming with differential effects on soil greenhouse gas emissions. Alpine grasslands may play huge roles in mitigating climate warming through such microbially-enhanced CH<sub>4</sub> uptake.</span></p>
Competition mode and soil nutrient status shape the role of soil microbes in the diversity–invasibility relationship
<p>Understanding the relationship between plant diversity and invasibility is essential in invasion ecology. Species-rich communities are hypothesized to be more resistant to invasions than species-poor communities. However, while soil microorganisms play a crucial role in regulating this diversity–invasibility relationship, the effects of plant competition mode and soil nutrient status on their role remain unclear. To address this, we conducted a two-stage greenhouse experiment. Soils were first conditioned by growing nine native species separately in them for 1 year, then mixed in various configurations with soils conditioned using one, three, or six species, respectively. Next, we inoculated the mixed soil into sterilized substrate soil and planted the alien species <em>Rhus typhina</em> and native species <em>Ailanthus altissima</em> as test plants. We set up two competition modes (intraspecific and interspecific) and two nutrient levels (fertilization using slow-release fertilizer and non-fertilization). Under intraspecific competition, regardless of fertilization, the biomass of the alien species was higher in soil conditioned by six native species. By contrast, under interspecific competition, the biomass increased without fertilization but remained stable with fertilization in soil conditioned by six native species. Analysis of soil microbes suggests that pathogens and symbiotic fungi in diverse plant communities influenced <em>R. typhina</em> growth, which varied with competition mode and nutrient status. Our findings suggest that the soil microbiome is pivotal in mediating the diversity–invasibility relationship, and this influence varies according to competition mode and nutrient status.</p>
Habitat quality drives the species-area relationship of plants and soil microbes in an ocean archipelago
<p>While the positive species-area relationship on islands is frequently observed, the mechanisms underlying this pattern remain poorly studied. By analyzing insular community diversity across spatial scales and the soil properties within the islands, we were able to explore potential mechanisms leading to the island species-area relationship of plants, as well as associated soil bacteria and fungi, from a tropical archipelago.<strong> </strong>We found that both plant and soil microbial communities showed similar positive species-area relationships across scales and the greater taxonomic diversity on larger islands was mainly driven by the higher richness within samples. These patterns arose primarily due to shifting habitat quality with island area, rather than spatial processes generally attributed to species-area relationships. Specifically, for plants, changes in soil total phosphorus content with island area were most explanatory, while changes in soil pH appeared to play the most important role in shaping soil bacteria and fungi patterns. By contrast, we found little evidence for the role of spatial processes (i.e., dispersal limitation or soil heterogeneity) within the island.<strong> </strong>Overall, this study highlights the importance of dissecting potential mechanisms underlying multi-trophic community dynamics to explain patterns of biodiversity and its variation on islands.</p>
Data for: Soil microbes alter competition between native and invasive plants
<p>Invasive plants can alter soil microbial communities and generate positive plant-soil feedbacks that facilitate their performance, but the magnitude and direction of feedbacks may change with novel conditions under climate change. We assessed how potential soil legacy effects of plant invasion and simulated drought influenced plant performance and competition in the longleaf pine ecosystem.</p> <p>We collected soil from a four-year factorial invasion (cogongrass, <i>Imperata cylindrica</i>) by drought (simulated with rainout shelters) field experiment and used it as live or sterilized soil inoculum in a greenhouse experiment that included two native foundation species, longleaf pine (<i>Pinus palustris</i>) and wiregrass (<i>Aristida stricta</i>), and cogongrass, grown individually or in competition.</p> <p>There was no evidence of biotic soil legacy effects of invasion or drought for any plant species, but microbes played a significant role in competition. When plants were grown alone, the invader had 12% greater biomass in live soil than sterile soil but both native species had 25% less biomass in live soil. When grown in competition, these effects were reversed for cogongrass (37% smaller in live soil) and pine (17% larger in live soil). In competition, the three species grown in sterile soil produced similar amounts of biomass, whereas live soil created a competitive hierarchy where pine was more competitive than wiregrass and cogongrass.</p> <p>Synthesis: These results emphasize the importance of soil biota in native plant restoration because, although the invader was highly successful when grown alone, plant-microbe interactions influenced the outcome of competition between native and invasive species by promoting native longleaf pine. There was little evidence that invasive cogongrass inhibited native plants via biotic soil legacies, instead, results suggested that plant-soil interactions can be highly resilient to global change such that the biotic legacy of invasion and drought may not promote or inhibit invasion.</p>
Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response
<p>We examined the role of the plant vs the environment in selecting for beneficial microbes to plants in their home moisture environment, in either wet vs dry conditions. To this end, we first conditioned soil microbial communities, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After 3 plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants, using the soil from the prior 3 generations as an inoculum. From plants inoculated with these ‘evolved’ soils, we measured plant biomass and height. We also measured soil nitrogen of the inoculum, and measured inoculum respiration across a water content gradient. <br> </p>
Data from: Soil microbes mediate the effects of resource variability on plant invasion
<p>A fundamental question in ecology is which species will prevail over others amid changes in both environmental mean conditions and their variability. Although the widely accepted fluctuating resource hypothesis predicts that increases in mean resource availability and variability therein will promote non-native plant invasion, it remains unclear to what extent these effects might be mediated by soil microbes. We grew eight invasive non-native plant species as target plants in pot-mesocosms planted with five different synthetic native communities as competitors and assigned them to eight combinations of two nutrient-fluctuation (constant vs pulsed), two nutrient-availability (low vs high) and two soil-microbe (living vs sterilized) treatments. We found that when plants grew in sterilized soil, nutrient fluctuation promoted the dominance of non-native plants under overall low nutrient availability, whereas the nutrient fluctuation had minimal effect under high nutrient availability. In contrast, when plants grew in living soil, nutrient fluctuation promoted the dominance of non-native plants under high nutrient availability rather than under low nutrient availability. Analysis of the soil microbial community suggests that this might reflect that nutrient fluctuation strongly increased the relative abundance of the most dominant pathogenic fungal family or genus under high nutrient availability, while decreasing it under low nutrient availability. Our findings are the first to indicate that besides its direct effect, environmental variability could also indirectly affect plant invasion via changes in soil microbial communities.</p>
Nutrient availability and invader density regulate the diversity–invasibility relationship mediated by soil microbes
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Data for: Soil microbes alter competition between native and invasive plants
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Data from: Soil microbes alter herbivore-induced volatile emissions in response to cereal cropping systems
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Interactions between soil microbes and native species drive a diversity-invasibility relationship
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