scholarly journals An Examination of Soil Microbial Communities and Litter Decomposition in Five Urban Land Uses in Metropolitan Milwaukee, WI, U.S.

2016 ◽  
Vol 42 (1) ◽  
Author(s):  
Keith Turnquist ◽  
Les Werner ◽  
Brian Sloss
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Fungal Community ◽  
C:N Ratio ◽  
Soil Microbial Communities ◽  
Urban Land ◽  
Land Uses ◽  
Fungal Community Composition ◽  
Soil Microbial ◽  
Physical And Chemical

The process of urbanization may alter the ability of microorganisms to supply nutrients to plants. However, both the composition and structure of soil biological communities, and the extent of variation within these communities, is not clear in urban areas. Therefore, baseline information regarding the impact of urban land management practices on soil microbial communities is essential to improving individuals’ ability to manage urban soils and the plants they support. This study examined soil microbial communities over five urban land uses with different degrees of urbanization in metropolitan Milwaukee, Wisconsin, U.S. The objectives were to 1) determine if differences exist in bacterial and fungal community composition, biological activity, and the soil physical and chemical environment across five urban land uses, and 2) determine if differences in the bacterial and fungal compositions compare to differences in the soil’s physical and chemical characteristics. Bulk density, soil organic matter, pH, magnesium, sodium, total nitrogen, and C:N ratio displayed significant differences between streets and forests. Microbial biomass did not differ between land uses, and the differences in bacterial and fungal community composition reflect only a small portion of the total microbial pool. The decomposition of transposed leaf litter showed significant decline in C:N ratio over time, but no statistical differences between land use were observed. The results display a highly redundant microbial assemblage, and suggest that in locations with adequate levels of soil carbon and where parent material and soil forming processes are homogeneous, urbanization and landscape management have less impact on soil microbiology than expected.

scholarly journals Fungal Community, Not Substrate Quality, Drives Soil Microbial Function in Northeastern U.S. Temperate Forests

2020 ◽  
Vol 3 ◽  
Author(s):  
Amelia A. Fitch ◽  
Ashley K. Lang ◽  
Emily D. Whalen ◽  
Kevin Geyer ◽  
Caitlin Hicks Pries
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Community Composition ◽  
Fungal Community ◽  
Enzyme Production ◽  
C:N Ratio ◽  
Am Fungi ◽  
Fungal Community Composition ◽  
Substrate Quality ◽  
Soil Microbial

Mycorrhizal fungi can affect soil organic matter cycling through several mechanisms including priming, nutrient competition, and direct enzyme production. Differences in nutrient foraging strategies between ectomycorrhizal (EcM) and arbuscular mycorrhizal (AM) fungi produce divergent belowground dynamics: where EcM can take up organic nitrogen and directly break down soil organic matter (SOM) by producing enzymes, AM fungi are limited to scavenging mineral N. EcM-associated tree species also have leaf litter with relatively higher ratios of carbon to nitrogen (C:N), and belowground saprotrophic communities more dominated by fungi. Consequently, free-living microbes in EcM-dominated soils should experience nitrogen limitation, with subsequent increases in enzyme production and decreased carbon use efficiency (CUE). However, the relative importance of the effects of substrate quality and fungal community composition on enzyme production and CUE are unclear. To assess this distinction, we sampled the organic horizon and 10 cm of the mineral horizon in northern temperate forest soils along a gradient of EcM dominance. We characterized fungal community composition by measuring EcM relative abundances from extracted fungal DNA and the fungal to bacterial (F:B) ratios from phospholipid fatty acid (PLFA) analysis. We assessed soil substrate quality as the soil C:N ratio. Soil microbial functions were measured as potential activities of five hydrolytic and two oxidative enzymes, and microbial CUE. We found that the fungal community, represented by either the F:B ratio, EcM relative abundance, or both, affected CUE and six measured enzyme activities, while the C:N ratio affected only oxidative and chitin-targeting extracellular enzyme activities. Our results highlight the use of EcM relative dominance as a predictor of soil microbial community composition and function independent of substrate quality.

Weed seed mortality in soils with contrasting agricultural management histories

Weed Science ◽  
2006 ◽  
Vol 54 (02) ◽  
pp. 291-297 ◽  
Author(s):  
Adam S. Davis ◽  
Kathleen I. Anderson ◽  
Steven G. Hallett ◽  
Karen A. Renner
Keyword(s):  
Soil Properties ◽  
Microbial Communities ◽  
Community Composition ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Weed Seed ◽  
Soil Microbial ◽  
Giant Foxtail ◽  
Seed Mortality

It has been proposed that cropping systems can be managed to promote the development of soil microbial communities that accelerate weed seed mortality. We examined soil fungal and bacterial communities, soil C:N ratio, soil particle size fractions, and weed seed mortality in soil from fields with over 10 yr of five contrasting management histories with the objective of determining if seed mortality could be explained by differences in soil properties. Seed mortality of giant foxtail and velvetleaf were greatest in soil from the conventionally managed systems and lowest in soil from a reduced input system. Principal-components analysis of soil microbial communities, as determined through denaturing gradient gel electrophoresis of polymerase chain reaction–amplified ribosomal RNA genes (PCR-DGGE), showed distinct differences in the composition of fungal and bacterial communities among the study soils. The first principal component of the 18S rDNA PCR-DGGE analysis of fungal community composition showed a strong negative correlation with both giant foxtail (− 0.52, P < 0.05) and velvetleaf (− 0.57, P < 0.01) seed mortality, as did ordination with nonmetric multidimensional scaling (NMS) [giant foxtail (− 0.54, P < 0.01) and velvetleaf (− 0.60, P < 0.01)], suggesting that seeds of the two species were affected similarly by changes in the soil fungal community. For giant foxtail, weed seed mortality was also positively correlated (r = 0.48, P < 0.05) with the first NMS axis of the bacterial 16S rDNA analysis. None of the other measured soil properties were significantly correlated with weed seed mortality. Thus, for the soils tested here, management history, microbial community composition, and weed seed mortality were linked. To extend these results to the field, more work is needed to identify components of the fungal and bacterial communities that are active in seed degradation, and to develop conservation biocontrol recommendations for these species.

scholarly journals Soil bacterial and fungal communities of six bahiagrass cultivars

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7014 ◽  
Author(s):  
Lukas Beule ◽  
Ko-Hsuan Chen ◽  
Chih-Ming Hsu ◽  
Cheryl Mackowiak ◽  
Jose C.B. Dubeux Jr. ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Relative Abundance ◽  
Fungal Community ◽  
Plant Pathogens ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Soil Dna ◽  
Soil Microbial ◽  
Soil Bacterial

BackgroundCultivars of bahiagrass (Paspalum notatumFlüggé) are widely used for pasture in the Southeastern USA. Soil microbial communities are unexplored in bahiagrass and they may be cultivar-dependent, as previously proven for other grass species. Understanding the influence of cultivar selection on soil microbial communities is crucial as microbiome taxa have repeatedly been shown to be directly linked to plant performance.ObjectivesThis study aimed to determine whether different bahiagrass cultivars interactively influence soil bacterial and fungal communities.MethodsSix bahiagrass cultivars (‘Argentine’, ‘Pensacola’, ‘Sand Mountain’, ‘Tifton 9’, ‘TifQuik’, and ‘UF-Riata’) were grown in a randomized complete block design with four replicate plots of 4.6 × 1.8 m per cultivar in a Rhodic Kandiudults soil in Northwest Florida, USA. Three soil subsamples per replicate plot were randomly collected. Soil DNA was extracted and bacterial 16S ribosomal RNA and fungal ribosomal internal transcribed spacer 1 genes were amplified and sequenced with one Illumina Miseq Nano.ResultsThe soil bacterial and fungal community across bahiagrass cultivars showed similarities with communities recovered from other grassland ecosystems. Few differences in community composition and diversity of soil bacteria among cultivars were detected; none were detected for soil fungi. The relative abundance of sequences assigned to nitrite-oxidizingNitrospirawas greater under ‘Sand Mountain’ than ‘UF-Riata’. Indicator species analysis revealed that several bacterial and fungal indicators associated with either a single cultivar or a combination of cultivars are likely to be plant pathogens or antagonists.ConclusionsOur results suggest a low impact of plant cultivar choice on the soil bacterial community composition, whereas the soil fungal community was unaffected. Shifts in the relative abundance ofNitrospiramembers in response to cultivar choice may have implications for soil N dynamics. The cultivars associated with presumptive plant pathogens or antagonists indicates that the ability of bahiagrass to control plant pathogens may be cultivar-dependent, however, physiological studies on plant-microbe interactions are required to confirm this presumption. We therefore suggest that future studies should explore the potential of different bahiagrass cultivars on plant pathogen control, particularly in sod-based crop rotation.

scholarly journals Consistent predictors of microbial community composition across scales in grasslands reveal low context-dependency

2021 ◽  
Author(s):  
Dajana Radujković ◽  
Sara Vicca ◽  
Margaretha van Rooyen ◽  
Peter Wilfahrt ◽  
Leslie Brown ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Spatial Scales ◽  
Regional Scale ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Plant Productivity ◽  
Context Dependency ◽  
Fungal Community Composition ◽  
Soil Microbial

Environmental circumstances shaping soil microbial communities have been studied extensively, but due to disparate study designs it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 sampled across regional plant productivity gradients) to examine i) if the same abiotic or biotic factors predict both large- and regional-scale patterns in bacterial and fungal community composition, and ii) if microbial community composition differs consistently with regional plant productivity (low vs high) across different sites. We found that there is high congruence between predictors of microbial community composition across spatial scales; bacteria were predominantly associated with soil properties and fungi with plant community composition. Moreover, there was a microbial community signal that clearly distinguished high and low productivity soils that was shared across worldwide distributed grasslands suggesting that microbial assemblages vary predictably depending on grassland productivity.

scholarly journals Response of Soil Microbial Communities to Warming and Clipping in Alpine Meadows in Northern Tibet

2020 ◽  
Vol 12 (14) ◽  
pp. 5617
Author(s):  
Haorui Zhang ◽  
Shaowei Li ◽  
Guangyu Zhang ◽  
Gang Fu
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Soil Microbial Communities ◽  
Alpine Meadows ◽  
Soil Microbial ◽  
Alpine Steppe ◽  
Total Plfa ◽  
Kobresia Meadow ◽  
Low Altitude ◽  
Steppe Meadow

In order to explore responses of soil microbial communities among different alpine meadows under warming and clipping, soil microorganisms of three alpine meadow sites (low altitude: 4313 m, alpine steppe meadow, 30°30′ N, 91°04′ E; mid-altitude: 4513 m, alpine steppe meadow, 30°31′ N, 91°04′ E; and high altitude: 4693, alpine Kobresia meadow, 30°32′ N, 91°03′ E) were measured using the phospholipid fatty acid (PLFA) method. Both warming and clipping significantly reduced PLFA content and changed the community composition of soil microbial taxa, which belong to bacterial and fungal communities in the alpine Kobresia meadow. Warming significantly reduced the soil total PLFA content by 36.1% and the content of soil fungi by 37.0%; the clipping significantly reduced the soil total PLFA content by 57.4%, the content of soil fungi by 49.9%, and the content of soil bacteria by 60.5% in the alpine Kobresia meadow. Only clipping changed the total fungal community composition at a low altitude. Neither clipping nor warming changed the microbial community composition at a moderate altitude. Soil temperature, soil moisture, and pH were the main factors affecting soil microbial communities. Therefore, the effects of warming and clipping on soil microbial communities in alpine meadows were related to grassland types and soil environmental conditions.

scholarly journals Intercropping with Potato-Onion Enhanced the Soil Microbial Diversity of Tomato

2020 ◽  
Vol 8 (6) ◽  
pp. 834
Author(s):  
Naihui Li ◽  
Danmei Gao ◽  
Xingang Zhou ◽  
Shaocan Chen ◽  
Chunxia Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Organic Carbon ◽  
Bacterial Community ◽  
Soil Organic Carbon ◽  
Microbial Communities ◽  
Fungal Community ◽  
Soil Microbial Communities ◽  
Tomato Seedling ◽  
Soil Microbial ◽  
Potato Onion

Intercropping can achieve sustainable agricultural development by increasing plant diversity. In this study, we investigated the effects of tomato monoculture and tomato/potato-onion intercropping systems on tomato seedling growth and changes of soil microbial communities in greenhouse conditions. Results showed that the intercropping with potato-onion increased tomato seedling biomass. Compared with monoculture system, the alpha diversity of soil bacterial and fungal communities, beta diversity and abundance of bacterial community were increased in the intercropping system. Nevertheless, the beta-diversity and abundance of fungal community had no difference between the intercropping and monoculture systems. The relative abundances of some taxa (i.e., Acidobacteria-Subgroup-6, Arthrobacter, Bacillus, Pseudomonas) and several OTUs with the potential to promote plant growth were increased, while the relative abundances of some potential plant pathogens (i.e., Cladosporium) were decreased in the intercropping system. Redundancy analysis indicated that bacterial community structure was significantly influenced by soil organic carbon and pH, the fungal community structure was related to changes in soil organic carbon and available phosphorus. Overall, our results suggested that the tomato/potato-onion intercropping system altered soil microbial communities and improved the soil environment, which may be the main factor in promoting tomato growth.

scholarly journals Transformation of Soil Microbial Community Structure and Rhizoctonia-Suppressive Potential in Response to Apple Roots

1999 ◽  
Vol 89 (10) ◽  
pp. 920-927 ◽  
Author(s):  
Mark Mazzola
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Burkholderia Cepacia ◽  
Soil Microbial Communities ◽  
Apple Trees ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Orchard Soil

Changes in the composition of soil microbial communities and relative disease-suppressive ability of resident microflora in response to apple cultivation were assessed in orchard soils from a site possessing trees established for 1 to 5 years. The fungal community from roots of apple seedlings grown in noncultivated orchard soil was dominated by isolates from genera commonly considered saprophytic. Plant-pathogenic fungi in the genera Phytophthora, Pythium, and Rhizoctonia constituted an increasing proportion of the fungal community isolated from seedling roots with increasing orchard block age. Bacillus megaterium and Burkholderia cepacia dominated the bacterial communities recovered from noncultivated soil and the rhizosphere of apple seedlings grown in orchard soil, respectively. Populations of the two bacteria in their respective habitats declined dramatically with increasing orchard block age. Lesion nematode populations did not differ among soil and root samples from orchard blocks of different ages. Similar changes in microbial communities were observed in response to planting noncultivated orchard soil to five successive cycles of ‘Gala’ apple seedlings. Pasteurization of soil had no effect on apple growth in noncultivated soil but significantly enhanced apple growth in third-year orchard block soil. Seedlings grown in pasteurized soil from the third-year orchard block were equal in size to those grown in noncultivated soil, demonstrating that suppression of plant growth resulted from changes in the composition of the soil microbial community. Rhizoctonia solani anastomosis group 5 (AG 5) had no effect on growth of apple trees in noncultivated soil but significantly reduced the growth of apple trees in soil from third-year orchard soil. Changes in the ability of the resident soil microflora to suppress R. solani AG 5 were associated with reductions in the relative populations of Burkholderia cepacia and Pseudomonas putida in the rhizosphere of apple.

scholarly journals Effects of Wildfire and Harvest Disturbances on Forest Soil Bacterial Communities

2007 ◽  
Vol 74 (1) ◽  
pp. 216-224 ◽  
Author(s):  
Nancy R. Smith ◽  
Barbara E. Kishchuk ◽  
William W. Mohn
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Biomass Carbon ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Microbial Biomass Nitrogen ◽  
Soil Microbial

ABSTRACT Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH4 + and NO3 − due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma- and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.

scholarly journals Short-Term Effects of Different Forest Management Methods on Soil Microbial Communities of a Natural Quercus aliena var. acuteserrata Forest in Xiaolongshan, China

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 161 ◽  
Author(s):  
Pan Wan ◽  
Gongqiao Zhang ◽  
Zhonghua Zhao ◽  
Yanbo Hu ◽  
Wenzhen Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Forest Management ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
Soil Microbial Communities ◽  
Short Term ◽  
Soil Microbial

One of the aims of sustainable forest management is to preserve the diversity and resilience of ecosystems. Unfortunately, changes in the soil microbial communities after forest management remain unclear. We analyzed and compared the soil microbial community of a natural Quercus aliena var. acuteserrata forest after four years of four different management methods using high-throughput sequencing technology. The forest management methods were close-to-nature management (CNFM), structure-based forest management (SBFM), secondary forest comprehensive silviculture (SFCS) and unmanaged control (CK). The results showed that: (1) the soil microbial community diversity indices were not significantly different among the different management methods. (2) The relative abundance of Proteobacteria in the SBFM treatment was lower than in the CK treatment, while the relative abundance of Acidobacteria in the SBFM was significantly higher than that in the CK treatment. The relative abundance of Ascomycota was highest in the CNFM treatment, and that of Basidiomycota was lowest in the CNFM treatment. However, the relative abundance of dominant bacterial and fungal phyla was not significantly different in CK and SFCS. (3) Redundancy analysis (RDA) showed that the soil organic matter (SOM), total nitrogen (TN), and available nitrogen (AN) significantly correlated with the bacterial communities, and the available potassium (AK) was the only soil nutrient, which significantly correlated with the composition of the fungal communities. The short-term SBFM treatment altered microbial bacterial community compositions, which may be attributed to the phyla present (e.g., Proteobacteria and Acidobacteria), and the short-term CNFM treatment altered microbial fungal community compositions, which may be attributed to the phyla present (e.g., Ascomycota and Basidiomycota). Furthermore, soil nutrients could affect the dominant soil microbial communities, and its influence was greater on the bacterial community than on the fungal community.

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