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 Soil Bacterial and Fungal Community Responses to Throughfall Reduction in a Eucalyptus Plantation in Southern China

Forests ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 37
Author(s):  
Yubiao Lin ◽  
Jiejun Kong ◽  
Ling Yang ◽  
Qian He ◽  
Yan Su ◽  
...  
Keyword(s):  
Community Structure ◽  
Relative Abundance ◽  
Fungal Community ◽  
Southern China ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Eucalyptus Plantation ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
Throughfall Reduction

In subtropical plantations in southern China, how soil microbial communities respond to climate change-induced drought is poorly understood. A field experiment was conducted in a subtropical Eucalyptus plantation to determine the impacts of 50% of throughfall reduction (TR) on soil microbial community composition, function, and soil physicochemical properties. Results showed that TR reduced soil water content (SWC) and soil available phosphorus (AP) content. TR significantly altered 196 bacterial operational taxonomic units (OTUs), most of them belonging to Acidobacteria, Actinobacteria, and Proteobacteria, while there were fewer changes in fungal OTUs. At the phylum level, TR increased the relative abundance of Acidobacteria at 0–20 cm soil depth by 37.18%, but failed to influence the relative abundance of the fungal phylum. Notably, TR did not alter the alpha diversity of the bacterial and fungal communities. The redundancy analysis showed that the bacterial communities were significantly correlated with SWC, and fungal communities were significantly correlated with AP content. According to predictions of bacterial and fungal community functions using PICRUSt2 and FUNGuild platforms, TR had different effects on both bacterial and fungal communities. Overall, SWC and AP decreased during TR, resulting in greater changes in soil bacterial community structure, but did not dramatically change soil fungal community structure.

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.

scholarly journals Long-Term Drought and Warming Alter Soil Bacterial and Fungal Communities in an Upland Heathland

Ecosystems ◽  
2021 ◽  
Author(s):  
Fiona M. Seaton ◽  
Sabine Reinsch ◽  
Tim Goodall ◽  
Nicola White ◽  
Davey L. Jones ◽  
...  
Keyword(s):  
Climate Change ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Fungal Communities ◽  
Its2 Region ◽  
Rrna Gene ◽  
Summer Drought ◽  
Soil Microbial ◽  
Soil Bacterial

AbstractThe response of soil microbial communities to a changing climate will impact global biogeochemical cycles, potentially leading to positive and negative feedbacks. However, our understanding of how soil microbial communities respond to climate change and the implications of these changes for future soil function is limited. Here, we assess the response of soil bacterial and fungal communities to long-term experimental climate change in a heathland organo-mineral soil. We analysed microbial communities using Illumina sequencing of the 16S rRNA gene and ITS2 region at two depths, from plots undergoing 4 and 18 years of in situ summer drought or warming. We also assessed the colonisation of Calluna vulgaris roots by ericoid and dark septate endophytic (DSE) fungi using microscopy after 16 years of climate treatment. We found significant changes in both the bacterial and fungal communities in response to drought and warming, likely mediated by changes in soil pH and electrical conductivity. Changes in the microbial communities were more pronounced after a longer period of climate manipulation. Additionally, the subsoil communities of the long-term warmed plots became similar to the topsoil. Ericoid mycorrhizal colonisation decreased with depth while DSEs increased; however, these trends with depth were removed by warming. We largely ascribe the observed changes in microbial communities to shifts in plant cover and subsequent feedback on soil physicochemical properties, especially pH. Our results demonstrate the importance of considering changes in soil microbial responses to climate change across different soil depths and after extended periods of time.

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.

Microbial temperature adaptation across a European gradient

2021 ◽  
Author(s):  
Carla Cruz Paredes ◽  
Daniel Tajmel ◽  
Johannes Rousk
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Bacterial Growth ◽  
Microbial Community Composition ◽  
Thermal Adaptation ◽  
Soil Microbial Communities ◽  
Fungal Growth ◽  
Fungal Communities ◽  
Soil Microbial

<p>Temperature is one of the most important environmental factors controlling both microbial growth and respiration. Warmer temperatures accelerate the rate at which microorganisms respire. Therefore, it is expected that climate warming will induce losses of carbon to the atmosphere through soil microbial respiration, representing a positive feedback to climate warming. However, there are multiple gaps in our understanding on responses of microorganisms to warming. For instance, long-term experiments have shown that the increase in soil respiration found in warming experiments diminishes with time, recovering to ambient values. This suggests that soil C losses might not be as extensive as previously suggested. This can be due to substrate depletion or shifts in the microbial community composition that led to thermal adaptation. To test thermal adaptation of soil microbial communities to their climate, variation along latitudinal gradients is a useful context. Such geographical gradients have long-term and large temperature differences thus patterns in thermal adaptation should have had sufficient time for ecological and evolutionary processes to act, allowing us to test if soil microbial communities have adapted to thermal regimes.</p><p>We investigated a latitudinal gradient across Europe with 76 sites that spanned a gradient of decadal mean annual temperature (MAT) from -3.1 to 18.3°C. We investigated if respiration, bacterial and fungal growth responses were adapted to long-term temperature differences in this gradient. We did this by estimating the temperature dependences of bacterial growth, fungal growth and respiration. We determined the temperature sensitivity (Q<sub>10</sub>), the minimum temperature (T<sub>min</sub>) for growth and the optimum temperature (T<sub>opt</sub>) for growth. These metrics were then correlated to MAT. Additionally, we sequenced bacterial (16S) and fungal (ITS) amplicons from the different sites to also assess variance in community composition and structure. We hypothesized that microbes should be adapted to their historical temperature; microbial communities in warmer environments will be warm-shifted and vice versa.</p><p>We could effectively represent temperature relationships for bacterial growth, fungal growth, and respiration for all soils. As expected, temperature relationships correlated with the environmental temperature of the site, such that higher temperatures resulted in microbial communities with warm-adapted growth and respiration. This could be seen as a strong positive correlation between T<sub>min</sub> values and environmental temperatures which range from -14 to -5°C for bacteria, -11.5 to -4°C for fungi and -8 to -2°C for respiration. We found that MAT explains the microbial communities’ temperature dependencies for bacterial growth and respiration, but not for fungal growth. With 1°C rise in MAT, T<sub>min</sub> increased 0.17°C for bacterial growth, while T<sub>min</sub> for respiration increased by 0.11. Similarly, bacterial and fungal communities’ composition were correlated with MAT (r<sup>2</sup>=0.38; r<sup>2</sup>=0.62), and T<sub>min</sub> (r<sup>2</sup>=0.16; r<sup>2</sup>=0.21). These findings suggest that thermal adaptation occurs in processes such as bacterial growth and respiration, probably due to shifts in the microbial community composition. However, fungal growth seems to be less sensitive to changes in temperature, even though fungal communities’ composition was correlated with MAT.</p>

scholarly journals Vegetation drives the structure of active microbial communities on an acidogenic mine tailings deposit

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10109
Author(s):  
Vanessa Gagnon ◽  
Michaël Rodrigue-Morin ◽  
Julien Tremblay ◽  
Jessica Wasserscheid ◽  
Julie Champagne ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Relative Abundance ◽  
Fungal Community ◽  
Mine Tailings ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Soil Microbial Communities ◽  
Vegetation Density ◽  
Mine Site ◽  
Soil Microbial

Plant-microbe associations are increasingly recognized as an inextricable part of plant biology and biogeochemistry. Microbes play an essential role in the survival and development of plants, allowing them to thrive in diverse environments. The composition of the rhizosphere soil microbial communities is largely influenced by edaphic conditions and plant species. In order to decipher how environmental conditions on a mine site can influence the dynamics of microbial communities, we characterized the rhizosphere soil microbial communities associated with paper birch, speckled alder, and spruce that had naturally colonized an acidogenic mine tailings deposit containing heavy metals. The study site, which had been largely undisturbed for five decades, had highly variable vegetation density; with some areas remaining almost barren, and others having a few stands or large thickets of mature trees. Using Illumina sequencing and ordination analyses (redundancy analysis and principal coordinate analysis), our study showed that soil bacterial and fungal community structures correlated mainly with vegetation density, and plant species. Tailings without any vegetation were the most different in bacterial community structure, compared to all other areas on the mine site, as well as an adjacent natural forest (comparison plot). The bacterial genera Acidiferrobacter and Leptospirillum were more abundant in tailings without vegetation than in any of the other sites, while Bradyrhizobium sp. were more abundant in areas of the tailings deposit having higher vegetation density. Frankia sp. is equally represented in each of the vegetation densities and Pseudomonas sp. present a greater relative abundance in boreal forest. Furthermore, alder rhizosphere showed a greater relative abundance of Bradyrhizobium sp. (in comparison with birch and spruce) as well as Haliangium sp. (in comparison with birch). In contrast, fungal community structures were similar across the tailings deposit regardless of vegetation density, showing a greater relative abundance of Hypocrea sp. Tailings deposit fungal communities were distinct from those found in boreal forest soils. Alder rhizosphere had greater relative abundances of Hypocrea sp. and Thelephora sp., while birch rhizosphere were more often associated with Mollisia sp. Our results indicate that, with increasing vegetation density on the mine site, the bacterial communities associated with the individual deciduous or coniferous species studied were increasingly similar to the bacterial communities found in the adjacent forest. In order to properly assess and restore disturbed sites, it is important to characterize and understand the plant-microbe associations that occur since they likely improve plant fitness in these harsh environments.

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 Phosphorus Reduces Negative Effects of Nitrogen Addition on Soil Microbial Communities and Functions

2020 ◽  
Vol 8 (11) ◽  
pp. 1828 ◽  
Author(s):  
Zongwei Xia ◽  
Jingyi Yang ◽  
Changpeng Sang ◽  
Xu Wang ◽  
Lifei Sun ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Diversity ◽  
Soil Microbial Communities ◽  
N Deposition ◽  
N Fixation ◽  
N Addition ◽  
Soil Bacterial Diversity ◽  
Soil Microbial ◽  
Soil Bacterial ◽  
P Addition

Increased soil nitrogen (N) from atmospheric N deposition could change microbial communities and functions. However, the underlying mechanisms and whether soil phosphorus (P) status are responsible for these changes still have not been well explained. Here, we investigated the effects of N and P additions on soil bacterial and fungal communities and predicted their functional compositions in a temperate forest. We found that N addition significantly decreased soil bacterial diversity in the organic (O) horizon, but tended to increase bacterial diversity in the mineral (A) horizon soil. P addition alone did not significantly change soil bacterial diversity but mitigated the negative effect of N addition on bacterial diversity in the O horizon. Neither N addition nor P addition significantly influenced soil fungal diversity. Changes in soil microbial community composition under N and P additions were mainly due to the shifts in soil pH and NO3− contents. N addition can affect bacterial functional potentials, such as ureolysis, N fixation, respiration, decomposition of organic matter processes, and fungal guilds, such as pathogen, saprotroph, and mycorrhizal fungi, by which more C probably was lost in O horizon soil under increased N deposition. However, P addition can alleviate or switch the effects of increased N deposition on the microbial functional potentials in O horizon soil and may even be a benefit for more C sequestration in A horizon soil. Our results highlight the different responses of microorganisms to N and P additions between O and A horizons and provides an important insight for predicting the changes in forest C storage status under increasing N deposition in the future.

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.

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