scholarly journals One-time Nitrogen Fertilization Shifts Switchgrass Soil Microbiomes within a Context of Larger Spatial and Temporal Variation

2019 ◽  
Author(s):  
Huaihai Chen ◽  
Zamin K. Yang ◽  
Dan Yip ◽  
Reese H. Morris ◽  
Steven J. Lebreux ◽  
...  
Keyword(s):  
Temporal Variation ◽  
Fungal Community ◽  
Temporal Variability ◽  
N Fertilization ◽  
Fungal Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Spatial And Temporal Variation ◽  
Vertical Heterogeneity ◽  
Over Time

AbstractSoil microbiome responses to short-term nitrogen (N) inputs within the context of existing spatio-temporal variability remain uncertain. Here, we examined soil bacterial and fungal communities pre/post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha-1 as NH4NO3) for the first time since planting. Soils were collected at two depths, 0-5 and 5-15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions, and soil metagenomic analysis. Baseline assessment prior to fertilization revealed no pre-existing differences in either bacterial or fungal communities across plots. The one-time N fertilization increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12-22 % of the variation in bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. Thus, variability within the field might override the changes induced by N addition. Continued analyses of these trends over time with fertilization and management are needed to understand whether these transient effects change over time.

scholarly journals The Response of the Soil Microbiota to Long-Term Mineral and Organic Nitrogen Fertilization is Stronger in the Bulk Soil than in the Rhizosphere

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 456 ◽  
Author(s):  
Massimiliano Cardinale ◽  
Stefan Ratering ◽  
Aitak Sadeghi ◽  
Sushil Pokhrel ◽  
Bernd Honermeier ◽  
...  
Keyword(s):  
N Fertilization ◽  
16S Rrna Genes ◽  
Bulk Soil ◽  
Rrna Genes ◽  
Soil Microbiome ◽  
Future Research ◽  
Arable Soils ◽  
Mineral N ◽  
Bacterial Microbiota

The effects of different agronomic practices, such as fertilization regimes, can be experimentally tested in long-term experiments (LTE). Here, we aimed to evaluate the effect of different nitrogen fertilizations on the bacterial microbiota in both rhizosphere and bulk soil of sugar beet, in the Giessen-LTE (Germany). Fertilization treatments included mineral-N, manure, mineral-N + manure and no N-amendment. Metabarcoding and co-occurrence analysis of 16S rRNA genes, qPCR of amoA, nirK, nirS, nosZ-I and nosZ-II genes and soil physico-chemical analyses were performed. The effect of the fertilization treatments was more evident in the bulk soil, involving 33.1% of the microbiota. Co-occurrence analysis showed a rhizosphere cluster, dominated by Proteobacteria, Actinobacteria and Verrucomicrobia (hub taxa: Betaproteobacteriales), and a bulk soil cluster, dominated by Acidobacteria, Gemmatominadetes and “Latescibacteria” (hub taxa: Acidobacteria). In the bulk soil, mineral N-fertilization reduced nirK, amoA, nosZ-I and nosZ-II genes. Thirteen Operational taxonomic units (OTUs) showed 23 negative correlations with gene relative abundances. These OTUs likely represent opportunistic species that profited from the amended mineral-N and outgrew the species carrying N-cycle genes. Our results indicate trajectories for future research on soil microbiome in LTE and add new experimental evidence that will be helpful for sustainable management of nitrogen fertilizations on arable soils.

Spatial and temporal variation in assemblages of Lutjanidae, Lethrinidae and associated fish species among mid-continental shelf reefs in the central Great Barrier Reef

2001 ◽  
Vol 52 (6) ◽  
pp. 843 ◽  
Author(s):  
Stephen J. Newman ◽  
David McB. Williams
Keyword(s):  
Continental Shelf ◽  
Temporal Variation ◽  
Fish Assemblages ◽  
Spatial And Temporal Variation ◽  
Shallow Trap ◽  
Fish Traps ◽  
Lutjanus Carponotatus ◽  
Plectropomus Leopardus ◽  
Trap Catches ◽  
Over Time

Visual censuses were used to survey shallow-water assemblages of the Lutjanidae and Lethrinidae among three mid-continental shelf reefs, and fish traps were used to survey deeper water assemblages below diveable depths. Significant differences were found in visual censuses of the Lutjanidae and Lethrinidae among reefs. Trap catches of the Lutjanidae and Lethrinidae varied more between depths and diel sampling periods than among reefs or over time. Lutjanus carponotatus, L. fulviflamma and Lethrinus miniatus were more abundant in shallow trap sets, whereas Lutjanus adetii, L. russelli, L. sebae, L. vitta, Gymnocranius audleyi, Lethrinus sp.2 and Abalistes stellaris were more abundant in deeper sets. Additionally, Lutjanus adetii, L. fulviflamma, L. quinquelineatus, L. russelli, L. sebae, L. vitta and Lethrinus miniatus were more abundant at night, whereas Lethrinus sp. 2, Abalistes stellarisand Plectropomus leopardus were more abundant during the day. The absence of significant temporal variation in the observed spatial patterns both among reefs and between depths indicates that these patterns may persist through time. The use of both visual censuses and fish traps to assess reef fish assemblages may provide an objective way of repeatedly censusing reefs for monitoring purposes, especially where differences among reefs and regions are important.

scholarly journals What drives the spatial distribution and dynamics of local species richness in tropical forest?

2017 ◽  
Vol 284 (1863) ◽  
pp. 20171503 ◽  
Author(s):  
Thorsten Wiegand ◽  
Felix May ◽  
Martin Kazmierczak ◽  
Andreas Huth
Keyword(s):  
Species Richness ◽  
Tropical Forest ◽  
Temporal Variation ◽  
Tropical Forests ◽  
Temporal Variability ◽  
Dynamic Models ◽  
Neutral Theory ◽  
Spatial And Temporal Variation ◽  
Demographic Stochasticity ◽  
Spatio Temporal

Understanding the structure and dynamics of highly diverse tropical forests is challenging. Here we investigate the factors that drive the spatio-temporal variation of local tree numbers and species richness in a tropical forest (including 1250 plots of 20 × 20 m 2 ). To this end, we use a series of dynamic models that are built around the local spatial variation of mortality and recruitment rates, and ask which combination of processes can explain the observed spatial and temporal variation in tree and species numbers. We find that processes not included in classical neutral theory are needed to explain these fundamental patterns of the observed local forest dynamics. We identified a large spatio-temporal variability in the local number of recruits as the main missing mechanism, whereas variability of mortality rates contributed to a lesser extent. We also found that local tree numbers stabilize at typical values which can be explained by a simple analytical model. Our study emphasized the importance of spatio-temporal variability in recruitment beyond demographic stochasticity for explaining the local heterogeneity of tropical forests.

scholarly journals Spatial and Temporal Variation in an Apple Orchard

HortScience ◽  
2019 ◽  
Vol 54 (12) ◽  
pp. 2182-2187
Author(s):  
Babak Talebpour ◽  
Maksut Barış Eminoğlu ◽  
Uğur Yegül ◽  
Ufuk Türker
Keyword(s):  
Temporal Variation ◽  
Precision Agriculture ◽  
Temporal Stability ◽  
Apple Orchard ◽  
The Other ◽  
Spatial And Temporal Variation ◽  
Spatial And Temporal Variability ◽  
Research Station ◽  
Temporal Variance ◽  
Over Time

One important goal of precision horticulture (PH), as well as precision agriculture (PA), is to measure and manage spatial and temporal variation in orchards. In this study, temporal and spatial analysis of yields were carried out over 2 years for a 0.5-ha apple orchard (at the Haymana Research Station of Ankara University, Turkey, from 2017 to 2018) to determine the variability of yields over time and included seven apple varieties: ‘Royal Gala’, ‘Red Chief’, ‘Braeburn’, ‘Mondial Gala’, ‘Jonagold’, ‘Fuji’, and ‘Mitch Gala’. To achieve this, yield data for two different years were analyzed for mean yield, temporal variance, and cv in terms of spatial and temporal stability, and their yield maps were produced. The results showed that ‘Jonagold’, ‘Braeburn’, and ‘Red Chief’ varieties yielded less than the average yield, whereas the other varieties produced average yields when the yield from 2 years was taken into account. Calculation of the values for determining temporal stability over time resulted in all existing varieties being identified as stable over time. For example, the ‘Jonagold’ and ‘Red Chief’ varieties showed 100% stability in terms of temporal variance. Results also showed that the ‘Gala’ varieties were stable for 2 years and produced high yields, whereas the other varieties were specified as stable and low yielding when spatial and temporal variability was considered in combination.

scholarly journals Hot spot detection and spatio-temporal dynamics of dengue in Queensland, Australia

2014 ◽  
Vol XL-8 ◽  
pp. 197-204 ◽  
Author(s):  
S. Naish ◽  
S. Tong
Keyword(s):  
Temporal Variation ◽  
Temporal Dynamics ◽  
Hot Spot ◽  
Seasonal Pattern ◽  
Temporal Distribution ◽  
Health Concern ◽  
Spatial And Temporal Variation ◽  
Dengue Case ◽  
Spatio Temporal ◽  
Over Time

Dengue has been a major public health concern in Australia since it re-emerged in Queensland in 1992–1993. This study explored spatio-temporal distribution and clustering of locally-acquired dengue cases in Queensland State, Australia and identified target areas for effective interventions. A computerised locally-acquired dengue case dataset was collected from Queensland Health for Queensland from 1993 to 2012. Descriptive spatial and temporal analyses were conducted using geographic information system tools and geostatistical techniques. Dengue hot spots were detected using SatScan method. Descriptive spatial analysis showed that a total of 2,398 locally-acquired dengue cases were recorded in central and northern regions of tropical Queensland. A seasonal pattern was observed with most of the cases occurring in autumn. Spatial and temporal variation of dengue cases was observed in the geographic areas affected by dengue over time. Tropical areas are potential high-risk areas for mosquito-borne diseases such as dengue. This study demonstrated that the locally-acquired dengue cases have exhibited a spatial and temporal variation over the past twenty years in tropical Queensland, Australia. There is a clear evidence for the existence of statistically significant clusters of dengue and these clusters varied over time. These findings enabled us to detect and target dengue clusters suggesting that the use of geospatial information can assist the health authority in planning dengue control activities and it would allow for better design and implementation of dengue management programs.

scholarly journals Investigation of sources, diversity, and variability of bacterial aerosols in Athens, Greece: a pilot study

2021 ◽  
Author(s):  
Angelina Metaxatos ◽  
Sydonia Manibusan ◽  
Gediminas Mainelis
Keyword(s):  
Field Application ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Airborne Bacteria ◽  
Bacterial Composition ◽  
Commensal Microbiota ◽  
High Prevalence ◽  
Bacterial Aerosols ◽  
The Impact ◽  
Over Time

Abstract This study is the first attempt to describe the composition, diversity, and potential sources of bacterial aerosols in the urban air of Athens by DNA barcoding (analysis of 16S rRNA genes). It is also the first field application of the recently developed Rutgers Electrostatic Passive Sampler (REPS) to study the microbial diversity of aerosols. Three sampling campaigns 6–10 days in duration were conducted in the summer and fall of 2019. The completely passive REPS captured a sufficient amount of biological material to demonstrate the diversity of airborne bacteria and their variability over time. Overall, in the air of Athens, 793 OTUs were detected. Firmicutes, Proteobacteria, and Actinobacteria were the dominant Phyla, while the Cyanobacteria, Bacteroidetes, and Fusobacteria were the minor Phyla. The observed Phyla were further classified into 54 families. The families with high prevalence across our samples contained genera known to have pathogenic species, e.g., Streptococcus, Corynebacterium, Gemella, Pseudomonas, Staphylococcus, Neisseria; many species belonging to human or animal commensal microbiota were also detected. The paper discusses the likely sources of observed airborne bacteria, including soil, plants, animals, humans. Given the variability in bacterial composition over time, it is obvious that the contribution of those sources to airborne microbiota is dynamic. However, a more accurate linkage between the sources and airborne bacteria requires further study. Also, the exact functional and ecological role and, even more importantly, the impact of observed bacterial aerosols on public health and the ecosystem is still unknown and required further analysis.

scholarly journals Dynamics of Bacterial and Fungal Communities on Decaying Salt Marsh Grass

2003 ◽  
Vol 69 (11) ◽  
pp. 6676-6687 ◽  
Author(s):  
Alison Buchan ◽  
Steven Y. Newell ◽  
Melissa Butler ◽  
Erin J. Biers ◽  
James T. Hollibaugh ◽  
...  
Keyword(s):  
Salt Marsh ◽  
Rflp Analysis ◽  
Fungal Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Natural Environments ◽  
Ecological Interactions ◽  
Decomposition Processes ◽  
Community Fingerprinting ◽  
Bacteria And Fungi

ABSTRACT Both bacteria and fungi play critical roles in decomposition processes in many natural environments, yet only rarely have they been studied as an integrated microbial community. Here we describe the bacterial and fungal assemblages associated with two decomposition stages of Spartina alterniflora detritus in a productive southeastern U.S. salt marsh. 16S rRNA genes and 18S-to-28S internal transcribed spacer (ITS) regions were used to target the bacterial and ascomycete fungal communities, respectively, based on DNA sequence analysis of isolates and environmental clones and by using community fingerprinting based on terminal restriction fragment length polymorphism (T-RFLP) analysis. Seven major bacterial taxa (six affiliated with the α-Proteobacteria and one with the Cytophagales) and four major fungal taxa were identified over five sample dates spanning 13 months. Fungal terminal restriction fragments (T-RFs) were informative at the species level; however, bacterial T-RFs frequently comprised a number of related genera. Amplicon abundances indicated that the salt marsh saprophyte communities have little-to-moderate variability spatially or with decomposition stage, but considerable variability temporally. However, the temporal variability could not be readily explained by either successional shifts or simple relationships with environmental factors. Significant correlations in abundance (both positive and negative) were found among dominant fungal and bacterial taxa that possibly indicate ecological interactions between decomposer organisms. Most associations involved one of four microbial taxa: two groups of bacteria affiliated with the α-Proteobacteria and two ascomycete fungi (Phaeosphaeria spartinicola and environmental isolate “4clt”).

scholarly journals Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate

2014 ◽  
Vol 80 (6) ◽  
pp. 1810-1820 ◽  
Author(s):  
Puja Jasrotia ◽  
Stefan J. Green ◽  
Andy Canion ◽  
Will A. Overholt ◽  
Om Prakash ◽  
...  
Keyword(s):  
Nitrous Oxide ◽  
Fungal Community ◽  
Ph Gradient ◽  
Fungal Communities ◽  
Rrna Genes ◽  
Acidic Ph ◽  
Watershed Scale ◽  
Subsurface Environment ◽  
Fungal Isolates ◽  
Groundwater Samples

ABSTRACTThe objective of this study was to characterize fungal communities in a subsurface environment cocontaminated with uranium and nitrate at the watershed scale and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semiquantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylumAscomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH <4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genusConiochaeta, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylumAscomycotaand within a single genus of theBasidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide underin situacidic pH conditions.

scholarly journals Seasonal dynamics of microbial diversity in the rhizosphere of Ulmus pumila L. var. sabulosa in a steppe desert area of Northern China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7526 ◽  
Author(s):  
Tianyu Liang ◽  
Guang Yang ◽  
Yunxia Ma ◽  
Qingzhi Yao ◽  
Yuan Ma ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Seasonal Dynamics ◽  
Bacterial Communities ◽  
Fungal Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ecological Guilds ◽  
Ulmus Pumila ◽  
Bacterial Phyla ◽  
Α Diversity

The seasonal dynamics of microbial diversity within the rhizosphere of Ulmus pumila L. var. sabulosa in the hinterland of the Otindag Sandy Land of China were investigated using high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences. A significant level of bacterial and fungal diversity was observed overall, with detection of 7,676 bacterial Operational Taxonomic Units (OTUs) belonging to 40 bacteria phyla and 3,582 fungal OTUs belonging to six phyla. Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial phyla among communities, while Ascomycota, Basidiomycota, and Zygomycota were the dominant phyla of fungal communities. Seasonal changes influenced the α-diversity and β-diversity of bacterial communities within elm rhizospheres more than for fungal communities. Inferred functional analysis of the bacterial communities identified evidence for 41 level two KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology groups, while guild-based analysis of the fungal communities identified eight ecological guilds. Metabolism was the most prevalent bacterial functional group, while saprotrophs prevailed among the identified fungal ecological guilds. Soil moisture and soil nutrient content were important factors that affected the microbial community structures of elm rhizospheres across seasons. The present pilot study provides an important baseline investigation of elm rhizosphere microbial communities.

scholarly journals P677 Fungal abundance is related to inflammatory status in Ulcerative Colitis

2021 ◽  
Vol 15 (Supplement_1) ◽  
pp. S598-S599
Author(s):  
C M Herrera De Guise ◽  
G Sarrabayrouse ◽  
E Varela ◽  
V Robles ◽  
N Borruel ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Fecal Samples ◽  
Inflammatory Status ◽  
Fungal Abundance ◽  
Gene Copies ◽  
16Srrna Gene ◽  
Over Time

Abstract Background Fungi account for approximately 0.1% of the total microorganisms in the gut. Despite the vast body of literature on the bacterial component of the gut microbiota, little has been published on the fungal microbiota. Fungal-bacterial interactions may be significant in inflammatory bowel disease (IBD), with several lines of evidence linking fungi and IBD. Our study aimed to explore and compare the fungal and bacterial loads in fecal samples from different ulcerative colitis (UC) patients’ groups. Methods Using two qPCR systems to amplify the ITS2 sequence from fungi and the 16srRNA gene from bacteria, we characterized and compared fungal and bacterial loads in 3 groups: 1) UClr: UC patients in long-term remission (≥5 years of flare-free disease, clinical, endoscopic and histological remission at inclusion); 2) UCsr: UC patients in short-term remission (3 months in clinical remission at inclusion and previously more than one relapse/year); 3) UCfl: UC patients with active disease (CAI &gt;4 at inclusion). We obtained two frozen fecal samples from all subjects, except for the UCfl group from which we obtained 1 sample at flare onset. Results were expressed in copies/g of feces. Results We included 87 UC patients, 29 in UClr, 20 in UCsr, and 38 in UCfl groups. Median age was 39 years, women comprised 52%. Fecal samples contained a significantly lower number of ITS2 gene copies (median 9.27E+05) than 16srRNA gene copies (median 4.28E+11). 16s rRNA gene copies were similar among the different groups with a median 3.88E+11 for UClr, median 5.29E+11 for UCsr, and median 4.315E+11 for UCfl patients (FDR p=0.65). In contrast, copies of ITS2 gene were increased in UCfl (median 1.95E+06) when compared to UClr (3.68E+04, FDR p=0.0036) but not significantly different to UCsr (5.24E+05 copies, FDR p=0.20). We analyzed the variation between samples over time; we compared the number of copies of ITS2 and 16s rRNA genes in fecal samples collected at two different time points: basal versus 8-weeks. We calculated overall fold changes that reflect stability over time. We found a trend for a more significant variation in the quantity of the ITS2 gene than the 16srRNA gene, but this was not significant. Analysis of the ITS2/16S rRNA ratio assessing the frequency of fungi compared to bacteria showed that this ratio was higher in UCfl (median 6.94E-06) when compared to UClr (median 2.63E-07, FDR p=0.0005) and UCsr patients (median 5.60E-07, FDR p=0.0072), there were no differences between UClr and UCsr patients. Conclusion Fungal abundance was increased in UC flare patients compared to UC patients in long remission, while there were no differences in bacterial abundance. This high number of fungi could be involved in the inflammatory response of UC patients.

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