Influence of soil factors on the microbiome of Rendzic Leptosols chronosequence in the Crimean Peninsula

2021 ◽  
Author(s):  
Anastasiia Kimeklis ◽  
Grigory Gladkov ◽  
Aleksei Zverev ◽  
Arina Kichko ◽  
Evgeny Andronov ◽  
...  
Keyword(s):  
Soil Formation ◽  
Alpha Diversity ◽  
Parent Material ◽  
Soil Microbiome ◽  
Soil Horizon ◽  
Rrna Gene ◽  
Reactive Component ◽  
Crimean Peninsula ◽  
Russian Scientific ◽  
Limestone Bedrock

<p>Pedogenesis depends on multiple factors, such as climate, vegetation, topography, parent material. Some of these factors are zonal, meaning they are determined by climate zone. But some factors are intrazonal, meaning that it has the same impact on soil formation in different climate zones. One example is parent material. The other peculiar feature of a parent material is that it determines the rates of pedogenesis. In this regard, Rendzic Leptosols – are intrazonal slowly developing soils formed on a limestone bedrock. In this study we approached the dynamics of microbiome formation in a chronosequence of these soils collected in Crimean Peninsula using analysis of 16S rRNA gene libraries and quantitative PCR. The chronosequence included benchmark soil, 700 year-old soil from the ancient city of Eski-Kermen, 70 year-old soil from WWII trenches and 50 year-old soil from the open quarry screenings. Our research demonstrated that soil type on a limestone rock is the driving force behind microbiome shaping, without any apparent influence of its age. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. CCA analysis, in combination with PERMANOVA, linked differences in microbiomes to the nutrients associated with the soil horizon, and our analysis showed that the reactive component of the soil microbiome shifted simultaneously in both soil horizons between different soil sites.</p><p>The work was supported by the grant of the Russian Scientific Foundation, project 17-16-01030.</p>

scholarly journals Soil microbiome in chronosequence of spoil heaps of Kursk Magnetic Anomaly

2019 ◽  
Vol 64 (3) ◽  
Author(s):  
Ekaterina Ivanova ◽  
Elizaveta Pershina ◽  
Dina Karpova ◽  
Olga Rogova ◽  
Evgeny Abakumov ◽  
...  
Keyword(s):  
Magnetic Anomaly ◽  
Soil Formation ◽  
Variable Region ◽  
Active Role ◽  
Taxonomic Diversity ◽  
Taxonomic Composition ◽  
Soil Microbiome ◽  
Rrna Gene ◽  
Kursk Magnetic Anomaly ◽  
Mining Areas

The physicochemical parameters, vegetation and biodiversity of microbiomes inhabiting 10-, 35- and 50-year-old embryonic soils (technozems) formed in the mining areas of the Kursk Magnetic Anomaly (Russia) were analyzed in the current study. Analysis of taxonomic diversity was carried out by 454-pyrosequencing of the V4 variable region of the 16S rRNA gene. All points of the chronosequence were characterized by microbiomes reliably differing in taxonomic composition. The older the dump, the higher the proportion of bacteria from the phyla Actinobacteria (mostly representatives of the Solirubrobacteriaceae family), Chloroflexi and Acidobacteria in the community. In 10-year-old dumps, bacteria from the phyla Proteobacteria, Gemmatimonadetes and Bacteroides prevailed. The most pronounced changes in the community structure at the early and middle stages of microbiological succession were demonstrated by bacteria from the genus Delftia, which may indicate their active role in the processes of soil formation in this ecosystem.

Mineralogical and weathering study of a red-brown earth formed on granodiorite

Soil Research ◽  
1966 ◽  
Vol 4 (2) ◽  
pp. 181 ◽  
Author(s):  
P Green
Keyword(s):  
Soil Formation ◽  
Progressive Increase ◽  
Particle Size Analysis ◽  
Parent Material ◽  
Soil Horizon ◽  
Size Analysis ◽  
Forming Process ◽  
Gains And Losses ◽  
In Situ Weathering

The development of a red-brown earth has been studied by means of mineral and fabric analyses. Data from particle-size analysis and zircon distribution indicate relative uniformity of the parent material throughout the profile, with a possible minor disconformity near the bottom of the B horizon. Calculations of gains and losses of major minerals during soil formation, based on the zircon content of each soil horizon and of the rock, show a break in the progressive increase in weathering towards the surface, suggesting that the soil is in fact a two-storied profile; micromorphological evidence supports this postulate. The constancy of the qualitative mineral assemblage, however, shows that both sola were formed entirely from the underlying weathered granodiorite. The top four horizons are interpreted as being a separate soil, probably developed from a surface movement layer composed of some material from the upper horizons of the older profile with accessions from weathering granodiorite boulders. Both soils are considered to have been formed dominantly by in situ weathering of primary minerals and removal of the weathering products by leaching; clay illuviation does not appear to have been more than a very minor soil-forming process.

scholarly journals Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10871
Author(s):  
Anastasiia K. Kimeklis ◽  
Grigory V. Gladkov ◽  
Aleksei O. Zverev ◽  
Arina A. Kichko ◽  
Evgeny E. Andronov ◽  
...  
Keyword(s):  
Anthropogenic Impacts ◽  
Rapid Development ◽  
Plant Litter ◽  
Soil Horizon ◽  
Rrna Gene ◽  
Soil Horizons ◽  
Crimean Peninsula ◽  
Microbiome Composition ◽  
Different Ages ◽  
The Crimean Peninsula

Rendzic Leptosols are intrazonal soils formed on limestone bedrock. The specialty of these soils is that parent rock material is more influential in shaping soil characteristics than zonal factors such as climate, especially during soil formation. Unlike fast evolving Podzols due to their leaching regime, Leptosols do not undergo rapid development due to the nature of the limestone. Little is known how microbiome reflects this process, so we assessed microbiome composition of Rendzic Leptosols of different ages, arising from disruption and subsequent reclamation. The mountains and foothills that cover much of the Crimean Peninsula are ideal for this type of study, as the soils were formed on limestone and have been subjected to anthropogenic impacts through much of human history. Microbiomes of four soil sites forming a chronosequence, including different soil horizons, were studied using sequencing of 16S rRNA gene libraries and quantitative PCR. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. The oldest and the youngest soils had the most similar microbiomes, which could have been caused by their geographic proximity. Oligotrophic bacteria from Chitinophagaceae, Blastocatellaceae and Rubrobacteriaceae dominated the microbiome of these soils. The microbiome of 700-year old soil was the most diverse. This soil was from the only study location with topsoil formed by plant litter, which provided additional nutrients and could have been the driving force of this differentiation. Consistent with this assumption, this soil was abundant in copiotrophic bacteria from Proteobacteria and Actinobacteria phyla. The microbiome of 50-year old Leptosol was more similar to the microbiome of benchmark soil than the microbiome of 700-year old soil, especially by weighted metrics. CCA analysis, in combination with PERMANOVA, linked differences in microbiomes to the joint change of all soil chemical parameters between soil horizons. Local factors, such as parent material and plant litter, more strongly influenced the microbiome composition in Rendzic Leptosols than soil age.

Contributions to the Knowledge of Sandy Soils from Oltenia Plain

2020 ◽  
Vol 71 (1) ◽  
pp. 192-200
Author(s):  
Anca-Luiza Stanila ◽  
Catalin Cristian Simota ◽  
Mihail Dumitru
Keyword(s):  
Chemical Properties ◽  
Soil Formation ◽  
Sandy Soils ◽  
Physical Geography ◽  
Parent Material ◽  
Negative Effects ◽  
Small Water ◽  
Wind Characteristic ◽  
The One ◽  
Physical And Chemical

Highlighting the sandy soil of Oltenia Plain calls for a better knowledge of their variability their correlation with major natural factors from each physical geography. Pedogenetic processes specific sandy soils are strongly influenced by nature parent material. This leads, on the one hand, climate aridity of the soil due to strong heating and accumulation of small water reserves, consequences emphasizing the moisture deficit in the development of the vegetation and favoring weak deflation, and on the other hand, an increase in mineralization organic matter. Relief under wind characteristic sandy land, soil formation and distribution has some particularly of flat land with the land formed on the loess. The dune ridges are less evolved soils, profile underdeveloped and poorly supplied with nutrients compared to those on the slopes of the dunes and the interdune, whose physical and chemical properties are more favorable to plant growth.Both Romanati Plain and the Blahnita (Mehedinti) Plain and Bailesti Plain, sand wind shaped covering a finer material, loamy sand and even loess (containing up to 26% clay), also rippled with negative effects in terms of overall drainage. Depending on the pedogenetic physical and geographical factors that have contributed to soil cover, in the researched were identified following classes of soils: protisols, cernisols, cambisols, luvisols, hidrisols and antrosols.Obtaining appropriate agricultural production requires some land improvement works (especially fitting for irrigation) and agropedoameliorative works. Particular attention should be paid to preventing and combating wind erosion.

scholarly journals Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert C. Kaplan ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
Martha L. Daviglus ◽  
...  
Keyword(s):  
Community Health ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Health Study ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Hispanic Community ◽  
The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

scholarly journals Comparative analysis of bacterioplankton assemblages from two subtropical karst reservoirs of southwestern China with contrasting trophic status

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qiang Li ◽  
Yadan Huang ◽  
Shenglin Xin ◽  
Zhongyi Li
Keyword(s):  
Trophic Status ◽  
Alpha Diversity ◽  
Decisive Role ◽  
Sensu Stricto ◽  
Karst Area ◽  
Southwestern China ◽  
Rrna Gene ◽  
Karst Water ◽  
Bacterioplankton Community ◽  
Generation Sequencing

AbstractAlthough bacterioplankton play an important role in aquatic ecosystems, less is known about bacterioplankton assemblages from subtropical karst reservoirs of southwestern China with contrasting trophic status. Here, 16S rRNA gene next-generation sequencing coupled with water chemistry analysis was applied to compare the bacterioplankton communities from a light eutrophic reservoir, DL Reservoir, and a mesotrophic reservoir, WL Reservoir, in subtropical karst area of southwestern China. Our findings indicated that Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia dominated bacterioplankton community with contrasting relative frequency in the two subtropical karst reservoirs. Proteobacteria and Bacteroidetes were the core communities, which played important roles in karst biogeochemical cycles. Though WT, TN and DOC play the decisive role in assembling karst aquatic bacterioplankton, trophic status exerted significantly negative direct effects on bacterioplankton community composition and alpha diversity. Due to contrasting trophic status in the two reservoirs, the dominant taxa such as Enterobacter, Clostridium sensu stricto, Candidatus Methylacidiphilum and Flavobacteriia, that harbor potential functions as valuable and natural indicators of karst water health status, differed in DL Reservoir and WL Reservoir.

scholarly journals Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hua Zha ◽  
Fengping Liu ◽  
Zongxin Ling ◽  
Kevin Chang ◽  
Jiezuan Yang ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Type 2 Diabetes ◽  
Type 2 Diabetes Mellitus ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Diversity Indices ◽  
Vital Role ◽  
Rrna Gene ◽  
Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

scholarly journals Effect of hay type on cecal and fecal microbiome and fermentation parameters in horses

2020 ◽  
Author(s):  
Rachel J Sorensen ◽  
James S Drouillard ◽  
Teresa L Douthit ◽  
Qinghong Ran ◽  
Douglas G Marthaler ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Volatile Fatty Acids ◽  
Random Effect ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Fecal Microbiome ◽  
Β Diversity ◽  
Fermentation Parameters

Abstract The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split plot design run as a crossover in 2 periods. Whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. Main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, all possible interactions and random effect of horse. Alpha and β diversity were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05) whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total volatile fatty acid (VFA) concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared to cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared to the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared to cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.

scholarly journals Effect of Bovine MFGM and LF in Infant Formula on Gut Microbiome and Metabolome at Four Months of Age

2021 ◽  
Author(s):  
Maciej Chichlowski ◽  
Nicholas Bokulich ◽  
Cheryl L Harris ◽  
Jennifer L Wampler ◽  
Fei Li ◽  
...  
Keyword(s):  
Infant Formula ◽  
Beta Diversity ◽  
Milk Fat ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Term Infants ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Metabolite Profiles

Abstract Background Milk fat globule membrane (MFGM) and lactoferrin (LF) are human milk bioactive components demonstrated to support gastrointestinal (GI) and immune development. Significantly fewer diarrhea and respiratory-associated adverse events through 18 months of age were previously reported in healthy term infants fed a cow's milk-based infant formula with added source of bovine MFGM and bovine LF through 12 months of age. Objectives To compare microbiota and metabolite profiles in a subset of study participants. Methods Stool samples were collected at Baseline (10–14 days of age) and Day 120 (MFGM + LF: 26, Control: 33). Bacterial community profiling was performed via16S rRNA gene sequencing (Illumina MiSeq) and alpha and beta diversity were analyzed (QIIME 2). Differentially abundant taxa were determined using Linear discriminant analysis effect size (LefSE) and visualized (Metacoder). Untargeted stool metabolites were analyzed (HPLC/mass spectroscopy) and expressed as the fold-change between group means (Control: MFGM + LF ratio). Results Alpha diversity increased significantly in both groups from baseline to 4 months. Subtle group differences in beta diversity were demonstrated at 4 months (Jaccard distance; R2 = 0.01, P = 0.042). Specifically, Bacteroides uniformis and Bacteroides plebeius were more abundant in the MFGM + LF group at 4 months. Metabolite profile differences for MFGM + LF vs Control included: lower fecal medium chain fatty acids, deoxycarnitine, and glycochenodeoxycholate, and some higher fecal carbohydrates and steroids (P < 0.05). After applying multiple test correction, the differences in stool metabolomics were not significant. Conclusions Addition of bovine MFGM and LF in infant formula was associated with subtle differences in stool microbiome and metabolome by four months of age, including increased prevalence of Bacteroides species. Stool metabolite profiles may be consistent with altered microbial metabolism. Trial registration:  https://clinicaltrials.gov/ct2/show/NCT02274883).

scholarly journals Modulation of Saliva Microbiota through Prebiotic Intervention in HIV-Infected Individuals

Nutrients ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 1346 ◽  
Author(s):  
Nuria Jiménez-Hernández ◽  
Sergio Serrano-Villar ◽  
Alba Domingo ◽  
Xavier Pons ◽  
Alejandro Artacho ◽  
...  
Keyword(s):  
Hiv Infection ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Microbiota Composition ◽  
Hiv Status ◽  
T Helper ◽  
Immunodeficiency Virus ◽  
Salivary Microbiota ◽  
Rrna Gene Sequencing

Human immunodeficiency virus (HIV) infection is characterized by an early depletion of the mucosal associated T helper (CD4+) cells that impair the host immunity and impact the oral and gut microbiomes. Although, the HIV-associated gut microbiota was studied in depth, few works addressed the dysbiosis of oral microbiota in HIV infection and, to our knowledge, no studies on intervention with prebiotics were performed. We studied the effect of a six-week-long prebiotic administration on the salivary microbiota in HIV patients and healthy subjects. Also, the co-occurrence of saliva microorganisms in the fecal bacteria community was explored. We assessed salivary and feces microbiota composition using deep 16S ribosomal RNA (rRNA) gene sequencing with Illumina methodology. At baseline, the different groups shared the same most abundant genera, but the HIV status had an impact on the saliva microbiota composition and diversity parameters. After the intervention with prebiotics, we found a drastic decrease in alpha diversity parameters, as well as a change of beta diversity, without a clear directionality toward a healthy microbiota. Interestingly, we found a differential response to the prebiotics, depending on the initial microbiota. On the basis of 100% identity clustering, we detected saliva sequences in the feces datasets, suggesting a drag of microorganisms from the upper to the lower gastrointestinal tract.

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