Effects of Rhizosphere Microbial Composition on the Growth of Cajanus Cajan in Coal Gangue Reclaimed Soil

Abstract Planting the economically sustainable Cajanus cajan crop in coal gangue dump as an approach for ecological management has attracted extensive attention from scholars worldwide. Microorganisms play important roles in ecological restoration. However, there have been few reports about the microbial composition and functions of Cajanus cajan root systems planted in plateau waste dumps. In this study, the gangue dump (1,390 m above sea level) in Guizhou Plateau was covered with soil and planted with YN and JX Cajanus cajans. After one year, the Cajanus cajan root system was collected, and high-throughput sequencing was utilized to examine the bacterial and fungal biodiversity. The bacteria in all samples were assigned to six phyla and 60 genera. The unclassified_f_Enterobacteriaceae and Cedecea were the most abundant genera. The fungi were assigned to six phyla and 143 genera and Fusarium was the most abundant genus. Venn and heatmap analyses revealed differences in the dominant root species among Cajanus cajan varieties, Lactococcus and Fusarium. In JX and YN, Pseudoarthrobacter is a unique genus of bacteria; in JX, Robillarda is a unique genus of fungi; and in YN, Scytalidium is a unique genus of fungi. The endophytic fungi mainly play the roles of saprotroph, plant pathogen, and endophyte. Among the bacterial properties, L-arabinose isomerase and adenosine triphosphatase were the most abundant in all samples, while chitinase, catalase, and laccase played important roles in photosynthesis, degradation of lignin, chitin, and chitosan. This study guides the selection of reclamation plants and strategies for the migration and restriction of heavy metals in soil.

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Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

Microorganisms ◽

10.3390/microorganisms9020211 ◽

2021 ◽

Vol 9 (2) ◽

pp. 211

Author(s):

Jie Gao ◽

Miao Liu ◽

Sixue Shi ◽

Ying Liu ◽

Yu Duan ◽

...

Keyword(s):

Microbial Community ◽

High Throughput Sequencing ◽

Carbon Fixation ◽

Microbial Community Composition ◽

Ecosystem Functions ◽

Microbial Composition ◽

Wetland Ecosystems ◽

Soil Microbial ◽

Geochemical Properties ◽

Microbial Groups

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles.

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Experimental infection with the hookworm, Necator americanus, is associated with stable gut microbial diversity in human volunteers with relapsing multiple sclerosis

BMC Biology ◽

10.1186/s12915-021-01003-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Timothy P. Jenkins ◽

David I. Pritchard ◽

Radu Tanasescu ◽

Gary Telford ◽

Marina Papaiakovou ◽

...

Keyword(s):

Multiple Sclerosis ◽

Experimental Infection ◽

High Throughput Sequencing ◽

Alpha Diversity ◽

Placebo Treatment ◽

Sequencing Data ◽

Faecal Microbiota ◽

Microbial Composition ◽

Necator Americanus ◽

Human Volunteers

Abstract Background Helminth-associated changes in gut microbiota composition have been hypothesised to contribute to the immune-suppressive properties of parasitic worms. Multiple sclerosis is an immune-mediated autoimmune disease of the central nervous system whose pathophysiology has been linked to imbalances in gut microbial communities. Results In the present study, we investigated, for the first time, qualitative and quantitative changes in the faecal bacterial composition of human volunteers with remitting multiple sclerosis (RMS) prior to and following experimental infection with the human hookworm, Necator americanus (N+), and following anthelmintic treatment, and compared the findings with data obtained from a cohort of RMS patients subjected to placebo treatment (PBO). Bacterial 16S rRNA high-throughput sequencing data revealed significantly decreased alpha diversity in the faecal microbiota of PBO compared to N+ subjects over the course of the trial; additionally, we observed significant differences in the abundances of several bacterial taxa with putative immune-modulatory functions between study cohorts. Parabacteroides were significantly expanded in the faecal microbiota of N+ individuals for which no clinical and/or radiological relapses were recorded at the end of the trial. Conclusions Overall, our data lend support to the hypothesis of a contributory role of parasite-associated alterations in gut microbial composition to the immune-modulatory properties of hookworm parasites.

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Effect of Biofertilizers Application on Soil Biodiversity and Litter Degradation in a Commercial Apricot Orchard

Agronomy ◽

10.3390/agronomy11061116 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1116

Author(s):

Elena Baldi ◽

Paola Gioacchini ◽

Daniela Montecchio ◽

Stefano Mocali ◽

Livio Antonielli ◽

...

Keyword(s):

Nir Spectroscopy ◽

Microbial Composition ◽

Trichoderma Spp ◽

Soil Biodiversity ◽

Decomposition Processes ◽

Dta Analysis ◽

Litter Deposition ◽

Litter Degradation ◽

Bacteria And Fungi ◽

One Year

The aim of the present experiment was to determine if the supply of biofertilizers could differently stimulate the native microbiota, thus determining different patterns of organic material decomposition processes. The microbial composition of soil and litter was investigated by next generation sequencing using a metabarcoding approach. The chemical structure of the decomposing litterbags was investigated through the TG-DTA analysis and NIR spectroscopy. The study was conducted in an apricot orchard in Italy, and two different type of biofertilizers (AMF and Trichoderma spp.) were compared to unfertilized control over one year. Bacteria and fungi in soil, 162 days from litter deposition, evidenced differentiated clusters for control and both biofertilizers; on the other hand, only fungal composition of litterbags was modified as a consequence of Trichoderma spp. supply; no effect was observed in the bacterial community of litterbags. NIR and TG-DTA analysis evidenced a significant change over time of the chemical composition of litterbags with a faster degradation as a consequence of Trichoderma spp. supply testified by a higher degradation coefficient (1.9) than control (1.6) and AMF (1.7). The supply of biofertilizers partially modified the bacteria community of soil, while Trichoderma spp. Influenced the fungal community of the litter. Moreover, Trichoderma spp. Evidenced a faster and higher degradation of litter than AMF-biofertilizers, laying the foundation for an efficient use in orchard.

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Bioconductor workflow for microbiome data analysis: from raw reads to community analyses

F1000Research ◽

10.12688/f1000research.8986.1 ◽

2016 ◽

Vol 5 ◽

pp. 1492 ◽

Cited By ~ 148

Author(s):

Ben J. Callahan ◽

Kris Sankaran ◽

Julia A. Fukuyama ◽

Paul J. McMurdie ◽

Susan P. Holmes

Keyword(s):

High Throughput Sequencing ◽

Linear Models ◽

Reference Database ◽

Rrna Gene ◽

Microbial Composition ◽

Nonparametric Testing ◽

Abundance Estimates ◽

Taxonomic Markers ◽

Microbiome Data ◽

Microbiome Data Analysis

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.

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Bioregional Alterations in Gut Microbiome Contribute to the Plasma Metabolomic Changes in Pigs Fed with Inulin

Microorganisms ◽

10.3390/microorganisms8010111 ◽

2020 ◽

Vol 8 (1) ◽

pp. 111 ◽

Cited By ~ 5

Author(s):

Weida Wu ◽

Li Zhang ◽

Bing Xia ◽

Shanlong Tang ◽

Lei Liu ◽

...

Keyword(s):

Gut Microbiota ◽

High Throughput Sequencing ◽

Mantel Test ◽

Plasma Metabolites ◽

Microbial Composition ◽

Regional Effects ◽

Host Interaction ◽

Β Diversity ◽

Branched Chain ◽

Host Metabolism

Inulin (INU) is a non-digestible carbohydrate, known for its beneficial properties in metabolic disorders. However, whether and how gut microbiota in its regulation contributes to host metabolism has yet to be investigated. We conduct this study to examine the possible associations between the gut microbiota and circulating gut microbiota–host co-metabolites induced by inulin interventions. Plasma and intestinal site samples were collected from the pigs that have consumed inulin diet for 60 days. High-throughput sequencing was adopted for microbial composition, and the GC-TOF-MS-based metabolomics were used to characterize featured plasma metabolites upon inulin intervention. Integrated multi-omics analyses were carried out to establish microbiota–host interaction. Inulin consumption decreased the total cholesterol (p = 0.04) and glucose (p = 0.03) level in serum. Greater β-diversity was observed in the cecum and colon of inulin-fed versus that of control-fed pigs (p < 0.05). No differences were observed in the ileum. In the cecum, 18 genera were altered by inulin, followed by 17 in the colon and 6 in the ileum. Inulin increased propionate, and isobutyrate concentrations but decreased the ratio of acetate to propionate in the cecum, and increased total short fatty acids, valerate, and isobutyrate concentrations in the colon. Metabolomic analysis reveals that indole-3-propionic acid (IPA) was significantly higher, and the branched-chain amino acids (BCAA), L-valine, L-isoleucine, and L-leucine are significantly lower in the inulin groups. Mantel test and integrative analysis revealed associations between plasma metabolites (e.g., IPA, BCAA, L-tryptophan) and inulin-responsive cecal microbial genera. These results indicate that the inulin has regional effects on the intestine microbiome in pigs, with the most pronounced effects occurring in the cecum. Moreover, cecum microbiota plays a pivotal role in the modulation of circulating host metabolites upon inulin intervention

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Clinical characteristics associated with the properties of gut microbiota in peritoneal dialysis patients

Peritoneal Dialysis International ◽

10.1177/0896860820976983 ◽

2020 ◽

pp. 089686082097698

Author(s):

Na Jiang ◽

Chenhong Zhang ◽

Hao Feng ◽

Jiangzi Yuan ◽

Li Ding ◽

...

Keyword(s):

Renal Function ◽

Peritoneal Dialysis ◽

Gut Microbiota ◽

Clinical Characteristics ◽

High Throughput Sequencing ◽

Residual Renal Function ◽

Microbial Composition ◽

Cross Sectional ◽

Dialysis Duration ◽

Glucose Exposure

Background: Gut microbiota alters in patients with end-stage renal disease, which contributes to inflammation, atherosclerosis, and results in increased incidence of cardiovascular diseases. The present study investigated the potential clinical factors, which influence the gut microbial structure and function in patients undergoing peritoneal dialysis (PD). Methods: This is a cross-sectional study performed in 81 prevalent PD patients. Gut microbiota was assessed by high throughput sequencing of 16S ribosomal ribonucleic acid gene in fecal samples. Gas chromatography was conducted to measure stool short-chain fat acid (SCFA) concentrations. Demographic parameters and clinical characteristics, including dialysis regimen, residual renal function, nutrition, and inflammation, were retrieved and related to the properties of gut microbiota. Results: PD duration, peritoneal glucose exposure, and estimated glomerulus filtration rate (eGFR) were identified to be associated with microbial variations. Significant separation of microbial composition was shown between patients with short or long PD duration ( p = 0.015) and marginal differences were found between patients grouped by different levels of peritoneal glucose exposure ( p = 0.056) or residual renal function ( p = 0.063). A couple of gut bacteria showed different abundance at amplicon sequencing variant level between these patient groups ( p < 0.05). In addition, stool isobutyric and isovaleric acid concentrations were significantly reduced in patients with longer dialysis duration, higher peritoneal glucose exposure, or declined eGFR ( p < 0.05). Conclusions: This pilot study demonstrated that long dialysis duration, high peritoneal glucose exposure, and loss of residual renal function were associated with gut microbiota alteration and reduced branched-chain SCFA production in PD patients.

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Intestinal epithelial cell-specific IGF1 promotes the expansion of intestinal stem cells during epithelial regeneration and functions on the intestinal immune homeostasis

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.00022.2018 ◽

2018 ◽

Vol 315 (4) ◽

pp. E638-E649 ◽

Cited By ~ 5

Author(s):

Yu Zheng ◽

Yongli Song ◽

Qi Han ◽

Wenjie Liu ◽

Jiuzhi Xu ◽

...

Keyword(s):

Stem Cells ◽

Epithelial Cell ◽

Intestinal Epithelial Cell ◽

High Throughput Sequencing ◽

Secretory Cells ◽

Intestinal Epithelial ◽

Epithelial Stem Cells ◽

Microbial Composition ◽

Epithelial Regeneration

It is well known that insulin-like growth factor 1 (IGF1) acts as a trophic factor in small intestine under both physiological and pathophysiological conditions. However, it still lacks direct in vivo evidence of the functions of intestinal epithelial cell (IEC)-specific IGF1 under both normal and pathological conditions. Using IEC-specific IGF1-knockout (cKO) mice and Lgr5-eGFP-CreERT mice, we demonstrate that IEC-specific IGF1 can enhance nutrient uptake, reduce protein catabolism and energy consumption, and promote the proliferation and expansion of intestinal epithelial cells, including intestinal epithelial stem cells and intestinal secretory cells. Next, we showed that IEC-specific IGF1 renders IECs resistant to irradiation and promotes epithelial regeneration. Strikingly, transcriptome profiling assay revealed that many differentially expressed genes involved in the differentiation and maturation of lymphoid lineages were significantly suppressed in the cKO mice as compared with the control mice. We demonstrated that deletion of IGF1 in IECs enhances bacterial translocation to the mesenteric lymph nodes and liver. Furthermore, high-throughput sequencing of 16S ribosomal RNA genes of gut microbiota revealed that IEC-specific IGF1 loss profoundly affected the gut microbial composition at various levels of classification. Therefore, our findings shed light on the in vivo roles of IEC-specific IGF1 in intestinal homeostasis, epithelial regeneration, and immunity, broadening our current insights on IGF1 functions.

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Biocontrol of Aspergillus flavus in Ensiled Sorghum by Water Kefir Microorganisms

Microorganisms ◽

10.3390/microorganisms7080253 ◽

2019 ◽

Vol 7 (8) ◽

pp. 253 ◽

Cited By ~ 3

Author(s):

Gonda ◽

Garmendia ◽

Rufo ◽

Peláez ◽

Wisniewski ◽

...

Keyword(s):

Aspergillus Flavus ◽

High Throughput Sequencing ◽

Management Practice ◽

Bacterial Phyla ◽

Mixed Inoculum ◽

Sorghum Grains ◽

Before And After ◽

Relevant Role ◽

Abundant Genus ◽

Water Kefir

The capacity of microorganisms from water kefir (WK) to control Aspergillus flavus growth during the aerobic phase of ensiled sorghum grains was determined. Sorghum inoculated with A. flavus was treated with filter-sterilized and non-sterilized water kefir, ensiled, and incubated 7 days at 25 °C. A. flavus growth was quantified by qPCR after incubation. Mold growth was inhibited in the presence of water kefir while no inhibition was observed when filter-sterilized water kefir was applied, demonstrating the relevant role of the microorganisms in the kefir water in the biocontrol process. Fungal and bacterial diversity in treated sorghum mini-silos was analyzed by high-throughput sequencing. Firmicutes was the predominant bacterial phyla and Lactobacillus represented the most abundant genus, while Ascomycota was the predominant fungal phyla with Saccharomyces and Pichia as the major genera. Bacterial and yeast counts before and after incubation indicated that the microbial community obtained from WK was able to grow in the sorghum mini-silos in the presence of A. flavus. Results of the present work indicate that the use of a mixed inoculum of microorganisms present in WK may represent an alternative management practice to avoid the growth of A. flavus in ensiled sorghum grains and the concomitant contamination with aflatoxins.

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Early Stage Root-Associated Fungi Show a High Temporal Turnover, but Are Independent of Beech Progeny

Microorganisms ◽

10.3390/microorganisms8020210 ◽

2020 ◽

Vol 8 (2) ◽

pp. 210 ◽

Cited By ~ 1

Author(s):

Kezia Goldmann ◽

Silke Ammerschubert ◽

Rodica Pena ◽

Andrea Polle ◽

Bin-Wei Wu ◽

...

Keyword(s):

High Throughput Sequencing ◽

Early Stage ◽

European Beech ◽

Fungal Species ◽

Fungal Communities ◽

Transplant Experiment ◽

Fungal Community Structure ◽

Temporal Turnover ◽

One Year ◽

The Impact

The relationship between trees and root-associated fungal communities is complex. By specific root deposits and other signal cues, different tree species are able to attract divergent sets of fungal species. Plant intraspecific differences can lead to variable fungal patterns in the root’s proximity. Therefore, within the Beech Transplant Experiment, we analyzed the impact of three different European beech ecotypes on the fungal communities in roots and the surrounding rhizosphere soil at two time points. Beech nuts were collected in three German sites in 2011. After one year, seedlings of the different progenies were out-planted on one site and eventually re-sampled in 2014 and 2017. We applied high-throughput sequencing of the fungal ITS2 to determine the correlation between tree progeny, a possible home-field advantage, plant development and root-associated fungal guilds under field conditions. Our result showed no effect of beech progeny on either fungal OTU richness or fungal community structure. However, over time the fungal OTU richness in roots increased and the fungal communities changed significantly, also in rhizosphere. In both plant compartments, the fungal communities displayed a high temporal turnover, indicating a permanent development and functional adaption of the root mycobiome of young beeches.

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High-Throughput, Sequence-Based Analysis of the Microbiota of Greek Kefir Grains from Two Geographic Regions

Food Technology and Biotechnology ◽

10.17113/ftb.58.02.20.6581 ◽

2020 ◽

Vol 58 (2) ◽

pp. 138-146

Author(s):

Mary S. Kalamaki ◽

Apostolos S. Angelidis

Keyword(s):

Bacterial Community ◽

High Throughput ◽

High Throughput Sequencing ◽

Geographic Origin ◽

Probiotic Properties ◽

Sequencing Analysis ◽

Microbial Composition ◽

Bacterial Phyla ◽

Geographic Regions ◽

Kefir Grains

Research background. Kefir is a natural probiotic drink traditionally produced by milk fermentation using kefir grains. Kefir grains are composed of a complex population of bacteria and yeasts embedded in a polysaccharide-protein matrix. The geographic origin of kefir grains may largely influence their microbial composition and the associated kefir drink properties. Although the detailed bacterial composition of kefir grains from several geographic regions has been reported, to date, analogous data about the microbiome of Greek kefir are lacking. Hence, the aim of this study is to investigate the structure and the diversity of the bacterial community of Greek kefir grains.Experimental approach. The bacterial community structure and diversity of two different kefir grains from distant geographic regions in Greece were examined via high-throughput sequencing analysis, a culture-independent metagenomic approach, targeting the 16S rRNA V4 variable region, in order to gain a deeper understanding of their bacterial population diversities.Results and conclusions. Firmicutes (a phylum that includes lactic acid bacteria) was strikingly dominant amongst the identified bacterial phyla, with over 99 % of the sequences from both kefir grains classified to this phylum. At the family level, Lactobacillaceae sequences accounted for more than 98 % of the operational taxonomic units (OTUs), followed by Ruminococcaceae, Lahnospiraceae, Bacteroidaceae and other bacterial families of lesser abundance. Α relatively small number of bacterial genera dominated, with Lactobacillus kefiranofaciens being the most abundant in both kefir grains (95.0 % of OTUs in kefir A and 96.3 % of OTUs in kefir B). However, a quite variable subdominant population was also present in both grains, including bacterial genera that have been previously associated with the gastrointestinal tract of humans and animals, some of which are believed to possess probiotic properties (Faecalibacterium spp., Bacteroides spp., Blautia spp.). Differences among the bacterial profiles of the two grains were very small indicating a high homogeneity despite the distant geographic origin.Novelty and scientific contribution. This is the first study to deeply explore and report on the bacterial diversity and species richness of Greek kefir.

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