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

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.

scholarly journals Deintensification of land use leads to recovery of soil microbial community composition and function after land use change in Ethiopia

2021 ◽  
Author(s):  
Yoseph Delelegn ◽  
Witoon Purahong ◽  
Ali Nawaz ◽  
Hans Sandén ◽  
Douglas Godbold ◽  
...  
Keyword(s):  
Land Use ◽  
Microbial Community ◽  
Land Use Change ◽  
Microbial Communities ◽  
Soil Microbial Community ◽  
Microbial Community Composition ◽  
Soil Microbial Communities ◽  
Natural Forest ◽  
Ecosystem Functions ◽  
Soil Microbial

Ethiopia has undergone significant land use change during the past centuries, particularly deforestation. These changes have resulted in the loss of topsoil as well as the associated soil ecosystem functions. Grazing exclusion and planting of eucalyptus are measures used to recover degraded lands and reduce deforestation, respectively. Using a gradient of the intensity of land use from natural forest to croplands, we investigated whether these measures also result in restoration of the soil microbial community. We identified the soil bacterial and fungal communities using paired-end amplicon sequencing. A total of 12,765 fungal and 12,325 bacterial OTUs were detected in the five land use types, and only ca. 2% and 17% were shared among the land uses, respectively. Total fungal and bacterial OTU richness was not significantly affected by land use change, but the conversion of forest to cropland resulted in the loss of approximately 40% and 11% of the total native fungal and bacterial OTUs, respectively. Soil pH, C, N, and aggregate stability were key factors corresponding to the overall bacterial and fungal community compositions. We also showed relationships between the microbial functional group and enzyme activities. The exclusion of grazing led to an enrichment of soil microbial communities that overlapped with the communities of the natural forest. Our results suggest that remnant native forests act as refugia for microbial communities and that restoration of microbial communities and concomitant recovery of ecosystem function via deintensification of land use is possible. Keywords: ectomycorrhiza, ericoid mycorrhiza, exclosure, microbial diversity, soil enzymes

scholarly journals Microbial Community Changes in the Rhizosphere Soil of Healthy and Rusty Panax ginseng and Discovery of Pivotal Fungal Genera Associated with Rusty Roots

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Xuemin Wei ◽  
Xiaoyue Wang ◽  
Pei Cao ◽  
Zitong Gao ◽  
Amanda Juan Chen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Panax Ginseng ◽  
Soil Microbial Community ◽  
Fungal Pathogens ◽  
High Throughput Sequencing ◽  
Microbial Community Composition ◽  
Pathogenic Fungi ◽  
Linear Discriminant ◽  
Rhizosphere Soils ◽  
Soil Microbial

Panax ginseng Meyer, a valuable medicinal plant, is severely threatened by rusty root, a condition that greatly affects its yield and quality. Studies investigating the relationship between soil microbial community composition and rusty roots are vital for the production of high-quality ginseng. Here, high-throughput sequencing was employed to systematically characterize changes in the soil microbial community associated with rusty roots. Fungal diversity was lower in the soils of rusty root-affected P. ginseng than in those of healthy plants. Importantly, principal coordinate analysis separated the fungal communities in the rhizosphere soils of rusty root-affected ginseng from those of healthy plants. The dominant bacterial and fungal genera differed significantly between rhizosphere soils of healthy and rusty root-affected P. ginseng, and linear discriminant analysis effect size (LEfSe) further indicated a strong imbalance in the soil microbial community of diseased plants. Significantly enriched bacterial genera (including Rhodomicrobium, Knoellia, Nakamurella, Asticcacaulis, and Actinomadura) were mainly detected in the soil of rusty root-affected P. ginseng, whereas significantly enriched fungal genera (including Xenopolyscytalum, Arthrobotrys, Chalara, Cryptococcus, and Scutellinia) were primarily detected in the soil of healthy plants. Importantly, five fungal genera (Cylindrocarpon, Acrophialophora, Alternaria, Doratomyces, and Fusarium) were significantly enriched in the soil of rusty root-affected plants compared with that of healthy plants, suggesting that an increase in the relative abundance of these pathogenic fungi (Cylindrocarpon, Alternaria, and Fusarium) may be associated with ginseng rusty roots. Additionally, this study is the first to report that an increase in the relative abundances of Acrophialophora and Doratomyces in the rhizosphere of P. ginseng may be associated with the onset of rusty root symptoms in this plant. Our findings provide potentially useful information for developing biological control strategies against rusty root, as well as scope for future screening of fungal pathogens in rusty roots of P. ginseng.

scholarly journals Effect of Litter-Derived Dissolved Organic Carbon Addition on Forest Soil Microbial Community Composition

2021 ◽  
Vol 1 ◽  
Author(s):  
Min Wang ◽  
Qiuxiang Tian ◽  
Chang Liao ◽  
Rudong Zhao ◽  
Feng Liu
Keyword(s):  
Microbial Community ◽  
Microbial Biomass ◽  
Organic Carbon ◽  
Dissolved Organic Carbon ◽  
Community Composition ◽  
Soil Microbial Biomass ◽  
Microbial Community Composition ◽  
Soil Microbial ◽  
Significant Difference ◽  
Microbial Groups

The input of dissolved organic carbon (DOC) into soil affects soil organic carbon mineralization and microbial community composition by changing carbon availability. However, up to now, there is little knowledge about the microbial groups that utilize the added DOC and how the incorporation process may vary over time. In this study, we added 13C-labeled litter-derived DOC (treatment) or pure water (control) to a forest soil from different layers to investigate the effects of DOC addition on soil microbial biomass and community composition in a 180-d laboratory incubation experiment. Soil microbial phospholipid fatty acid (PLFA) were measured to assess changes in the microbial community composition. The 13C incorporation into microbial biomass and PLFAs was analyzed to trace the microbial utilization of litter-derived DOC. Our results indicated that DOC addition increased the biomass of gram-negative bacteria, gram-positive bacteria, fungi, and actinomycetes, but the microbial community composition manifested a similar trend for both treatment and control soils at the end of incubation. Proportions of added DOC in different depths of soil microbial PLFAs had no significant difference. Moreover, 17:0 cy and 15:0 PLFAs which are described as the bacterial biomarkers had a greater amount of 13C incorporation than other PLFAs for the topsoil, which indicated that 13C-labeled litter-derived DOC was more easily assimilated by some specific bacterial community. Soil microbial biomass and the incorporation of 13C into PLFA reached its maximum around 30 days after DOC addition and then rapidly reduced to the level comparable to control. Overall, this study demonstrated that the incorporation of 13C-labeled litter-derived DOC into PLFA in different depth soil had no significant difference, and the incorporation of 13C by bacteria was higher than other microbial groups.

Real time interactions between soil microorganisms and microplastics at microscale

2021 ◽  
Author(s):  
P. Micaela Mafla-Endara ◽  
Pelle Ohlsson ◽  
Edith Hammer
Keyword(s):  
Microbial Community ◽  
Soil Microorganisms ◽  
Pore Space ◽  
Microbial Community Composition ◽  
Terrestrial Ecosystems ◽  
Microbial Colonization ◽  
Soil Mesofauna ◽  
Soil Macrofauna ◽  
Soil Microbial ◽  
Microbial Groups

<p>Terrestrial ecosystems are under threat due to the continuous accumulation of plastics in soils. Particularly, microplastics have been proven to negatively affect the performance of soil macrofauna such as earthworms, as well as soil mesofauna including springtails and nematodes. Unfortunately, two big groups remain largely unexplored: the soil microfauna and microflora.</p><p>Recent studies have shown that soil microbial community composition can significantly vary depending on the concentration and type of plastic, favouring some groups and disfavouring others. To have a better understanding of these relationships, it is necessary to study them at relevant scale: the microscale.</p><p>Considering that in situ observations are hard to achieve due to the opacity of soil and ever-changing soil architecture, we used transparent micro-engineered chips to study interactions between microplastics and soil microorganisms live. We hypothesized that different concentrations of microplastics interfere with a natural microbial community in terms of 1. Soil microbial colonization/succession of the chips and 2. Soil microbial growth inside the chips’ pore space.</p><p>We fabricated chips containing different microstructures that simulate soil pore spaces. The chips were bonded to a glass slide and one side was opened to allow microbial colonization. Each chip was filled with a mix of liquid nutrient medium and 1.0 µm polystyrene microbeads at microplastic concentrations of 0.0, 0.006, 0.001 and 0.0005 mg/ml. The chip´s opening was inoculated with 5 g of soil and incubated in the laboratory at room temperature for one month. We documented the presence/absence and abundance of different soil microbial groups changing over time by using an inverted microscope.</p><p>Our preliminary study reveals that larger microorganisms are sensitive to the presence of microbeads 1.0 µm size. We found that all major soil microbial groups (fungi, bacteria, and protists) and nematodes colonized the chips. However, their abundance was affected by the presence of microplastics, irrespective of the concentration. Particularly protists and nematodes were lower in number during the first days of the exposure. The beads were clearly visibly taken up into the cells of the protists or the digestive tract of the nematodes.</p><p>We are now investigating what consequences the lower abundance of certain soil microbial groups have for the soil food web. As seen here, micro-engineered chips are useful tools to provide visual access at the scale where most cell-to-cell interactions occur.</p>

scholarly journals Changes in Microbial Community Composition and Function during a Polyaromatic Hydrocarbon Phytoremediation Field Trial

2003 ◽  
Vol 69 (1) ◽  
pp. 483-489 ◽  
Author(s):  
Steven D. Siciliano ◽  
James J. Germida ◽  
Kathy Banks ◽  
Charles W. Greer
Keyword(s):  
Microbial Community ◽  
Festuca Arundinacea ◽  
Rhizosphere Soil ◽  
Microbial Community Composition ◽  
Hydrocarbon Degradation ◽  
Bulk Soil ◽  
Catabolic Gene ◽  
Soil Microbial ◽  
Catabolic Genes ◽  
And Function

ABSTRACT The purpose of this study was to investigate the mechanism by which phytoremediation systems promote hydrocarbon degradation in soil. The composition and degradation capacity of the bulk soil microbial community during the phytoremediation of soil contaminated with aged hydrocarbons was assessed. In the bulk soil, the level of catabolic genes involved in hydrocarbon degradation (ndoB, alkB, and xylE) as well as the mineralization of hexadecane and phenanthrene was higher in planted treatment cells than in treatment cells with no plants. There was no detectable shift in the 16S ribosomal DNA (rDNA) composition of the bulk soil community between treatments, but there were plant-specific and -selective effects on specific catabolic gene prevalence. Tall Fescue (Festuca arundinacea) increased the prevalence of ndoB, alkB, and xylE as well as naphthalene mineralization in rhizosphere soil compared to that in bulk soil. In contrast, Rose Clover (Trifolium hirtum) decreased catabolic gene prevalence and naphthalene mineralization in rhizosphere soil. The results demonstrated that phytoremediation systems increase the catabolic potential of rhizosphere soil by altering the functional composition of the microbial community. This change in composition was not detectable by 16S rDNA but was linked to specific functional genotypes with relevance to petroleum hydrocarbon degradation.

scholarly journals New Soil, Old Plants, and Ubiquitous Microbes: Evaluating the Potential of Incipient Basaltic Soil to Support Native Plant Growth and Influence Belowground Soil Microbial Community Composition

2018 ◽  
Author(s):  
Aditi Sengupta ◽  
Priyanka Kushwaha ◽  
Antonia Jim ◽  
Peter A. Troch ◽  
Raina Maier
Keyword(s):  
Microbial Community ◽  
Plant Growth ◽  
Community Composition ◽  
Plant Species ◽  
Soil Microbial Community ◽  
Soil Loss ◽  
Microbial Community Composition ◽  
Parent Material ◽  
Native Plant ◽  
Soil Microbial

The plant-microbe-soil nexus is critical in maintaining biogeochemical balance of the biosphere. However, soil loss and land degradation are occurring at alarmingly high rates, with soil loss exceeding soil formation rates. This necessitates evaluating marginal soils for their capacity to support and sustain plant growth. In a greenhouse study, we evaluated the capacity of marginal incipient basaltic parent material to support native plant growth, and the associated variation in soil microbial community dynamics. Three plant species, native to the Southwestern Arizona-Sonora region were tested with three soil treatments including basaltic parent material, parent material amended with 20% compost, and potting soil. The parent material with and without compost supported germination and growth of all the plant species, though germination was lower than the potting soil. A 16S rRNA amplicon sequencing approach showed Proteobacteria to be the most abundant phyla in both parent material and potting soil, followed by Actinobacteria. Microbial community composition had strong correlations with soil characteristics but not plant attributes within a given soil material. Predictive functional potential capacity of the communities revealed chemoheterotrophy as the most abundant metabolism within the parent material, while photoheterotrophy and anoxygenic photoautotrophy were prevalent in the potting soil. These results show that marginal incipient basaltic soil has the ability to support native plant species growth, and non-linear associations may exist between plant-marginal soil-microbial interactions.

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