Different responses of bacteria and fungi to environmental variables and corresponding community assembly in Sb-contaminated soil

2022 ◽  
pp. 118812
Author(s):  
Weiqi Wang ◽  
Hongmei Wang ◽  
Xiaoyu Cheng ◽  
Mengxiaojun Wu ◽  
Yuyang Song ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Community Assembly ◽  
Environmental Variables ◽  
Bacteria And Fungi

Petroleum biodegradation capacity of bacteria and fungi isolated from petroleum-contaminated soil

2017 ◽  
Vol 116 ◽  
pp. 48-57 ◽  
Author(s):  
Charlotte Marchand ◽  
Marc St-Arnaud ◽  
William Hogland ◽  
Terrence H. Bell ◽  
Mohamed Hijri
Keyword(s):  
Contaminated Soil ◽  
Petroleum Contaminated Soil ◽  
Bacteria And Fungi

scholarly journals Reduction of Some Heavy Metals in Fibre Cement Roofing Sheet Waste-Contaminated Soil by Consortium of Bacteria and Fungi

2020 ◽  
Vol 10 (3) ◽  
pp. 43
Author(s):  
Olubunmi Olufunmi Akpomie ◽  
Catherine Ese Balogun ◽  
Timothy Marhiere Akpomie
Keyword(s):  
Heavy Metals ◽  
Contaminated Soil ◽  
Fibre Cement ◽  
Bacteria And Fungi

Reduction of Some Heavy Metals in Fibre Cement Roofing Sheet Waste-Contaminated Soil by Consortium of Bacteria and Fungi

scholarly journals Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
E. N. Melekhina ◽  
E. S. Belykh ◽  
M. Yu. Markarova ◽  
A. A. Taskaeva ◽  
E. E. Rasova ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Taxonomic Diversity ◽  
Northern Taiga ◽  
Contaminated Sites ◽  
Oil Contamination ◽  
Polluted Soils ◽  
Degrading Bacteria ◽  
Upper Level ◽  
Bacteria And Fungi ◽  
Soil Level

AbstractThe present comprehensive study aimed to estimate the aftermath of oil contamination and the efficacy of removing the upper level of polluted soil under the conditions of the extreme northern taiga of northeastern European Russia. Soil samples from three sites were studied. Two sites were contaminated with the contents of a nearby sludge collector five years prior to sampling. The highly contaminated upper soil level was removed from one of them. The other was left for self-restoration. A chemical analysis of the soils was conducted, and changes in the composition of the soil zoocoenosis and bacterial and fungal microbiota were investigated. At both contaminated sites, a decrease in the abundance and taxonomic diversity of indicator groups of soil fauna, oribatid mites and collembolans compared to the background site were found. The pioneer eurytopic species Oppiella nova, Proisotoma minima and Xenyllodes armatus formed the basis of the microarthropod populations in the contaminated soil. A complete change in the composition of dominant taxonomic units was observed in the microbiota, both the bacterial and fungal communities. There was an increase in the proportion of representatives of Proteobacteria and Actinobacteria in polluted soils compared to the background community. Hydrocarbon-degrading bacteria—Alcanivorax, Rhodanobacter ginsengisoli, Acidobacterium capsulatum, and Acidocella—and fungi—Amorphotheca resinae abundances greatly increased in oil-contaminated soil. Moreover, among both bacteria and fungi, a sharp increase in the abundance of uncultivated organisms that deserve additional attention as potential oil degraders or organisms with a high resistance to oil contamination were observed. The removal of the upper soil level was partly effective in terms of decreasing the oil product concentration (from approximately 21 to 2.6 g/kg of soil) and preventing a decrease in taxonomic richness but did not prevent alterations in the composition of the microbiota or zoocoenosis.

Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms

2019 ◽  
Vol 95 (6) ◽  
Author(s):  
Anders Bjørnsgaard Aas ◽  
Carrie J Andrew ◽  
Rakel Blaalid ◽  
Unni Vik ◽  
Håvard Kauserud ◽  
...  
Keyword(s):  
Microbial Community ◽  
Spatial Structure ◽  
Community Assembly ◽  
High Throughput Sequencing ◽  
Spatial Scales ◽  
Microbial Community Composition ◽  
Diversity Patterns ◽  
Bistorta Vivipara ◽  
Adjacent Soil ◽  
Bacteria And Fungi

ABSTRACT The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.

scholarly journals Microbial abundance, composition, and function in nectar are shaped by flower visitor identity

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Megan M Morris ◽  
Natalie J Frixione ◽  
Alexander C Burkert ◽  
Elizabeth A Dinsdale ◽  
Rachel L Vannette
Keyword(s):  
Community Assembly ◽  
Culturable Bacteria ◽  
Microbial Abundance ◽  
Floral Nectar ◽  
Shotgun Metagenomics ◽  
Carpenter Bees ◽  
Vector Identity ◽  
Bacteria And Fungi ◽  
And Function ◽  
Nectar Robbers

ABSTRACT Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacterium, among visitor treatments. Visitation increased microbial abundance, but robbing resulted in 10× higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism and specialized transporters. Gene differences were mirrored in function: robbed nectar contained a higher percentage of monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.

scholarly journals Trait-Environment Relationships and Tiered Forward Model Selection in Linear Mixed Models

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Tahira Jamil ◽  
Wout Opdekamp ◽  
Rudy van Diggelen ◽  
Cajo J. F. ter Braak
Keyword(s):  
Model Selection ◽  
Community Assembly ◽  
Environmental Variables ◽  
Fixed Effects ◽  
Mixed Model ◽  
Information Criterion ◽  
Species Traits ◽  
Forward Selection ◽  
Interaction Terms ◽  
Important Trait

To understand patterns of variation in species biomass in terms of species traits and environmental variables a one-to-one approach might not be sufficient, and a multitrait multienvironment approach will be necessary. A multitrait multienvironment approach is proposed, based on a mixed model for species biomass. In the model, environmental variables are species-dependent random terms, whereas traits are fixed terms, and trait-environment relationships are fixed interaction terms. In this approach, identifying the important trait-environment relationship becomes a model selection problem. Because of the mix of fixed and random terms, we propose a novel tiered forward selection approach for this. In the first tier, the random factors are selected; in the second, the fixed effects; in the final tier, nonsignificant terms are removed using a modified Akaike information criterion. We complement this tiered selection with an alternative selection method, namely, type II maximum likelihood. A mesocosm experiment on early community assembly in wetlands with three two-level environmental factors is analyzed by the new approach. The results are compared with the fourth corner problem and the linear trait-environment method. Traits related to germination and seedling establishment are selected as being most important in the community assembly in these wetland mesocosms.

scholarly journals Fungal alpha-diversity drives the stochasticity of bacterial and fungal community assembly in soil aggregates in the apple orchard

2020 ◽  
Author(s):  
Wei Zheng ◽  
Zhiyuan Zhao ◽  
Fenglian Lv ◽  
Yanan Yin ◽  
Zhaohui Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Fungal Community ◽  
Community Assembly ◽  
Fungal Diversity ◽  
Soil Aggregates ◽  
Alpha Diversity ◽  
Apple Orchard ◽  
Community Diversity ◽  
Agricultural Practice ◽  
Bacteria And Fungi

Abstract Background In soil ecosystems, bacteria and fungi always co-exist in the same niche and interact with each other, especially in different sized soil aggregates. The bacterial and fungal community assembly process and bacteria-fungi interactions in soil aggregates, which is important for bacterial and fungal community diversity and composition, is still unclear.Methods We examined bacterial and fungal community assembly in soil macroaggregate (> 0.25 mm), microaggregate (0.053–0.25 mm) and smaller microaggregate (silt + clay, < 0.053 mm) in an apple orchard. The microbial community assembly processes were analyzed by normalized stochasticity ratio index (NST).Results Bacterial community diversity, composition and assembly were more affected by agricultural practice and aggregate than fungal community. Bacterial community assembly was more stochastic in silt + clay than in macroaggregate, and was more stochastic (NST > 50%) than fungal community in soil aggregates. Meanwhile, bacterial NST was negatively correlated with fungal diversity, and fungal NST was positively correlated with fungal diversity. Co-occurrence network suggested that the bacteria and fungi were less strongly interacting in the network of silt + clay, compared to macroaggregate. The results indicated that fungi impact on the bacterial community assembly in soil aggregate, and the stochasticity of bacterial community assembly was increased with the decrease of interaction between bacteria and fungi in soil aggregates.Conclusions This study enhances our understanding of the mechanism of bacterial and fungal community assembly and co-exists pattern of bacteria and fungi in soil aggregates.

scholarly journals Fungi are more dispersal-limited than bacteria among flowers

2020 ◽  
Author(s):  
Rachel Vannette ◽  
Griffin Hall ◽  
Ivan Munkres
Keyword(s):  
Community Assembly ◽  
Dispersal Ability ◽  
Numerical Abundance ◽  
Flower Traits ◽  
Biodiversity Maintenance ◽  
Dispersal Abilities ◽  
Dispersal Routes ◽  
The Difference ◽  
Bacteria And Fungi ◽  
Plant Pollinator

AbstractDispersal, particularly variation in dispersal ability among taxa, affects community assembly in individual communities and biodiversity maintenance within metacommunities. Although fungi and bacteria frequently coexist, their relative dispersal abilities are poorly understood. Here, we compare the incidence and abundance of culturable flower-inhabiting bacteria and fungi among individual flowers. Using collections that span two coflowering communities across two years, we assess viable bacterial and fungal incidence and abundance within individual flower samples, and examine patterns across plant species that differ in flower traits. Our results demonstrate that bacteria can be detected in more flowers and in greater numerical abundance than fungi, particularly in flowers with more exposed corollas. For fungi, however, flowers with long corollas were equally likely as exposed flowers to contain cells, and hosted higher numbers of fungal cells, primarily yeasts. Across all flowers, bacteria and fungal incidence was positively related, but within flowers containing microbes, bacterial and fungal incidence was negatively related, suggesting shared dispersal routes but competition among microbes within flowers. The difference in dispersal abilities of bacteria and fungi identified here may have broad relevance for community assembly of microbes and plant-pollinator interactions.

scholarly journals Effects of Ametryn on Microbial Activity in Soil with Biofertilizer Addition

2018 ◽  
Vol 5 (4) ◽  
pp. 214
Author(s):  
Ana Paula Justiniano Régo ◽  
Kassio Ferreira Mendes ◽  
Cassiana Maria Reganhan Coneglian ◽  
Valdemar Luiz Tornisielo
Keyword(s):  
Enzymatic Activity ◽  
Microbial Activity ◽  
Contaminated Soil ◽  
Food Production ◽  
Pesticide Application ◽  
Soil Microbiota ◽  
Bacteria And Fungi ◽  
Microbial Action

In recent years, pesticide application has increased worldwide due to the need for increased food production. In this way, understanding of the effects that these xenobiotic molecules can result in the soil microbiota becomes fundamental. Thus, this work aimed to evaluate microbial enzymatic activity by FDA, as well as quantify bacteria and fungi contaminated soil by ametryn herbicide. In addition, biofertilizer was added as a form of microbial biostimulation in order to cause enrichment of the affected site. The ametryn herbicide was chosen because it is widely used in sugarcane crops in Brazil, in the control of weeds, and is moderately persistent in the environment. It can be evaluated that the biofertilizer was fundamental in increasing the microbial activity of the soil, even in the presence of ametryn, probably contributing to its biodegradation. The estimation of the enzymatic activity by FDA, was essential for the evaluation of the increase of the microbial action, contributing to the verification of the active microbiota in the soil. It is suggested the application of biofertilizer in soils contaminated by ametryn, as a way to mitigate affected sites.

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