Diversity of the bphA1 Genes in a Microbial Community from Anthropogenically Contaminated Soil and Isolation of New Pseudomonads Degrading Biphenyl/Chlorinated Biphenyls

Characterization of redox-related soil microbial communities along a river floodplain continuum by fatty acid methyl ester (FAME) and 16S rRNA genes

No studies have examined the effect of experimental warming on the microbial biomass and community composition of soil in agricultural ecosystem on the Qinghai-Tibet Plateau. Thus it is unclear whether the influences of experimental warming on microbial communities in soil are related to warming magnitude in croplands on this Plateau. This study performed warming experiment (control, low- and high-level) in a highland barley system of the Lhasa River in May 2014 to examine the correlation between the response of microbial communities in soil to warming and warming magnitude. Topsoil samples (0–10 and 10–20 cm) were collected on September 14, 2014. Experimental warming at both low and high levels significantly increased soil temperature by 1.02 °C and 1.59 °C, respectively at the depth of 15 cm. Phospho lipid fatty acid (PLFA) method was used to determine the microbial community in soil. The low-level experimental warming did not significantly affect the soil's total PLFA, fungi, bacteria, arbuscular mycorrhizal fungi (AMF), actinomycetes, gram-positive bacteria (G+), gram-negative bacteria (G–), protozoa, the ratio of fungi to bacteria (F/B ratio), and ratio of G+ to G– (G+/G– ratio) at the 0–10 and 10–20 cm depth. The low-level experimental warming also did not significantly alter the composition of microbial community in soil at the 0–10 and 10–20 cm depth. The high-level experimental warming significantly increased total PLFA by 74.4%, fungi by 78.0%, bacteria by 74.0%, AMF by 66.9%, actinomycetes by 81.4%, G+ by 67.0% and G– by 74.4% at the 0–10 cm depth rather than at 10–20 cm depth. The high-level experimental warming significantly altered microbial community composition in soil at the 0–10 cm depth rather than at 10-20 cm depth. Our findings suggest that the response of microbial communities in soil to warming varied with warming magnitudes in the highland barley system of the Lhasa River.

Phosphorus (P)-modified biochar demonstrates dual capabilities for heavy metal immobilization and soil quality enhancement. However, the underlying mechanism of microbial response to changes in soil properties is still unclear. In this study, P-modified biochar, prepared by co-pyrolysis of apple tree branches with K3PO4, was used for removal of heavy metals from the soils near a mining area. Effects of P-modified biochar on the microbial communities in soil were investigated and the key driving factors were identified. Adding P-modified biochar reduced the bioavailable cadmium and lead contents of the soil by 28.21% and 28.64%, respectively, mainly through improved co-precipitation and cation exchange. In turn, the cadmium and lead concentrations in maize grains were reduced by 36.52% and 61.82% respectively. Meanwhile, the richness and diversity of soil bacteria significantly decreased with the addition of P-modified biochar (P < 0.05). Microbial multi-trophic ecological network module analysis and partial least squares pathway modeling indicated that biochar changed the capacity of the soil to provide microorganisms with nitrogen and P, requiring the key microbial taxa (modules 1 and 3) to adjust. Modules 1 and 3 played important but opposite functions in the nitrogen and P cycle of the soil. This further led to variations in the composition and structure of microbial communities in soil. Particularly, changes in the bioavailability of heavy metals showed a negligible effect on soil microbial communities. This study emphasizes that P-modified biochar can efficiently reduce soil heavy metal bioavailability and alter the microbial community by regulating nutrient supply balance. Graphical Abstract

Wildland fire is increasingly recognized as a driver of bioaerosol emissions, but the effects that smoke-emitted microbes have on the diversity and community assembly patterns of the habitats where they are deposited remain unknown. In this study, we examined whether microbes aerosolized by biomass burning smoke detectably impact the composition and function of soil sinks using lab-based mesocosm experiments. Soils either containing the native microbial community or presterilized by γ-irradiation were inundated with various doses of smoke from native tallgrass prairie grasses. Smoke-inundated, γ-irradiated soils exhibited significantly higher respiration rates than both smoke-inundated, native soils and γ-irradiated soils exposed to ambient air only. Microbial communities in γ-irradiated soils were significantly different between smoke-treated and control soils, which supports the hypothesis that wildland fire smoke can act as a dispersal agent. Community compositions differed based on smoke dose, incubation time, and soil type. Concentrations of phosphate and microbial biomass carbon and nitrogen together with pH were significant predictors of community composition. Source tracking analysis attributed smoke as contributing nearly 30% of the taxa found in smoke-inundated, γ-irradiated soils, suggesting smoke may play a role in the recovery of microbial communities in similar damaged soils. Our findings demonstrate that short-distance microbial dispersal by biomass burning smoke can influence the assembly processes of microbial communities in soils and has implications for a broad range of subjects including agriculture, restoration, plant disease, and biodiversity.

Battery waste is one of the most destructive hazards to our environment, especially to the soil. In order to understand the effect of the battery waste on the microbial communities in soil, microcosm soils were treated with the powder made from the battery waste. Microbial biomass and respiration were measured after 15,30,45, and 60 days of the treatments, while microbial respiratory quotient, catabolic capability were enhanced. Although microbial biomass recovered after a period of incubation, microbial respiratory quotient, catabolic capability and community structure remained significantly affected. Our results also suggest that microbial; respiratory quotient and Biology parameters are more sensitive than microbial biomass to the battery stress on bioavailability. *Supported by the Outstanding Young Scientists Foundation of Shandong Province (Grant No. 2005BS08010), the China Geological Survey Project (No. 1212010310306) and Key Project of Natural Science Foundation of Shandong Province (No. ...

Using community trait-distributions to assign microbial responses to pH changes and Cd in forest soils treated with wood ash

To explore the differences in structure and diversity of nirK-type denitrifying microbial community in marsh soils at different invasion stages of Spartina alterniflora, the mudflat (MF, before invasion) and the S. alterniflora marsh after seaward invasion for 1-2 years (SAN) and 6-7 years (SA) in Shanyutan of the Minjiang River estuary were investigated by high-through put sequencing method. Results showed that the seaward invasion of S. alterniflora reduced the richness and diversity of nirK-type denitrifying microbial community in marsh soils. The nirK-type denitrifying microbial community in soils at different invasion stages included Proteobacteria and Actinobacteria, with Proteobacteria as the dominant one. The seaward invasion of S. alterniflora greatly altered the composition of nirK-type denitrifying microbial community in marsh soils. The highest relative abundance of genus in soils from different invasion stages were Bradyrhizobium, Mesorhizobium and Alcaligenes, respectively. The seaward invasion of S. alterniflora increased the spatial heterogeneity of nirK-type denitrifying microbial community composition in marsh soils. In SAN plot, the enhancement of spatial heterogeneity was primarily due to higher environmental disturbances in plots and the increased spatial heterogeneity of environmental variables caused by the seaward invasion of S. alterniflora. The seaward invasion of S. alterniflora altered the physico-chemical properties (e.g., grain composition, pH and moisture) and N nutrient conditions (total N, NH4+-N and NO3--N) in marsh soils, which greatly altered the structure and diversity of nirK-type denitrifying microbial community. Our findings reveal the microbial mechanism of denitrification process in marsh soils during the seaward invasion of S. alterniflora.

Sugarcane (inter-specific hybrids of Saccharum) is grown largely under long-term monoculture production in Louisiana. This can lead to a complex problem termed "yield decline" that results in poor root health and reduced productive capacity of sugarcane. This problem has been documented to be a limiting factor for sugarcane production in diverse regions, including Louisiana, Hawaii, Jamaica, and Australia. Previous work showed that biological factors affect root health and contribute to yield decline. The objectives of this study were to increase our understanding of microbial communities in sugarcane soils, to determine if there are differences in microbial communities associated with sugarcane roots in soil with and without a sugarcane cropping history, and to provide information on possible changes in the microbial communities resulting from monoculture that may contribute to yield decline. To achieve these objectives, two approaches were used for comparing culturable organisms in soil microbial communities from soil with and without a sugarcane cropping history, and methods were adapted to reliably obtain DNA from soil microbial communities for molecular comparisons. In one approach, colonies grown on different types of culture media were quantified and characterized. In the other approach, sole carbon source utilization profiles (SCSUP) of soil communities grown in Biolog(tm) GN2 microplates were compared. Comparisons of the numbers and types of microorganisms that grew on various culture media demonstrated that differences exist between microbial communities associated with sugarcane roots in Louisiana soils with and without a recent sugarcane cropping history. The differences in community functional diversity detected by SCSUP supported the differences found in types of microorganisms isolated on selective media. The SCSUP results showed that differences in community functional diversity exist between sites in soils with a long-term sugarcane cropping history in common. Methods for DNA extraction and polymerase chain reaction (PCR) amplification were optimized for sugarcane soil microbial community samples from Louisiana. This will allow molecular characterization of sugarcane rhizosphere microbial communities in the future.

Many studies have investigated patterns in the near-surface soil microbial community over large spatial scales. However, less is known about variation in subsurface (15-30 cm of depth) microbial communities. Here we studied depth profiles of microbial communities in high-elevation soils from Tibet. The relative abundance of Acidobacteria, Chloroflexi and Alphaproteobacteria was higher in near-surface layers, while the relative abundance of Actinobacteria, Gemmatimonadetes and Betaproteobacteria was higher in the subsurface samples. The microbial community structure was distinct between the surface and subsurface soil layers, strongly correlating with variation in total carbon (TC) and carbon to nitrogen ratio (C/N). The differences in the microbial community between the layers were about the same as the horizontal differences between sites separated by many kilometers. Overall, we found that TC and C/N were the best predictors for both surface and subsurface microbial community distribution. Exploration of the relative contribution of distance and environmental variables to community composition suggests that the contemporary environment is the primary driver of microbial distribution in this region. Reflecting niche conservatism in evolution, the microbial communities in each soil site and layer tended to be more phylogenetically clustered than expected by chance, and surface soil layer samples were more likely to be clustered than subsurface samples.

A meta-analysis on the responses of soil microbial biomass and community structure to antibiotics

Effects of cultivation of OsrHSA transgenic rice on functional diversity of microbial communities in the soil rhizosphere

Cadmium (Cd) contamination in soil has become the focus of widespread concern in society today. In this paper, with Eisenia fetida as research subjects, an indoor simulation experiment was conducted. A BIOLOG microplate technique was used to determine the carbon source (single-carbon) utilization of the microbial communities in the contaminated soil and earthworms under Cd stress. Contour line analysis was used for the first time to study the difference of carbon source metabolism in microbial communities. And the effects of Cd stress on the functional diversity of the microbial communities and the detoxification mechanism in earthworms were researched. With two test groups, a short-term test and the long-term test were performed. The former test lasted for 10days, with the removal of an earthworm every day for analysis; the latter test lasted for 30days, with the removal of an earthworm every 10days. The Cd2+ concentration was set at 0, 50, 100, 125, 250, or 500mgkg-1 dry weight, and 10 earthworms were inoculated in each concentration treatment. The earthworm homogenate and soil extracts were used to determine the carbon source utilization of the microbial communities. The results show that Cd stress changed the functional diversity of the microbial communities in the soil and earthworms. With the extension of stress time and the increase of stress concentration, earthworms will adjust their own physiological functions (including the microbial community structure and stress mechanism in the body) and regulate the microbial community structure in the external environment to obtain the necessary substances for growth. In addition, 2-hydroxybenzoic acid, γ-hydroxybutyric acid, glutamyl-L-glutamic acid, α-butyric acid, threonine, and α-cyclodextrin were important carbon sources for the earthworms to maintain their normal physiological metabolism under Cd stress. This study confirms that changes in microbial communities can be used to reveal the detoxification mechanisms of earthworm under heavy metal stress.

In this study soils at different depths were collected in a Zn smelting site located in Zhuzhou City, China, in order to understand toxic metal(loid)s distribution and microbial community in vertical soil profile at a smelting site. Except Soil properties and metal(loid)s content, the richness and diversity of microbial communities in soil samples were analyzed via high-throughput Illumina sequencing of 16s rRNA gene amplicons. The results showed that the content of As, Pb, Cu, Cd, Zn, and Mn was relatively high in top soil in comparison to subsoil, while the concentration of Cr in subsoil was comparable with that in top soil due to its relative high background value in this soil layer. The bioavailability of Cd, Mn, Zn, and Pb was relative higher than that of As, Cr, and Cu. The diversity of soil microbial communities decreased with increasing depth, which might be ascribed to the decrease in evenness with increase in depth duo to the influence by environmental conditions, such as pH, TK (total potassium), CEC (cation exchange capacity), ORP (oxidation reduction potential), and Bio-Cu (bioavailable copper). The results also found Acidobacteria, Proteobacteria, Firmicutes, and Chloroflexi were dominant phyla in soil samples. At the genus level, Acinetobacter, Pseudomonas, and Gp7 were dominant soil microorganism. Besides, Environmental factors, such as SOM (soil organic matter), pH, Bio-Cu, Bio-Cd (bioavailable cadmium), and Bio-Pb (bioavailable lead), greatly impacted microbial community in surface soil (1–3 m), while ORP, TK, and AN concentration influenced microbial community in the subsoil (4–10 m).

Biochar is a promising material for the improvement of soil quality. However, studies on biochar have mostly been carried out in laboratory conditions or have focused on agricultural aspects. The impacts of the application of biochar on soil characteristics and related ecological processes of the forest ecosystem have not been fully resolved. In this study, we investigated the effects of regular biochar and bacteria-loaded biochar on the microbial communities in the bulk soil and the rhizosphere soil of an annual Chinese fir plantation. In early spring (April), the two types of biochar were added to the soil at the rates of 2.22 t·ha−1, 4.44 t·ha−1, 6.67 t·ha−1, 8.89 t·ha−1, and 11.11 t·ha−1 by ring furrow application around the seedlings, and soil samples were collected at the end of autumn (November). The results showed that biochar addition increased the soil nutrient content and promoted the growth and diversity of soil microbial communities. The diversity of soil fungi was significantly increased, and the diversity of soil bacteria was significantly decreased. Principal component analysis under the different biochar types and application rates demonstrated that microbial communities differed significantly between the treatments and controls and that the effect of biochar on the microbial community of the bulk soil was more significant than that of the rhizosphere soil. Under the same dosage, the effect of bacteria-loaded biochar on soil was more significant than that of regular biochar.

Mobility and toxicity of heavy metal contamination in the environment are highly dependent on its bioavailability. Most of previous studies focused on total heavy metal contents and their influence on microbial community in soils and sediments. Little were concerned about bioavailable fractions. In the current study, soil and sediment samples were collected near an abandoned realgar mine in Shimen County, China. Bioavailable heavy metals including Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Cd, Sb, and Pb in the samples were extracted using three-step sequential extraction method. Interactions among physicochemical parameters, total and bioavailable heavy metals, and microbial community in the collected samples were investigated. The study area has been severely contaminated by As with a concentration up to 2158mg·kg-1 detected. The result of principal component analysis showed that the abundance of operational taxonomic units (OTUs) in the soils were obviously different from those in the sediments. In the soil samples, pH made a dominant contribution on the OTU abundance of microbial community. Correlation analyses revealed that the alpha diversity indices and microbial taxon were most correlated with bioavailable fractions of heavy metals in all the samples. That means bioavailable heavy metals rather than total heavy metals or physicochemical parameters played a more important role on richness and diversity of microbial community. Little connections were observed between microbial community and As no matter total concentration or bioavailable fraction. However, bioavailable Fe and Mn were recognized as the major driving force shaping the taxonomic structure of microbial community due to their relatively high concentrations and high affinity to other heavy metal contamination in soils and sediments.