Combined Effect of Laboratory-Simulated Fire and Chromium Pollution on Microbial Communities in an Agricultural Soil.
Ontology highlight
ABSTRACT:
SUBMITTER: Rascio I
PROVIDER: S-EPMC8301050 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Extensive use of chromium (Cr) and arsenic (As) based preservatives from the leather tanning industry in Pakistan has had a deleterious effect on the soils surrounding production facilities. Bacteria have been shown to be an active component in the geochemical cycling of both Cr and As, but it is unknown how these compounds affect microbial community composition or the prevalence and form of metal resistance. Therefore, we sought to understand the effects that long-term exposure to As and Cr had on the diversity and structure of soil microbial communities. Soils from three spatially isolated tanning facilities in the Punjab province of Pakistan were analyzed. The structure, diversity and abundance of microbial 16S rRNA genes were highly influenced by the concentration and presence of hexavalent chromium (Cr (VI)) and arsenic. When compared to control soils, contaminated soils were dominated by Proteobacteria while Actinobacteria and Acidobacteria (which are generally abundant in pristine soils) were minor components of the bacterial community. Shifts in community composition were significant and revealed that Cr (VI)-containing soils were more similar to each other than to As contaminated soils lacking Cr (VI). Diversity of the arsenic resistance genes, arsB and ACR3 were also determined. Results showed that ACR3 becomes less diverse as arsenic concentrations increase with a single OTU dominating at the highest concentration. Chronic exposure to either Cr or As not only alters the composition of the soil bacterial community in general, but affects the arsenic resistant individuals in different ways.
| S-EPMC3386950 | biostudies-other
Project description:Copper has long been applied for agricultural practices. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on Folsomia candida, an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure explained the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. Combined analysis at various trophic levels is highly relevant in the context of assessing long-term soil pollution.
2012-04-04 | GSE29644 | GEO
Project description:Plant and soil properties cooperatively structure soil microbial communities, with implications for ecosystem functioning. However, the extent to which each factor contributes to community structuring is not fully understood. To quantify the influence of plants and soil properties on microbial diversity and composition in an agricultural context, we conducted an experiment within a corn-based annual cropping system and a perennial switchgrass cropping system across three topographic positions. We sequenced barcoded 16S ribosomal RNA genes from whole soil three times throughout a single growing season and across two years in July. To target the belowground effects of plants, we also sampled rhizosphere soil in July. We hypothesized that microbial community α-diversity and composition (β-diversity) would be more sensitive to cropping system effects (annual vs. perennial inputs) than edaphic differences among topographic positions, with greater differences occurring in the rhizosphere compared to whole soil. We found that microbial community composition consistently varied with topographic position, and cropping system and the rhizosphere influenced α-diversity. In July, cropping system and rhizosphere structured a small but specific group of microbes implying a subset of microbial taxa, rather than broad shifts in community composition, may explain previously observed differences in resource cycling between treatments. Using rank abundance analysis, we detected enrichment of Saprospirales and Actinomycetales, including cellulose and chitin degraders, in the rhizosphere soil and enrichment of Nitrospirales, Syntrophobacterales, and MND1 in the whole soil. Overall, these findings support environmental filtering for the soil microbial community first by soil and second by the rhizosphere. Across cropping systems, plants selected for a general rhizosphere community with evidence for plant-specific effects related to time of sampling.
| S-EPMC4520589 | biostudies-literature
Project description:Soil pollution is an important stressor affecting biodiversity and ecosystem functioning. However, we lack a holistic understanding of how soil microbial communities respond to heavy metal pollution in agricultural ecosystems. Here, we explored the distribution patterns and inter-kingdom interactions of entire soil microbiome (including bacteria, fungi, and protists) in 47 paired paddy and upland fields along a gradient of legacy mercury (Hg) pollution. We found that the richness and composition of protistan community had stronger responses to Hg pollution than those of bacterial and fungal communities in both paddy and upland soils. Mercury polluted soils harbored less protistan phototrophs but more protistan consumers. We further revealed that long-term Hg pollution greatly increased network complexity of protistan community than that of bacterial and fungal communities, as well as intensified the interactions between protists and the other microorganisms. Moreover, our results consistently indicated that protistan communities had stronger responses to long-term Hg pollution than bacterial and fungal communities in agricultural soils based on structural equation models and random forest analyses. Our study highlights that soil protists can be used as bioindicators of Hg pollution, with important implications for the assessment of contaminated farmlands and the sustainable management of agricultural ecosystems.
| S-EPMC9723755 | biostudies-literature
Project description:The impacts of increased flooding frequency on soil microbial communities and potential functions, in line with predicted environmental changes, were investigated in a laboratory-controlled environment. More frequent flooding events altered microbial community composition and significantly increased the resolved species alpha-diversity (Shannon index). The Bacteria:Archaea ratio was greater at the end of the experiment than at the start, more-so after only one flood. Significant changes in taxa and functional gene abundances were identified and quantified. These include genes related to the reduction and oxidation of substances associated with anoxia, for example, those involved in nitrogen and sulfur cycling. No significant changes were observed in the methanogenesis pathway, another function associated with anoxia and which contributes to the emission of greenhouse gases.
| S-EPMC5822339 | biostudies-literature
Project description:Copper has long been applied for agricultural practices. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on Folsomia candida, an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure explained the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. Combined analysis at various trophic levels is highly relevant in the context of assessing long-term soil pollution. A single channel, interwoven loop design was used to test animals exposed to the copper-spiked field soil samples. The field soil was spiked with 4 copper and 4 pH treatments yielding 16 combinations. Combinations are displayed in the Sample descriptions, with 1 M-bM-^@M-^S 4 representing the copper concentrations from low to high, and A-D representing the soil pH from low to high. 4 biological replicates per copper/pH combination were used. Each replicate contained 25 grams of soil and thirty 23-day-old animals.
2012-04-03 | E-GEOD-29644 | biostudies-arrayexpress
Project description:Fire disturbances are becoming more common, more intense, and further-reaching across the globe, with consequences for ecosystem functioning. Importantly, fire can have strong effects on the soil microbiome, including community and functional changes after fire, but surprisingly little is known regarding the role of soil fire legacy in shaping responses to recent fire. To address this gap, we conducted a manipulative field experiment administering fire across 32 soils with varying fire legacies, including combinations of 1-7 historic fires and 1-33 years since most recent fire. We analyzed soil metatranscriptomes, determining for the first time how fire and fire legacy interactively affect metabolically-active soil taxa, the microbial regulation of important carbon (C), nitrogen (N) and phosphorus (P) cycling, expression of carbohydrate-cycling enzyme pathways, and functional gene co-expression networks. Experimental fire strongly downregulated fungal activity while upregulating many bacterial and archaeal phyla. Further, fire decreased soil capacity for microbial C and N cycling and P transport, and drastically rewired functional gene co-expression. Perhaps most importantly, we highlight a novel role of soil fire legacy in regulation of microbial C, N, and P responses to recent fire. We observed a greater number of functional genes responsive to the interactive effects of fire and fire legacy than those affected solely by recent fire, indicating that many functional genes respond to fire only under certain fire legacy contexts. Therefore, without incorporating fire legacy of soils, studies will miss important ways that fire shapes microbial roles in ecosystem functioning. Finally, we showed that fire caused significant downregulation of carbon metabolism and nutrient cycling genes in microbiomes under abnormal soil fire histories, producing a novel warning for the future: human manipulation of fire legacies, either indirectly through global change-induced fire intensification or directly through fire suppression, can negatively impact soil microbiome functional responses to new fires.
2024-08-12 | GSE274211 | GEO
Project description:UnlabelledThe abundance of libA, encoding a hydrolase that initiates linuron degradation in the linuron-metabolizing Variovorax sp. strain SRS16, was previously found to correlate well with linuron mineralization, but not in all tested environments. Recently, an alternative linuron hydrolase, HylA, was identified in Variovorax sp. strain WDL1, a strain that initiates linuron degradation in a linuron-mineralizing commensal bacterial consortium. The discovery of alternative linuron hydrolases poses questions about the respective contribution and competitive character of hylA- and libA-carrying bacteria as well as the role of linuron-mineralizing consortia versus single strains in linuron-exposed settings. Therefore, dynamics of hylA as well as dcaQ as a marker for downstream catabolic functions involved in linuron mineralization, in response to linuron treatment in agricultural soil and on-farm biopurification systems (BPS), were compared with previously reported libA dynamics. The results suggest that (i) organisms containing either libA or hylA contribute simultaneously to linuron biodegradation in the same environment, albeit to various extents, (ii) environmental linuron mineralization depends on multispecies bacterial food webs, and (iii) initiation of linuron mineralization can be governed by currently unidentified enzymes.ImportanceA limited set of different isofunctional catabolic gene functions is known for the bacterial degradation of the phenylurea herbicide linuron, but the role of this redundancy in linuron degradation in environmental settings is not known. In this study, the simultaneous involvement of bacteria carrying one of two isofunctional linuron hydrolysis genes in the degradation of linuron was shown in agricultural soil and on-farm biopurification systems, as was the involvement of other bacterial populations that mineralize the downstream metabolites of linuron hydrolysis. This study illustrates the importance of the synergistic metabolism of pesticides in environmental settings.
| S-EPMC4836412 | biostudies-literature
Project description:Edaphic cyanobacteria and algae have been extensively studied in dryland soils because they play key roles in the formation of biological soil crusts and the stabilization of soil surfaces. Yet, in temperate agricultural crop soils, little is understood about the functional significance of indigenous photosynthetic microbial communities for various soil processes. This study investigated how indigenous soil algae and cyanobacteria affected topsoil aggregate stability in cereal cropping systems. Topsoil aggregates from conventional and organic cropping systems were incubated in microcosms under dark or photoperiodic conditions with or without a treatment with an herbicide (isoproturon). Physicochemical parameters (bound exopolysaccharides, organic carbon) and microbial parameters (esterase activity, chlorophyll a biomass, and pigment profiles) were measured for incubated aggregates. Aggregate stability were analyzed on the basis of aggregate size distribution and the mean weight diameter (MWD) index, resulting from disaggregation tests. Soil photosynthetic microbial biomass (chl a) was strongly and positively correlated with aggregate stability indicators. The development of microalgae crusts in photoperiodic conditions induced a strong increase of the largest aggregates (>2 mm), as compared to dark conditions (up to 10.6 fold and 27.1 fold, in soil from organic and conventional cropping systems, respectively). Concomitantly, the MWD significantly increased by 2.4 fold and 4.2 fold, for soil from organic and conventional cropping systems. Soil microalgae may have operated directly via biochemical mechanisms, by producing exopolymeric matrices surrounding soil aggregates (bound exopolysaccharides: 0.39-0.45 μg C g-1 soil), and via biophysical mechanisms, where filamentous living microbiota enmeshed soil aggregates. In addition, they may have acted indirectly by stimulating heterotrophic microbial communities, as revealed by the positive effect of microalgal growth on total microbial activity. The herbicide treatment negatively impacted soil microalgal community, resulting in significant decreases of the MWD of the conventional soil aggregates (up to -42% of the value in light treatment). This study underscores that indigenous edaphic algae and cyanobacteria can promote aggregate formation, by forming photosynthetic microbiotic crusts, thus improving the structural stability of topsoil, in temperate croplands. However, the herbicide uses can impair the functional abilities of algal and cyanobacterial communities in agricultural soils.Originality/significanceEdaphic algal and cyanobacterial communities are known to form photosynthetic microbial crusts in arid soils, where they drive key ecosystem functions. Although less well characterized, such communities are also transiently abundant in temperate and mesic cropped soils. This microcosm study investigated the communities' functional significance in topsoil aggregate formation and stabilization in two temperate cropping systems. Overall, our results showed that the development of indigenous microalgal communities under our experimental conditions drove higher structural stability in topsoil aggregates in temperate cropland soils. Also, herbicide use affected photosynthetic microbial communities and consequently impaired soil aggregation.
| S-EPMC6587365 | biostudies-literature
Project description:Plants in their natural and agricultural environments are continuously exposed to a plethora of diverse microorganisms resulting in microbial colonization of plants in the rhizosphere. This process is believed to be accompanied by an intricate network of ongoing simultaneous interactions. In this study, we compared transcriptional patterns of Arabidopsis thaliana roots and shoots in the presence and absence of whole microbial communities extracted from compost soil. The results show a clear growth promoting effect of Arabidopsis shoots in the presence of soil microbes compared to axenically grown plants under identical conditions. Element analyses showed that iron uptake was facilitated by these mixed microbial communities which also lead to transcriptional downregulation of genes required for iron transport. In addition, soil microbial communities suppressed the expression of marker genes involved in oxidative stress/redox signalling, cell wall modification and plant defense. While most previous studies have focussed on individual plant-microbe interactions, our data suggest that multi-species transcriptional profiling, using simultaneous plant and metatranscriptomics coupled to metagenomics may be required to further increase our understanding of the intricate networks underlying plant-microbe interactions in their diverse environments.
2013-03-09 | GSE44984 | GEO