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... Plant microbiome referred to as plant second genome, plays pivotal role in determination of vigor and productivity of plant. Current high-throughput sequence technologies provide remarkable insight into microbial diversity and host microbe interaction. The obtained dataset aimed to reveal the core bacterial community residing the rhizosphere of two leading cereal crops Zea mays and Triticum aestiv ...
... Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon tar ...
... The rhizomicrobiome is composed of microbes that live in association with plant roots. From nutrient cycling to carbon sequestration, soil microorganisms have provided a solid base for natural and agricultural ecosystems to function. The relationship between plant roots and soil microorganisms is especially relevant in food staples such as rice (Oryza sativa L.), as the various properties of these ...
... Bergen Community College (BCC) soils were used to generate mud suspensions to construct microbial fuel cells (MFCs) with the anode buried with the mud, while the cathode rested on top. MFCs incubated at 37°C showed more electrical output and electrogenic bacteria than those grown at 25°C. The most productive MFC generated a maximum of 80 microwatts with 1.67 × 10⁹ electrogenic microorganisms. 16S ...
... To gain an in-depth insight into the diversity and the distribution of genes under the particular evolutionary pressure of an arsenic-rich acid mine drainage (AMD), the genes involved in bacterial arsenic detoxification (arsB, ACR3) and arsenite oxidation (aioA) were investigated in sediment from Carnoulès (France), in parallel to the diversity and global distribution of the metabolically active b ...
Acidobacteria; Desulfovibrionales; Firmicutes; Spirochaetales; Syntrophobacterales; bacterial communities; clones; community structure; organic matter; oxygen; phylogeny; ribosomal RNA; sediments; statistics; Arabian Sea; India
Abstract:
... The eastern Arabian Sea has a unique and permanent oxygen minimum zone (OMZ) that extends along the western continental margin of India. The sediment below this region is rich in organic matter. This study describes the bacterial community structure and diversity in OMZ sediments of the eastern Arabian Sea (AS) through 16S rRNA clone library analysis. Phylogenetic analysis of the sequences demonst ...
... Although the consequences of long-term inorganic fertilizer application on microbial communities have been widely investigated, the potential links between soil properties, microbial communities, and functions remain unclear in reddish paddy soil in southern China. Herein, we used Illumina Miseq sequencing technology to evaluate bacterial communities after extensive application of fertilizers star ...
... In agriculture, soil health is disturbed by various anthropogenic activities, including applications of chemicals, and highly mechanized cropping methods, leading to a gradual loss in soil fertility and microbial diversity. Therefore, it is the need of the hour to shift towards eco-friendly and sustainable agri-management practices. The practice of conservation agriculture (CA) is considered a hol ...
... Indigenous bacterial communities are essential for biofiltration processes in drinking water treatment systems. In this study, we examined the microbial community composition and abundance of three different biofilter types (rapid sand, granular activated carbon, and slow sand filters) and their respective effluents in a full-scale, multi-step treatment plant (Zürich, CH). Detailed analysis of org ...
... Hydrocarbon catabolic genes were investigated in soils and sediments in nine different locations around Syowa Station, Antarctica, using conventional PCR, real-time PCR, cloning, and sequencing analysis. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD)-coding genes from both Gram-positive and Gram-negative bacteria were observed. Clone libraries of Gram-positive RHD genes w ...
... Acidobacteria is a new bacterial group, identified by molecular research, which is widely distributed and has specific ecological functions in forest soil. In this study, we investigated Acidobacteria response to N input, and the effects were related to N form and dose. The experimental design included two N forms (NH₄ ⁺-N and NO₃ ⁻-N) and five levels of N deposition (0, 20, 40, 60, 80 kg N ha⁻¹) ...
... The Acidobacteria show a widespread distribution in natural ecosystems. In this study, we analyzed the presence of Acidobacteria in freshwater ponds at Doñana National Park (southwestern Spain). Nucleic acid sequence analysis, quantitative, real-time RT-PCR, and fluorescence in situ hybridization (FISH) were carried out. Acidobacteria in these aquatic environments were investigated using their 16S ...
... Bacterial communities of the lichens from a Sphagnum bog (Karelia) and tundra (Vorkuta oblast) were investigated. Members of the phylum Acidobacteria were numerous in the thallus of living and decaying lichens (3.8 Ã 108 cells/g), constituting 6 to 32% of the total bacterial number. Pure cultures of acidobacteria were isolated from the samples of living and decaying lichen thallus. Ten of them we ...
... Easily visible colonies of bacteria continued to form on plates inoculated with soil and incubated for 24 weeks. Using two different media, 13% and 29% of easily visible colonies appeared after more than 12 weeks. In addition, 10% and 18% of all colonies had diameters of 25-200 µm (mini-colonies), which could not be readily seen with the unaided eye. Members of soil bacterial groups that are only ...
Angela Cirigliano; Francesco Mura; Adele Cecchini; Maria Cristina Tomassetti; Daniele Federico Maras; Monica Di Paola; Niccolò Meriggi; Duccio Cavalieri; Rodolfo Negri; Andrea Quagliariello; John E. Hallsworth; Teresa Rinaldi
... Earth's microbial biosphere extends down through the crust and much of the subsurface, including those microbial ecosystems located within cave systems. Here, we elucidate the microbial ecosystems within anthropogenic 'caves'; the Iron‐Age, subterranean tombs of central Italy. The interior walls of the rock (calcium‐rich macco) were painted ~2500 years ago and are covered with CaCO₃ needles (known ...
... This study investigated the acute effects of hexavalent chromium (Cr(VI)) shock load at 2.5, 6 and 25 mg/L on the performance and bacterial community structures in aerobiotic activated sludge reactors. The results showed that eight-day Cr(VI) toxicity made the removal rates of COD and NH₃–N to obviously decrease in all reactors. Furthermore, the higher the Cr(VI) concentration was, the more severe ...
... Soil around the gold tailing due to the smelting process of wastewater and solid waste can lead to metal (loids) contamination, especially arsenic (As). Soil microorganisms have gradually evolved adaptive mechanisms in the process of long-term adaptation to As contamination. However, comprehensive investigations on As metabolism genes and their host microbial communities in soil profiles with diff ...
... The feeding of high-grain diets to dairy cows commonly results in lowered pH and ruminal dysbiosis, characterized by changes in absorption dynamics of short-chain fatty acids (SCFA) across the reticuloruminal wall, epithelial function, and the epithelial bacteria community structure. Therefore, the present study evaluated the effect of high-grain feeding persistence on the absorption kinetics of r ...
... Hospital wastewater represents an important source of pharmaceutical active compounds (PhACs) as contaminants of emerging concern for urban wastewater treatment plants. This work evaluates a fungal biological treatment of a hospital effluent before discharging in the municipal sewer system. This treatment was performed in rotating biological contactors (RBCs) covered with wooden planks in order to ...
Acidobacteria; Actinobacteria; Crenarchaeota; Euryarchaeota; bacterial communities; carbon; community structure; delta-Proteobacteria; ecosystems; environmental factors; fauna; food quality; gamma-Proteobacteria; life history; microorganisms; phylotype; sediments; North Sea
Abstract:
... Knowledge on the spatial distribution of prokaryotic taxa is an essential basis to understand microbial diversity and the factors shaping its patterns. Large-scale patterns of faunal distribution are thought to be influenced by physical environmental factors, whereas smaller scale spatial heterogeneity is maintained by species-specific life-history characteristics, the quantity and quality of food ...
... Soil bacteria have been widely investigated and their roles in terrestrial ecosystems are relatively well understood. The soil bacterial community and potential function are controlled by vegetation and bacteria are factors indicating changes in soil microenvironment. However, there is a knowledge gap regarding microbial influence and their use to predict the change in metabolic function after aff ...
... Diversified cropping systems provide yield benefits that may result from enhanced nutrient availability via the root microbiome. We hypothesized that root-associated microbial communities in diversified and conventional systems would differ most during high plant nitrogen demand, reflecting microbiome-derived benefits, and that these effects would be greatest nearest the root. We compared maize bu ...
Acidobacteria; Ascomycota; Glomeromycota; Proteobacteria; agriculture; agroecosystems; community structure; edaphic factors; equations; fungal communities; fungi; intensive farming; soil microorganisms; soil organic carbon; soil quality; structural equation modeling; total nitrogen; China
Abstract:
... The stability of soil microbial community plays a key role in nutrient cycling, soil organic carbon reservoirs, and plant productivity, making them crucial players in agroecosystems. Although the effect of agricultural intensification on microbial communities has been extensively studied, little is known about the stability of the microbial networks. In this study, we examined the changes in soil ...
... BACKGROUND: Agricultural management and temporal change including climate conditions and soil properties can result in the alteration of soil enzymatic activity and bacterial community, respectively. Therefore, different agricultural practices have been used globally to explore the soil quality. In this study, the temporal variations in soil property, enzymatic activity, and bacterial community at ...
... BACKGROUND: The soil quality and health of the tea plantations are dependent on agriculture management practices, and long-term chemical fertilizer use is implicated in soil decline. Hence, several sustainable practices are used to improve and maintain the soil quality. Here, in this study, changes in soil properties, enzymatic activity, and dysbiosis in bacterial community composition were compar ...
... Adding alkaline into an anaerobic waste activated sludge (WAS) fermentation with thermophilic bacteria pretreatment could efficiently improve short-chain fatty acids (SCFAs) accumulation to 3550 ± 120 mg COD/L. The acidification rate in combined test was 21.2%, while that was 15.6% and 10.7% in sole thermophilic bacteria pretreatment and control tests respectively. Four distinct groups of microbes ...
... 2-Methyl-4-chlorophenoxyacetic acid (MCPA) is a widely used phenoxyalkanoic acid herbicide and subject to aerobic microbial degradation. Earthworms stimulate both growth and activity of MCPA-degrading bacteria in soil. Thus, active MCPA degraders in soil and drilosphere (i.e. burrow walls, gut content and cast) were assessed by 16S rRNA stable isotope probing in soil columns under experimental con ...
Acidobacteria; Actinobacteria; Bacteroidetes; Gemmatimonadetes; Nitrospirae; Proteobacteria; climate change; community structure; drought; ecosystems; environmental science; microbial communities; phosphorus; principal component analysis; soil microorganisms; soil pH; soil water; technology; total nitrogen; total organic carbon; water content; water solubility; wetlands
Abstract:
... The Zoige alpine wetland is one of the most sensitive ecosystems to global climate change. It is the largest alpine wetland in the world and currently suffers from serious drought and degradation. In this study, soil microbial communities of five soils with different moisture content were investigated by Illumina MiSeq high-throughput sequencing of 16S rRNA. The results showed that soil acidity an ...
... We selected 42 early‐stage primary biliary cirrhosis (PBC) patients and 30 healthy controls (HC). Metagenomic sequencing of the 16S rRNA gene was used to characterize the fecal microbiome. UPLC‐MS/MS assaying of small molecules was used to characterize the metabolomes of the serum, urine and feces. Liquid chip assaying of serum cytokines was used to characterize the immune profiles. The gut of PBC ...
... In order to better understand the variations in soil bacterial community and associated drivers following plant invasion, we investigated changes in soil bacterial community along with 9-, 13-, 20- and 23-year-old Spartina alterniflora Loisel. (SA) invasion in comparison with bare flat (BF) in the eastern Chinese coastal wetlands, based on analyses of quantitative polymerase chain reaction (qPCR) ...
... Afforestation can modify terrestrial carbon (C) pools, some of which are primarily fixed in the plant dead biomass and then incorporated into the microbial dead biomass. Soil microorganisms exert a critical role in C flow and potentially influence C balance through the degradation of plant and microbial dead biomass. Here, we compared sites along a 45-year Robinia pseudoacacia (RP) afforestation ch ...
... Tomato–rice rotation is prevalent in subtropical and tropical regions in China. This practice enhances crop productivity and the disease suppression property of soils against soil-borne plant pathogens. To explore the variations and dynamics of bacterial and fungal communities, bulk soil samples were collected during two consecutive years under a rotation system between tomato and rice originated ...
... Unraveling the distribution patterns of plants and animals along the elevational gradients has been attracting growing scientific interests of ecologists, whether the microbial communities exhibit similar elevational patterns, however, remains largely less documented. Here, we investigate the biogeographic distribution of soil archaeal and bacterial communities across three vertical climate zones ...
Acidobacteria; Actinobacteria; agricultural land; aluminum; beta-Proteobacteria; biodiversity; cations; fertilizer application; land use change; liming; long term experiments; metabolism; metagenomics; microbiome; no-tillage; nucleic acids; potassium; rhizosphere; root systems; soil; soybeans; tropical forests; virulence
Abstract:
... The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity ...
Acidobacteria; Archaea; Cyanobacteria; DNA; DNA fingerprinting; Flexibacter; Pseudomonas; bacteria; calcium; carbon; carbon sinks; cation exchange capacity; cluster analysis; databases; denaturing gradient gel electrophoresis; gels; land use; landscapes; longevity; microbial communities; paddies; phosphorus; restriction fragment length polymorphism; soil management; soil microorganisms; soil mineralogy; soil pH; soil sampling; terra preta; tropics; Amazonia; Brazil
Abstract:
... We compared the microbial community composition in soils from the Brazilian Amazon with two contrasting histories; anthrosols and their adjacent non-anthrosol soils of the same mineralogy. The anthrosols, also known as the Amazonian Dark Earths or terra preta, were managed by the indigenous pre-Colombian Indians between 500 and 8,700 years before present and are characterized by unusually high cat ...
restriction fragment length polymorphism; sequence analysis; Senna alata; soil chemical properties; rhizosphere; ribosomal RNA; terra preta; community structure; Acidobacteria; genes; soil fertility; bacterial communities; Mimosa; Actinobacteria; Verrucomicrobium; roots; forests; Amazonia
Abstract:
... Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects ...
... Soil pH is a dominant factor affecting bacterial community composition in acidic, neutral, and alkaline soils but not in severely acidic soils (pH<4.5). We conducted a nitrogen (N) addition experiment in the field in severely acidic forest soil to determine the response of the soil bacterial community and identified the dominant factor in determining community composition. Using a high-throughput ...
... The discharge of solid and liquid waste from domestic, municipal, and hospital premises pollutes the soil and river ecosystems. However, the diversity and functions of the microbial communities present in these polluted environments are not well understood and may contain harmful microbial communities with specialized metabolic potential. In this present study, we adapted the Illumina sequencing t ...
... In this work, anammox-denitrification process was verified by 15N stable isotopic tracing methods and variations and effects of microbial community structures were studied using Illumina MiSeq sequencing and Quantitative Polymerase Chain Reaction (qPCR). The results showed that higher nitrogen removal efficiency and richer microbial consortia was observed at hydraulic loading rate (HLR) of 15L/m3· ...
... This study explored the differences among various artificial morel cultivations as well as the factors that influence these differences, including soil bacterial community structure, yield, and mineral element contents of ascocarp and the cultivated soil. High-throughput sequencing results revealed that the dominant bacterial phyla in all the samples, including Proteobacteria, Acidobacteria, Chlor ...
... Biological soil crusts (BSCs) provide important ecosystem services in dryland regions, including erosion control and contribution to nitrogen and CO₂ fixation. As soil microorganisms are still rarely studied within the context of biodiversity planning, we describe, as a contribution to the Soil Crust International project, an approach that addresses this gap in biodiversity assessments. The purpos ...
... Bacterial communities in rhizosphere soil of healthy and diseased cotton (infected by the pathogenic fungus Verticillium dahliae Kleb.) were examined at different plant growth stages using T-RFLP and 16S rDNA clone library. At flowering and bolling, soil samples from the rhizosphere of healthy cotton had the highest richness, whereas the highest evenness was found in the rhizosphere of diseased co ...
... The bacteria resident in sponges collected from Chuuk Lagoon and Kosrae Island of Micronesia were investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. These sponges were clustered into 5 groups based on their bacterial composition. Diversity indexes and cumulative rank abundance curves showed the different compositions of bacterial communities in the various groups of sponges. Re ...
Acidobacteria; Actinobacteria; Proteobacteria; microbiology; sequence analysis; Korean Peninsula
Abstract:
... The bacterial diversity of 14 sponges belonging to 5 different orders that were collected around Chuja Island, Korea was investigated using barcoded 454 pyrosequencing. The sponges contained many unidentified bacterial groups (e.g. more than half of the taxa at the family level) that were known only in environmental sequences and obtained from culture-independent methods. Five of the sponges were ...
Acidobacteria; Cyanobacteria; Paeonia; Proteobacteria; ecological function; economic valuation; endophytes; medicinal plants; metagenomics; plant growth; rhizosphere; soil; traditional medicine; China
Abstract:
... Paeonia ludlowii is indigenous to Tibet and has an important ecological and economic value in China. In Tibet, P. ludlowii has been used in folk medicine with relative success. Plant microbial endophytes play an important role in plant growth, health and ecological function. The diversity of endophytic bacteria associated with P. ludlowii remains poorly understood. In this study, the structure of ...
Acidobacteria; Actinobacteria; Bacteroidetes; Cyanobacteria; DNA; DNA repair; catenas; heavy metals; humans; metagenomics; metal tolerance; methane; nitrification; oxidation; permafrost; pollution; sulfur; China
Abstract:
... The relationship between heavy metals and the expression of heavy metal resistance genes (HMRGs) in the active layer (AL) and the permafrost layer (PL) are not well understood, despite being closely linked to the impact of human activity on heavy metal levels and bacterial response to heavy metal stress. Herein, we conducted a metagenomics sequencing analysis to understand how bacteria adapt to su ...
... Soil pollution occurring at mining sites has adverse impacts on soil microbial diversity. New approaches, such as metagenomics approach, have become a powerful tool to investigate biodiversity of soil microbial communities. In the current study, metagenomics approach was used to investigate the microbial diversity of soils contaminated with different concentrations of lead (Pb) and zinc (Zn). The ...
... Microorganisms in grape skins play vital roles in grapevine health, productivity, wine quality and organoleptic properties. To investigate microbial diversity of muscadine grape skins, 16S and ITS sequences of 30 samples from six muscadine (Muscadinia rotundifolia Michx.) cultivars grown in Guangxi, China, were sequenced using Illumina Novaseq platform. A total of 7,317 bacterial operational taxon ...
Acidobacteria; Actinobacteria; Archaea; Dothideomycetes; Eurotiomycetes; Fusarium solani; Leotiomycetes; Proteobacteria; biodegradability; community structure; humans; plastics; soil; soil microorganisms; Europe
Abstract:
... BACKGROUND: Bio-based and biodegradable plastics are considered as plastics of the future owing to their ability to decompose under various environmental conditions. However, their effects on the soil microbiome are poorly characterised. In this study, we aimed to investigate the effects of an important bio-based and biodegradable plastic, polybutylene succinate-co-adipate (PBSA), on soil microbia ...
... Rusty root is a widespread problem in ginseng production, which can reduce ginseng quality and root price. The formation of rusty root is a complex process caused by multiple factors, primarily soil physicochemical factors and microorganisms. However, the precise roles played by these factors in the development of this disease remain unclear, especially the role of microorganisms. Deciphering the ...