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48 results for “soil bacterial community”
Soil properties and plant functional traits have different importance in shaping rhizosphere soil bacterial and fungal communities in a meadow steppe
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Data for: Can heavy metal pollution induce soil bacterial community resistance to antibiotics in boreal forests?
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Contrasting early successional dynamics of bacterial and fungal communities in recently deglaciated soils of the maritime Antarctic
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Slow soil enzyme recovery following invasive tree removal through gradual changes in bacterial and fungal communities
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Taxonomic and functional biogeographies of soil bacterial communities across the Tibet plateau are better explained by abiotic conditions than distance and plant community composition
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Bacterial communities and soil chemistry from ten established invasions of Lupinus polyphyllus in southwestern Finland, 2020
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Correlations between dominant vegetation type and composition and diversity of soil bacterial communities in a subtropical forest
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Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: a field-based experiment
<p>Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove <i>Rhizophora mangle</i> on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting, we found that bacterial community composition differed among <i>R. mangle</i> maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of <i>R. mangle</i>. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.</p>
Data from: The bacterial community structure and functional profile in the heavy metal contaminated paddy soils,surrounding a nonferrous smelter in South Korea
The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. The present study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes, involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.
Data from: Smooth brome invasion increases rare soil bacterial species prevalence and alters soil bacterial community composition
Plant and soil communities are tightly linked, but the mechanisms by which the invasion of an exotic plant and the resulting shifts in plant diversity and productivity influence soil bacterial community structure remain poorly understood. We investigated the effects of invasive smooth brome (Bromus inermis) on grassland soil bacterial community structure using massively-parallel sequencing of the 16S rRNA gene to determine bacterial community richness, evenness, composition, and beta diversity (UniFrac indices) of soils collected along a gradient of smooth brome abundance. We evaluated several hypotheses including: a) that the declines in native plant diversity associated with smooth brome invasion would cause declines in bacterial community diversity, and b) that mechanisms driving smooth brome effects on bacterial community structure involved altered soil edaphic properties rather than preferential invasion in areas of high soil nitrogen and distinct soil microbial communities. Smooth brome invasion led to increased soil nitrogen, soil carbon and root biomass. Bacterial evenness and bacterial richness increased with increasing smooth brome cover, while bacterial beta diversity declined. We found no evidence of a dominant direct link between the alteration of soil edaphic properties by brome and the changes in the soil bacterial community. Rather, the main controls on the soil bacterial community were direct effects of pH and smooth brome that could not be linked to the edaphic changes. The most important effect of brome on the bacterial community was the selective suppression of dominant bacterial species, which allowed rarer bacteria to increase in relative abundance. Synthesis: Here we show that plant community composition influences bacterial community structure at a very fine scale, but that these changes are not due to altered soil total nitrogen or carbon content. The dominant direct effect of smooth brome invasion on soil communities suggests non-edaphic, i.e. inter and intra-trophic, interactions among smooth brome and non-bacterial components of the soil ecosystem are key drivers of soil community structure. Some of the data in this repository were also reported in the following paper: Piper, C.L., Lamb, E.G. & Siciliano, S.D. (In Press) Smooth brome changes gross soil nitrogen cycling processes during invasion of a rough fescue grassland. Plant Ecology. doi:10.1007/s11258-014-0431-y
Large-scale homogenization of soil bacterial communities in response to agricultural practices in paddy fields, China
<div>This dataset contains data from 257 sites in four typical rice-growing regions across a 4,000-km transect in China, including geographic location data and environment factors data.</div> <div> <br> The study was conducted across a 4,000-km transect of China's rice-growing areas, from Heilong Jiang province to Yunnan province (100°55′ E to 134°08′° E, 22°46′ N to 48°02′ N, Table S1). Four typical rice-growing regions were selected along this transect: Sanjiang Plain (modern mechanical farming), Taihu Plain (mechanical plus minor manual farming), Lianghu Plain (manual plus minor mechanical farming), and Hani Terrace (traditional manual farming).</div> <div> <br> Field sampling was conducted during July and August in 2014 and 2015. Soil samples were collected from 178 flooded paddy fields and 79 surrounding non-paddy areas across four typical rice-growing regions of China. At each site, one homogenized sample was obtained, which was then separated into two parts. One part, which was obtained for DNA extraction, was placed into a sterile plastic tube then immediately placed in liquid nitrogen for short-term transportation. After shipping to the laboratory, these tubes were stored at −80 °C. The second part of the soil sample was placed into a plastic bag and stored at 4.0 °C for determining the soil physicochemical properties.</div> <div> <br> Main results of the experiments are that: (1) Distance–decay patterns of bacterial communities in paddy fields revealed reduced β-diversity compared to surrounding natural habitats. (2) Modern rice farming practices (plowing with machines) caused stronger homogenization of soil bacterial communities than traditional farming (plowing by hand). Among the four paddy regions, plowing by hand retained the highest soil bacterial β-diversity. (3) Moreover, a significant inverse correlation was observed between bacterial β-diversity and the agricultural mechanization level. (4) Among multiple environmental factors, dramatic spatial homogenization of soil physicochemical properties, particularly soil nutrient contents, and reduced dispersal limitation caused by modern farming activities both strongly predict a reduction of bacterial β-diversity in modern paddy fields.</div>
Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils.
<p>This repository holds the final data products from metagenomics processing of bacteria and viruses from the article : "Differences in the genomic potential of soil bacterial and phage communities between urban greenspaces and natural arid soils"</p> <p>Contents: </p> <ul> <li>LU_metadata.csv: information on the samples</li> <li>soil_chemistry.txt: physicochemical information on samples</li> <li>*_len.csv: tables containing the length information for annotated genes, divided by database. These are used to calculate RPKM abundances from count tables. </li> <li>BACTERIA</li> <li>ko_table, ko_unknown, ko2level, ko_description: count table of KEGG annotations, total counts for unnanotated genes, match of ko number to level and description</li> <li>all_bracken.csv: count table of taxonomic bacterial annotations using kraken2 and bracken</li> <li>mags_tax.csv: taxonomy assignments to MAGs (metagenome assembled genomes)</li> <li>mags_count_table.csv: abundante table of MAGs in counts</li> <li>ags_result, gc_mean, gc_variance: functional traits results, average genome size, and gc content</li> <li>lu_c_count, lu_n_count, card_d0, metals_count_table: abundance tables of genes annotated with Cazy (carbon), Ncydb (nitrogen), CARD (antibiotic resistance genes), and Bacmet (heavy metal resistance genes)</li> <li>VIRUS</li> <li>amg_summary.csv: results from AMG annotation with DRAM-V, filtered to keep genes of interest</li> <li>genomad_virus_summary.tsv: viral taxonomy annotations with geNomad</li> <li>virus_len.txt: length of inferred viruses (used for calculation of RPKM from count tables)</li> <li>all_host_prediction_to_genus.csv: virus host annotation with IPhop</li> <li>final_checkv.tsv: table of final viral inferences with quality estimates</li> <li>viral_species_count_table.txt: abundance table of infered viral contigs in counts</li> </ul>
Impact of transgenic maize Ruifeng125 on diversity and dy-namics of bacterial community in rhizosphere soil
<p><span>With the development of commercialized planting of genetically modified crops, their ecological security risks remain a hot topic of public concern. Insect-resistant genetically modified maize Ruifeng125 which expressing a fusion Bt protein (Cry1Ab-Cry2Aj) has obtained the application safety certificate issued by the Chinese government. To determine the effects of Ruifeng125 on the diversity and dynamics of bacterial communities, the accumulation and degradation pattern of the fusion Bt protein in the rhizosphere soil of transgenic maize were detected firstly. Results showed that the contents of Bt protein varied significantly at different developmental stages, but after straw returning to the field, over 97% of Bt proteins has been degraded quickly at the early stages (≤ 10 d) and then they were degraded at a relative slow rate. In addition, the variations of bacterial community diversity in the rhizosphere soil were detected by 16S ribosomal RNA (Rrna) high-throughput sequencing technology. A total of 44 phyla, 435 families and 842 genera were obtained by 16S rRNA sequencing, among which <em>Proteobacteria</em>, <em>Actinobacia</em>, <em>Acidobacter</em> <em>Acidobacterium</em> and <em>Chloroflexi</em> were the dominant taxa. At the same developmental stage, no significant differences in soil bacterial diversity were detected between Ruifeng125 and its non-transgenic control variety. Further analysis revealed that developmental stage, rather than the transgenic event, made the greatest contribution for the changes in soil microbial diversity. This research provides important information for evaluating the impacts of Bt crops on the soil microbiome and establish a theoretical foundation for their environmental safety assessment.</span></p>
Dataset of manuscript "Divergent responses of soil bacterial and fungal communities to climate warming in an alpine tundra ecosystem"
<p>Our study conducts a translocation experiment in the alpine tundra of the Changbai Mountains to explore how climate warming will affect soil bacterial and fungal communities in the alpine tundra and what are the underlying ecological mechanisms for their potential community changes. Soil samples (n = 24) were respectively collected during the early growing season (June 5, EGS), peak growing season (July 30, PGS), and late growing season (September 20, LGS) of 2021. The uploaded data contains the soil properties and OTU abundance measurements for these soil samples, as well as air and soil temperature from June 1, 2020 to September 15, 2021. </p>
Soil fauna-microbial interactions complexity triggers shifts in both fungal and bacterial communities under a contamination disturbance
<p>meta.otu.june2020.txt : Willow morphological data, data related to qPCR of PAH-RHD genes and phenanthrene amounts found by GC-MS in soil, associated to the paper entitled: Soil fauna-microbial interactions complexity triggers shifts in both fungal and bacterial communities under a contamination disturbance.</p> <p>Files starting by 16s, its, gn and gp are data tables of bioinformatically processed amplicon sequencing data containing filtered and rarefied counts corresponding to 4 set of genes (16S rRNA gene, fungal ITS, PAH-RHD Gram Negative and Gram Positive bacteria) and corresponding taxonomy. </p>
Data from: Smooth brome invasion increases rare soil bacterial species prevalence and alters soil bacterial community composition
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Data from: Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: a field-based experiment
Open the record for dataset details and reuse information.
Large-scale homogenization of soil bacterial communities in response to agricultural practices in paddy fields, China
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Data from: The bacterial community structure and functional profile in the heavy metal contaminated paddy soils,surrounding a nonferrous smelter in South Korea
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Data from: Positive selection inhibits gene mobilization and transfer in soil bacterial communities
Horizontal gene transfer (HGT) between bacterial lineages is a fundamental evolutionary process that accelerates adaptation. Sequence analyses show that conjugative plasmids are principal agents of HGT in natural communities. However, we lack understanding of how the ecology of bacterial communities and their environments affect the dynamics of plasmid-mediated gene mobilization and transfer. Here we show, in simple experimental soil bacterial communities containing a conjugative mercury resistance plasmid, the repeated, independent mobilization of transposon-borne genes from chromosome to plasmid, plasmid to chromosome and, in the absence of mercury selection, interspecific gene transfers from the chromosome of one species to the other via the plasmid. By reducing conjugation, positive selection for plasmid-encoded traits, like mercury resistance, can consequently inhibit HGT. Our results suggest that interspecific plasmid-mediated gene mobilization is most likely to occur in environments where plasmids are infectious, parasitic elements rather than those where plasmids are positively selected, beneficial elements.
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International Brain Laboratory public data
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