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1. 16S metagenomics dataset of Zea mays and Triticum aestivum rhizosphere from Kallar Syedan Punjab, Pakistan

Author:
Sadia Latif; Rizwana Kousar; Anum Fatima; Hina Fatimah; Saba Farooq; Naeem Khan; Tayyaba Andleeb; Tariq Shah
Source:
Data in Brief 2022 v.42 pp. 108057
ISSN:
2352-3409
Subject:
Acidobacteria; Actinobacteria; Bacteroidetes; Firmicutes; Gemmatimonadetes; Nitrospirae; Proteobacteria; Thermomicrobia; Triticum aestivum; Verrucomicrobia; Zea mays; bacterial communities; climate change; data collection; genome; host-pathogen relationships; meta-analysis; metagenomics; phytobiome; population growth; rhizosphere; statistical analysis; vigor; Pakistan
Abstract:
... 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 ...
DOI:
10.1016/j.dib.2022.108057

2. 16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments

Author:
Dechamma Mundanda Muthappa; Sakshi Lamba; Sathesh K. Sivasankaran; Ankita Naithani; Noel Rogers; Shabarinath Srikumar; Guerrino Macori; Amalia G.M. Scannell; Séamus Fanning
Source:
Foodborne pathogens & disease 2022 v.19 no.7 pp. 485-494
ISSN:
1556-7125
Subject:
Acidobacteria; Actinobacteria; Bacteroidetes; Deinococcus-Thermus; Firmicutes; Proteobacteria; Tenericutes; Verrucomicrobia; bacterial communities; food matrix; food production; genes; metagenomics; microbiome; processed foods; ribosomal RNA; spring; summer; winter; Ireland
Abstract:
... 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 ...
DOI:
10.1089/fpd.2022.0014

3. 16S rRNA Gene-Based Metagenomic Analysis of Rhizosphere Soil Bacteria in Arkansas Rice Crop Fields

Author:
Cássia Oliveira; Ehsan Shakiba; Dustin North; Madison McGraw; Ethan Ballard; Marissa Barrett-D’Amico; Galina Glazko; Yasir Rahmatallah
Source:
Agronomy 2022 v.12 no.1 pp. -
ISSN:
2073-4395
Subject:
Acidobacteria; Actinobacteria; Bacteroidetes; Oryza sativa; Proteobacteria; agronomy; carbon sequestration; community structure; crop rotation; crop yield; food availability; metagenomics; no-tillage; phylogeny; plant health; rhizosphere; rice; soil; Arkansas
Abstract:
... 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 ...
DOI:
10.3390/agronomy12010222

4. 16S rRNA analysis of electrogenic bacterial communities in microbial fuel cells developed from temperate soils

Author:
Luis Jimenez; Margarita Kulko; Ryan Kim; Theranda Jashari; Tina Choe
Source:
Bios 2020 v.91 no.1 pp. 9-20
ISSN:
0005-3155
Subject:
Acidobacteria; Actinobacteria; Chloroflexi; Firmicutes; Planctomycetes; Proteobacteria; anodes; bacterial communities; biofilm; cathodes; electricity generation; soil bacteria
Abstract:
... 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 ...
DOI:
10.1893/BIOS-D-18-00006

5. 16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage

Author:
Anne Fahy; Ludovic Giloteaux; Philippe Bertin; Denis Le Paslier; Claudine Médigue; Jean Weissenbach; Robert Duran; Béatrice Lauga
Source:
Microbial ecology 2015 v.70 no.1 pp. 154-167
ISSN:
0095-3628
Subject:
Acidithiobacillus; Acidobacteria; Actinobacteria; Thiomonas; acid mine drainage; amino acid sequences; arsenic; arsenites; bacteria; evolution; functional diversity; genes; oxidation; ribosomal RNA; sediments; transporters; France
Abstract:
... 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 ...
DOI:
10.1007/s00248-014-0558-3

6. 16S rRNA-based bacterial diversity in the organic-rich sediments underlying oxygen-deficient waters of the eastern Arabian Sea

Author:
Baby Divya; Ammini Parvathi; P. A. Loka Bharathi; Shanta Nair
Source:
World journal of microbiology & biotechnology 2011 v.27 no.12 pp. 2821-2833
ISSN:
0959-3993
Subject:
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 ...
DOI:
10.1007/s11274-011-0760-0

7. The 19-years inorganic fertilization increased bacterial diversity and altered bacterial community composition and potential functions in a paddy soil

Author:
Qiong Huang; Jianlei Wang; Cong Wang; Qing Wang
Source:
Applied soil ecology 2019 v.144 pp. 60-67
ISSN:
0929-1393
Subject:
Acidobacteria; Actinobacteria; Bacteroidetes; Chloroflexi; Gemmatimonadetes; Nitrospirae; Planctomycetes; Proteobacteria; autotrophs; bacterial communities; biodiversity; community structure; denitrification; fertilizer application; mineral fertilizers; multidimensional scaling; nitrate reduction; nitrates; nitrites; nitrogen; nitrogen fixation; nitrous oxide; oxidation; paddy soils; phosphorus; photoheterotrophs; phylogeny; potassium; soil ecology; sulfates; sulfides; sulfur; China
Abstract:
... 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 ...
DOI:
10.1016/j.apsoil.2019.07.009

8. A 3-year field study reveals that agri-management practices drive the dynamics of dominant bacterial taxa in the rhizosphere of Cajanus cajan

Author:
Upma Singh; Anil K. Choudhary; Shilpi Sharma
Source:
Symbiosis 2022 v.86 no.2 pp. 215-227
ISSN:
0334-5114
Subject:
Acidobacteria; Actinobacteria; Cajanus cajan; Firmicutes; agricultural conservation practice; bacterial communities; community structure; crop residues; disturbed soils; microbial activity; organic production; rhizosphere; soil fertility; soil quality; species richness; symbiosis; tillage
Abstract:
... 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 ...
DOI:
10.1007/s13199-022-00834-3

9. Abundance and composition of indigenous bacterial communities in a multi-step biofiltration-based drinking water treatment plant

Author:
Karin Lautenschlager; Chiachi Hwang; Fangqiong Ling; Wen-Tso Liu; Nico Boon; Oliver Köster; Thomas Egli; Frederik Hammes
Source:
Water research 2014 v.62 pp. 40-52
ISSN:
0043-1354
Subject:
Acidobacteria; Chloroflexi; Planctomycetes; Proteobacteria; activated carbon; bacteria; bacterial communities; biodegradation; biofilters; biofiltration; cluster analysis; community structure; drinking water; effluents; microbial biomass; phylogeny; ribosomal RNA; sand; sequence analysis; water treatment
Abstract:
... 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 ...
DOI:
10.1016/j.watres.2014.05.035

10. Abundance and diversity of functional genes involved in the degradation of aromatic hydrocarbons in Antarctic soils and sediments around Syowa Station

Author:
C. Muangchinda; S. Chavanich; V. Viyakarn; K. Watanabe; S. Imura; A. S. Vangnai; O. Pinyakong
Source:
Environmental science and pollution research international 2015 v.22 no.6 pp. 4725-4735
ISSN:
0944-1344
Subject:
Acidobacteria; Burkholderia glathei; Chlorobium; Cyanobacteria; Gram-negative bacteria; Mycobacterium; Sphingomonas; Terrabacter; Verrucomicrobium; bioremediation; denaturing gradient gel electrophoresis; functional diversity; genes; naphthalene; polycyclic aromatic hydrocarbons; quantitative polymerase chain reaction; sediments; sequence analysis; soil; Antarctic region; Antarctica
Abstract:
... 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 ...
DOI:
10.1007/s11356-014-3721-y

11. Acidobacteria Community Responses to Nitrogen Dose and Form in Chinese Fir Plantations in Southern China

Author:
Caixia Liu; Yuhong Dong; Lingyu Hou; Nan Deng; Ruzhen Jiao
Source:
Current microbiology 2017 v.74 no.3 pp. 396-403
ISSN:
0343-8651
Subject:
Acidobacteria; Cunninghamia lanceolata; RNA; ammonium nitrogen; ecological function; environmental factors; experimental design; nitrate nitrogen; nitrogen; pH; plantations; sequence analysis; China
Abstract:
... 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) ...
DOI:
10.1007/s00284-016-1192-8

12. Acidobacteria in Freshwater Ponds at Doñana National Park, Spain

Author:
Johannes Zimmermann; M. Carmen Portillo; Laura Serrano; Wolfgang Ludwig; Juan M. Gonzalez
Source:
Microbial ecology 2012 v.63 no.4 pp. 844-855
ISSN:
0095-3628
Subject:
Acidobacteria; aquatic environment; ecosystems; enrichment culture; fluorescence in situ hybridization; freshwater; geographical distribution; metabolism; national parks; nucleotide sequences; organic matter; ponds; ribosomal DNA; ribosomal RNA; sediments; sequence analysis; Spain
Abstract:
... 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 ...
DOI:
10.1007/s00248-011-9988-3
PubMed:
22167078

13. Acidobacteria in microbial communities of the bog and tundra lichens

Author:
T. A. Pankratov
Source:
Microbiology 2012 v.81 no.1 pp. 51-58
ISSN:
0026-2617
Subject:
Acidobacteria; Sphagnum; bacterial communities; lichens; pectins; starch; thallus; tundra; xylan
Abstract:
... 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 × 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 ...
DOI:
10.1134/S0026261711060166

14. Acidobacteria, Rubrobacteridae and Chloroflexi are abundant among very slow-growing and mini-colony-forming soil bacteria

Author:
Davis, Kathryn E.R.; Sangwan, Parveen; Janssen, Peter H.
Source:
Environmental microbiology 2011 v.13 no.3 pp. 798-805
ISSN:
1462-2912
Subject:
soil bacteria; eyes; Acidobacteria; Rubrobacteridae; soil
Abstract:
... 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 ...
DOI:
10.1111/j.1462-2920.2010.02384.x
PubMed:
21108723

15. Active microbial ecosystem in Iron‐Age tombs of the Etruscan civilization

Author:
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
Source:
Environmental microbiology 2021 v.23 no.7 pp. 3957-3969
ISSN:
1462-2912
Subject:
Acidobacteria; Actinobacteria; Bacteroidetes; Brevundimonas; Calothrix; Chroococcidiopsis; Polaromonas; acid tolerance; biosphere; limestone; mineralogy; nutrition; photosynthesis; primary productivity; temperature; Italy
Abstract:
... 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 ...
DOI:
10.1111/1462-2920.15327

16. Acute effects of hexavalent chromium on the performance and microbial community of activated sludge in aerobiotic reactors

Author:
Quan Zheng; Situ Na; Xinhui Li; Nankun Li; Reti Hai; Xiaohui Wang
Source:
Environmental technology 2019 v.40 no.14 pp. 1871-1880
ISSN:
1479-487X
Subject:
Acidobacteria; Coxiella; Planctomycetes; Rhodanobacter; activated sludge; acute effects; ammonium nitrogen; bacteria; bacterial communities; chemical oxygen demand; chromium; community structure; nitrification; oxygen; toxicity
Abstract:
... 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 ...
DOI:
10.1080/09593330.2018.1432695

17. Adaptation mechanisms of arsenic metabolism genes and their host microorganisms in soils with different arsenic contamination levels around abandoned gold tailings

Author:
Xianhong Li; Xiaoxia Liu; Neng Cao; Songjun Fang; Caihong Yu
Source:
Environmental pollution 2021 v.291 pp. 117994
ISSN:
0269-7491
Subject:
Acidobacteria; Actinobacteria; Chloroflexi; Proteobacteria; arsenic; genes; gold; metabolism; metagenomics; methylation; oxidation; pollution; prediction; solid wastes; wastewater
Abstract:
... 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 ...
DOI:
10.1016/j.envpol.2021.117994

18. Adaptive responses in short-chain fatty acid absorption, gene expression, and bacterial community of the bovine rumen epithelium recovered from a continuous or transient high-grain feeding

Author:
R.M. Petri; S.U. Wetzels; M. Qumar; R. Khiaosa-ard; Q. Zebeli
Source:
Journal of dairy science 2019 v.102 no.6 pp. 5361-5378
ISSN:
0022-0302
Subject:
Acetivibrio; Acidobacteria; Anaerorhabdus; Coprococcus; DNA; Dethiobacter; Holstein; bacteria; bacterial communities; biopsy; community structure; cross-over studies; dairy cows; diet; dysbiosis; experimental design; forage; gene expression; genes; homeostasis; intestinal absorption; models; pH; ribosomal RNA; rumen epithelium; short chain fatty acids; Switzerland
Abstract:
... 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 ...
DOI:
10.3168/jds.2018-15691

19. Advanced bio-oxidation of fungal mixed cultures immobilized on rotating biological contactors for the removal of pharmaceutical micropollutants in a real hospital wastewater

Author:
A. Cruz del Álamo; M.I. Pariente; R. Molina; F. Martínez
Source:
Journal of hazardous materials 2022 v.425 pp. 128002
ISSN:
0304-3894
Subject:
Acidobacteria; Ascomycota; Coriolus versicolor; Firmicutes; azithromycin; bacterial communities; biofilm; biological treatment; bioreactors; carbon; fungal biomass; hospitals; metronidazole; mixed culture; nitrogen; phosphorus; pollutants; sewer systems; sulfamethoxazole; temperature; wastewater; wastewater treatment
Abstract:
... 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 ...
DOI:
10.1016/j.jhazmat.2021.128002

20. Advancing the understanding of biogeography-diversity relationships of benthic microorganisms in the North Sea

Author:
Sapp, Melanie; Parker, Eleanor Ruth; Teal, Lorna Rachel; Schratzberger, Michaela
Source:
FEMS microbiology ecology 2010 v.74 no.2 pp. 410-429
ISSN:
0168-6496
Subject:
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 ...
DOI:
10.1111/j.1574-6941.2010.00957.x
PubMed:
20735476