1
|
Hernández-Guzmán M, Pérez-Hernández V, Navarro-Noya YE, Luna-Guido ML, Verhulst N, Govaerts B, Dendooven L. Application of ammonium to a N limited arable soil enriches a succession of bacteria typically found in the rhizosphere. Sci Rep 2022; 12:4110. [PMID: 35260645 PMCID: PMC8904580 DOI: 10.1038/s41598-022-07623-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/01/2022] [Indexed: 12/30/2022] Open
Abstract
Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha−1 and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.) rotation. Soil samples, fertilized or unfertilized, were amended or not (control) with a solution of (NH4)2SO4 (300 kg N ha−1) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO2 emission, mineral N and the bacterial community were monitored. Application of NH4+ significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH4+ and NO2− was faster in the fertilized soil than in the unfertilized soil. The relative abundance of Nitrosovibrio, the sole ammonium oxidizer detected, was higher in the fertilized than in the unfertilized soil; and similarly, that of Nitrospira, the sole nitrite oxidizer. Application of NH4+ enriched Pseudomonas, Flavisolibacter, Enterobacter and Pseudoxanthomonas in the first week and Rheinheimera, Acinetobacter and Achromobacter between day 7 and 28. The application of ammonium to a soil cultivated with wheat and maize enriched a sequence of bacterial genera characterized as rhizospheric and/or endophytic independent of the application of urea, retention or burning of the crop residue, or tillage.
Collapse
Affiliation(s)
- Mario Hernández-Guzmán
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico
| | - Valentín Pérez-Hernández
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico.,Department of Chemistry and Biochemistry, Instituto Tecnológico de Tuxtla-Gutiérrez, Tuxtla Gutiérrez, Mexico
| | - Yendi E Navarro-Noya
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, México
| | - Marco L Luna-Guido
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico
| | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Bram Govaerts
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico.,Cornell University, Ithaca, USA
| | - Luc Dendooven
- Laboratory of Soil Ecology, CINVESTAV, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A Madero, Mexico City, Mexico.
| |
Collapse
|
2
|
Lawal OU, Barata M, Fraqueza MJ, Worning P, Bartels MD, Goncalves L, Paixão P, Goncalves E, Toscano C, Empel J, Urbaś M, Domiìnguez MA, Westh H, de Lencastre H, Miragaia M. Staphylococcus saprophyticus From Clinical and Environmental Origins Have Distinct Biofilm Composition. Front Microbiol 2021; 12:663768. [PMID: 34163443 PMCID: PMC8216562 DOI: 10.3389/fmicb.2021.663768] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Biofilm formation has been shown to be critical to the success of uropathogens. Although Staphylococcus saprophyticus is a common cause of urinary tract infections, its biofilm production capacity, composition, genetic basis, and origin are poorly understood. We investigated biofilm formation in a large and diverse collection of S. saprophyticus (n = 422). Biofilm matrix composition was assessed in representative strains (n = 63) belonging to two main S. saprophyticus lineages (G and S) recovered from human infection, colonization, and food-related environment using biofilm detachment approach. To identify factors that could be associated with biofilm formation and structure variation, we used a pangenome-wide association study approach. Almost all the isolates (91%; n = 384/422) produced biofilm. Among the 63 representative strains, we identified eight biofilm matrix phenotypes, but the most common were composed of protein or protein-extracellular DNA (eDNA)-polysaccharides (38%, 24/63 each). Biofilms containing protein-eDNA-polysaccharides were linked to lineage G and environmental isolates, whereas protein-based biofilms were produced by lineage S and infection isolates (p < 0.05). Putative biofilm-associated genes, namely, aas, atl, ebpS, uafA, sasF, sasD, sdrH, splE, sdrE, sdrC, sraP, and ica genes, were found with different frequencies (3-100%), but there was no correlation between their presence and biofilm production or matrix types. Notably, icaC_1 was ubiquitous in the collection, while icaR was lineage G-associated, and only four strains carried a complete ica gene cluster (icaADBCR) except one that was without icaR. We provided evidence, using a comparative genomic approach, that the complete icaADBCR cluster was acquired multiple times by S. saprophyticus and originated from other coagulase-negative staphylococci. Overall, the composition of S. saprophyticus biofilms was distinct in environmental and clinical isolates, suggesting that modulation of biofilm structure could be a key step in the pathogenicity of these bacteria. Moreover, biofilm production in S. saprophyticus is ica-independent, and the complete icaADBCR was acquired from other staphylococci.
Collapse
Affiliation(s)
- Opeyemi U. Lawal
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Marta Barata
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Maria J. Fraqueza
- Centre for Interdisciplinary Research in Animal Health, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal
| | - Peder Worning
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Mette D. Bartels
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | | | | | | | | | - Joanna Empel
- Department of Epidemiology and Clinical Microbiology, Narodowy Instytut Leków, Warszawa, Poland
| | - Malgorzata Urbaś
- Department of Epidemiology and Clinical Microbiology, Narodowy Instytut Leków, Warszawa, Poland
| | | | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
- Institute of Clinical Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- The Laboratory of Microbiology and Infectious Diseases, The Rockefeller University, New York, NY, United States
| | - Maria Miragaia
- Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| |
Collapse
|
3
|
Roland FAE, Borges AV, Darchambeau F, Llirós M, Descy JP, Morana C. The possible occurrence of iron-dependent anaerobic methane oxidation in an Archean Ocean analogue. Sci Rep 2021; 11:1597. [PMID: 33452366 PMCID: PMC7810693 DOI: 10.1038/s41598-021-81210-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/05/2021] [Indexed: 11/24/2022] Open
Abstract
In the ferruginous and anoxic early Earth oceans, photoferrotrophy drove most of the biological production before the advent of oxygenic photosynthesis, but its association with ferric iron (Fe3+) dependent anaerobic methane (CH4) oxidation (AOM) has been poorly investigated. We studied AOM in Kabuno Bay, a modern analogue to the Archean Ocean (anoxic bottom waters and dissolved Fe concentrations > 600 µmol L-1). Aerobic and anaerobic CH4 oxidation rates up to 0.12 ± 0.03 and 51 ± 1 µmol L-1 d-1, respectively, were put in evidence. In the Fe oxidation-reduction zone, we observed high concentration of Bacteriochlorophyll e (biomarker of the anoxygenic photoautotrophs), which co-occurred with the maximum CH4 oxidation peaks, and a high abundance of Candidatus Methanoperedens, which can couple AOM to Fe3+ reduction. In addition, comparison of measured CH4 oxidation rates with electron acceptor fluxes suggest that AOM could mainly rely on Fe3+ produced by photoferrotrophs. Further experiments specifically targeted to investigate the interactions between photoferrotrophs and AOM would be of considerable interest. Indeed, ferric Fe3+-driven AOM has been poorly envisaged as a possible metabolic process in the Archean ocean, but this can potentially change the conceptualization and modelling of metabolic and geochemical processes controlling climate conditions in the Early Earth.
Collapse
Affiliation(s)
- Fleur A E Roland
- Chemical Oceanography Unit, Université de Liège, Liège, Belgium.
| | | | | | - Marc Llirós
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Girona Biomedical Research Institute, Salt, Catalunya, Spain
| | | | - Cédric Morana
- Department of Earth and Environmental Sciences, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| |
Collapse
|
4
|
Wang Y, Osman JR, DuBow MS. Bacterial Communities on the Surface of the Mineral Sandy Soil from the Desert of Maine (USA). Curr Microbiol 2020; 77:1429-1437. [PMID: 32193606 DOI: 10.1007/s00284-020-01946-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 03/07/2020] [Indexed: 12/19/2022]
Abstract
The Desert of Maine, not a real desert, is a 160,000 m2 tourist attraction of glacial silt which resembles a desert, surrounded by a pine forest in the state of Maine located in the northeastern USA. Though not a true desert, the soil of the Desert of Maine has a sandy texture with poor water-holding abilities, nutrient retention capabilities, and a relatively low pH value (pH 5.09). Samples from this site may be of interest to examine the bacterial diversity present on mineral sandy loam soils with an acidic pH, low concentrations of organic materials though surrounded by a pine forest, and compare it with true desert soil microbial populations. Two surface sand samples from the Desert of Maine were obtained, and pyrosequencing of PCR amplified 16S rRNA genes from total extracted DNA was used to assess bacterial diversity, community structure, and the relative abundance of major bacterial taxa. We found that the soil samples from the Desert of Maine displayed high levels of bacterial diversity, with a predominance of members belonging to the Proteobacteria and Actinobacteria phyla. Bacteria from the most abundant genus, Acidiphilium, represent 12.5% of the total 16S rDNA sequences. In total, 1394 OTUs were observed in the two samples, with 668 OTUs being observed in both samples. By comparing Desert of Maine bacterial populations with studies on similar soil environments, we found that the samples contained less Acidobacteria than soils from acid soil forests, and less Firmicutes plus more Proteobacteria than oligotrophic desert soils. Interestingly, our samples were found to be highly similar in their composition to an oak forest soil in France.
Collapse
Affiliation(s)
- Yang Wang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Jorge R Osman
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
- Laboratoire de Géologie de Lyon, Université Claude Bernard Lyon-1, UMR5276, Lyon, France
| | - Michael S DuBow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France.
| |
Collapse
|
5
|
El-Sayed WS, Elbahloul Y, Saad ME, Hanafy AM, Hegazi AH, ElShafei GMS, Elbadry M. Impact of nanoparticles on transcriptional regulation of catabolic genes of petroleum hydrocarbon-degrading bacteria in contaminated soil microcosms. J Basic Microbiol 2018; 59:166-180. [PMID: 30468270 DOI: 10.1002/jobm.201800186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 09/29/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022]
Abstract
This study was conducted to determine what effects nanoparticles (NPs) like TiO2 , ZnO, and Ag may pose on natural attenuation processes of petroleum hydrocarbons in contaminated soils. The solid NPs used were identified using x-ray diffraction technique and their average size was certified as 18.2, 16.9, and 18.3 nm for Ag-NPs, ZnO-NPs, and TiO2 -NPs, respectively. NPs in soil microcosms behave differently where it was dissolved as in case of Ag-NPs, partially dissolved as in ZnO-NPs or changed into other crystalline phase as in TiO2 -NPs. In this investigation, catabolic gene encoding catechol 2,3 dioxygenase (C23DO) was selected specifically as biomarker for monitoring hydrocarbon biodegradation potential by measuring its transcripts by RT-qPCR. TiO2 -NPs amended microcosms showed almost no change in C23DO expression profile or bacterial community which were dominated by Bacillus sp., Mycobacterium sp., Microbacterium sp., Clostridium sp., beside uncultured bacteria, including uncultured proteobacteria, Thauera sp. and Clostridia. XRD pattern suggested that TiO2 -NPs in microcosms were changed into other non-inhibitory crystalline phase, consequently, showing the maximum degradation profile for most low molecular weight oil fractions and partially for the high molecular weight ones. Increasing ZnO-NPs concentration in microcosms resulted in a reduction in the expression of C23DO with a concomitant slight deteriorative effect on bacterial populations ending up with elimination of Clostridium sp., Thauera sp., and uncultured proteobacteria. The oil-degradation efficiency was reduced compared to TiO2 -NPs amended microcosms. In microcosms, Ag-NPs were not detected in the crystalline form but were available in the ionic form that inhibited most bacterial populations and resulted in a limited degradation profile of oil, specifically the low molecular weight fractions. Ag-NPs amended microcosms showed a significant reduction (80%) in C23DO gene expression and a detrimental effect on bacterial populations including key players like Mycobacterium sp., Microbacterium sp., and Thauera sp. involved in the biodegradation of petroleum hydrocarbons.
Collapse
Affiliation(s)
- Wael S El-Sayed
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Yasser Elbahloul
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Mohamed E Saad
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Ahmed M Hanafy
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Microbiology Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Abdelrahman H Hegazi
- Chemistry Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Gamal M S ElShafei
- Chemistry Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Chemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Medhat Elbadry
- Biology Department, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia.,Agricultural Microbiology Department, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| |
Collapse
|
6
|
Qi D, Wieneke X, Tao J, Zhou X, Desilva U. Soil pH Is the Primary Factor Correlating With Soil Microbiome in Karst Rocky Desertification Regions in the Wushan County, Chongqing, China. Front Microbiol 2018; 9:1027. [PMID: 29896164 PMCID: PMC5987757 DOI: 10.3389/fmicb.2018.01027] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/01/2018] [Indexed: 01/22/2023] Open
Abstract
Karst rocky desertification (KRD) is a process of land degradation, which causes desert-like landscapes, deconstruction of endemic biomass, and declined soil quality. The relationship of KRD progression with above-ground communities (e.g. vegetation and animal) is well-studied. Interaction of soil desertification with underground communities, such as soil microbiome, however, is vastly unknown. This study characterizes change in soil bacterial community in response to KRD progression. Soil bacterial communities were surveyed by deep sequencing of 16S amplicons. Eight soil properties, pH, soil organic matter (SOM), total and available nitrogen (TN and AN), total and available phosphorus (TP and AP), and total and available potassium (TK and AK), were measured to assess soil quality. We find that the overall soil quality decreases along with KRD progressive gradient. Soil bacterial community compositions are distinguishingly different in KRD stages. The richness and diversity in bacterial community do not significantly change with KRD progression although a slight increase in diversity was observed. A slight decrease in richness was seen in SKRD areas. Soil pH primarily correlates with bacterial community composition. We identified a core microbiome for KRD soils consisting of; Acidobacteria, Alpha-Proteobacteria, Planctomycetes, Beta-Proteobacteria, Actinobacteria, Firmicutes, Delta-Proteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Gemmatimonadetes in this study. Phylum Cyanobacteria is significantly abundant in non-degraded soils, suggesting that Cyanobacterial activities might be correlated to soil quality. Our results suggest that Proteobacteria are sensitive to changes in soil properties caused by the KRD progression. Alpha- and beta-Proteobacteria significantly predominated in SKRD compared to NKRD, suggesting that Proteobacteria, along with many others in the core microbiome (Acidobacteria, Actinobacteria, Firmicutes, and Nitrospirae), were active in nutrient limiting degraded soils. This study demonstrates the relationship of soil properties with bacterial community in KRD areas. Our results fill the gap of knowledge on change in soil bacterial community during KRD progression.
Collapse
Affiliation(s)
- Daihua Qi
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Xuwen Wieneke
- Department of Animal Science, Oklahoma State University, Stillwater, OK, United States
| | - Jianping Tao
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Xu Zhou
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| | - Udaya Desilva
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, China
| |
Collapse
|
7
|
Shah V, Subramaniam S. Bradyrhizobium japonicum USDA110: A representative model organism for studying the impact of pollutants on soil microbiota. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:963-967. [PMID: 29275259 DOI: 10.1016/j.scitotenv.2017.12.185] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 12/17/2017] [Indexed: 06/07/2023]
Abstract
Photobacteria phosoreum or Escherichia coli are widely used in the scientific, industrial, and regulatory industries for evaluating the toxicity of pollutants against the soil microbial community. The organisms, however, are not part of the soil microbiota and the toxicity data obtained using these organisms could be misleading. Analysis of microbiota present in the soil obtained from across the world indicates that organisms from the Bradyrhizobium genus are the most ubiquitous of all microorganisms. Playing a critical role in nitrogen fixation and soil fertility, organisms from this genus should be used for studying the toxicity of pollutants. Indeed, we propose that Bradyrhizobium japonicum USDA110 be used as a model organism for screening pollutants for toxicity against a soil microbial community.
Collapse
Affiliation(s)
- Vishal Shah
- College of the Sciences and Mathematics, West Chester University of Pennsylvania, West Chester, PA, United States.
| | | |
Collapse
|
8
|
Pelagic photoferrotrophy and iron cycling in a modern ferruginous basin. Sci Rep 2015; 5:13803. [PMID: 26348272 PMCID: PMC4562300 DOI: 10.1038/srep13803] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/05/2015] [Indexed: 11/08/2022] Open
Abstract
Iron-rich (ferruginous) ocean chemistry prevailed throughout most of Earth’s early history. Before the evolution and proliferation of oxygenic photosynthesis, biological production in the ferruginous oceans was likely driven by photoferrotrophic bacteria that oxidize ferrous iron {Fe(II)} to harness energy from sunlight, and fix inorganic carbon into biomass. Photoferrotrophs may thus have fuelled Earth’s early biosphere providing energy to drive microbial growth and evolution over billions of years. Yet, photoferrotrophic activity has remained largely elusive on the modern Earth, leaving models for early biological production untested and imperative ecological context for the evolution of life missing. Here, we show that an active community of pelagic photoferrotrophs comprises up to 30% of the total microbial community in illuminated ferruginous waters of Kabuno Bay (KB), East Africa (DR Congo). These photoferrotrophs produce oxidized iron {Fe(III)} and biomass, and support a diverse pelagic microbial community including heterotrophic Fe(III)-reducers, sulfate reducers, fermenters and methanogens. At modest light levels, rates of photoferrotrophy in KB exceed those predicted for early Earth primary production, and are sufficient to generate Earth’s largest sedimentary iron ore deposits. Fe cycling, however, is efficient, and complex microbial community interactions likely regulate Fe(III) and organic matter export from the photic zone.
Collapse
|
9
|
Llirós M, Inceoğlu Ö, García-Armisen T, Anzil A, Leporcq B, Pigneur LM, Viroux L, Darchambeau F, Descy JP, Servais P. Bacterial community composition in three freshwater reservoirs of different alkalinity and trophic status. PLoS One 2014; 9:e116145. [PMID: 25541975 PMCID: PMC4277477 DOI: 10.1371/journal.pone.0116145] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/03/2014] [Indexed: 11/21/2022] Open
Abstract
In order to investigate the factors controlling the bacterial community composition (BCC) in reservoirs, we sampled three freshwater reservoirs with contrasted physical and chemical characteristics and trophic status. The BCC was analysed by 16S rRNA gene amplicon 454 pyrosequencing. In parallel, a complete dataset of environmental parameters and phytoplankton community composition was also collected. BCC in the analysed reservoirs resembled that of epilimnetic waters of natural freshwater lakes with presence of Actinobacteria, Alpha- and Betaproteobacteria, Cytophaga–Flavobacteria–Bacteroidetes (CFB) and Verrucomicrobia groups. Our results evidenced that the retrieved BCC in the analysed reservoirs was strongly influenced by pH, alkalinity and organic carbon content, whereas comparatively little change was observed among layers in stratified conditions.
Collapse
Affiliation(s)
- Marc Llirós
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | - Özgül Inceoğlu
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Adriana Anzil
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussels, Belgium
| | - Bruno Leporcq
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | | | - Laurent Viroux
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | | | - Jean-Pierre Descy
- Laboratory of Freshwater Ecology, University of Namur, Namur, Belgium
| | - Pierre Servais
- Ecologie des Systèmes Aquatiques, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
| |
Collapse
|
10
|
Rispoli FJ, Green T, Fasano TA, Shah V. The effect of environmental remediation on the cesium-137 levels in white-tailed deer. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:11598-11602. [PMID: 25028321 DOI: 10.1007/s11356-014-3143-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/02/2014] [Indexed: 06/03/2023]
Abstract
Due to activities involving nuclear energy research during the latter half of the 1900 s, environmental contamination in the form of elevated cesium-137 levels was observed within the Brookhaven National Laboratory, a US Department of Energy facility. Between the years 2000 and 2005, the laboratory carried out a major soil cleanup effort to remove cesium-137 from contaminated sites. In this study, we examine the effectiveness of the cleanup effort by comparing the levels of cesium-137 in the meat of white-tailed deer found within and around the laboratory. Results suggest that the cleanup was effective, with mean concentration of cesium-137 in the meat from within the laboratory decreasing from 2.04 Bq/g prior to 1.22 Bq/g after cleanup. At the current level, the consumption of deer would not pose any human health hazard. Nevertheless, statistically higher levels of cesium-137 were detected in the deer within the laboratory as opposed to levels found in deer 1 mi beyond the laboratory site.
Collapse
Affiliation(s)
- Fred J Rispoli
- Department of Mathematics, Dowling College, Oakdale, NY, 11769, USA,
| | | | | | | |
Collapse
|
11
|
Shah V, Jones J, Dickman J, Greenman S. Response of soil bacterial community to metal nanoparticles in biosolids. JOURNAL OF HAZARDOUS MATERIALS 2014; 274:399-403. [PMID: 24801897 DOI: 10.1016/j.jhazmat.2014.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/04/2014] [Accepted: 04/05/2014] [Indexed: 06/03/2023]
Abstract
The increasing use of engineered nanoparticles (NPs) in industrial and household applications will very likely lead to the increased release of such materials into the public sewer systems. During the wastewater treatment process, some fraction of NPs would always be concentrated in the biosolids. When biosolids is applied on the agricultural land, NPs are introduced into the soil matrix. In the current study we investigate the influence of five different metal nanoparticles present in biosolids on soil microbial community as a function of time. Results indicate that ZnO and Zero Valent Cu NPs were not toxic to soil bacterial community. Biosolids mixed with Ag NPs and TiO2 (both anatase and rutile phase) in contrast changed the bacterial richness and composition in wavering pattern as a function of time. Based on the observations made in the study, we suggest caution when interpreting the toxicity of NPs based on single time point study.
Collapse
Affiliation(s)
- Vishal Shah
- Department of Biology, Dowling College, Oakdale, NY 11769, USA.
| | - Jamilee Jones
- Department of Biology, Dowling College, Oakdale, NY 11769, USA
| | - Jenifer Dickman
- Department of Biology, Dowling College, Oakdale, NY 11769, USA
| | - Steven Greenman
- Department of Biology, Dowling College, Oakdale, NY 11769, USA
| |
Collapse
|
12
|
Kumar N, Palmer GR, Shah V, Walker VK. The effect of silver nanoparticles on seasonal change in arctic tundra bacterial and fungal assemblages. PLoS One 2014; 9:e99953. [PMID: 24926877 PMCID: PMC4057283 DOI: 10.1371/journal.pone.0099953] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/20/2014] [Indexed: 11/29/2022] Open
Abstract
The impact of silver nanoparticles (NPs) and microparticles (MPs) on bacterial and fungal assemblages was studied in soils collected from a low arctic site. Two different concentrations (0.066% and 6.6%) of Ag NPs and Ag MPs were tested in microcosms that were exposed to temperatures mimicking a winter to summer transition. Toxicity was monitored by differential respiration, phospholipid fatty acid analysis, polymerase chain reaction-denaturing gradient gel electrophoresis and DNA sequencing. Notwithstanding the effect of Ag MPs, nanosilver had an obvious, additional impact on the microbial community, underscoring the importance of particle size in toxicity. This impact was evidenced by levels of differential respiration in 0.066% Ag NP-treated soil that were only half that of control soils, a decrease in signature bacterial fatty acids, and changes in both richness and evenness in bacterial and fungal DNA sequence assemblages. Prominent after Ag NP-treatment were Hypocreales fungi, which increased to 70%, from only 1% of fungal sequences under control conditions. Genera within this Order known for their antioxidant properties (Cordyceps/Isaria) dominated the fungal assemblage after NP addition. In contrast, sequences attributed to the nitrogen-fixing Rhizobiales bacteria appeared vulnerable to Ag NP-mediated toxicity. This combination of physiological, biochemical and molecular studies clearly demonstrate that Ag NPs can severely disrupt the natural seasonal progression of tundra assemblages.
Collapse
Affiliation(s)
- Niraj Kumar
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Gerald R. Palmer
- Department of Biology, Queen's University, Kingston, Ontario, Canada
| | - Vishal Shah
- Department of Biology, Dowling College, Oakdale, New York, United States of America
| | - Virginia K. Walker
- Department of Biology, Queen's University, Kingston, Ontario, Canada
- School of Environmental Studies, Queen's University, Kingston, Ontario, Canada
- * E-mail:
| |
Collapse
|
13
|
454 pyrosequencing analysis on microbial diversity of an expanded granular sludge bed reactor treating high NaCl and nitrate concentration wastewater. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0387-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
14
|
Shah V, Shah S, Mackey H, Kambhampati M, Collins D, Dowd SE, Colichio R, McDonnell KT, Green T. Microbial community in the soil determines the forest recovery post-exposure to gamma irradiation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:11396-11402. [PMID: 24063597 DOI: 10.1021/es400923k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Exposure of an ecosystem to ionizing radiation remains a possibility either due to accidents involving nuclear fuel rods or contamination with high-level radioactive wastes. While the short and long-term effect of ionizing radiation on higher eukaryotes has been well documented, we do not have an understanding on the recovery of the microbial community post radiation. Here we report that at a site within Brookhaven National Laboratory that was radiated from 1961 to 1978 with γ rays (Gamma Forest), the ecosystem has not yet fully recovered from the effects of radiation. The current vegetation type in the Gamma Forest varies as one goes away from the source of ionizing radiation, with the region closest to the source having no vegetation. The microbial tag-encoded FLX amplicon pyrosequencing analysis of the soil from different regions suggests that the current microbial community structure is identical in all the Zones. When soil samples from each vegetation zone of the Gamma Forest were radiated with 1.8 kGy γ radiation and survival microbial community analyzed, clear difference in the microbial communities were observed. It is evident based on the experimental data that the colonization of soil with Nitrosomonadaceae is critical for the higher plants in pine barrens to reestablish and grow after the area had been exposed to ionizing radiation.
Collapse
Affiliation(s)
- Vishal Shah
- Department of Biology, Dowling College , 150 Idle Hour Boulevard, Oakdale, New York 11769, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Rohini-Kumar M, Osborne JW, Saravanan VS. Comparison of soil bacterial communities of Pinus patula of Nilgiris, western ghats with other biogeographically distant pine forest clone libraries. MICROBIAL ECOLOGY 2013; 66:132-144. [PMID: 23274880 DOI: 10.1007/s00248-012-0167-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 12/13/2012] [Indexed: 06/01/2023]
Abstract
The bacterial community structure of the rhizosphere and non-rhizosphere soil of Pinus patula, found in the Nilgiris region of Western Ghats, was studied by constructing 16S rRNA gene clone libraries. In the rhizosphere and non-rhizosphere soil clone libraries constructed, 13 and 15 bacterial phyla were identified, respectively. The clone libraries showed the predominance of members of culturally underrepresented phyla like Acidobacteria and Verrucomicrobia. The Alphaproteobacteria and Acidobacteria clones were predominant in rhizosphere and non-rhizosphere soil samples, respectively. In rhizosphere, amongst Alphaproteobacteria members, Bradyrhizobium formed the significant proportion, whereas in non-rhizosphere, members of subdivision-6 of phylum Acidobacteria were abundant. The diversity analysis of P. patula soil libraries showed that the phylotypes (16S rRNA gene similarity cutoff, ≥97 %) of Acidobacteria and Bacteroidetes were relatively predominant and diverse followed by Alphaproteobacteria and Verrucomicrobia. The diversity indices estimated higher richness and abundance of bacteria in P. patula soil clone libraries than the pine forest clone libraries retrieved from previous studies. The tools like principal co-ordinate analysis and Jackknife cluster analysis, which were under UniFrac analysis indicated that variations in soil bacterial communities were attributed to their respective geographical locations due to the phylogenetic divergence amongst the clone libraries. Overall, the P. patula rhizosphere and non-rhizosphere clone libraries were found significantly unique in composition, evenly distributed and highly rich in phylotypes, amongst the biogeographically distant clone libraries. It was finally hypothesised that the phylogenetic divergence amongst the bacterial phylotypes and natural selection plays a pivotal role in the variations of bacterial communities across the geographical distance.
Collapse
Affiliation(s)
- M Rohini-Kumar
- School of Bio Sciences and Technology, Vellore Institute of Technology University, Vellore, 632014, India.
| | | | | |
Collapse
|
16
|
Impact of short-term acidification on nitrification and nitrifying bacterial community dynamics in soilless cultivation media. Appl Environ Microbiol 2012; 78:6576-82. [PMID: 22773643 DOI: 10.1128/aem.01545-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soilless medium-based horticulture systems are highly prevalent due to their capacity to optimize growth of high-cash crops. However, these systems are highly dynamic and more sensitive to physiochemical and pH perturbations than traditional soil-based systems, especially during nitrification associated with ammonia-based fertilization. The objective of this study was to assess the impact of nitrification-generated acidification on ammonia oxidation rates and nitrifying bacterial community dynamics in soilless growth media. To achieve this goal, perlite soilless growth medium from a commercial bell pepper greenhouse was incubated with ammonium in bench-scale microcosm experiments. Initial quantitative real-time PCR analysis indicated that betaproteobacterial ammonia oxidizers were significantly more abundant than ammonia-oxidizing archaea, and therefore, research focused on this group. Ammonia oxidation rates were highest between 0 and 9 days, when pH values dropped from 7.4 to 4.9. Pyrosequencing of betaproteobacterial ammonia-oxidizing amoA gene fragments indicated that r-strategist-like Nitrosomonas was the dominant ammonia-oxidizing bacterial genus during this period, seemingly due to the high ammonium concentration and optimal growth conditions in the soilless media. Reduction of pH to levels below 4.8 resulted in a significant decrease in both ammonia oxidation rates and the diversity of ammonia-oxidizing bacteria, with increased relative abundance of the r-strategist-like Nitrosospira. Nitrite oxidizers (Nitrospira and Nitrobacter) were on the whole more abundant and less sensitive to acidification than ammonia oxidizers. This study demonstrates that nitrification and nitrifying bacterial community dynamics in high-N-load intensive soilless growth media may be significantly different from those in in-terra agricultural systems.
Collapse
|