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Vijayan A, Vattiringal Jayadradhan RK, Pillai D, Prasannan Geetha P, Joseph V, Isaac Sarojini BS. Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity. J Basic Microbiol 2021; 61:88-109. [PMID: 33448079 DOI: 10.1002/jobm.202000485] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/30/2020] [Accepted: 12/28/2020] [Indexed: 12/14/2022]
Abstract
The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.
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Affiliation(s)
- Ardhra Vijayan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Rejish Kumar Vattiringal Jayadradhan
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India.,Department of Aquaculture, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Devika Pillai
- Department of Aquatic Animal Health Management, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Preena Prasannan Geetha
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
| | - Bright Singh Isaac Sarojini
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Kochi, Kerala, India
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Sangwan P, Nain T, Singal K, Hooda N, Sharma N. Soil as a tool of revelation in forensic science: a review. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:5150-5159. [PMID: 33135702 DOI: 10.1039/d0ay01634a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Soil contains diverse and complex natural elements having physical, chemical, mineralogical and biological components. Soil being a transferable physical component (it can be transferred from one location to another with the help of shoes, tires, clothes, tools etc.), acts as a tool of forensic investigation to correlate a specific crime scene with criminal suspects. A variety of techniques and combinations of methods can be used to discriminate soil from different geographical locations. The present review highlights various analytical techniques (ATR-FTIR, pyGC-MS, SEM-EDX, ICP-MS/OES and XRD) for soil analysis (colour comparison, texture and particle size determination, density gradient methods and organic matter estimation) and discusses some of the famous cases solved with soil trace evidence. The objective of the present study is to provide an overview of the importance of soil as physical evidence in forensic science based on literature analysis that will help forensic scientists and researchers to select appropriate methods to discriminate different soil samples. This article reviews various analytical techniques used to differentiate soils and provides compiled information regarding soil as trace evidence in order to help academicians, researchers and forensic soil scientists.
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Affiliation(s)
- Preeti Sangwan
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, India
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Babujia LC, Silva AP, Nakatani AS, Cantão ME, Vasconcelos ATR, Visentainer JV, Hungria M. Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome. Transgenic Res 2016; 25:425-40. [PMID: 26873023 DOI: 10.1007/s11248-016-9938-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/04/2016] [Indexed: 01/21/2023]
Abstract
The transgenic soybean [Glycine max (L.) Merrill] occupies about 80 % of the global area cropped with this legume, the majority comprising the glyphosate-resistant trait (Roundup Ready(®), GR or RR). However, concerns about possible impacts of transgenic crops on soil microbial communities are often raised. We investigated soil chemical, physical and microbiological properties, and grain yields in long-term field trials involving conventional and nearly isogenic RR transgenic genotypes. The trials were performed at two locations in Brazil, with different edaphoclimatic conditions. Large differences in physical, chemical and classic microbiological parameters (microbial biomass of C and N, basal respiration), as well as in grain production were observed between the sites. Some phyla (Proteobacteria, Actinobacteria, Acidobacteria), classes (Alphaproteobacteria, Actinomycetales, Solibacteres) and orders (Rhizobiales, Burkholderiales, Myxococcales, Pseudomonadales), as well as some functional subsystems (clustering-based subsystems, carbohydrates, amino acids and protein metabolism) were, in general, abundant in all treatments. However, bioindicators related to superior soil fertility and physical properties at Londrina were identified, among them a higher ratio of Proteobacteria:Acidobacteria. Regarding the transgene, the metagenomics showed differences in microbial taxonomic and functional abundances, but lower in magnitude than differences observed between the sites. Besides the site-specific differences, Proteobacteria, Firmicutes and Chlorophyta were higher in the transgenic treatment, as well as sequences related to protein metabolism, cell division and cycle. Although confirming effects of the transgenic trait on soil microbiome, no differences were recorded in grain yields, probably due to the buffering capacity associated with the high taxonomic and functional microbial diversity observed in all treatments.
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Affiliation(s)
- Letícia Carlos Babujia
- Department of Chemistry, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil
- Embrapa Soja, C.P. 231, Londrina, Paraná, 86001-970, Brazil
| | | | | | | | | | - Jesuí Vergilio Visentainer
- Department of Chemistry, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil
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Tambong JT, Xu R. Culture-independent analysis of Pseudomonas community structures in fertilized and unfertilized agricultural soils. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-012-0477-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Tongarun R, Luepromchai E, Vangnai AS. Natural Attenuation, Biostimulation, and Bioaugmentation in 4-Chloroaniline-Contaminated Soil. Curr Microbiol 2007; 56:182-8. [DOI: 10.1007/s00284-007-9055-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Accepted: 09/08/2007] [Indexed: 10/22/2022]
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DNA extraction method affects microbial community profiles from soils and sediment. Appl Microbiol Biotechnol 2007; 77:955-64. [DOI: 10.1007/s00253-007-1219-y] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 09/17/2007] [Accepted: 09/18/2007] [Indexed: 11/29/2022]
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Bordenave S, Goñi-Urriza MS, Caumette P, Duran R. Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl Environ Microbiol 2007; 73:6089-97. [PMID: 17704271 PMCID: PMC2075027 DOI: 10.1128/aem.01352-07] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of petroleum contamination on the bacterial community of a pristine microbial mat from Salins-de-Giraud (Camargue, France) have been investigated. Mats were maintained as microcosms and contaminated with no. 2 fuel oil from the wreck of the Erika. The evolution of the complex bacterial community was monitored by combining analyses based on 16S rRNA genes and their transcripts. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) analyses clearly showed the effects of the heavy fuel oil after 60 days of incubation. At the end of the experiment, the initial community structure was recovered, illustrating the resilience of this microbial ecosystem. In addition, the responses of the metabolically active bacterial community were evaluated by T-RFLP and clone library analyses based on 16S rRNA. Immediately after the heavy fuel oil was added to the microcosms, the structure of the active bacterial community was modified, indicating a rapid microbial mat response. Members of the Gammaproteobacteria were initially dominant in the contaminated microcosms. Pseudomonas and Acinetobacter were the main genera representative of this class. After 90 days of incubation, the Gammaproteobacteria were superseded by "Bacilli" and Alphaproteobacteria. This study shows the major changes that occur in the microbial mat community at different time periods following contamination. At the conclusion of the experiment, the RNA approach also demonstrated the resilience of the microbial mat community in resisting environmental stress resulting from oil pollution.
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Affiliation(s)
- Sylvain Bordenave
- Equipe Environnement et Microbiologie, IPREM UMR5254, IBEAS, Université de Pau, BP1155, 64013 Pau Cedex, France
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Muckian L, Grant R, Doyle E, Clipson N. Bacterial community structure in soils contaminated by polycyclic aromatic hydrocarbons. CHEMOSPHERE 2007; 68:1535-41. [PMID: 17482237 DOI: 10.1016/j.chemosphere.2007.03.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 02/28/2007] [Accepted: 03/04/2007] [Indexed: 05/15/2023]
Abstract
Bacterial community structure was examined in polycyclic aromatic hydrocarbon (PAH) contaminated soil taken from a timber treatment facility in southern Ireland. Profiles of soil bacterial communities were generated using a molecular fingerprinting technique, terminal restriction fragment length polymorphism (TRFLP), and results were interpreted using sophisticated multivariate statistical analysis. Findings suggested that there was a correlation between PAH structure and bacterial community composition. Initial characterisation of soil from the timber treatment facility indicated that PAH contamination was unevenly distributed across the site. Bacterial community composition was correlated with the type of PAH present, with microbial community structure associated with soil contaminated with two-ringed PAHs only being distinctly different to communities in soils contaminated with multi-component PAH mixtures. Typically the number of bacterial ribotypes detected in samples did not appear to be adversely affected by the level of contamination.
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Affiliation(s)
- Lorraine Muckian
- Microbial Ecology and Biodegradation Group, School of Biology and Environmental Science, University College Dublin, Ardmore House, Belfield, Dublin 4, Ireland
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Supaphol S, Panichsakpatana S, Trakulnaleamsai S, Tungkananuruk N, Roughjanajirapa P, O'Donnell AG. The selection of mixed microbial inocula in environmental biotechnology: Example using petroleum contaminated tropical soils. J Microbiol Methods 2006; 65:432-41. [PMID: 16226327 DOI: 10.1016/j.mimet.2005.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2005] [Revised: 08/29/2005] [Accepted: 09/02/2005] [Indexed: 10/25/2022]
Abstract
The impact of inorganic N and P additions on a tropical soil contaminated with petroleum hydrocarbons was investigated using molecular and culture techniques. Microcosms were incubated for 42 days and sampled at 0, 1, 7, 28 and 42 days. Changes in bacterial community structure were determined using denaturing gradient gel electrophoresis (DGGE) of the rRNA following reverse transcription PCR using primers specific to the V3 region of the 16S rRNA gene. To identify which components of the microbial community were changing during incubation, PCR amplicons were resolved using DGGE and the banding patterns analyzed using stepwise discriminant function analysis (SDA). SDA showed that the number of bands needed to recover the differences between samples over time could be reduced from the initial 11 bands for the 16S rRNA transcript to 3 bands. Sequences originating from the rRNA gels (16S rRNA transcripts) were recovered in clades containing known cultured isolates of Bacillus marisflavi, Microbacterium oxydans and Pseudomonas oleovorans. Isolation studies on these soils using lubricant oil as a carbon source yielded 317 bacterial isolates, 3 of which showed high sequence similarity (>96%) with the 16S rRNA transcripts identified using SDA as being important in differentiating between bacterial communities over time. These isolates were then tested singly and in combination for their ability to degrade lubricant oil. These analyses demonstrated that the consortium selected using the combined molecular-SDA approach was more effective at degrading the lubricant in both liquid media and in contaminated sand than the single isolates.
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Affiliation(s)
- Savaporn Supaphol
- Department of Soil Science, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
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Girvan MS, Bullimore J, Ball AS, Pretty JN, Osborn AM. Responses of active bacterial and fungal communities in soils under winter wheat to different fertilizer and pesticide regimens. Appl Environ Microbiol 2004; 70:2692-701. [PMID: 15128520 PMCID: PMC404392 DOI: 10.1128/aem.70.5.2692-2701.2004] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The composition of the active microbial (bacterial and fungal) soil community in an arable wheat field subjected to different management practices was examined at five times during a 1-year period. Field sections were fertilized either at good agricultural practice (GAP) levels or at reduced levels (0.5x GAP) and were inoculated with vesicular arbuscular mycorrhizae (VAM) at the same time. Field subsections were treated either with or without pesticides. Changes in the active microbial communities were investigated by denaturing gradient gel electrophoresis analysis of reverse transcription-PCR-amplified 16S and 18S rRNA. Microbial community structure was primarily determined by season, and the seasonal trends were similar for the fungal and bacterial components. Between-sample microbial heterogeneity decreased under a mature crop in the summer but increased following harvesting and plowing. Although similar overall trends were seen for the two microbial components, sample variability was greater for the fungal community than for the bacterial community. The greatest management effects were due to GAP fertilization, which caused increases in the bacterial numbers in the total and culturable communities. Microbial biomass similarly increased. GAP fertilization also caused large shifts in both the active bacterial community structure and the active fungal community structure and additionally resulted in a decrease in the heterogeneity of the active bacterial community. Pesticide addition did not significantly affect bacterial numbers or heterogeneity, but it led to major shifts in the active soil bacterial community structure. PCR primers specific for Glomales 25S rRNA genes were used to monitor the VAM population following inoculation. Glomales were detected initially only in VAM-inoculated field sections but were subsequently detected in noninoculated field sections as the season progressed. After plowing, the level of Glomales was reduced in noninoculated field sections but remained high in VAM-inoculated field sections. Inoculation of VAM correlated with elevated soil phosphate and carbon levels.
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Affiliation(s)
- Martina S Girvan
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England, United Kingdom
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Griffiths RI, Whiteley AS, O'Donnell AG, Bailey MJ. Physiological and community responses of established grassland bacterial populations to water stress. Appl Environ Microbiol 2004; 69:6961-8. [PMID: 14660337 PMCID: PMC309888 DOI: 10.1128/aem.69.12.6961-6968.2003] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effects of water stress upon the diversity and culturable activity of bacterial communities in the rhizosphere of an established upland grassland soil have been investigated. Intact monoliths were subjected to different watering regimens over a 2-month period to study community adaptation to moisture limitation and subsequent response to stress alleviation following rewetting. Genetic diversity was analyzed with 16S-based denaturing gradient gel electrophoresis (DGGE) of total soil-extracted DNA (rRNA genes) and RNA (rRNA transcripts) in an attempt to discriminate between total and active communities. Physiological response was monitored by plate counts, total counts, and BIOLOG-GN2 substrate utilization analyses. Controlled soil drying decreased the total number of CFU on all the media tested and also decreased the substrate utilization response. Following rewetting of dried soil, culture-based analyses indicated physiological recovery of the microbial population by the end of the experiment. In contrast, DGGE analyses of community 16S rRNA genes, rRNA transcripts and cultured communities did not reveal any changes relating to the moisture regimens, despite the observed physiological effects. We conclude that the imposed moisture regimen modulated the physiological status of the bacterial community and that bacterial communities in this soil are resistant to water stress. Further, we highlight the need for a reexamination of rRNA transcript-based molecular profiling techniques as a means of describing the active component of soil bacterial communities.
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Affiliation(s)
- Robert I Griffiths
- Molecular Microbial Ecology Laboratory, CEH-Oxford, Oxford OX1 3SR, United Kingdom
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Whiteley AS, Griffiths RI, Bailey MJ. Analysis of the microbial functional diversity within water-stressed soil communities by flow cytometric analysis and CTC+ cell sorting. J Microbiol Methods 2003; 54:257-67. [PMID: 12782381 DOI: 10.1016/s0167-7012(03)00066-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Total and active cell counts within soil samples were determined by culture-independent methods using flow cytometry and preparative Nycodenz gradient centrifugation. Whole cells were purified from soil cores and total extractable cell counts assessed by SYBR Green II fluorescence, while active cell counts were determined by 5-cyano-2,3-ditolyl tetrazolium chloride reduction (CTC+ cells). Parallel microcosms, maintained at either field water capacity or subjected to drying, indicated that the total extractable cell count remained between 10(8) and 10(9) g(-1) (dry weight). In contrast, the CTC+ active count fell threefold in dried microcosms (6% of total cell count) when compared to wetted microcosms (18% of total cell count). Specifically, these data highlighted an overall deactivation of microbial biomass during water stress, with 16S rDNA analyses of flow-sorted CTC+ cells demonstrating shifts within the active diversity. Flow cytometry coupled with cell purification techniques represents a significant tool for operationally defining an active and redundant microbial component within soil communities and is demonstrated during water stress.
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Affiliation(s)
- Andrew S Whiteley
- Molecular Microbial Ecology Laboratory, CEH-Oxford, Mansfield Road, Oxford OX1 3SR, UK.
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