1
|
Fatoyinbo HO, McDonnell MC, Hughes MP. Dielectrophoretic sample preparation for environmental monitoring of microorganisms: Soil particle removal. BIOMICROFLUIDICS 2014; 8:044115. [PMID: 25379100 PMCID: PMC4189292 DOI: 10.1063/1.4892036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/22/2014] [Indexed: 05/04/2023]
Abstract
Detection of pathogens from environmental samples is often hampered by sensors interacting with environmental particles such as soot, pollen, or environmental dust such as soil or clay. These particles may be of similar size to the target bacterium, preventing removal by filtration, but may non-specifically bind to sensor surfaces, fouling them and causing artefactual results. In this paper, we report the selective manipulation of soil particles using an AC electrokinetic microfluidic system. Four heterogeneous soil samples (smectic clay, kaolinitic clay, peaty loam, and sandy loam) were characterised using dielectrophoresis to identify the electrical difference to a target organism. A flow-cell device was then constructed to evaluate dielectrophoretic separation of bacteria and clay in a continous flow through mode. The average separation efficiency of the system across all soil types was found to be 68.7% with a maximal separation efficiency for kaolinitic clay at 87.6%. This represents the first attempt to separate soil particles from bacteria using dielectrophoresis and indicate that the technique shows significant promise; with appropriate system optimisation, we believe that this preliminary study represents an opportunity to develop a simple yet highly effective sample processing system.
Collapse
Affiliation(s)
- Henry O Fatoyinbo
- Centre for Biomedical Engineering, Department of Mechanical Engineering Sciences, University of Surrey , Guildford, Surrey GU2 7XH, United Kingdom
| | | | - Michael P Hughes
- Centre for Biomedical Engineering, Department of Mechanical Engineering Sciences, University of Surrey , Guildford, Surrey GU2 7XH, United Kingdom
| |
Collapse
|
2
|
|
3
|
Liu J, Li J, Feng L, Cao H, Cui Z. An improved method for extracting bacteria from soil for high molecular weight DNA recovery and BAC library construction. J Microbiol 2011; 48:728-33. [DOI: 10.1007/s12275-010-0139-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 07/15/2010] [Indexed: 10/18/2022]
|
4
|
García-Villaraco Velasco A, Probanza A, Gutierrez Mañero F, Ramos B, Lucas García J. Functional diversity of rhizosphere microorganisms from different genotypes ofArabidopsis thaliana. COMMUNITY ECOL 2009. [DOI: 10.1556/comec.10.2009.1.13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
5
|
Högberg MN, Bååth E, Nordgren A, Arnebrant K, Högberg P. Contrasting effects of nitrogen availability on plant carbon supply to mycorrhizal fungi and saprotrophs - a hypothesis based on field observations in boreal forest. THE NEW PHYTOLOGIST 2003; 160:225-238. [PMID: 33873541 DOI: 10.1046/j.1469-8137.2003.00867.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• Soil microorganisms are considered C-limited, while plant productivity is frequently N-limited. Large stores of organic C in boreal forest soils are attributed to negative effects of low temperature, soil acidity and plant residue recalcitrance upon microbial activity. • We examined microbial activity, biomass and community composition along a natural 90-m-long soil N supply gradient, where plant species composition varies profoundly, forest productivity three-fold and soil pH by three units. • There was, however, no significant variation in soil respiration in the field across the gradient. Neither did microbial biomass C determined by fumigation-extraction vary, while other estimates of activity and biomass showed a weak increase with increasing N supply and soil pH. Simultaneously, a phospholipid fatty acid attributed mainly to mycorrhizal fungi declined drastically, while bacterial biomass increased. • We hypothesize that low N supply and plant productivity, and hence low litter C supply to saprotrophs is associated with a high plant C supply to mycorrhizal fungi, while the reverse occurs under high N supply. This should mean that effects of N availability on C supply to these functional groups of microbes acts in opposing directions.
Collapse
Affiliation(s)
- Mona N Högberg
- Section of Soil Science, Department of Forest Ecology, SLU, SE-901 83 Umeå, Sweden
| | - Erland Bååth
- Department of Microbial Ecology, Lund University, SE-223 62 Lund, Sweden
| | - Anders Nordgren
- Section of Soil Science, Department of Forest Ecology, SLU, SE-901 83 Umeå, Sweden
| | - Kristina Arnebrant
- Department of Microbial Ecology, Lund University, SE-223 62 Lund, Sweden
| | - Peter Högberg
- Section of Soil Science, Department of Forest Ecology, SLU, SE-901 83 Umeå, Sweden
| |
Collapse
|
6
|
dos Santos Furtado AL, Casper P. Different methods for extracting bacteria from freshwater sediment and a simple method to measure bacterial production in sediment samples. J Microbiol Methods 2000; 41:249-57. [PMID: 10958970 DOI: 10.1016/s0167-7012(00)00163-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The efficiency of different treatments was tested to extract bacterial cells from freshwater sediment samples. The influence of sonication, density gradient centrifugation, fixation by formalin and centrifugation speed on bacterial recovery was investigated. The method developed by Smith and Azam [Mar. Microb. Food Webs 6 (1992) 107] to measure microbial activity on bacterioplankton (3H-leucine incorporation), was also evaluated in sediment samples. After 1 min of sonication bacterial abundance was reduced by about 47% in diluted sediments with tetrasodium pyrophosphate. With the addition of Percoll after sonication, bacterial counts were not significantly different (P<0.05). Fixation by formalin increased bacterial counts using sonication. However, higher bacterial abundance was estimated in non-sonicated samples. Bacterial abundance in samples centrifuged at 7000xg with and without Percoll was not significantly different (P<0.05). Highest bacterial abundance was obtained after centrifugation at low speed (750xg). Bacterial abundance decreased with higher centrifugation speed (750, 1500 and 3000xg), the difference, however, was not significant. Bacterial production ranged from 0.10 microg C cm(-3) d(-1) in autoclaved sediment to 0. 27 microg C cm(-3) d(-1) in untreated sediment. The radioactivity measured in controls of both untreated and autoclaved sediment was high (70 and 91%, respectively), indicating a high level of leucine adsorption in sediment particles. In contrast, radioactivity in control samples previously centrifuged was markedly lower (6%). Despite the high values of radioactivity in the controls, bacterial production in untreated sediment was significantly higher than in centrifuged sediment (P<0.05).
Collapse
Affiliation(s)
- A L dos Santos Furtado
- Lab. de Limnologia, Depto. de Ecologia, Inst. de Biologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, 21.941-590, Rio de Janeiro, Brazil
| | | |
Collapse
|
7
|
Mayr C, Winding A, Hendriksen NB. Community level physiological profile of soil bacteria unaffected by extraction method. J Microbiol Methods 1999; 36:29-33. [PMID: 10353797 DOI: 10.1016/s0167-7012(99)00008-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Extraction and purification of bacteria from soil by the Nycodenz gradient centrifugation procedure described by Bakken and Lindahl (1995; Recovery of bacterial cells from soil. In: van Elsas, J.D., Trevors, J.T. (Eds.), Nucleic Acids in the Environment: Methods and Applications. Springer Verlag, Berlin, pp. 9-27) were compared to soil slurry extractions. Bacterial communities from four different soils were described by the bacterial abundance, CTC-reducing capacity, culturability and the community level physiological profiles (CLPP) in BIOLOG GN plates. A significant loss of both total and culturable number of bacteria g(-1) soil dry weight were found after extraction and purification of cells. The origin of soil influenced the yield of cells and a difference between the four soils and an interaction between the soils and extraction procedure were found. The culturability and the CLPP were different between the four soils but were unaffected by the extraction procedure. The bacterial community obtained after extraction and purification thus represented the same fraction of the indigenous bacterial community.
Collapse
Affiliation(s)
- C Mayr
- Department of Marine Ecology and Microbiology, National Environmental Research Institute, Roskilde, Denmark
| | | | | |
Collapse
|
8
|
Christensen H, Hansen M, Sorensen J. Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe. Appl Environ Microbiol 1999; 65:1753-61. [PMID: 10103277 PMCID: PMC91247 DOI: 10.1128/aem.65.4.1753-1761.1999] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A fluorescence in situ hybridization (FISH) technique based on binding of a rhodamine-labelled oligonucleotide probe to 16S rRNA was used to estimate the numbers of ribosome-rich bacteria in soil samples. Such bacteria, which have high cellular rRNA contents, were assumed to be active (and growing) in the soil. Hybridization to an rRNA probe, EUB338, for the domain Bacteria was performed with a soil slurry, and this was followed by collection of the bacteria by membrane filtration (pore size, 0.2 micrometer). A nonsense probe, NONEUB338 (which has a nucleotide sequence complementary to the nucleotide sequence of probe EUB338), was used as a control for nonspecific staining. Counting and size classification into groups of small, medium, and large bacteria were performed by fluorescence microscopy. To compensate for a difference in the relative staining intensities of the probes and for binding by the rhodamine part of the probe, control experiments in which excess unlabelled probe was added were performed. This resulted in lower counts with EUB338 but not with NONEUB338, indicating that nonspecific staining was due to binding of rhodamine to the bacteria. A value of 4.8 x 10(8) active bacteria per g of dry soil was obtained for bulk soil incubated for 2 days with 0.3% glucose. In comparison, a value of 3.8 x 10(8) active bacteria per g of dry soil was obtained for soil which had been air dried and subsequently rewetted. In both soils, the majority (68 to 77%) of actively growing bacteria were members of the smallest size class (cell width, 0.25 to 0.5 micrometer), but the active (and growing) bacteria still represented only approximately 5% of the total bacterial population determined by DAPI (4', 6-diamidino-2-phenylindole) staining. The FISH technique in which slurry hybridization is used holds great promise for use with phylogenetic probes and for automatic counting of soil bacteria.
Collapse
Affiliation(s)
- H Christensen
- Department of Veterinary Microbiology, Royal Veterinary and Agricultural University, 1870 Frederiksberg C, Denmark.
| | | | | |
Collapse
|
9
|
Nicholson WL, Law JF. Method for purification of bacterial endospores from soils: UV resistance of natural Sonoran desert soil populations of Bacillus spp. with reference to B. subtilis strain 168. J Microbiol Methods 1999; 35:13-21. [PMID: 10076626 DOI: 10.1016/s0167-7012(98)00097-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Endospores of Bacillus spp. were purified from three Sonoran desert soil samples by Chelex extraction and NaBr density gradient centrifugation and their UV resistances compared with that of B. subtilis strain 168. Natural spore populations exhibited tight adherence to soil particles which was not readily overcome by the extraction and purification procedure. It was observed that spores purified from soil exhibited 2-3 fold higher resistance to UV (as measured by the 90% lethal dose, LD90) than did B. subtilis strain 168 grown on NSM, a standard laboratory sporulation medium, and purified by the same extraction procedure. Cultivation of spore-forming bacteria isolated from soil on NSM resulted in production of spores with essentially identical UV resistance as strain 168, suggesting that spore UV resistance is influenced by the environment in which spores are produced.
Collapse
Affiliation(s)
- W L Nicholson
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson 85721, USA.
| | | |
Collapse
|
10
|
Lindahl V, Aa K, Olsen RA. Effects on microbial activity by extraction of indigenous cells from soil slurries. FEMS Microbiol Ecol 1996. [DOI: 10.1111/j.1574-6941.1996.tb00349.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|