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Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales. Appl Environ Microbiol 2019; 85:AEM.00324-19. [PMID: 31076430 DOI: 10.1128/aem.00324-19] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e., small (<2 mm), strongly bound clusters of minerals and organic carbon that persist through mechanical disruptions and wetting events. Their spatial structure is important for biogeochemical cycling, and we cannot reliably predict soil biological activities and variability by studying bulk soils alone. To fully understand the biogeochemical processes at work in soils, it is necessary to understand the micrometer-scale interactions that occur between soil particles and their microbial inhabitants. Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as "microbial villages" that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining "model system" approaches (e.g., developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members, like viruses. Initial studies suggest that aggregate-based approaches are a critical next step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.
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Williamson KE, Fuhrmann JJ, Wommack KE, Radosevich M. Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory. Annu Rev Virol 2017; 4:201-219. [PMID: 28961409 DOI: 10.1146/annurev-virology-101416-041639] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viral abundance in soils can range from below detection limits in hot deserts to over 1 billion per gram in wetlands. Abundance appears to be strongly influenced by water availability and temperature, but a lack of informational standards creates difficulties for cross-study analysis. Soil viral diversity is severely underestimated and undersampled, although current measures of viral richness are higher for soils than for aquatic ecosystems. Both morphometric and metagenomic analyses have raised questions about the prevalence of nontailed, ssDNA viruses in soils. Soil is complex and critically important to terrestrial biodiversity and human civilization, but impacts of viral activities on soil ecosystem services are poorly understood. While information from aquatic systems and medical microbiology suggests the potential for viral influences on nutrient cycles, food web interactions, gene transfer, and other key processes in soils, very few empirical data are available. To understand the soil virome, much work remains.
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Affiliation(s)
- Kurt E Williamson
- Biology Department, College of William and Mary, Williamsburg, Virginia 23185;
| | - Jeffry J Fuhrmann
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716
| | - K Eric Wommack
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716.,Department Biological Sciences, University of Delaware, Newark, Delaware 19716.,College of Earth, Ocean, and Environment, University of Delaware, Newark, Delaware 19716
| | - Mark Radosevich
- Biosystems Engineering and Soil Science Department, University of Tennessee, Knoxville, Tennessee 37996
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Stotzky G. Influence of Soil Mineral Colloids on Metabolic Processes, Growth, Adhesion, and Ecology of Microbes and Viruses. SSSA SPECIAL PUBLICATIONS 2015. [DOI: 10.2136/sssaspecpub17.c10] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- G. Stotzky
- Laboratory of Microbial Ecology, Dep. of Biology; New York University; New York NY 10003 USA
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Bellou MI, Syngouna VI, Tselepi MA, Kokkinos PA, Paparrodopoulos SC, Vantarakis A, Chrysikopoulos CV. Interaction of human adenoviruses and coliphages with kaolinite and bentonite. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 517:86-95. [PMID: 25723960 DOI: 10.1016/j.scitotenv.2015.02.036] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 02/10/2015] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
Human adenoviruses (hAdVs) are pathogenic viruses responsible for public health problems worldwide. They have also been used as viral indicators in environmental systems. Coliphages (e.g., MS2, ΦX174) have also been studied as indicators of viral pollution in fecally contaminated water. Our objective was to evaluate the distribution of three viral fecal indicators (hAdVs, MS2, and ΦΧ174), between two different phyllosilicate clays (kaolinite and bentonite) and the aqueous phase. A series of static and dynamic experiments were conducted under two different temperatures (4, 25°C) for a time period of seven days. HAdV adsorption was examined in DNase I reaction buffer (pH=7.6, and ionic strength (IS)=1.4mM), whereas coliphage adsorption in phosphate buffered saline solution (pH=7, IS=2mM). Moreover, the effect of IS on hAdV adsorption under static conditions was evaluated. The adsorption of hAdV was assessed by real-time PCR and its infectivity was tested by cultivation methods. The coliphages MS2 and ΦΧ174 were assayed by the double-layer overlay method. The experimental results have shown that coliphage adsorption onto both kaolinite and bentonite was higher for the dynamic than the static experiments; whereas hAdV adsorption was lower under dynamic conditions. The adsorption of hAdV increased with decreasing temperature, contrary to the results obtained for the coliphages. This study examines the combined effect of temperature, agitation, clay type, and IS on hAdV adsorption onto clays. The results provide useful new information on the effective removal of viral fecal indicators (MS2, ΦX174 and hAdV) from dilute aqueous solutions by adsorption onto kaolinite and bentonite. Factors enabling enteric viruses to penetrate soils, groundwater and travel long distances within aquifers are important public health issues. Because the observed adsorption behavior of surrogate coliphages MS2 and ΦΧ174 is substantially different to that of hAdV, neither MS2 nor ΦΧ174 is recommended as a suitable model for adenovirus.
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Affiliation(s)
- Maria I Bellou
- Environmental Microbiology Unit, Department of Public Health, University of Patras, 26500 Patras, Greece
| | - Vasiliki I Syngouna
- Environmental Engineering Laboratory, Department of Civil Engineering, University of Patras, 26500 Patras, Greece
| | - Maria A Tselepi
- Environmental Microbiology Unit, Department of Public Health, University of Patras, 26500 Patras, Greece
| | - Petros A Kokkinos
- Environmental Microbiology Unit, Department of Public Health, University of Patras, 26500 Patras, Greece
| | - Spyros C Paparrodopoulos
- Environmental Microbiology Unit, Department of Public Health, University of Patras, 26500 Patras, Greece
| | - Apostolos Vantarakis
- Environmental Microbiology Unit, Department of Public Health, University of Patras, 26500 Patras, Greece.
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Soil Phage Ecology: Abundance, Distribution, and Interactions with Bacterial Hosts. SOIL BIOLOGY 2011. [DOI: 10.1007/978-3-642-14512-4_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Williamson KE, Radosevich M, Smith DW, Wommack KE. Incidence of lysogeny within temperate and extreme soil environments. Environ Microbiol 2008; 9:2563-74. [PMID: 17803780 DOI: 10.1111/j.1462-2920.2007.01374.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A companion study indicated that approximately 30% of cultivable soil bacteria may contain inducible prophage; however, the degree to which this cultivation-based estimate applies to autochthonous communities of soil bacteria is unknown. To estimate the prevalence of lysogeny within soil bacterial communities, induction assays were carried out by extracting bacteria from soil and subsequently exposing extracts to mitomycin C (MC; 0.5 microg ml(-1)), or by exposing bacteria to MC (1.0 microg ml(-1)) through direct addition to soil slurries. Induction was assessed as an increase in viral direct counts relative to those obtained in controls, as detected by epifluorescence microscopy. Extracting bacteria from soils followed by 18 h MC exposure generated significantly higher prophage induction than all other treatments (P < 0.05). For three Antarctic soil samples, estimates of inducible fraction (IF) were statistically indistinguishable across two independent assays (P = 0.82), indicating that this approach is highly reproducible. Although IF was lower in Antarctic soils (4-20%) and higher in temperate Delaware soils (22-68%), no clear correlations were found between lysogeny and soil physical properties. For Delaware soils, IF estimates were similar between whole soil assays (44%) and cultivation-based approaches (30%). While these data suggest that lysogeny is common among soil bacteria, the specific factors which promote temperate interactions remain unclear.
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Affiliation(s)
- Kurt E Williamson
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
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Williamson KE, Wommack KE, Radosevich M. Sampling natural viral communities from soil for culture-independent analyses. Appl Environ Microbiol 2004; 69:6628-33. [PMID: 14602622 PMCID: PMC262263 DOI: 10.1128/aem.69.11.6628-6633.2003] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An essential first step in investigations of viruses in soil is the evaluation of viral recovery methods suitable for subsequent culture-independent analyses. In this study, four elution buffers (10% beef extract, 250 mM glycine buffer, 10 mM sodium pyrophosphate, and 1% potassium citrate) and three enumeration techniques (plaque assay, epifluorescence microscopy [EFM], and transmission electron microscopy [TEM]) were compared to determine the best method of extracting autochthonous bacteriophages from two Delaware agricultural soils. Beef extract and glycine buffer were the most effective in eluting viable phages inoculated into soils (up to 29% recovery); however, extraction efficiency varied significantly with phage strain. Potassium citrate eluted the highest numbers of virus-like particles from both soils based on enumerations by EFM (mean, 5.3 x 10(8) g of dry soil(-1)), but specific soil-eluant combinations posed significant problems to enumeration by EFM. Observations of virus-like particles under TEM gave confidence that the particles were, in fact, phages, but TEM enumerations yielded measurements of phage abundance (mean, 1.5 x 10(8) g of dry soil(-1)) that were about five times lower. Clearly, the measurement of phage abundance in soils varies with both the extraction and enumeration methodology; thus, it is important to assess multiple extraction and enumeration approaches prior to undertaking ecological studies of phages in a particular soil.
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Affiliation(s)
- Kurt E Williamson
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716, USA
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Yin X, Stotzky G. Gene transfer among bacteria in natural environments. ADVANCES IN APPLIED MICROBIOLOGY 1997; 45:153-212. [PMID: 9342828 DOI: 10.1016/s0065-2164(08)70263-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- X Yin
- SRA Technologies, Inc., Rockville, Maryland 20850, USA
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Stotzky G, Babich H. Survival of, and genetic transfer by, genetically engineered bacteria in natural environments. ADVANCES IN APPLIED MICROBIOLOGY 1986; 31:93-138. [PMID: 3521212 DOI: 10.1016/s0065-2164(08)70440-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Abstract
Organic matter in sewage, soil, and aquatic systems may enhance or inhibit the infectivity of viruses associated with particulates (e.g., clay minerals, sediments). The purpose of this investigation was to identify the mechanisms whereby organic matter, in the form of defined proteins, affects the adsorption of reovirus to the clay minerals kaolinite and montmorillonite and its subsequent infectivity. Chymotrypsin and ovalbumin reduced the adsorption of reovirus to kaolinite and montmorillonite homoionic to sodium. Lysozyme did not reduce the adsorption of the virus to kaolinite, but it did reduce adsorption to montmorillonite. The proteins apparently competed with the reovirus for sites on the clay. As lysozyme does not adsorb to kaolinite by cation exchange, it did not inhibit the adsorption of reovirus to this clay. The amount of reovirus desorbed from lysozyme-coated montmorillonite was approximately 38% less (compared with the input population) than that from uncoated or chymotrypsin-coated montmorillonite after six washings with sterile distilled water. Chymotrypsin and lysozyme markedly decreased reovirus infectivity in distilled water, whereas infectivity of the virus was enhanced after recovery from an ovalbumin-distilled water-reovirus suspension (i.e., from the immiscible pelleted fraction plus supernatant). The results of these studies indicate that the persistence of reovirus in terrestrial and aquatic environments may vary with the type of organic matter and clay mineral with which the virus comes in contact.
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Bitton G, Pancorbo OC, Farrah SR. Virus transport and survival after land application of sewage sludge. Appl Environ Microbiol 1984; 47:905-9. [PMID: 6331308 PMCID: PMC240010 DOI: 10.1128/aem.47.5.905-909.1984] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The survival and transport patterns of poliovirus 1 and echovirus 1 were studied in undisturbed soil cores which were treated with digested sludge and exposed to natural weather conditions prevailing in north central Florida. It was shown that, under those experimental conditions, enteroviruses are relatively rapidly inactivated in the soil. A more rapid virus decline was observed during the warm and dry fall season than during the warm and wet summer season. The monitoring of soil core leachates has shown that both viruses were effectively retained by the sludge-treated soil.
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Chang PL, Yen TF. Interaction of
Escherichia coli
B and B/4 and Bacteriophage T4D with Berea Sandstone Rock in Relation to Enhanced Oil Recovery. Appl Environ Microbiol 1984; 47:544-50. [PMID: 16346492 PMCID: PMC239718 DOI: 10.1128/aem.47.3.544-550.1984] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Much research and development is needed to recover oil reserves presently unattainable, and microbially enhanced oil recovery is a technology that may be used for this purpose. To address the problem of bacterial contamination in an oil field injection well region, we connected each end of a Teflon-sleeved Berea sandstone rock to a flask containing nutrient medium. By inoculating one flask with
Escherichia coli
B, we could observe bacterial growth in the uninoculated flask resulting from the transport and establishment of cells across the rock. Differences in bacterial populations occurred depending on whether bacteriophage T4D was first adsorbed to the rock. The results of these experiments indicate that the inhibition of bacterial establishment within a rock matrix is possible via lytic interaction. Some nonlytic effects are also implied by experiments with B/4 cells, which are T4D-resistant mutants of
E. coli
B. A 10 to 40% retention of T4 by the rock occurred when it was loaded with 10
5
to 10
6
PFU. We also describe a lysogenic system for possible use in microbially enhanced oil recovery techniques.
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Affiliation(s)
- P L Chang
- Department of Environmental Engineering, University of Southern California, University Park, California 90089
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Abstract
Coliphages T1 and T7 of Escherichia coli were absorbed by kaolinite (K) and montmorillonite (M). Maximum adsorption of T7 (96%) to M was greater than that of T1 (84%), but the adsorption of both coliphages to K was the same (99%). Positively charged sites (i.e., anion exchange sites) on the clays appeared to be primarily responsible for the adsorption of T1 to K but only partially responsible for the adsorption of T1 to M; equilibrium adsorption isotherms of T1 to K and M did not show a correlation between adsorption and the cation exchange capacity of the clays, and the reduction in adsorption caused by sodium metaphosphate (a polyanion that interacts with positively charged sites on clay) was more pronounced with K than with M. The equilibrium adsorption isotherms of T7 to K and M suggested a correlation between adsorption and the cation exchange capacity of the clays. However, studies with sodium metaphosphate indicated that T7 also adsorbed to positively charged sites on the clays, especially on K. Adsorption of the coliphages to positively charged sites was greater with K than with M, probably because the ratio of positively charged sites to negatively charged sites was greater on K than on M.
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MICROBIOLOGICAL HEALTH EFFECTS ASSOCIATED WITH THE USE OF MUNICIPAL WASTEWATER FOR IRRIGATION. MUNICIPAL WASTEWATER IN AGRICULTURE 1981. [PMCID: PMC7271177 DOI: 10.1016/b978-0-12-214880-4.50018-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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