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1
McDaniel, Marshall D., Marcela Hernández, Marc G. Dumont, Lachlan J. Ingram, and Mark A. Adams. "Disproportionate CH4 Sink Strength from an Endemic, Sub-Alpine Australian Soil Microbial Community." Microorganisms 9, no. 3 (March 15, 2021): 606. http://dx.doi.org/10.3390/microorganisms9030606.
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Soil-to-atmosphere methane (CH4) fluxes are dependent on opposing microbial processes of production and consumption. Here we use a soil–vegetation gradient in an Australian sub-alpine ecosystem to examine links between composition of soil microbial communities, and the fluxes of greenhouse gases they regulate. For each soil/vegetation type (forest, grassland, and bog), we measured carbon dioxide (CO2) and CH4 fluxes and their production/consumption at 5 cm intervals to a depth of 30 cm. All soils were sources of CO2, ranging from 49 to 93 mg CO2 m−2 h−1. Forest soils were strong net sinks for CH4, at rates of up to −413 µg CH4 m−2 h−1. Grassland soils varied, with some soils acting as sources and some as sinks, but overall averaged −97 µg CH4 m−2 h−1. Bog soils were net sources of CH4 (+340 µg CH4 m−2 h−1). Methanotrophs were dominated by USCα in forest and grassland soils, and Candidatus Methylomirabilis in the bog soils. Methylocystis were also detected at relatively low abundance in all soils. Our study suggests that there is a disproportionately large contribution of these ecosystems to the global soil CH4 sink, which highlights our dependence on soil ecosystem services in remote locations driven by unique populations of soil microbes. It is paramount to explore and understand these remote, hard-to-reach ecosystems to better understand biogeochemical cycles that underpin global sustainability.
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Eskov, Alen K., Alexei O. Zverev, and Evgeny V. Abakumov. "Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other." Microorganisms 9, no. 5 (May 11, 2021): 1033. http://dx.doi.org/10.3390/microorganisms9051033.
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Microbial biodiversity parameters for tropical rainforests remain poorly understood. Whilst the soil microbiome accounts up to 95% of the total diversity of microorganisms in terrestrial ecosystems, the microbiome of suspended soils formed by vascular epiphytes remains completely unexplored. Samples of ground and suspended soils were collected in Cat Tien National Park, southern Vietnam. DNA extraction and sequencing were performed, and libraries of 16s rDNA gene sequences were analyzed. Alpha diversity indices of the microorganisms were the highest in the forest ground soil. In general, the microbiological diversity of all the soil types was found to be similar at the phylum level. Taxonomic composition of the bacterial communities in the suspended soils of plants from the same species are not closer than the taxonomic compositions of the communities in the suspended soils of different plant species. However, the beta diversity analysis revealed significant differences in the movement of mineral elements in terrestrial versus suspended soils. Our data showed that the suspended soils associated with vascular epiphytes were a depository of unique microbiological biodiversity. A contributing factor was the presence of large amounts of organic matter in the suspended soils—deposits collected by the epiphytes—which would have been degraded by termites if it had reached the ground. Further, the nutrient content of the suspended soils was prime for soil respiration activity and taxonomic microbial community biodiversity.
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Czarny, Jakub, Justyna Staninska-Pięta, Jolanta Powierska-Czarny, Jacek Nowak, Łukasz Wolko, and Agnieszka Piotrowska-Cyplik. "Metagenomic Analysis of Soil Bacterial Community and Level of Genes Responsible for Biodegradation of Aromatic Hydrocarbons." Polish Journal of Microbiology 66, no. 3 (September 27, 2017): 345–52. http://dx.doi.org/10.5604/01.3001.0010.4865.
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The aim of the studies was to compare the composition of soil bacterial metabiomes originating from urbanized areas and areas con¬taminated with hydrocarbons with those from agricultural soil and forest soil obtained from a protected wild-life park area. It should be noted that hydrocarbons are everywhere therefore bacteria capable of their utilization are present in every soil type. In the hydrocarbon-contaminated soil and in the soil of anthropogenic origin, the bacteria belonging to Gammaproteobacteria were dominant (28.4–36.6%), whereas in the case of agricultural soil and protected wild-life park soil their ratios decreased (22.8–23.0%) and were similar to that of Alphaproteobacteria. No statistically significant changes were observed in terms of the Operational Taxonomic Unit identified in the studies soils, however, based on the determined alpha-diversity it can be established that contaminated soils were characterized by lower biodiversity indices compared to agricultural and forest soils. Furthermore, the dioxygenase level was also evaluated in the studied soils, which are genes encoding crucial enzymes for the decomposition of mono- and polycyclic aromatic hydrocarbons during the biodegradation of diesel oil (PAHRHDαGN, PAHRHDαGP, xylE, Cat 2,3, ndoB). It was concluded that both the population structure of the soil metabiome and the number of genes crucial for biodegradation processes differed significantly between the soils. The level of analysed genes showed a similar trend, as their highest number in relations to genes encoding 16S RNA was determined in urban and hydrocarbon-contaminated soil.
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Lee, Jung Yeop, and Byung Kook Hwang. "Diversity of antifungal actinomycetes in various vegetative soils of Korea." Canadian Journal of Microbiology 48, no. 5 (May 1, 2002): 407–17. http://dx.doi.org/10.1139/w02-025.
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Diversity of actinomycetes and their antifungal activities against some plant pathogenic fungi were examined in various vegetative soils from 14 different sites in the western part of Korea. Actinomycete counts ranged from 1.17 × 106to 4.20 × 106cfu·g-1dried soil. A total of 1510 actinomycetes were isolated from the soil samples. Streptomyces was predominant in soils with a pH range of 5.1-6.5, 9.1-13.0% moisture, and 9.1-11.0% organic matter. Most Micromonospora, Dactylosporangium, and Streptosporangium were distributed in soils with pH 4.0-5.0, 2.0-9.0% moisture, and 4.0-7.0% organic matter. Actinomadura and nocardioform actinomycetes were abundant in soils with pH 4.0-5.0 and 13.1-20.0% moisture and with 9.1-11.0 and 4.0-7.0% organic matter, respectively. Populations of Streptomyces were predominant in all the soils, but were highest in grassland and lowest in mountain-forest soils. Micromonospora was most abundant in pepper-field soil and nocardioform actinomycetes were highest in rice paddy field soil. Dactylosporangium was predominant in lake-mud sediments and pepper-field soil, Streptosporangium in lake-mud sediments, and Actinomadura in mountain-forest soil. Antifungal actinomycetes were abundant in orchard soil and lake mud. More than 50% of antifungal isolates from most soils were classified as genus Streptomyces. Actinomycete isolates that showed strong antifungal activity against Alternaria mali, Colletotrichum gloeosporioides, Fusarium oxysporum f.sp. cucumerinum, and Rhizoctonia solani were predominant in pepper-field soils, whereas those against Magnaporthe grisea and Phytophthora capsici were abundant in radish-field soils.Key words: actinomycetes, antifungal activity, plant pathogenic fungi, vegetative soils.
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Cullings, Ken, and Shilpa Makhija. "Ectomycorrhizal Fungal Associates of Pinus contorta in Soils Associated with a Hot Spring in Norris Geyser Basin, Yellowstone National Park, Wyoming." Applied and Environmental Microbiology 67, no. 12 (December 1, 2001): 5538–43. http://dx.doi.org/10.1128/aem.67.12.5538-5543.2001.
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ABSTRACT Molecular methods and comparisons of fruiting patterns (i.e., presence or absence of fungal fruiting bodies in different soil types) were used to determine ectomycorrhizal (EM) associates of Pinus contorta in soils associated with a thermal soil classified as ultra-acidic to extremely acidic (pH 2 to 4). EM were sampled by obtaining 36 soil cores from six paired plots (three cores each) of both thermal soils and forest soils directly adjacent to the thermal area. Fruiting bodies (mushrooms) were collected for molecular identification and to compare fruiting body (above-ground) diversity to below-ground diversity. Our results indicate (i) that there were significant decreases in both the level of EM infection (130 ± 22 EM root tips/core in forest soil; 68 ± 22 EM root tips/core in thermal soil) and EM fungal species richness (4.0 ± 0.5 species/core in forest soil; 1.2 ± 0.2 species/core in thermal soil) in soils associated with the thermal feature; (ii) that the EM mycota of thermal soils was comprised of a small set of dominant species and included very few rare species, while the EM mycota of forest soils contained a few dominant species and several rare EM fungal species; (iii) that Dermocybe phoenecius and a species of Inocybe, which was rare in forest soils, were the dominant EM fungal species in thermal soils; (iv) that other than the single Inocybe species, there was no overlap in the EM fungal communities of the forest and thermal soils; and (v) that the fungal species forming the majority of the above-ground fruiting structures in thermal soils (Pisolithus tinctorius, which is commonly used in remediation of acid soils) was not detected on a single EM root tip in either type of soil. Thus, P. tinctorius may have a different role in these thermal soils. Our results suggest that this species may not perform well in remediation of all acid soils and that factors such as pH, soil temperature, and soil chemistry may interact to influence EM fungal community structure. In addition, we identified at least one new species with potential for use in remediation of hot acidic soil.
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Ibekwe, A. Mark, Sharon K. Papiernik, Catherine M. Grieve, and Ching-Hong Yang. "Quantification of Persistence ofEscherichia coliO157:H7 in Contrasting Soils." International Journal of Microbiology 2011 (2011): 1–11. http://dx.doi.org/10.1155/2011/421379.
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Persistence ofEscherichia coli (E. coli)O157:H7 in the environment is a major concern to vegetable and fruit growers where farms and livestock production are in close proximity. The objectives were to determine the effects of preplant fumigation treatment on the survival ofE. coliO157:H7 in two soils and the effects of indigenous bacterial populations on the survival of this pathogen. Real-time PCR and plate counts were used to quantify the survival ofE. coliO157:H7 in two contrasting soils after fumigation with methyl bromide (MeBr) and methyl iodide (MeI). Ten days after fumigation,E. coliO157:H7 counts were significantly lower () in fumigated soils than in the non-fumigated. Direct comparison between MeBr and MeI within each soil indicated that these two fumigants showed similar impacts onE. coliO157:H7 survival. Microbial species diversity as determined by DGGE was significantly higher in clay soil than sandy soil and this resulted in higher initial decline in population in clay soil than in sandy soil. This study shows that if soil is contaminated withE. coliO157:H7, fumigation alone may not eliminate the pathogen, but may cause decrease in microbial diversity which may enhance the survival of the pathogen.
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Mahaney, William C., Jessica Zippin, Michael W. Milner, Kandiah Sanmugadas, R. G. V. Hancock, Susan Aufreiter, Sean Campbell, et al. "Chemistry, mineralogy and microbiology of termite mound soil eaten by the chimpanzees of the Mahale Mountains, Western Tanzania." Journal of Tropical Ecology 15, no. 5 (September 1999): 565–88. http://dx.doi.org/10.1017/s0266467499001029.
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Subsamples of termite mound soil used by chimpanzees for geophagy, and topsoil never ingested by them, from the forest floor in the Mahale Mountains National Park, Tanzania, were analysed to determine the possible stimulus or stimuli for geophagy. The ingested samples have a dominant clay texture equivalent to a claystone, whereas the control samples are predominantly sandy clay loam or sandy loam, which indicates that particle size plays a significant role in soil selection for this behaviour. One potential function of the clays is to bind and adsorb toxins. Although both termite mound and control samples have similar alkaloid-binding capacities, they are in every case very high, with the majority of the samples being above 80%. The clay size material (<2 μm) contains metahalloysite and halloysite, the latter a hydrated aluminosilicate (Al2Si2O4·nH2O), present in the majority of both the termite mound soil and control soil samples.Metahalloysite, one of the principal ingredients found in the pharmaceutical Kaopectate™, is used to treat minor gastric ailments in humans. The soils commonly ingested could also function as antacids, as over half had pH values between 7.2 and 8.6. The mean concentrations of the majority of elements measured were greater in the termite mound soils than in the control soils. The termite mound soils had more filamentous bacteria, whereas the control soils contained greater numbers of unicellular bacteria and fungi.
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Chen, Danmei, Yuqi Duan, Yan Jin, Yuhong Yang, and Ling Yuan. "Soil quality and microbiology in response to fertilizations in a paddy-upland rotation with multiple crops and frequent tillage." Experimental Agriculture 56, no. 2 (October 14, 2019): 227–38. http://dx.doi.org/10.1017/s0014479719000322.
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AbstractBoth short- and long-term effects of fertilizers on crops and soils are often studied only in arid or paddy soils, whereas less is known about the long-term effects in paddy-upland rotations, particularly with multiple crops and frequent tillage in subtropical areas. Therefore, an 18-year field experiment was initialized to assess the effects of different types of fertilization (no fertilizer; chemical fertilizer (CF); and manure in combination with CF (MCF)) on yield and soil chemical and microbial properties in a crop rotation involving rice (Oryza sativa L., summer), rapeseed (Brassica campestris L., winter), tobacco (Nicotiana tabacum L., the following summer), and hairy vetch (Vicia villosa Roth, the following winter). MCF caused higher yields of rapeseed grains and tobacco leaves than CF after 3 or 4 years of implementing the experiment, while rice yields varied little between MCF and CF, with one exception in 2011. Compared with the initial soil properties, providing soil with MCF increased organic matter (OM), while the opposite trend was found with CF. Higher microbial biomasses, enzyme activities, bacterial operational taxonomic units, and richness and diversity indexes of bacterial communities were found in soils receiving MCF, implying the improvement of soil microbial properties in the paddy-upland rotation system with multiple crops and frequent tillage. The experimental soils under varying fertilization were dominated by four bacterial phyla (Proteobacteria, Acidobacteria, Actinobacteria, and unclassified groups), which accounted for approximately 70% of the 16S rDNA sequences. Among the top 20 predominant bacteria, 14 were commonly found in all soil samples irrespective of which fertilizer treatment was implemented. Thus, the presence of those bacteria was stable in the soil and to some extent was influenced by fertilization. Most of them were facultative anaerobic bacteria, which can adapt to both anaerobic paddy soil and aerobic drylands. The dominant bacteria at various taxonomic levels found in soils might reflect multiple soil processes such as OM turnover, nutrient cycling, physical structure formation, and xenobiotic detoxification.
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Martin, S. Bruce, G. S. Abawi, and H. C. Hoch. "The relation of population densities of the antagonist, Laetisaria arvalis, to seedling diseases of table beet incited by Pythium ultimum." Canadian Journal of Microbiology 32, no. 2 (February 1, 1986): 156–59. http://dx.doi.org/10.1139/m86-031.
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Sclerotia of Laetisaria arvalis were added to raw or steamed table beet field soils infested with Pythium ultimum and other low-temperature Pythium spp. to determine the relationship between soil population densities of the antagonist to disease incidence. Decrease in disease incidence of table beet seedlings and final Pythium spp. inoculum densities were linearly related to increasing population density of the antagonist in raw field soils. In P. ultimum infested steamed soils, decreasing disease incidence was also related to increasing population densities of L. arvalis, but the relationship was curvilinear and was described by a quadratic model. The latter models also described the decrease in P. ultimum inoculum densities with increasing levels of the antagonist. Percentages of healthy plants (those surviving the pre- and post-emergence damping-off disease phases) were increased approximately 20% in raw soils containing 100 sclerotia of L. arvalis per gram soil in comparison with those of unamended soils. However, in Pythium infested steamed soils, percentages of healthy plants in soil amended with 100 sclerotia of L. arvalis per gram soil were increased by 40–60%.
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de Freitas, J. R., J. J. Schoenau, S. M. Boyetchko, and S. A. Cyrenne. "Soil microbial populations, community composition, and activity as affected by repeated applications of hog and cattle manure in eastern Saskatchewan." Canadian Journal of Microbiology 49, no. 9 (September 1, 2003): 538–48. http://dx.doi.org/10.1139/w03-069.
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A field site near Humboldt, Saskatchewan, was annually treated with hog or cattle manure and cropped to canola, spring wheat, barley, and canola from 1997 to 2000. During each growing season, soil was analyzed for microbial populations in terms of activity and community structure, and crops were assessed for root rot and foliar diseases. Microbial activity in soils treated with cattle manure was higher than in soils treated with hog manure or urea. Similarly, nitrous oxide emissions from soil increased with increasing rates of hog and cattle manure. Potential human pathogens, including Rahnella, Serratia, Proteus, Leclercia, and Salmonella species, were identified in soils that received cattle manure, whereas pseudomonads were the dominant species in the hog-manure-treated soil. Fecal coliforms were confirmed in soils that received hog or cattle manure. However, Enterobacteriaceae populations were 10-fold higher in soils receiving cattle manure than in soils receiving the other treatments. Increasing cattle manure rates increased fecal coliform population, but there was no indication that increased hog manure rates increased fecal coliform populations. Addition of urea, hog manure, or cattle manure to the soil did not increase foliar disease in wheat, barley, and canola and had variable effects on root rot incidence in cereals.Key words: soil microbial activity, soil microbial populations, microbial community, plant disease, hog manure, cattle manure, urea.
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Fillhart, Ronald C., George D. Bachand, and John D. Castello. "Detection of Infectious Tobamoviruses in Forest Soils." Applied and Environmental Microbiology 64, no. 4 (April 1, 1998): 1430–35. http://dx.doi.org/10.1128/aem.64.4.1430-1435.1998.
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ABSTRACT Our objectives were to evaluate elution and bait plant methods to detect infectious tobamoviruses in forest soils in New York State. Soils were collected from two forest sites: Whiteface Mountain (WF) and Heiberg Forest (HF). The effectiveness of four buffers to elute tomato mosaic tobamovirus (ToMV) from organic and mineral fractions of WF soil amended with ToMV was tested, and virus content was assessed by enzyme-linked immunosorbent assay (ELISA). The effectiveness ofChenopodium quinoa (Willd.) bait plants to detect the virus also was tested. Both methods then were utilized to detect tobamoviruses in 11 WF and 2 HF soil samples. A phosphate buffer (100 mM, pH 7.0) eluted more ToMV from soil than the other buffers tested. Mineral soil bound more virus than organic soil. Virus recoveries from virus-amended organic and mineral soils were 3 and 10%, respectively, and the detection sensitivity was 10 to 20 ng/g of soil. Roots of bait plants grown in all virus-amended soils tested positive by ELISA, and virus concentrations averaged 10 ng/g. Both ToMV and tobacco mosaic tobamovirus (TMV) were transmitted to C. quinoa by elution from one of two HF soil samples but not from the WF soil samples. A tobamovirus was detected by bait planting in 12 of 73 (16%) root extracts representing 5 of 13 soil samples (38%). Tobamovirus-like particles were seen by transmission electron microscopy in 6 of 12 infected root extracts. Tobamoviruses occur in forest soils in New York State. Abiotic soil transmission to trees may permit localized spread and persistence of these viruses in forest ecosystems.
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Dashko, Regina, and Anna Shidlovskaya. "Impact of microbial activity on soil properties." Canadian Geotechnical Journal 53, no. 9 (September 2016): 1386–97. http://dx.doi.org/10.1139/cgj-2015-0649.
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There are microorganisms in soils and their activity can have a positive or negative impact on soil properties and groundwater. The positive effect of microorganisms includes the self-purification and self-regulation of contaminated groundwater and soil. The negative effect on soil is the change in grain-size composition; the weakening of engineering properties of soils; and the development processes, such as biogas generation, microbial quick-sand formation, and soil liquefaction. This paper addresses the negative effects of microbial activity on soil. Research on the impact of microbial activity in an underground space has been motivated by observations associated with underground infrastructure, such as subway tunnels, utilities tunnels, deep mines including those with tailings, and infrastructure with shallow and deep foundations. An overview of microorganisms in soil and an analysis of microbial activity in soils under the influence of natural and human-made factors are presented. Field and laboratory experiments show the significant impact of microbial activity on the engineering properties and consistency of the soil. Due to the complexity of the process, a study of microbial activity in the soil profile requires an integration of microbiology, biochemistry, engineering geology, and geotechnical engineering knowledge and experience.
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Uttarotai, Toungporn, Boyd A. McKew, Farid Benyahia, J. Colin Murrell, Wuttichai Mhuantong, Sunanta Wangkarn, Thararat Chitov, Sakunnee Bovonsombut, and Terry J. McGenity. "Isoprene-Degrading Bacteria from Soils Associated with Tropical Economic Crops and Framework Forest Trees." Microorganisms 9, no. 5 (May 10, 2021): 1024. http://dx.doi.org/10.3390/microorganisms9051024.
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Isoprene, a volatile hydrocarbon emitted largely by plants, plays an important role in regulating the climate in diverse ways, such as reacting with free radicals in the atmosphere to produce greenhouse gases and pollutants. Isoprene is both deposited and formed in soil, where it can be consumed by some soil microbes, although much remains to be understood about isoprene consumption in tropical soils. In this study, isoprene-degrading bacteria from soils associated with tropical plants were investigated by cultivation and cultivation-independent approaches. Soil samples were taken from beneath selected framework forest trees and economic crops at different seasons, and isoprene degradation in soil microcosms was measured after 96 h of incubation. Isoprene losses were 4–31% and 15–52% in soils subjected to a lower (7.2 × 105 ppbv) and a higher (7.2 × 106 ppbv) concentration of isoprene, respectively. Sequencing of 16S rRNA genes revealed that bacterial communities in soil varied significantly across plant categories (framework trees versus economic crops) and the presence of isoprene, but not with isoprene concentration or season. Eight isoprene-degrading bacterial strains were isolated from the soils and, among these, four belong to the genera Ochrobactrum, Friedmanniella, Isoptericola and Cellulosimicrobium, which have not been previously shown to degrade isoprene.
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Lestari, Widya, and Kamsia Dorliana Sitanggang. "KARAKTERISASI BAKTERI TANAH PERTANIAN ORGANIK DAN TANAH PERTANIAN ANORGANIK DAN UJI ANTAGONIS TERHADAP JAMUR AKAR PUTIH (Rigidoporus microporus)." JURNAL AGROPLASMA 7, no. 1 (May 20, 2020): 1–11. http://dx.doi.org/10.36987/agroplasma.v7i1.1684.
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Research on the Characterization and Antagonist Test of Organic Soil Bacteria and Inorganic Farm Soils Against White Root Fungi (Rigidoporus microporus), was studied at the USU FMIPA Microbiology Laboratory, Medan, in May 2018. The method used was the characterization of agricultural soil bacteria with scatter plates and Yeast media. Extract 1%, obtained 3 soil bacterial isolates namely Sp01, Sp02 and Sp03 and 3 isolates from the inorganic agricultural soils Spa1, Spa2, and Spa3 which were characterized by shape, color, elevation edge and edge of the colony. Sp02 and Sp03 bacteria have greater ability to inhibit the growth of Rigidoporus microporus than Sp01 with inhibition zones of 2.5 and 3.5 mm. Sp a1 bacterium has the highest inhibitory ability of 30 mm against Rigidoporus microporus compared to Spa2 and Spa3. Keywords: Bacteria, Rigidoporus microporus, Faarm soils
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Nijjer, Somereet, William E. Rogers, and Evan Siemann. "Negative plant–soil feedbacks may limit persistence of an invasive tree due to rapid accumulation of soil pathogens." Proceedings of the Royal Society B: Biological Sciences 274, no. 1625 (August 21, 2007): 2621–27. http://dx.doi.org/10.1098/rspb.2007.0804.
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Soil organisms influence plant species coexistence and invasion potential. Plant–soil feedbacks occur when plants change soil community composition such that interactions with that soil community in turn may positively or negatively affect the performance of conspecifics. Theories predict and studies show that invasions may be promoted by stronger negative soil feedbacks for native compared with exotic species. We present a counter-example of a successful invader with strong negative soil feedbacks apparently caused by host-specific, pathogenic soil fungi. Using a feedback experiment in pots, we investigated whether the relative strength of plant–soil feedbacks experienced by a non-native woody invader, Sapium sebiferum , differed from several native tree species by examining their performance in soils collected near conspecifics (‘home soils’) or heterospecifics (‘away soils’) in the introduced range. Sapium seedlings, but no native seedlings, had lower survival and biomass in its home soils compared with soils of other species (‘negative feedback’). To investigate biotic agents potentially responsible for the observed negative feedbacks, we conducted two additional experiments designed to eliminate different soil taxa (‘rescue experiments’). We found that soil sterilization (pot experiment) or soil fungicide applications (pot and field experiments) restored Sapium performance in home soil thereby eliminating the negative feedbacks we observed in the original experiment. Such negative feedbacks apparently mediated by soil fungi could have important effects on persistence of this invader by limiting Sapium seedling success in Sapium dominated forests (home soils) though their weak effects in heterospecific (away) soils suggest a weak role in limiting initial establishment.
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Zheng, Xuefang, Bo Liu, Yujing Zhu, Jieping Wang, Haifeng Zhang, and Ziran Wang. "Bacterial community diversity associated with the severity of bacterial wilt disease in tomato fields in southeast China." Canadian Journal of Microbiology 65, no. 7 (July 2019): 538–49. http://dx.doi.org/10.1139/cjm-2018-0637.
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Tomato bacterial wilt caused by Ralstonia solanacearum is a devastating plant disease. The aims of this study were to investigate the relationship among soil nutrients, rhizobacterial community, and abundance of R. solanacearum, and to gather useful information for controlling the disease. Fifteen tomato rhizosphere soils were collected from three regions, encompassing five disease grades. Then, soil physicochemical properties and rhizobacterial communities were investigated. The content of soil organic carbon (SOC), total phosphorus (TP), total potassium (TK), and exchangeable calcium was significantly higher in the healthy plant rhizosphere soils than in diseased plant rhizosphere soils (P < 0.05). The healthy soils had a relatively higher abundance of Proteobacteria and a lower abundance of Acidobacteria than the diseased soils from the same region. Redundancy analysis demonstrated that R. solanacearum abundance was positively correlated with total nitrogen content and negatively correlated with soil pH, SOC, TP, TK, and exchangeable calcium. Ralstonia solanacearum abundance correlated positively with Chloroflexi, Acidobacteria, and Planctomycetes abundance but negatively with Nitrospirae, Bacteroidetes, and Proteobacteria abundance. These results suggested that improving soil pH, applying the amount of P and K fertilizers, and controlling the dosage of N fertilizer might be an effective approach in controlling bacterial wilt disease.
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Lauber, Christian L., Micah Hamady, Rob Knight, and Noah Fierer. "Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale." Applied and Environmental Microbiology 75, no. 15 (June 5, 2009): 5111–20. http://dx.doi.org/10.1128/aem.00335-09.
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ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.
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Ibekwe, A. Mark, Catherine M. Grieve, and Ching-Hong Yang. "Survival ofEscherichia coliO157:H7 in soil and on lettuce after soil fumigation." Canadian Journal of Microbiology 53, no. 5 (May 2007): 623–35. http://dx.doi.org/10.1139/w07-003.
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Long-term survival of Escherichia coli O157:H7 in soil and in the rhizosphere of many crops after fumigation is relatively unknown. One of the critical concerns with food safety is the transfer of pathogens from contaminated soil to the edible portion of the plants. Multiplex fluorogenic polymerase chain reaction was used in conjunction with plate counts to quantify the survival of E. coli O157:H7 in soil after fumigation with methyl bromide and methyl iodide in growth chamber and microcosm laboratory experiments. Plants were grown at 20 °C in growth chambers during the first experiment and soils were irrigated with water contaminated with E. coli O157:H7. For the second experiment, soil microcosms were used in the laboratory without plants and were inoculated with E. coli O157:H7 and spiked with the two fumigants. Primers and probes were designed to amplify and quantify the Shiga-like toxin 1 (stx1) and 2 (stx2) genes and the intimin (eae) gene of E. coli O157:H7. Both fumigants were effective in reducing pathogen concentrations in soil, and when fumigated soils were compared with nonfumigated soils, pathogen concentrations were significantly higher in the nonfumigated soils throughout the study. This resulted in a longer survival of the pathogen on the leaf surface especially in sandy soil than observed in fumigated soils. Therefore, application of fumigant may play some roles in reducing the transfer of E. coli O157:H7 from soil to leaf. Regression models showed that survival of the pathogen in the growth chamber study followed a linear model while that of the microcosm followed a curvilinear model, suggesting long-term survival of the pathogen in soil. Both experiments showed that E. coli O157:H7 can survive in the environment for a long period of time, even under harsh conditions, and the pathogen can survive in soil for more than 90 days. This provides a very significant pathway for pathogen recontamination in the environment.
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Vreulink, Jo-Marie, Annerina Esterhuyse, Karin Jacobs, and Alfred Botha. "Soil properties that impact yeast and actinomycete numbers in sandy low nutrient soils." Canadian Journal of Microbiology 53, no. 12 (December 2007): 1369–74. http://dx.doi.org/10.1139/w07-092.
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To explore the beneficial qualities or detrimental consequences of cultureable soil yeasts, it is important to understand which physicochemical soil properties most impact populations of these unicellular fungi in their natural habitat. The goal of this study was to determine which soil properties dictate yeast numbers in pristine sandy, low nutrient soils within a semi-arid region. A correlation matrix of the data obtained for 19 different environmental variables indicated a negative correlation between soil pH and yeast numbers. Using general regression models, it was demonstrated that soil pH and copper concentration were the 2 variables that correlated best with soil yeast counts in these soils. However, soil moisture content was found to be the environmental factor with the most impact on cultureable actinomycetes and heterotrophic microbes. The study also demonstrated that divalent cation availability might impact the size of both yeast and prokaryote populations in these soils.
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Brandes Ammann, Andrea, Linda Kölle, and Helmut Brandl. "Detection of Bacterial Endospores in Soil by Terbium Fluorescence." International Journal of Microbiology 2011 (2011): 1–5. http://dx.doi.org/10.1155/2011/435281.
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Spore formation is a survival mechanism of microorganisms when facing unfavorable environmental conditions resulting in “dormant” states. We investigated the occurrence of bacterial endospores in soils from various locations including grasslands (pasture, meadow), allotment gardens, and forests, as well as fluvial sediments. Bacterial spores are characterized by their high content of dipicolinic acid (DPA). In the presence of terbium, DPA forms a complex showing a distinctive photoluminescence spectrum. DPA was released from soil by microwaving or autoclaving. The addition of aluminium chloride reduced signal quenching by interfering compounds such as phosphate. The highest spore content (up to 109spores per gram of dry soil) was found in grassland soils. Spore content is related to soil type, to soil depth, and to soil carbon-to-nitrogen ratio. Our study might provide a basis for the detection of “hot spots” of bacterial spores in soil.
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Hugoni, Mylène, William Galland, Solène Lecomte, Maxime Bruto, Mohamed Barakat, Florence Piola, Wafa Achouak, and Feth el Zahar Haichar. "Effects of the Denitrification Inhibitor “Procyanidins” on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome." Microorganisms 9, no. 7 (June 29, 2021): 1406. http://dx.doi.org/10.3390/microorganisms9071406.
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Some plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca2+ in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil.
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Hsiao, Che-Jen, Gretchen F. Sassenrath, Lydia H. Zeglin, Ganga M. Hettiarachchi, and Charles W. Rice. "Vertical changes of soil microbial properties in claypan soils." Soil Biology and Biochemistry 121 (June 2018): 154–64. http://dx.doi.org/10.1016/j.soilbio.2018.03.012.
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BROOKES, P., C. HEIJNEN, S. MCGRATH, and E. VANCE. "Soil microbial biomass estimates in soils contaminated with metals." Soil Biology and Biochemistry 18, no. 4 (1986): 383–88. http://dx.doi.org/10.1016/0038-0717(86)90042-8.
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Germida, James J. "Isolation of Bdellovibrio spp. that prey on Azospirillum brasilense in soil." Canadian Journal of Microbiology 33, no. 5 (May 1, 1987): 459–61. http://dx.doi.org/10.1139/m87-076.
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Bdellovibrios that prey on Azospirillum brasilense were isolated from a Latosol and a Podzolic soil from Brazil which were stored air-dried for 2 years. The addition of A. brasilense strain Cd or Sp 7 cells and nutrients to these soils stimulated growth of indigenous bdellovibrios; direct assay of these soils did not yield bdellovibrios. Two other Podzolic soils from Brazil and three Chernozemic soils from Canada did not contain detectable bdellovibrios. After enrichment with strain Cd cells, the Podzolic soil yielded 1340 bdellovibrios per g of soil, whereas enrichment with strain Sp 7 cells yielded only 50. Escherichia coli and Enterobacter aerogenes cells did not stimulate growth of bdellovibrios in this soil, but did stimulate growth of bdellovibrios in the Latosol as did strains Cd and Sp 7. The morphology of an azospirilla-attacking Bdellovibrio, isolated from the Podzolic soil, was typical of the genus; attack-phase cells were curved rods, 0.2–0.4 by 1.0–1.3 μm, motile by means of a single polar flagellum. In broth culture this Bdellovibrio isolate preyed on several different gram-negative bacteria, although the apparent growth rate on prey cells was A. brasilense strain Cd > strain Sp 7 > A. lipoferum strain Sp Br 17 = E. coli = E. aerogenes > A. brasilense strain Sp 35. Pseudomonas fluorescens, Ensifer adhaerens, and 20 unidentified bacterial isolates from the Podzolic soil were not suitable prey. These results indicate that Bdellovibrio survive in some air-dry soils at undetectable levels but respond quickly to the presence of a large number of prey cells. In addition, the presence in soil of bdellovibrios that exhibit a faster growth rate on A. brasilense strain Cd than on strain Sp 7 cells and other azospirilla indicates potential problems when using strain Cd as a crop inoculant in certain soils.
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Lodygin, Evgeny, Vasily Beznosikov, and Evgeny Abakumov. "Humic substances elemental composition of selected taiga and tundra soils from Russian European North-East." Polish Polar Research 38, no. 2 (June 27, 2017): 125–47. http://dx.doi.org/10.1515/popore-2017-0007.
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Abstract Soils of Russian European North were investigated in terms of stability and quality of organic matter as well as in terms of soils organic matter elemental composition. Therefore, soil humic acids (HAs), extracted from soils of different natural zones of Russian North-East were studied to characterize the degree of soil organic matter stabilization along a zonal gradient. HAs were extracted from soil of different zonal environments of the Komi Republic: south, middle and north taiga as well as south tundra. Data on elemental composition of humic acids and fulvic acids (FAs) extracted from different soil types were obtained to assess humus formation mechanisms in the soils of taiga and tundra of the European North-East of Russia. The specificity of HAs elemental composition are discussed in relation to environmental conditions. The higher moisture degree of taiga soils results in the higher H/C ratio in humic substances. This reflects the reduced microbiologic activity in Albeluvisols sods and subsequent conservation of carbohydrate and amino acid fragments in HAs. HAs of tundra soils, shows the H/C values decreasing within the depth of the soils, which reflects increasing of aromatic compounds in HA structure of mineral soil horizons. FAs were more oxidized and contains less carbon while compared with the HAs. Humic acids, extracted from soil of different polar and boreal environments differ in terms of elemental composition winch reflects the climatic and hydrological regimes of humification.
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KAISER, MICHELLE L., MICHELE L. WILLIAMS, NICHOLAS BASTA, MICHELLE HAND, and SARAH HUBER. "When Vacant Lots Become Urban Gardens: Characterizing the Perceived and Actual Food Safety Concerns of Urban Agriculture in Ohio." Journal of Food Protection 78, no. 11 (November 1, 2015): 2070–80. http://dx.doi.org/10.4315/0362-028x.jfp-15-181.
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This study was intended to characterize the perceived risks of urban agriculture by residents of four low-income neighborhoods in which the potential exists for further urban agriculture development and to provide data to support whether any chemical hazards and foodborne pathogens as potential food safety hazards were present. Sixty-seven residents participated in focus groups related to environmental health, food security, and urban gardening. In addition, soils from six locations were tested. Residents expressed interest in the development of urban gardens to improve access to healthy, fresh produce, but they had concerns about soil quality. Soils were contaminated with lead (Pb), zinc, cadmium (Cd), and copper, but not arsenic or chromium. Results from our study suggest paint was the main source of soil contamination. Detectable polyaromatic hydrocarbon (PAH) levels in urban soils were well below levels of concern. These urban soils will require further management to reduce Pb and possibly Cd bioavailability to decrease the potential for uptake into food crops. Although the number of locations in this study is limited, results suggest lower levels of soil contaminants at well-established gardens. Soil tillage associated with long-term gardening could have diluted the soil metal contaminants by mixing the contaminants with clean soil. Also, lower PAH levels in long-term gardening could be due to enhanced microbial activity and PAH degradation, dilution, or both due to mixing, similar to metals. No foodborne pathogen targets were detected by PCR from any of the soils. Residents expressed the need for clearness regarding soil quality and gardening practices in their neighborhoods to consume food grown in these urban areas. Results from this study suggest long-term gardening has the potential to reduce soil contaminants and their potential threat to food quality and human health and to improve access to fresh produce in low-income urban communities.
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Mahmoudi, Nagissa, Greg F. Slater, and Roberta R. Fulthorpe. "Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils." Canadian Journal of Microbiology 57, no. 8 (August 2011): 623–28. http://dx.doi.org/10.1139/w11-049.
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Molecular characterization of the microbial populations of soils and sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) is often a first step in assessing intrinsic biodegradation potential. However, soils are problematic for molecular analysis owing to the presence of organic matter, such as humic acids. Furthermore, the presence of contaminants, such as PAHs, can cause further challenges to DNA extraction, quantification, and amplification. The goal of our study was to compare the effectiveness of four commercial soil DNA extraction kits (UltraClean Soil DNA Isolation kit, PowerSoil DNA Isolation kit, PowerMax Soil DNA Isolation kit, and FastDNA SPIN kit) to extract pure, high-quality bacterial and eukaryotic DNA from PAH-contaminated soils. Six different contaminated soils were used to determine if there were any biases among the kits due to soil properties or level of contamination. Extracted DNA was used as a template for bacterial 16S rDNA and eukaryotic 18S rDNA amplifications, and PCR products were subsequently analyzed using denaturing gel gradient electrophoresis (DGGE). We found that the FastDNA SPIN kit provided significantly higher DNA yields for all soils; however, it also resulted in the highest levels of humic acid contamination. Soil texture and organic carbon content of the soil did not affect the DNA yield of any kit. Moreover, a liquid–liquid extraction of the DNA extracts found no residual PAHs, indicating that all kits were effective at removing contaminants in the extraction process. Although the PowerSoil DNA Isolation kit gave relatively low DNA yields, it provided the highest quality DNA based on successful amplification of both bacterial and eukaryotic DNA for all six soils. DGGE fingerprints among the kits were dramatically different for both bacterial and eukaryotic DNA. The PowerSoil DNA Isolation kit revealed multiple bands for each soil and provided the most consistent DGGE profiles among replicates for both bacterial and eukaryotic DNA.
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Johnsen, Anders R., Anne Winding, Ulrich Karlson, and Peter Roslev. "Linking of Microorganisms to Phenanthrene Metabolism in Soil by Analysis of 13C-Labeled Cell Lipids." Applied and Environmental Microbiology 68, no. 12 (December 2002): 6106–13. http://dx.doi.org/10.1128/aem.68.12.6106-6113.2002.
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ABSTRACT Phenanthrene-metabolizing soil microbial communities were characterized by examining mineralization of [14C]phenanthrene, by most-probable-number (MPN) counting, by 16S-23S spacer DNA analysis of the numerically dominant, culturable phenanthrene-degrading isolates, and by examining incorporation of [13C]phenanthrene-derived carbon into sterols and polar lipid fatty acids (PLFAs). An unpolluted agricultural soil, a roadside soil diffusely polluted with polycyclic aromatic hydrocarbons (PAHs), and two highly PAH-polluted soils from industrial sites were analyzed. Microbial phenanthrene degraders were not detected by MPN counting in the agricultural soil and the roadside soil. In the industrial soils, phenanthrene degraders constituted 0.04 and 3.6% of the total number of CFU. 16S-23S spacer DNA analysis followed by partial 16S DNA sequencing of representative isolates from one of the industrial soils showed that one-half of the isolates belonged to the genus Sphingomonas and the other half were closely related to an unclassified beta-proteobacterium. The 13C-PLFA profiles of the two industrial soils were relatively similar and resembled the profiles of phenanthrene-degrading Sphingomonas reference strains and unclassified beta-proteobacterium isolates but did not match the profiles of Pseudomonas, Mycobacterium, or Nocardia reference strains. The 13C-PLFA profiles of phenanthrene degraders in the agricultural soil and the roadside soil were different from each other and different from the profiles of the highly polluted industrial soils. Only in the roadside soil were 10me/12me18:0 PLFAs enriched in 13C, suggesting that actinomycetes metabolized phenanthrene in this soil. The 13C-PLFA profiles of the unpolluted agricultural soil did not resemble the profiles of any of the reference strains. In all of the soils investigated, no excess 13C was recovered in the 18:2ω6,9 PLFA, suggesting that fungi did not contribute significantly to assimilation of [13C]phenanthrene.
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Williamson, Kurt E., Mark Radosevich, and K. Eric Wommack. "Abundance and Diversity of Viruses in Six Delaware Soils." Applied and Environmental Microbiology 71, no. 6 (June 2005): 3119–25. http://dx.doi.org/10.1128/aem.71.6.3119-3125.2005.
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ABSTRACT The importance of viruses in marine microbial ecology has been established over the past decade. Specifically, viruses influence bacterial abundance and community composition through lysis and alter bacterial genetic diversity through transduction and lysogenic conversion. By contrast, the abundance and distribution of viruses in soils are almost completely unknown. This study describes the abundance and diversity of autochthonous viruses in six Delaware soils: two agricultural soils, two coastal plain forest soils, and two piedmont forest soils. Viral abundance was measured using epifluorescence microscopy, while viral diversity was assessed from morphological data obtained through transmission electron microscopy. Extracted soil virus communities were dominated by bacteriophages that demonstrated a wide range of capsid diameters (20 nm to 160 nm) and morphologies, including filamentous forms and phages with elongated capsids. The reciprocal Simpson's index suggests that forest soils harbor more diverse assemblages of viruses, particularly in terms of morphological distribution. Repeated extractions of virus-like particles (VLPs) from soils indicated that the initial round of extraction removes approximately 70% of extractable viruses. Higher VLP abundances were observed in forest soils (1.31 × 109 to 4.17 × 109 g−1 dry weight) than in agricultural soils (8.7 × 108 to 1.1 × 109 g−1 dry weight). Soil VLP abundance was significantly correlated to moisture content (r = 0.988) but not to soil texture. Land use (agricultural or forested) was significantly correlated to both bacterial (r = 0.885) and viral (r = 0.812) abundances, as were soil organic matter and water content. Thus, land use is a significant factor influencing viral abundance and diversity in soils.
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Cosgrove, Lee, Paula L. McGeechan, Geoff D. Robson, and Pauline S. Handley. "Fungal Communities Associated with Degradation of Polyester Polyurethane in Soil." Applied and Environmental Microbiology 73, no. 18 (July 27, 2007): 5817–24. http://dx.doi.org/10.1128/aem.01083-07.
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ABSTRACT Soil fungal communities involved in the biodegradation of polyester polyurethane (PU) were investigated. PU coupons were buried in two sandy loam soils with different levels of organic carbon: one was acidic (pH 5.5), and the other was more neutral (pH 6.7). After 5 months of burial, the fungal communities on the surface of the PU were compared with the native soil communities using culture-based and molecular techniques. Putative PU-degrading fungi were common in both soils, as <45% of the fungal colonies cleared the colloidal PU dispersion Impranil on solid medium. Denaturing gradient gel electrophoresis showed that fungal communities on the PU were less diverse than in the soil, and only a few species in the PU communities were detectable in the soil, indicating that only a small subset of the soil fungal communities colonized the PU. Soil type influenced the composition of the PU fungal communities. Geomyces pannorum and a Phoma sp. were the dominant species recovered by culturing from the PU buried in the acidic and neutral soils, respectively. Both fungi degraded Impranil and represented >80% of cultivable colonies from each plastic. However, PU was highly susceptible to degradation in both soils, losing up to 95% of its tensile strength. Therefore, different fungi are associated with PU degradation in different soils but the physical process is independent of soil type.
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Singh, Brajesh K., Allan Walker, J. Alun W. Morgan, and Denis J. Wright. "Role of Soil pH in the Development of Enhanced Biodegradation of Fenamiphos." Applied and Environmental Microbiology 69, no. 12 (December 2003): 7035–43. http://dx.doi.org/10.1128/aem.69.12.7035-7043.2003.
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ABSTRACT Repeated treatment with fenamiphos (ethyl 4-methylthio-m-tolyl isopropylphosphoramidate) resulted in enhanced biodegradation of this nematicide in two United Kingdom soils with a high pH (≥7.7). In contrast, degradation of fenamiphos was slow in three acidic United Kingdom soils (pH 4.7 to 6.7), and repeated treatments did not result in enhanced biodegradation. Rapid degradation of fenamiphos was observed in two Australian soils (pH 6.7 to 6.8) in which it was no longer biologically active against plant nematodes. Enhanced degrading capability was readily transferred from Australian soil to United Kingdom soils, but only those with a high pH were able to maintain this capability for extended periods of time. This result was confirmed by fingerprinting bacterial communities by 16S rRNA gene profiling of extracted DNA. Only United Kingdom soils with a high pH retained bacterial DNA bands originating from the fenamiphos-degrading Australian soil. A degrading consortium was enriched from the Australian soil that utilized fenamiphos as a sole source of carbon. The 16S rRNA banding pattern (determined by denaturing gradient gel electrophoresis) from the isolated consortium migrated to the same position as the bands from the Australian soil and those from the enhanced United Kingdom soils in which the Australian soil had been added. When the bands from the consortium and the soil were sequenced and compared they showed between 97 and 100% sequence identity, confirming that these groups of bacteria were involved in degrading fenamiphos in the soils. The sequences obtained showed similarity to those from the genera Pseudomonas, Flavobacterium, and Caulobacter. In the Australian soils, two different degradative pathways operated simultaneously: fenamiphos was converted to fenamiphos sulfoxide (FSO), which was hydrolyzed to the corresponding phenol (FSO-OH) or was hydrolyzed directly to fenamiphos phenol. In the United Kingdom soils in which enhanced degradation had been induced, fenamiphos was oxidized to FSO and then hydrolyzed to FSO-OH, but direct conversion to fenamiphos phenol did not occur.
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Mohamed Zubi, Wafa S., Masratul Hawa Mohd, Nik Mohd Izham Mohamed Nor, and Latiffah Zakaria. "Fusarium Species in Mangrove Soil in Northern Peninsular Malaysia and the Soil Physico-Chemical Properties." Microorganisms 9, no. 3 (February 26, 2021): 497. http://dx.doi.org/10.3390/microorganisms9030497.
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Fusarium genus comprises important saprophytic and phytopathogenic fungi and is widespread in nature. The present study reports the occurrence of Fusarium spp. in soils from two mangrove forests in northern Peninsular Malaysia and analyzed physico-chemical properties of the mangrove soil. Based on TEF-1α sequences, nine Fusarium species were identified: Fusarium solani species complex (FSSC) (n = 77), Fusarium verticillioides (n = 20), Fusarium incarnatum (n = 10), Fusarium proliferatum (n = 7), Fusarium lateritium (n = 4), Fusarium oxysporum (n = 3), Fusarium rigidiuscula (n = 2), Fusarium chlamydosporum (n = 1), and Fusarium camptoceras (n = 1); FSSC isolates were the most prevalent. Phylogenetic analysis of the combined TEF-1α and ITS sequences revealed diverse phylogenetic affinities among the FSSC isolates and potentially new phylogenetic clades of FSSC. Soil analysis showed varied carbon content, pH, soil moisture, and salinity, but not nitrogen content, between sampling locations. Regardless of the physico-chemical properties, various Fusarium species were recovered from the mangrove soils. These were likely saprophytes; however, some were well-known plant pathogens and opportunistic human pathogens. Thus, mangrove soils might serve as inoculum sources for plant and human pathogenic Fusarium species. The present study demonstrates the occurrence of various Fusarium species in the extreme environment of mangrove soil, thereby contributing to the knowledge on species diversity in Fusarium.
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Naether, Astrid, Bärbel U. Foesel, Verena Naegele, Pia K. Wüst, Jan Weinert, Michael Bonkowski, Fabian Alt, et al. "Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils." Applied and Environmental Microbiology 78, no. 20 (August 10, 2012): 7398–406. http://dx.doi.org/10.1128/aem.01325-12.
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ABSTRACTIn soil,Acidobacteriaconstitute on average 20% of all bacteria, are highly diverse, and are physiologically activein situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1Acidobacteria. The analysis of a large number of sites (n= 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed thatAcidobacteriadiversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations ofAcidobacteriasubpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters withAcidobacteria, individual populations within subgroups have to be considered.
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Turner, Benjamin L. "Variation in pH Optima of Hydrolytic Enzyme Activities in Tropical Rain Forest Soils." Applied and Environmental Microbiology 76, no. 19 (August 13, 2010): 6485–93. http://dx.doi.org/10.1128/aem.00560-10.
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ABSTRACT Extracellular enzymes synthesized by soil microbes play a central role in the biogeochemical cycling of nutrients in the environment. The pH optima of eight hydrolytic enzymes involved in the cycles of carbon, nitrogen, phosphorus, and sulfur, were assessed in a series of tropical forest soils of contrasting pH values from the Republic of Panama. Assays were conducted using 4-methylumbelliferone-linked fluorogenic substrates in modified universal buffer. Optimum pH values differed markedly among enzymes and soils. Enzymes were grouped into three classes based on their pH optima: (i) enzymes with acidic pH optima that were consistent among soils (cellobiohydrolase, β-xylanase, and arylsulfatase), (ii) enzymes with acidic pH optima that varied systematically with soil pH, with the most acidic pH optima in the most acidic soils (α-glucosidase, β-glucosidase, and N-acetyl-β-glucosaminidase), and (iii) enzymes with an optimum pH in either the acid range or the alkaline range depending on soil pH (phosphomonoesterase and phosphodiesterase). The optimum pH values of phosphomonoesterase were consistent among soils, being 4 to 5 for acid phosphomonoesterase and 10 to 11 for alkaline phosphomonoesterase. In contrast, the optimum pH for phosphodiesterase activity varied systematically with soil pH, with the most acidic pH optima (3.0) in the most acidic soils and the most alkaline pH optima (pH 10) in near-neutral soils. Arylsulfatase activity had a very acidic optimum pH in all soils (pH ≤3.0) irrespective of soil pH. The differences in pH optima may be linked to the origins of the enzymes and/or the degree of stabilization on solid surfaces. The results have important implications for the interpretation of hydrolytic enzyme assays using fluorogenic substrates.
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Singh, Brajesh K., Allan Walker, J. Alun W. Morgan, and Denis J. Wright. "Effects of Soil pH on the Biodegradation of Chlorpyrifos and Isolation of a Chlorpyrifos-Degrading Bacterium." Applied and Environmental Microbiology 69, no. 9 (September 2003): 5198–206. http://dx.doi.org/10.1128/aem.69.9.5198-5206.2003.
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ABSTRACT We examined the role of microorganisms in the degradation of the organophosphate insecticide chlorpyrifos in soils from the United Kingdom and Australia. The kinetics of degradation in five United Kingdom soils varying in pH from 4.7 to 8.4 suggested that dissipation of chlorpyrifos was mediated by the cometabolic activities of the soil microorganisms. Repeated application of chlorpyrifos to these soils did not result in the development of a microbial population with an enhanced ability to degrade the pesticide. A robust bacterial population that utilized chlorpyrifos as a source of carbon was detected in an Australian soil. The enhanced ability to degrade chlorpyrifos in the Australian soil was successfully transferred to the five United Kingdom soils. Only soils with a pH of ≥6.7 were able to maintain this degrading ability 90 days after inoculation. Transfer and proliferation of degrading microorganisms from the Australian soil to the United Kingdom soils was monitored by molecular fingerprinting of bacterial 16S rRNA genes by PCR-denaturing gradient gel electrophoresis (DGGE). Two bands were found to be associated with enhanced degradation of chlorpyrifos. Band 1 had sequence similarity to enterics and their relatives, while band 2 had sequence similarity to strains of Pseudomonas. Liquid enrichment culture using the Australian soil as the source of the inoculum led to the isolation of a chlorpyrifos-degrading bacterium. This strain had a 16S rRNA gene with a sequence identical to that of band 1 in the DGGE profile of the Australian soil. DNA probing indicated that genes similar to known organophosphate-degrading (opd) genes were present in the United Kingdom soils. However, no DNA hybridization signal was detected for the Australian soil or the isolated degrader. This indicates that unrelated genes were present in both the Australian soil and the chlorpyrifos-degrading isolate. These results are consistent with our observations that degradation of chlorpyrifos in these systems was unusual, as it was growth linked and involved complete mineralization. As the 16S rRNA gene of the isolate matched a visible DGGE band from the Australian soil, the isolate is likely to be both prominent and involved in the degradation of chlorpyrifos in this soil.
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Srinivasiah, Sharath, Jacqueline Lovett, Shawn Polson, Jaysheel Bhavsar, Dhritiman Ghosh, Krishnakali Roy, Jeffry J. Fuhrmann, Mark Radosevich, and K. Eric Wommack. "Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA." Applied and Environmental Microbiology 79, no. 18 (June 21, 2013): 5450–57. http://dx.doi.org/10.1128/aem.00268-13.
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ABSTRACTViruses are the most abundant and diverse biological entities within soils, yet their ecological impact is largely unknown. Defining how soil viral communities change with perturbation or across environments will contribute to understanding the larger ecological significance of soil viruses. A new approach to examining the composition of soil viral communities based on random PCR amplification of polymorphic DNA (RAPD-PCR) was developed. A key methodological improvement was the use of viral metagenomic sequence data for the design of RAPD-PCR primers. This metagenomically informed approach to primer design enabled the optimization of RAPD-PCR sensitivity for examining changes in soil viral communities. Initial application of RAPD-PCR viral fingerprinting to soil viral communities demonstrated that the composition of autochthonous soil viral assemblages noticeably changed over a distance of meters along a transect of Antarctic soils and across soils subjected to different land uses. For Antarctic soils, viral assemblages segregated upslope from the edge of dry valley lakes. In the case of temperate soils at the Kellogg Biological Station, viral communities clustered according to land use treatment. In both environments, soil viral communities changed along with environmental factors known to shape the composition of bacterial host communities. Overall, this work demonstrates that RAPD-PCR fingerprinting is an inexpensive, high-throughput means for addressing first-order questions of viral community dynamics within environmental samples and thus fills a methodological gap between narrow single-gene approaches and comprehensive shotgun metagenomic sequencing for the analysis of viral community diversity.
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Sagova-Mareckova, Marketa, Ladislav Cermak, Jitka Novotna, Kamila Plhackova, Jana Forstova, and Jan Kopecky. "Innovative Methods for Soil DNA Purification Tested in Soils with Widely Differing Characteristics." Applied and Environmental Microbiology 74, no. 9 (March 14, 2008): 2902–7. http://dx.doi.org/10.1128/aem.02161-07.
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ABSTRACT Seven methods of soil DNA extraction and purification were tested in a set of 14 soils differing in bedrock, texture, pH, salinity, moisture, organic matter content, and vegetation cover. The methods introduced in this study included pretreatment of soil with CaCO3 or purification of extracted DNA by CaCl2. The performance of innovated methods was compared to that of the commercial kit Mo Bio PowerSoil and the phenol-chloroform-based method of D. N. Miller, J. E. Bryant, E. L. Madsen, and W. C. Ghiorse (Appl. Environ. Microbiol. 65:4715-4724, 1999). This study demonstrated significant differences between the tested methods in terms of DNA yield, PCR performance, and recovered bacterial diversity. The differences in DNA yields were correlated to vegetation cover, soil pH, and clay content. The differences in PCR performances were correlated to vegetation cover and soil pH. The innovative methods improved PCR performance in our set of soils, in particular for forest acidic soils. PCR was successful in 95% of cases by the method using CaCl2 purification and in 93% of cases by the method based on CaCO3 pretreatment, but only in 79% by Mo Bio PowerSoil, for our range of soils. Also, the innovative methods recovered a higher percentage of actinomycete diversity from a subset of three soils. Recommendations include the assessment of soil characteristics prior to selecting the optimal protocol for soil DNA extraction and purification.
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Hirkala, Danielle L. M., and J. J. Germida. "Field and soil microcosm studies on the survival and conjugation of aPseudomonas putidastrain bearing a recombinant plasmid, pADPTel." Canadian Journal of Microbiology 50, no. 8 (August 1, 2004): 595–604. http://dx.doi.org/10.1139/w04-045.
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Pseudomonas putida CR30RNS (pADPTel) is an antibiotic-resistant strain with a recombinant plasmid that confers resistance to tellurite and the ability to catabolize atrazine. The survival of this strain as well as its ability to transfer genes for atrazine degradation and tellurite resistance to indigenous soil bacteria were tested in both fallow soil and canola (Brassica napus) rhizosphere by the use of parallel field and laboratory releases. Culturable CR30RNS (pADPTel) were enumerated in field and microcosm soils at 7- to 14-day intervals over 49 d. Strain CR30RNS (pADPTel) survived for up to 7 weeks in microcosm soils at a density of 104CFU/g soil, whereas in field soils the population declined to 103CFU/g soil by the fourth week. In contrast, when CR30RNS (pADPTel) was introduced into the soil as a seed coating of canola (B. napus 'Karoo'), the bacterium established at higher cell densities in the rhizosphere (106–105CFU/g fresh root mass), with no subsequent decrease in numbers. The presence of selective pressure (i.e., atrazine) had no significant effect on the survival of CR30RNS (pADPTel) in either field or microcosm soils. One year postinoculation field sites were examined for the presence of CR30RNS (pADPTel) and no evidence of culturable parental cells was observed when samples were plated onto selective media. However, the atzC and telAB gene segments were amplified from the field soils at that time. Under laboratory conditions, indigenous soil bacteria were capable of receiving and expressing the engineered plasmid construct at frequencies ranging from 1 to 10-3transconjugants per donor. However, no plasmid transfer to indigenous soil bacteria was detected in the field or microcosm soils regardless of the presence of canola rhizosphere and (or) the application of atrazine. Our results show that the survival and population size of P. putida CR30RNS (pADPTel) might be sufficient for degradation of environmental pollutants but that the transfer frequency was too low to be detected under the conditions of this study.Key words: Pseudomonas putida CR30RNS (pADPTel), survival, gene transfer, field, microcosm.
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Redman, Regina S., Anastassia Litvintseva, Kathy B. Sheehan, Joan M. Henson, and Rusty J. Rodriguez. "Fungi from Geothermal Soils in Yellowstone National Park." Applied and Environmental Microbiology 65, no. 12 (December 1, 1999): 5193–97. http://dx.doi.org/10.1128/aem.65.12.5193-5197.1999.
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ABSTRACT Geothermal soils near Amphitheater Springs in Yellowstone National Park were characterized by high temperatures (up to 70°C), high heavy metal content, low pH values (down to pH 2.7), sparse vegetation, and limited organic carbon. From these soils we cultured 16 fungal species. Two of these species were thermophilic, and six were thermotolerant. We cultured only three of these species from nearby cool (0 to 22°C) soils. Transect studies revealed that higher numbers of CFUs occurred in and below the root zone of the perennial plant Dichanthelium lanuginosum (hot springs panic grass). The dynamics of fungal CFUs in geothermal soil and nearby nongeothermal soil were investigated for 12 months by examining soil cores and in situ mesocosms. For all of the fungal species studied, the temperature of the soil from which the organisms were cultured corresponded with their optimum axenic growth temperature.
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Falardeau, Justin, Khalil Walji, Maxime Haure, Karen Fong, Greg Taylor, Yussanne Ma, Sean Smukler, and Siyun Wang. "Native bacterial communities and Listeria monocytogenes survival in soils collected from the Lower Mainland of British Columbia, Canada." Canadian Journal of Microbiology 64, no. 10 (October 2018): 695–705. http://dx.doi.org/10.1139/cjm-2018-0115.
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Soil is an important reservoir for Listeria monocytogenes, a foodborne pathogen implicated in numerous produce-related outbreaks. Our objectives were to (i) compare the survival of L. monocytogenes among three soils, (ii) compare the native bacterial communities across these soils, and (iii) investigate relationships between L. monocytogenes survival, native bacterial communities, and soil properties. Listeria spp. populations were monitored on PALCAM agar in three soils inoculated with L. monocytogenes (∼5 × 106 CFU/g): conventionally farmed (CS), grassland transitioning to conventionally farmed (TS), and uncultivated grassland (GS). Bacterial diversity of the soils was analyzed using 16S rRNA targeted amplicon sequencing. A 2 log reduction of Listeria spp. was observed in all soils within 10 days, but at a significantly lower rate in GS (Fisher’s least significant difference test; p < 0.05). Survival correlated with increased moisture and a neutral pH. GS showed the highest microbial diversity. Acidobacteria was the dominant phylum differentiating CS and TS from GS, and was negatively correlated with pH, carbon, nitrogen, and moisture. High moisture content and neutral pH are likely to increase the ability of L. monocytogenes to persist in soil. This study confirmed that native bacterial communities and short-term survival of L. monocytogenes varies across soils.
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Mamedzadeh, V. "Quantitative Indicators of Microorganisms in Alluvial Soils of Natural Biotopes on the Southern Slope of the Greater Caucasus." Bulletin of Science and Practice 6, no. 11 (November 15, 2020): 174–78. http://dx.doi.org/10.33619/2414-2948/60/20.
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This article discusses the results of studies on the microbiology of alluvial soils on the southern slope of the Greater Caucasus. The first information on the number of microorganisms in alluvial soils of natural biotopes is presented. The changes are associated with alluvial (river) sediments of the Shinchay River; the riverbed and above-floodplain terrace are compared. The analysis of soils of meadow-herbaceous (gramineous) and undersized shrubs (wild rose, blackberry, tamarix) vegetation is presented. Differences were revealed in quantitative indicators and the percentage ratio of individual groups of microbiota biotopes. In conclusion, it is concluded that the alluvial deposits of Shinchai in the 0–30 cm soil layer contain 3119.23 thousand/g microorganisms, and in soil samples taken from the above-floodplain terrace in a similar 0–30 cm layer — 4406.53 thousand/g.
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Yao, Huaiying, Yangmei Gao, Graeme W. Nicol, Colin D. Campbell, James I. Prosser, Limei Zhang, Wenyan Han, and Brajesh K. Singh. "Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils." Applied and Environmental Microbiology 77, no. 13 (May 13, 2011): 4618–25. http://dx.doi.org/10.1128/aem.00136-11.
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ABSTRACTAmmonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOBamoAgene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOAamoAsequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches.
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Watson, Tristan T., Tom A. Forge, and Louise M. Nelson. "Pseudomonads contribute to regulation ofPratylenchus penetrans(Nematoda) populations on apple." Canadian Journal of Microbiology 64, no. 11 (November 2018): 775–85. http://dx.doi.org/10.1139/cjm-2018-0040.
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Inoculation with antagonistic soil microorganisms has shown potential to suppress replant disease of apple in orchard soils. Pseudomonas spp. may have the potential to reduce Pratylenchus penetrans populations on apple. Pseudomonas spp. were isolated from the rhizosphere of sweet cherry and screened for antagonistic characteristics. Two highly antagonistic Pseudomonas isolates, P10-32 and P10-42, were evaluated for growth promotion of apple seedlings, suppression of P. penetrans populations, and root colonization in soil from three orchards. During the isolate screening, Pseudomonas fluorescens P10-32 reduced in vitro growth of fungal pathogens, had protease activity, had capacity to produce pyrrolnitrin, suppressed P. penetrans populations, and increased plant biomass. Pseudomonas fluorescens P10-42 reduced in vitro growth of fungal pathogens, had protease activity, suppressed P. penetrans populations, and increased plant biomass. In potted orchard soil, inoculating apple with P. fluorescens P10-32 suppressed P. penetrans populations in one of the three soils examined. Inoculation with P. fluorescens P10-42 improved plant growth in two of the soils and suppressed P. penetrans abundance in one soil. In one of the soils, P. fluorescens P10-42 was detected on the roots 56 days postinoculation. Overall, we conclude that Pseudomonas spp. play a role in suppressing P. penetrans on apple in orchard soil.
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Xiong, Jinbo, Liyou Wu, Shuxin Tu, Joy D. Van Nostrand, Zhili He, Jizhong Zhou, and Gejiao Wang. "Microbial Communities and Functional Genes Associated with Soil Arsenic Contamination and the Rhizosphere of the Arsenic-Hyperaccumulating Plant Pteris vittata L." Applied and Environmental Microbiology 76, no. 21 (September 10, 2010): 7277–84. http://dx.doi.org/10.1128/aem.00500-10.
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ABSTRACT To understand how microbial communities and functional genes respond to arsenic contamination in the rhizosphere of Pteris vittata, five soil samples with different arsenic contamination levels were collected from the rhizosphere of P. vittata and nonrhizosphere areas and investigated by Biolog, geochemical, and functional gene microarray (GeoChip 3.0) analyses. Biolog analysis revealed that the uncontaminated soil harbored the greatest diversity of sole-carbon utilization abilities and that arsenic contamination decreased the metabolic diversity, while rhizosphere soils had higher metabolic diversities than did the nonrhizosphere soils. GeoChip 3.0 analysis showed low proportions of overlapping genes across the five soil samples (16.52% to 45.75%). The uncontaminated soil had a higher heterogeneity and more unique genes (48.09%) than did the arsenic-contaminated soils. Arsenic resistance, sulfur reduction, phosphorus utilization, and denitrification genes were remarkably distinct between P. vittata rhizosphere and nonrhizosphere soils, which provides evidence for a strong linkage among the level of arsenic contamination, the rhizosphere, and the functional gene distribution. Canonical correspondence analysis (CCA) revealed that arsenic is the main driver in reducing the soil functional gene diversity; however, organic matter and phosphorus also have significant effects on the soil microbial community structure. The results implied that rhizobacteria play an important role during soil arsenic uptake and hyperaccumulation processes of P. vittata.
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Chiba, Akane, Yoshitaka Uchida, Susanne Kublik, Gisle Vestergaard, Franz Buegger, Michael Schloter, and Stefanie Schulz. "Soil Bacterial Diversity Is Positively Correlated with Decomposition Rates during Early Phases of Maize Litter Decomposition." Microorganisms 9, no. 2 (February 11, 2021): 357. http://dx.doi.org/10.3390/microorganisms9020357.
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This study aimed to investigate the effects of different levels of soil- and plant-associated bacterial diversity on the rates of litter decomposition, and bacterial community dynamics during its early phases. We performed an incubation experiment where soil bacterial diversity (but not abundance) was manipulated by autoclaving and reinoculation. Natural or autoclaved maize leaves were applied to the soils and incubated for 6 weeks. Bacterial diversity was assessed before and during litter decomposition using 16S rRNA gene metabarcoding. We found a positive correlation between litter decomposition rates and soil bacterial diversity. The soil with the highest bacterial diversity was dominated by oligotrophic bacteria including Acidobacteria, Nitrospiraceae, and Gaiellaceae, and its community composition did not change during the incubation. In the less diverse soils, those taxa were absent but were replaced by copiotrophic bacteria, such as Caulobacteraceae and Beijerinckiaceae, until the end of the incubation period. SourceTracker analysis revealed that litter-associated bacteria, such as Beijerinckiaceae, only became part of the bacterial communities in the less diverse soils. This suggests a pivotal role of oligotrophic bacteria during the early phases of litter decomposition and the predominance of copiotrophic bacteria at low diversity.
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Yeager, Chris M., Diana E. Northup, Christy C. Grow, Susan M. Barns, and Cheryl R. Kuske. "Changes in Nitrogen-Fixing and Ammonia-Oxidizing Bacterial Communities in Soil of a Mixed Conifer Forest after Wildfire." Applied and Environmental Microbiology 71, no. 5 (May 2005): 2713–22. http://dx.doi.org/10.1128/aem.71.5.2713-2722.2005.
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ABSTRACT This study was undertaken to examine the effects of forest fire on two important groups of N-cycling bacteria in soil, the nitrogen-fixing and ammonia-oxidizing bacteria. Sequence and terminal restriction fragment length polymorphism (T-RFLP) analysis of nifH and amoA PCR amplicons was performed on DNA samples from unburned, moderately burned, and severely burned soils of a mixed conifer forest. PCR results indicated that the soil biomass and proportion of nitrogen-fixing and ammonia-oxidizing species was less in soil from the fire-impacted sites than from the unburned sites. The number of dominant nifH sequence types was greater in fire-impacted soils, and nifH sequences that were most closely related to those from the spore-forming taxa Clostridium and Paenibacillus were more abundant in the burned soils. In T-RFLP patterns of the ammonia-oxidizing community, terminal restriction fragments (TRFs) representing amoA cluster 1, 2, or 4 Nitrosospira spp. were dominant (80 to 90%) in unburned soils, while TRFs representing amoA cluster 3A Nitrosospira spp. dominated (65 to 95%) in fire-impacted soils. The dominance of amoA cluster 3A Nitrosospira spp. sequence types was positively correlated with soil pH (5.6 to 7.5) and NH3-N levels (0.002 to 0.976 ppm), both of which were higher in burned soils. The decreased microbial biomass and shift in nitrogen-fixing and ammonia-oxidizing communities were still evident in fire-impacted soils collected 14 months after the fire.
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Aldén, L., F. Demoling, and E. Bååth. "Rapid Method of Determining Factors Limiting Bacterial Growth in Soil." Applied and Environmental Microbiology 67, no. 4 (April 1, 2001): 1830–38. http://dx.doi.org/10.1128/aem.67.4.1830-1838.2001.
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ABSTRACT A technique to determine which nutrients limit bacterial growth in soil was developed. The method was based on measuring the thymidine incorporation rate of bacteria after the addition of C, N, and P in different combinations to soil samples. First, the thymidine incorporation method was tested in two different soils: an agricultural soil and a forest humus soil. Carbon (as glucose) was found to be the limiting substance for bacterial growth in both of these soils. The effect of adding different amounts of nutrients was studied, and tests were performed to determine whether the additions affected the soil pH and subsequent bacterial activity. The incubation time required to detect bacterial growth after adding substrate to the soil was also evaluated. Second, the method was used in experiments in which three different size fractions of straw (1 to 2, 0.25 to 1, and <0.25 mm) were mixed into the agricultural soil in order to induce N limitation for bacterial growth. When the straw fraction was small enough (<0.25 mm), N became the limiting nutrient for bacterial growth after about 3 weeks. After the addition of the larger straw fractions (1 to 2 and 0.25 to 1 mm), the soil bacteria were C limited throughout the incubation period (10 weeks), although an increase in the thymidine incorporation rate after the addition of C and N together compared with adding them separately was seen in the sample containing the size fraction from 0.25 to 1 mm. Third, soils from high-pH, limestone-rich areas were examined. P limitation was observed in one of these soils, while tendencies toward P limitation were seen in some of the other soils.
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Gnangui, Sara Laetitia Elphège, Romain Kouakou Fossou, Anicet Ebou, Chiguié Estelle Raïssa Amon, Dominique Kadio Koua, Claude Ghislaine Zaka Kouadjo, Don A. Cowan, and Adolphe Zézé. "The Rhizobial Microbiome from the Tropical Savannah Zones in Northern Côte d’Ivoire." Microorganisms 9, no. 9 (August 30, 2021): 1842. http://dx.doi.org/10.3390/microorganisms9091842.
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Over the past decade, many projects have been initiated worldwide to decipher the composition and function of the soil microbiome, including the African Soil Microbiome (AfSM) project that aims at providing new insights into the presence and distribution of key groups of soil bacteria from across the African continent. In this national study, carried out under the auspices of the AfSM project, we assessed the taxonomy, diversity and distribution of rhizobial genera in soils from the tropical savannah zones in Northern Côte d’Ivoire. Genomic DNA extracted from seven sampled soils was analyzed by sequencing the V4-V5 variable region of the 16S rDNA using Illumina’s MiSeq platform. Subsequent bioinformatic and phylogenetic analyses showed that these soils harbored 12 out of 18 genera of Proteobacteria harboring rhizobia species validly published to date and revealed for the first time that the Bradyrhizobium genus dominates in tropical savannah soils, together with Microvirga and Paraburkholderia. In silico comparisons of different 16S rRNA gene variable regions suggested that the V5-V7 region could be suitable for differentiating rhizobia at the genus level, possibly replacing the use of the V4-V5 region. These data could serve as indicators for future rhizobial microbiome explorations and for land-use decision-making.
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Zeng, Quanchao, and Shaoshan An. "Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau." Microorganisms 9, no. 1 (January 9, 2021): 139. http://dx.doi.org/10.3390/microorganisms9010139.
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High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3–V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.
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Poly, Franck, Lionel Ranjard, Sylvie Nazaret, François Gourbière, and Lucile Jocteur Monrozier. "Comparison of nifH Gene Pools in Soils and Soil Microenvironments with Contrasting Properties." Applied and Environmental Microbiology 67, no. 5 (May 1, 2001): 2255–62. http://dx.doi.org/10.1128/aem.67.5.2255-2262.2001.
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ABSTRACT The similarities and differences in the structures of thenifH gene pools of six different soils (Montrond, LCSA-p, Vernon, Dombes, LCSA-c, and Thysse Kaymor) and five soil fractions extracted from LCSA-c were studied. Bacterial DNA was directly extracted from the soils, and a region of thenifH gene was amplified by PCR and analyzed by restriction. Soils were selected on the basis of differences in soil management, plant cover, and major physicochemical properties. Microenvironments differed on the basis of the sizes of the constituent particles and the organic carbon and clay contents. Restriction profiles were subjected to principal-component analysis. We showed that the composition of the diazotrophic communities varied both on a large scale (among soils) and on a microscale (among microenvironments in LCSA-c soil). Soil management seemed to be the major parameter influencing differences in the nifH gene pool structure among soils by controlling inorganic nitrogen content and its variation. However, physicochemical parameters (texture and total C and N contents) were found to correlate with differences amongnifH gene pools on a microscale. We hypothesize that the observed nifH genetic structures resulted from the adaptation to fluctuating conditions (cultivated soil, forest soil, coarse fractions) or constant conditions (permanent pasture soil, fine fractions). We attempted to identify a specific band within the profile of the clay fraction by cloning and sequencing it and comparing it with the gene databases. Unexpectedly, the nifH sequences of the dominant bacteria were most similar to sequences of unidentified marine eubacteria.