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Schumacher K, Braun D, Kleigrewe K, Jung K. Motility-activating mutations upstream of flhDC reduce acid shock survival of Escherichia coli. Microbiol Spectr 2024; 12:e0054424. [PMID: 38651876 PMCID: PMC11237407 DOI: 10.1128/spectrum.00544-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Many neutralophilic bacterial species try to evade acid stress with an escape strategy, which is reflected in the increased expression of genes coding for flagellar components. Extremely acid-tolerant bacteria, such as Escherichia coli, survive the strong acid stress, e.g., in the stomach of vertebrates. Recently, we were able to show that the induction of motility genes in E. coli is strictly dependent on the degree of acid stress, i.e., they are induced under mild acid stress but not under severe acid stress. However, it was not known to what extent fine-tuned expression of motility genes is related to fitness and the ability to survive periods of acid shock. In this study, we demonstrate that the expression of FlhDC, the master regulator of flagellation, is inversely correlated with the acid shock survival of E. coli. We encountered this phenomenon when analyzing mutants from the Keio collection, in which the expression of flhDC was altered by an insertion sequence element. These results suggest a fitness trade-off between acid tolerance and motility.IMPORTANCEEscherichia coli is extremely acid-resistant, which is crucial for survival in the gastrointestinal tract of vertebrates. Recently, we systematically studied the response of E. coli to mild and severe acidic conditions using Ribo-Seq and RNA-Seq. We found that motility genes are induced at pH 5.8 but not at pH 4.4, indicating stress-dependent synthesis of flagellar components. In this study, we demonstrate that motility-activating mutations upstream of flhDC, encoding the master regulator of flagella genes, reduce the ability of E. coli to survive periods of acid shock. Furthermore, we show an inverse correlation between motility and acid survival using a chromosomal isopropyl β-D-thio-galactopyranoside (IPTG)-inducible flhDC promoter and by sampling differentially motile subpopulations from swim agar plates. These results reveal a previously undiscovered trade-off between motility and acid tolerance and suggest a differentiation of E. coli into motile and acid-tolerant subpopulations, driven by the integration of insertion sequence elements.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Djanna Braun
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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Zhang H, Chen W, Dong L, Wang W. Grassland degradation amplifies the negative effect of nitrogen enrichment on soil microbial community stability. GLOBAL CHANGE BIOLOGY 2024; 30:e17217. [PMID: 38456565 DOI: 10.1111/gcb.17217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/27/2024] [Accepted: 02/07/2024] [Indexed: 03/09/2024]
Abstract
Although nitrogen (N) enrichment is known to threaten the temporal stability of aboveground net primary productivity, it remains unclear how it alters that of belowground microbial abundance and whether its impact can be regulated by grassland degradation. Using data from N enrichment experiments at temperate grasslands with no, moderate, severe, and extreme degradation degrees, we quantified the temporal stability of soil microbial abundance (hereafter 'microbial community stability') using the ratio of the mean quantitative PCR to its standard deviation over 4 years. Both bacterial and fungal community stability sharply decreased when N input exceeded 30 g N m-2 year-1 in non-degraded grasslands, whereas a reduction in this threshold occurred in degraded grasslands. Microbial species diversity, species asynchrony, and species associations jointly altered microbial community stability. Interestingly, the linkages between plant and microbial community stability were strengthened in degraded grasslands, suggesting that plants and soil microbes might depend on each other to keep stable communities in harsh environments. Our findings highlighted the importance of grassland degradation in regulating the responses of microbial community stability to N enrichment and provided experimental evidence for understanding the relationships between plant and microbial community stability.
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Affiliation(s)
- Hongjin Zhang
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Weile Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lizheng Dong
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Wei Wang
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
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Seward J, Bräuer S, Beckett P, Roy-Léveillée P, Emilson E, Watmough S, Basiliko N. Recovery of Smelter-Impacted Peat and Sphagnum Moss: a Microbial Perspective. MICROBIAL ECOLOGY 2023; 86:2894-2903. [PMID: 37632540 DOI: 10.1007/s00248-023-02289-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
Peatlands store approximately one-half of terrestrial soil carbon and one-tenth of non-glacial freshwater. Some of these important ecosystems are located near heavy metal emitting smelters. To improve the understanding of smelter impacts and potential recovery after initial pollution controls in the 1970s (roughly 50 years of potential recovery), we sampled peatlands along a distance gradient of 134 km from a smelter in Sudbury, Ontario, Canada, an area with over a century of nickel (Ni) and copper (Cu) mining activity. This work is aimed at evaluating potential shifts in bacterial and archaeal community structures in Sphagnum moss and its underlying peat within smelter-impacted poor fens. In peat, total Ni and Cu concentrations were higher (0.062-0.067 and 0.110-0.208 mg/g, respectively) at sites close to the smelter and exponentially dropped with distance from the smelter. This exponential decrease in Ni concentrations was also observed in Sphagnum. 16S rDNA amplicon sequencing showed that peat and Sphagnum moss host distinct microbiomes with peat accommodating a more diverse community structure. The microbiomes of Sphagnum were dominated by Proteobacteria (62.5%), followed by Acidobacteria (11.9%), with no observable trends with distance from the smelter. Dominance of Acidobacteria (32.4%) and Proteobacteria (29.6%) in peat was reported across all sites. No drift in taxonomy was seen across the distance gradient or from the reference sites, suggesting a potential microbiome recovery toward that of the reference peatlands microbiomes after decades of pollution controls. These results advance the understanding of peat and Sphagnum moss microbiomes, as well as depict the sensitivities and the resilience of peatland ecosystems.
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Affiliation(s)
- James Seward
- Vale Living with Lakes Centre and the School of Natural Sciences, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada.
| | - Suzanna Bräuer
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608, USA
| | - Peter Beckett
- Vale Living with Lakes Centre and the School of Natural Sciences, Laurentian University, 935 Ramsey Lake Rd, Sudbury, ON, P3E 2C6, Canada
| | - Pascale Roy-Léveillée
- Department of Geography, Université Laval, Pavillon Abitibi-Price, Quebec, G1V 0A6, Canada
| | - Erik Emilson
- Natural Resources Canada, Great Lakes Forestry Centre, 1219 Queen St. East, Sault Ste. Marie, ON, P6A 2E5, Canada
| | - Shaun Watmough
- School of the Environment, Trent University, Peterborough, Ontario, Canada
| | - Nathan Basiliko
- Department of Natural Resources Management, Lakehead University, 955 Oliver Rd., Thunder Bay, ON, P7B 5E1, Canada
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4
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Świecimska M, Golińska P, Goodfellow M. Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy. Front Microbiol 2023; 13:1054384. [PMID: 36741889 PMCID: PMC9893292 DOI: 10.3389/fmicb.2022.1054384] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Introduction Filamentous actinomycetes, notably members of the genus Streptomyces, remain a rich source of new specialized metabolites, especially antibiotics. In addition, they are also a valuable source of anticancer and biocontrol agents, biofertilizers, enzymes, immunosuppressive drugs and other biologically active compounds. The new natural products needed for such purposes are now being sought from extreme habitats where harsh environmental conditions select for novel strains with distinctive features, notably an ability to produce specialized metabolites of biotechnological value. Methods A culture-based bioprospecting strategy was used to isolate and screen filamentous actinomycetes from three poorly studied extreme biomes. Actinomycetes representing different colony types growing on selective media inoculated with environmental suspensions prepared from high-altitude, hyper-arid Atacama Desert soils, a saline soil from India and from a Polish pine forest soil were assigned to taxonomically predictive groups based on characteristic pigments formed on oatmeal agar. One hundred and fifteen representatives of the colour-groups were identified based on 16S rRNA gene sequences to determine whether they belonged to validly named or to putatively novel species. The antimicrobial activity of these isolates was determined using a standard plate assay. They were also tested for their capacity to produce hydrolytic enzymes and compounds known to promote plant growth while representative strains from the pine forest sites were examined to determine their ability to inhibit the growth of fungal and oomycete plant pathogens. Results Comparative 16S rRNA gene sequencing analyses on isolates representing the colour-groups and their immediate phylogenetic neighbours showed that most belonged to either rare or novel species that belong to twelve genera. Representative isolates from the three extreme biomes showed different patterns of taxonomic diversity and characteristic bioactivity profiles. Many of the isolates produced bioactive compounds that inhibited the growth of one or more strains from a panel of nine wild strains in standard antimicrobial assays and are known to promote plant growth. Actinomycetes from the litter and mineral horizons of the pine forest, including acidotolerant and acidophilic strains belonging to the genera Actinacidiphila, Streptacidiphilus and Streptomyces, showed a remarkable ability to inhibit the growth of diverse fungal and oomycete plant pathogens. Discussion It can be concluded that selective isolation and characterization of dereplicated filamentous actinomyctes from several extreme biomes is a practical way of generating high quality actinomycete strain libraries for agricultural, industrial and medical biotechnology.
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Affiliation(s)
- Magdalena Świecimska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland,*Correspondence: Magdalena Świecimska, ✉
| | - Patrycja Golińska
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland,Patrycja Golińska, ✉
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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Sridhar B, Lawrence GB, Debenport SJ, Fahey TJ, Buckley DH, Wilhelm RC, Goodale CL. Watershed-scale liming reveals the short- and long-term effects of pH on the forest soil microbiome and carbon cycling. Environ Microbiol 2022; 24:6184-6199. [PMID: 35799501 DOI: 10.1111/1462-2920.16119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/28/2022] [Indexed: 01/12/2023]
Abstract
Soil microbial community composition routinely correlates with pH, reflecting both direct pH effects on microbial physiology and long-term biogeochemical feedbacks. We used two watershed-scale liming experiments to identify short- (2 years) and long-term (25 years) changes in the structure and function of bacterial and fungal communities in organic horizons (Oe and Oa ) of acid forest soils. Liming increased soil pH, extractable calcium, and soil carbon stocks, reduced biomass-specific respiration, and caused major changes in the soil microbiome in the short and long term. More taxa responded to liming in the short term (70%) than in the long term (30%), with most showing consistent directional responses at both sites. The ratio of change in relative abundance between limed and reference sites was twofold higher at the long than the short-term site, indicating that the effects of liming grew over time. Liming impacts were most pronounced in fungi, as steep declines of dominant ectomycorrhizal fungi (Cenococcum and Russula) occurred at both sites. Liming favoured neutrophilic bacteria over acidophilic populations according to estimated environmental pH optima. Collectively, these results demonstrate that a liming-induced change of one pH unit has an immediate and persistent effect on the structure and function of microbial communities in acid forest soils. The corresponding suppression of respiration indicates that anthropogenic alterations of soil pH, as driven by acid deposition or liming, can affect forest floor C stocks due to pH-driven shifts in community structure.
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Affiliation(s)
- Bhavya Sridhar
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Spencer J Debenport
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Timothy J Fahey
- Department of Natural Resources, Cornell University, Ithaca, New York, USA
| | - Daniel H Buckley
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Roland C Wilhelm
- School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Christine L Goodale
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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Foley JR, McAvoy TJ, Grubb C, Mayfield AE, Strahm B, Salom SM. Subterranean Survivorship and Seasonal Emergence of Laricobius spp. (Coleoptera: Derodontidae), Biological Control Agents for the Hemlock Woolly Adelgid. ENVIRONMENTAL ENTOMOLOGY 2022; 51:63-70. [PMID: 35171282 DOI: 10.1093/ee/nvab124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 06/14/2023]
Abstract
Following the adventive arrival, subsequent spread, and ensuing impact of Adelges tsugae Annand (Hemiptera: Adelgidae), the hemlock woolly adelgid (HWA) in the eastern United States, a robust initiative was launched with the goal of decreasing ecosystem impacts from the loss of eastern hemlock (Pinales: Pinaceae). This initiative includes the use of biological control agents, including Laricobius spp. (Insecta: Coleoptera). Laboratory production of these agents is limited by subterranean mortality and early emergence. Therefore, the subterranean survivorship and timing of emergence of a mixture of Laricobius spp. was investigated. PVC traps internally lined with a sticky card and covered with a mesh screen were inserted into the soil to measure the percent emergence of adults based on the number of larvae placed within. The number of emerged adults in the field and laboratory-reared larval treatments was adjusted based on emergence numbers in the control and used as the response variable. Independent variables included in the final model were: treatment (field-collected vs. laboratory-reared), organic layer depth (cm), soil pH, and April-to-December mean soil moisture. No differences were found in survivorship between field-collected and laboratory-reared treatments. As pH and organic layer increased survivorship decreased, significantly. Although the majority of emergence occurred in the fall, emergence also occurred in spring and summer. The occurrence of spring and summer emergence and low survivorship (17.1 ± 0.4%) in the field across all treatments suggests that these are characteristics of Laricobius spp. field biology in their introduced range and not artifacts of the laboratory rearing process.
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Affiliation(s)
- Jeremiah R Foley
- Department of Entomology, Virginia Tech, 170 Drillfield Drive, Blacksburg, VA 24060, USA
| | - Thomas J McAvoy
- Department of Entomology, Virginia Tech, 170 Drillfield Drive, Blacksburg, VA 24060, USA
| | - Christopher Grubb
- Department of Statistics, Virginia Tech, 250 Drillfield Drive, Blacksburg, VA 24061, USA
| | - Albert E Mayfield
- USDA Forest Service, Southern Research Station, 200 W.T. Weaver Boulevard, Asheville, NC 28804, USA
| | - Brian Strahm
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 310 West Campus Drive, Blacksburg, VA 24060, USA
| | - Scott M Salom
- Department of Entomology, Virginia Tech, 170 Drillfield Drive, Blacksburg, VA 24060, USA
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Hansen JC, Schillinger WF, Sullivan TS, Paulitz TC. Decline in Soil Microbial Abundance When Camelina Introduced Into a Monoculture Wheat System. Front Microbiol 2020; 11:571178. [PMID: 33329427 PMCID: PMC7710528 DOI: 10.3389/fmicb.2020.571178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/26/2020] [Indexed: 12/04/2022] Open
Abstract
Camelina [Camelina sativa (L.) Crantz] of the Brassicaceae family is a potential alternative and oilseed biofuel crop for wheat (Triticum aestivum L.)-based cropping systems of the Inland Pacific Northwest (PNW) of the United States. We investigated the effect of this relatively new rotational crop on soil microbial communities. An 8-year cropping systems experiment was initiated in 2007 at Lind, WA, to compare a 3-year rotation of winter wheat (WW)-camelina (C)-fallow (F) to the typical 2-year WW-F rotation. All phases of both rotations (total = 20 plots) were present every year to allow valid statistical analysis and data interpretations. Monoculture WW-F is the dominant system practiced by the vast majority of farmers on 1.56 million ha of cropland in the PNW drylands that receive <300 mm average annual precipitation. Microbial abundance and community composition were determined using phospholipid fatty acid analysis (PLFA) from soil samples collected during 3 consecutive years beginning in 2010. The abundance of fungi, mycorrhizae, Gram positive and negative bacteria, and total microbial abundance all declined over the 3-year period in the WW-C-F rotation compared to the WW-F rotation. All microbial lipid biomarkers were significantly less in fallow compared to WW of the WW-C-F rotation. The 2-year WW-F rotation demonstrated few differences in microbial lipid abundance and community structure between the rotation phases. Microbial abundance declined and community structure shifted in the 3-year WW-C-F rotation likely due to the combination of a Brassica crop followed by a 13-month-long fallow. The results of this study suggest that camelina in combination with a fallow period may disrupt microbial communities that have become stable under historical WW-F monocropping. Such disturbances have the potential to affect soil processes that have been provided by wheat-adapted microbial communities. However, the disruption appears to be short-lived with the microbial abundance of WW in the WW-C-F rotation, returning to similar levels observed in the WW-F rotation.
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Affiliation(s)
- Jeremy C Hansen
- Northwest Sustainable Agroecosystems Research Unit, USDA-Agricultural Research Service, Washington State University, Pullman, WA, United States
| | - William F Schillinger
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Tarah S Sullivan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Timothy C Paulitz
- Wheat Health, Genetics, and Quality Research, USDA-Agricultural Research Service, Washington State University, Pullman, WA, United States
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Seward J, Carson MA, Lamit LJ, Basiliko N, Yavitt JB, Lilleskov E, Schadt CW, Smith DS, Mclaughlin J, Mykytczuk N, Willims-Johnson S, Roulet N, Moore T, Harris L, Bräuer S. Peatland Microbial Community Composition Is Driven by a Natural Climate Gradient. MICROBIAL ECOLOGY 2020; 80:593-602. [PMID: 32388577 DOI: 10.1007/s00248-020-01510-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/30/2020] [Indexed: 05/20/2023]
Abstract
Peatlands are important players in climate change-biosphere feedbacks via long-term net carbon (C) accumulation in soil organic matter and as potential net C sources including the potent greenhouse gas methane (CH4). Interactions of climate, site-hydrology, plant community, and groundwater chemical factors influence peatland development and functioning, including C dioxide (CO2) and CH4 fluxes, but the role of microbial community composition is not well understood. To assess microbial functional and taxonomic dissimilarities, we used high throughput sequencing of the small subunit ribosomal DNA (SSU rDNA) to determine bacterial and archaeal community composition in soils from twenty North American peatlands. Targeted DNA metabarcoding showed that although Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla on average, intermediate and rich fens hosted greater diversity and taxonomic richness, as well as an array of candidate phyla when compared with acidic and nutrient-poor poor fens and bogs. Moreover, pH was revealed to be the strongest predictor of microbial community structure across sites. Predictive metagenome content (PICRUSt) showed increases in specific genes, such as purine/pyrimidine and amino-acid metabolism in mid-latitude peatlands from 38 to 45° N, suggesting a shift toward utilization of microbial biomass over utilization of initial plant biomass in these microbial communities. Overall, there appears to be noticeable differences in community structure between peatland classes, as well as differences in microbial metabolic activity between latitudes. These findings are in line with a predicted increase in the decomposition and accelerated C turnover, and suggest that peatlands north of 37° latitude may be particularly vulnerable to climate change.
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Affiliation(s)
- James Seward
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608-2026, USA.
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada.
| | - Michael A Carson
- Department of Renewable Resources, Earth Sciences Building, University of Alberta, 116 St. and 85 Ave., Edmonton, Alberta, T6G 2R3, Canada
| | - L J Lamit
- Department of Biology, Syracuse University, Syracuse, NY, USA
| | - Nathan Basiliko
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, 14853, USA
| | - Erik Lilleskov
- USDA Forest Service, Northern Research Station, 410 MacInnes Dr, Houghton, MI, 49931, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6038, USA
| | - Dave Solance Smith
- Department of Biology, California State University, San Bernardino, CA, 92407, USA
| | - Jim Mclaughlin
- Ontario Forest Research Institute, Sault Ste. Marie, ON, Canada
| | - Nadia Mykytczuk
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada
| | - Shanay Willims-Johnson
- Vale Living with Lakes Centre and the Department of Biology, Laurentian University, 935 Ramsey Lake Rd., Sudbury, ON, P3E 2C6, Canada
| | - Nigel Roulet
- Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Tim Moore
- Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Lorna Harris
- Department of Geography, McGill University, 805 Sherbrooke St. W., Montreal, QC, H3A 0B9, Canada
| | - Suzanna Bräuer
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608-2026, USA
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Silva R, de Almeida DM, Cabral BCA, Dias VHG, Mello ICDTE, Ürményi TP, Woerner AE, Neto RSDM, Budowle B, Nassar CAG. Microbial enrichment and gene functional categories revealed on the walls of a spent fuel pool of a nuclear power plant. PLoS One 2018; 13:e0205228. [PMID: 30286173 PMCID: PMC6171911 DOI: 10.1371/journal.pone.0205228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/21/2018] [Indexed: 11/28/2022] Open
Abstract
Microorganisms developing in the liner of the spent fuel pool (SFP) and the fuel transfer channel (FTC) of a Nuclear Power Plant (NPP) can form high radiation resistant biofilms and cause corrosion. Due to difficulties and limitations to obtain large samples from SFP and FTC, cotton swabs were used to collect the biofilm from the wall of these installations. Molecular characterization was performed using massively parallel sequencing to obtain a taxonomic and functional gene classification. Also, samples from the drainage system were evaluated because microorganisms may travel over the 12-meter column of the pool water of the Brazilian Nuclear Power Plant (Angra1), which has been functioning since 1985. Regardless of the treatment of the pool water, our data reveal the unexpected presence of Fungi (Basidiomycota and Ascomycota) as the main contaminators of the SFP and FTC. Ustilaginomycetes (Basidiomycota) was the major class contributor (70%) in the SFP and FTC reflecting the little diversity in these sites; nevertheless, Proteobacteria, Actinobacteria, Firmicutes (Bacilli) were present in small proportions. Mapping total reads against six fungal reference genomes indicate that there is, in fact, a high abundance of fungal sequences in samples collected from SFP and FTC. Analysis of the ribosomal internal transcribed spacer (ITS) 1 and 2 regions and the protein found in the mitochondria of eukaryotic cells, cytochrome b (cytb) grouped our sample fungi in the clade 7 as Ustilago and Pseudozyma. In contrast, in the drainage system, Alphaproteobacteria were present in high abundances (55%). The presence of Sphingopyxis, Mesorhizobium, Erythrobacter, Sphingomonas, Novosphingobium, Sphingobium, Chelativorans, Oceanicaulis, Acidovorax, and Cyanobacteria was observed. Based on genomic annotation data, the assessment of the biological function found a higher proportion of protein-coding sequences related to respiration and protein metabolism in SFP and FTC samples. The knowledge of this biological inventory present in the system may contribute to further studies of potential microorganisms that might be useful for bioremediation of nuclear waste.
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Affiliation(s)
- Rosane Silva
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
| | - Darcy Muniz de Almeida
- Escola Politécnica & Escola de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Victor Hugo Giordano Dias
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Turán Péter Ürményi
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - August E. Woerner
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, United States of America
| | | | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, United States of America
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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Cortes-Tolalpa L, Norder J, van Elsas JD, Falcao Salles J. Halotolerant microbial consortia able to degrade highly recalcitrant plant biomass substrate. Appl Microbiol Biotechnol 2018; 102:2913-2927. [PMID: 29397428 PMCID: PMC5847192 DOI: 10.1007/s00253-017-8714-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/29/2017] [Accepted: 12/11/2017] [Indexed: 12/30/2022]
Abstract
The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent downstream processes. Here, we constructed halotolerant lignocellulose degrading microbial consortia by enriching a salt marsh soil microbiome on a recalcitrant carbon and energy source, i.e., wheat straw. The consortia were obtained after six cycles of growth on fresh substrate (adaptation phase), which was followed by four cycles on pre-digested (highly-recalcitrant) substrate (stabilization phase). The data indicated that typical salt-tolerant bacteria made up a large part of the selected consortia. These were “trained” to progressively perform better on fresh substrate, but a shift was observed when highly recalcitrant substrate was used. The most dominant bacteria in the consortia were Joostella marina, Flavobacterium beibuense, Algoriphagus ratkowskyi, Pseudomonas putida, and Halomonas meridiana. Interestingly, fungi were sparsely present and negatively affected by the change in the substrate composition. Sarocladium strictum was the single fungal strain recovered at the end of the adaptation phase, whereas it was deselected by the presence of recalcitrant substrate. Consortia selected in the latter substrate presented higher cellulose and lignin degradation than consortia selected on fresh substrate, indicating a specialization in transforming the recalcitrant regions of the substrate. Moreover, our results indicate that bacteria have a prime role in the degradation of recalcitrant lignocellulose under saline conditions, as compared to fungi. The final consortia constitute an interesting source of lignocellulolytic haloenzymes that can be used to increase the efficiency of the degradation process, while decreasing the associated costs.
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Affiliation(s)
- Larisa Cortes-Tolalpa
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Justin Norder
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Joana Falcao Salles
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
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Fang BZ, Salam N, Han MX, Jiao JY, Cheng J, Wei DQ, Xiao M, Li WJ. Insights on the Effects of Heat Pretreatment, pH, and Calcium Salts on Isolation of Rare Actinobacteria from Karstic Caves. Front Microbiol 2017; 8:1535. [PMID: 28848538 PMCID: PMC5550672 DOI: 10.3389/fmicb.2017.01535] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 07/28/2017] [Indexed: 01/10/2023] Open
Abstract
The phylum Actinobacteria is one of the most ubiquitously present bacterial lineages on Earth. In the present study, we try to explore the diversity of cultivable rare Actinobacteria in Sigangli Cave, Yunnan, China by utilizing a combination of different sample pretreatments and under different culture conditions. Pretreating the samples under different conditions of heat, setting the isolation condition at different pHs, and supplementation of media with different calcium salts were found to be effective for isolation of diverse rare Actinobacteria. During our study, a total of 204 isolates affiliated to 30 genera of phylum Actinobacteria were cultured. Besides the dominant Streptomyces, rare Actinobacteria of the genera Actinocorallia, Actinomadura, Agromyces, Alloactinosynnema, Amycolatopsis, Beutenbergia, Cellulosimicrobium, Gordonia, Isoptericola, Jiangella, Knoellia, Kocuria, Krasilnikoviella, Kribbella, Microbacterium, Micromonospora, Mumia, Mycobacterium, Nocardia, Nocardioides, Nocardiopsis, Nonomuraea, Oerskovia, Pseudokineococcus, Pseudonocardia, Rhodococcus, Saccharothrix, Streptosporangium, and Tsukamurella were isolated from these cave samples.
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Affiliation(s)
- Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Ming-Xian Han
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China.,Medical Faculty of Kunming University of Science and TechnologyKunming, China
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Juan Cheng
- Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
| | - Da-Qiao Wei
- Medical Faculty of Kunming University of Science and TechnologyKunming, China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China.,Yunnan Institute of Microbiology, Yunnan UniversityKunming, China
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Siridechakorn I, Yue Z, Mittraphab Y, Lei X, Pudhom K. Identification of spirobisnaphthalene derivatives with anti-tumor activities from the endophytic fungus Rhytidhysteron rufulum AS21B. Bioorg Med Chem 2017; 25:2878-2882. [PMID: 28274675 DOI: 10.1016/j.bmc.2017.02.054] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 11/25/2022]
Abstract
The cultivation of the mangrove-derived fungus Rhytidhysteron rufulum AS21B in acidic condition changed its secondary metabolite profile. Investigation of the culture broth extract led to the isolation and identification of two new spirobisnaphthalenes (1 and 2) together with eleven known compounds (3-13) from the crude extract of the fungus grown under an acidic condition as well as six known compounds (4, 10, 14-17) were isolated from the crude extract of the fungus grown under a neutral condition. Their structures were elucidated on the basis of extensive spectroscopic data. The isolated compounds were evaluated for their cytotoxicity against two human cancer cell lines, Ramos lymphoma and drug resistant NSCLC H1975. Compounds 2 and 10 displayed the most promising anti-tumor activity against both cancer cell lines.
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Affiliation(s)
- Ittipon Siridechakorn
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zongwei Yue
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yanisa Mittraphab
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Khanitha Pudhom
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Machamangalath R, Arekar C, Lele S. Exotic tropical fruit wines from Garcinia indica
and Musa acuminate. JOURNAL OF THE INSTITUTE OF BREWING 2016. [DOI: 10.1002/jib.379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Reena Machamangalath
- Food Engineering and Technology Department; Institute of Chemical Technology, Matunga; Mumbai Maharashtra 400019 India
| | - Chetan Arekar
- Food Engineering and Technology Department; Institute of Chemical Technology, Matunga; Mumbai Maharashtra 400019 India
| | - S.S. Lele
- Food Engineering and Technology Department; Institute of Chemical Technology, Matunga; Mumbai Maharashtra 400019 India
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Yang SH, Lim JS, Khan MA, Kim BS, Choi DY, Lee EY, Ahn HK. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses. Genet Mol Biol 2015; 38:373-80. [PMID: 26500442 PMCID: PMC4612598 DOI: 10.1590/s1415-475738320140252] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 02/10/2015] [Indexed: 12/03/2022] Open
Abstract
The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses) and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.
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Affiliation(s)
- Seung Hak Yang
- Animal Nutrition Physiology Team, National Institute of Animal Science, Jeonbuk, South Korea
| | - Joung Soo Lim
- Animal Environment Division, National Institute of Animal Science, Jeonbuk, South Korea
| | - Modabber Ahmed Khan
- Animal Environment Division, National Institute of Animal Science, Jeonbuk, South Korea
| | - Bong Soo Kim
- Department of Life Sciences, Hallym University, Chuncheon, Gangwon-do, South Korea
| | - Dong Yoon Choi
- Animal Environment Division, National Institute of Animal Science, Jeonbuk, South Korea
| | - Eun Young Lee
- Department of Environmental and Energy Engineering, Suwon University, South Korea
| | - Hee Kwon Ahn
- Department of Animal Biosystems Science, Chungnam National University, Daejeon, South Korea
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15
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Goyari S, Devi SS, Kalita MC, Talukdar NC. Population, diversity and characteristics of cellulolytic microorganisms from the Indo-Burma Biodiversity hotspot. SPRINGERPLUS 2014; 3:700. [PMID: 26034690 PMCID: PMC4447715 DOI: 10.1186/2193-1801-3-700] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022]
Abstract
Forest ecosystem harbour a large number of biotic components where cellulolytic microorganisms participate actively in the biotransformation of dead and decaying organic matter and soil nutrient cycling. This study explores the aerobic culturable cellulolytic microorganisms in the forest soils of North East India. Soil samples rich in dead and decaying organic matter were collected from eight conserved forests during the season when microbes were found to be most active. Cellulolytic microorganisms were isolated using selective media in which cellulose was the sole carbon source. Population of culturable, aerobic, cellulolytic microorganisms were found to be higher at the incubation temperature that corresponds to the natural ambient temperature of the site of sample collection. Bacterial population was higher in all of the sites than fungal population. Bacterial population ranged from 1.91 × 10(5) to 3.35 × 10(6) CFU g(-1) dry soil while actinomycetes and fungal population ranged from 9.13 × 10(2) to 3.46 × 10(4) CFU g(-1) dry soil and 9.36 × 10(2) to 4.31 × 10(4) CFU g(-1) dry soil, respectively. It was observed that though many isolates showed activity on the CMC plate assay, very few isolates showed significant filter paper activity. Three cellulolytic fungal isolates showing high FPase activity were characterised, identified and submitted to GenBank as Talaromyces verruculosus SGMNPf3 (KC937053), Trichoderma gamsii SGSPf7 (KC937055) and Trichoderma atroviride SGBMf4 (KC937054).
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Affiliation(s)
- Sailendra Goyari
- />Institute of Bioresources and Sustainable Development (IBSD), Imphal, India
| | - Shantibala S Devi
- />Institute of Bioresources and Sustainable Development (IBSD), Imphal, India
| | | | - Narayan C Talukdar
- />Institute of Bioresources and Sustainable Development (IBSD), Imphal, India
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16
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Magdich S, Ben Ahmed C, Jarboui R, Ben Rouina B, Boukhris M, Ammar E. Dose and frequency dependent effects of olive mill wastewater treatment on the chemical and microbial properties of soil. CHEMOSPHERE 2013; 93:1896-1903. [PMID: 23880238 DOI: 10.1016/j.chemosphere.2013.06.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 06/20/2013] [Accepted: 06/25/2013] [Indexed: 06/02/2023]
Abstract
Olive mill wastewater (OMW) is a problematic by-product of olive oil production. While its high organic load and polyphenol concentrations are associated with troublesome environmental effects, its rich mineral and organic matter contents represent valuable nutrients. This study aimed to investigate the valorization of this waste biomass as a potential soil conditioner and fertilizer in agriculture. OMW was assayed at three doses 50, 100, and 200 m(3) ha(-1) year(-1)) over three successive years in olive fields. The effects of the effluent on the physico-chemical and microbial properties of soil-layers were assessed. The findings revealed that the pH of the soil decreased but electrical conductivity and organic matter, total nitrogen, sodium, and potassium soil contents increased in proportion with OMW concentration and frequency of application. While no variations were observed in phosphorus content, slow increases were recorded in calcium and magnesium soil contents. Compared to their control soil counterparts, aerobic bacteria and fungi increased in proportion with OMW spreading rates. The models expressing the correlation between progress parameters and OMW doses were fitted into a second degree polynomial model. Principal component analysis showed a strong correlation between soil mineral elements and microorganisms. These parameters were not related to phosphorus and pH.
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Affiliation(s)
- Salwa Magdich
- Laboratoire d'Amélioration de la Productivité Oléicole et des Arbres Fruitiers, Institut de l'Olivier de Sfax, B.P. 1087, 3000 Sfax, Tunisia; UR Etude et Gestion des Environnements Urbains et Côtiers, Université de Sfax, Ecole Nationale d'Ingénieurs de Sfax, B.P. 1173, 3038 Sfax, Tunisia; Laboratoire d'Ecologie Végétale, Faculté des Sciences de Sfax, B.P. 1082, 3018 Sfax, Tunisia
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17
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Geiser E, Wierckx N, Zimmermann M, Blank LM. Identification of an endo-1,4-beta-xylanase of Ustilago maydis. BMC Biotechnol 2013; 13:59. [PMID: 23889751 PMCID: PMC3737115 DOI: 10.1186/1472-6750-13-59] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/22/2013] [Indexed: 12/04/2022] Open
Abstract
Background The utilization of raw biomass components such as cellulose or hemicellulose for the production of valuable chemicals has attracted considerable research interest in recent years. One promising approach is the application of microorganisms that naturally convert biomass constituents into value added chemicals. One of these organisms – Ustilago maydis – can grow on xylan, the second most abundant polysaccharide in nature, while at the same time it produces chemicals of biotechnological interest. Results In this study, we present the identification of an endo-1,4-beta xylanase responsible for xylan degradation. Xylanase activity of U. maydis cells was indirectly detected by the quantification of released reducing sugars and could be confirmed by visualizing oligosaccharides as degradation products of xylan by thin layer chromatography. A putative endo-1,4-beta-xylanase, encoded by um06350.1, was identified in the supernatant of xylan-grown cells. To confirm the activity, we displayed the putative xylanase on the surface of the xylanase negative Saccharomyces cerevisiae EBY100. The presented enzyme converted xylan to xylotriose, similar to the source organism U. maydis. Conclusions The xylan degradation ability together with its unicellular and yeast-like growth makes U. maydis MB215 a promising candidate for the production of valuable chemicals such as itaconic acid or glycolipids from lignocellulosic biomass. Therefore, the characterization of the endo-1,4-beta-xylanase, encoded by um06350.1, is a further step towards the biotechnological application of U. maydis and its enzymes.
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Affiliation(s)
- Elena Geiser
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, Aachen D-52074, Germany
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18
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Belyaeva ON, Haynes RJ, Sturm EC. Chemical, physical and microbial properties and microbial diversity in manufactured soils produced from co-composting green waste and biosolids. WASTE MANAGEMENT (NEW YORK, N.Y.) 2012; 32:2248-57. [PMID: 22770779 DOI: 10.1016/j.wasman.2012.05.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 05/16/2012] [Accepted: 05/22/2012] [Indexed: 05/03/2023]
Abstract
The effects of adding biosolids to a green waste feedstock (100% green waste, 25% v/v biosolids or 50% biosolids) on the properties of composted products were investigated. Following initial composting, 20% soil or 20% fly ash/river sand mix was added to the composts as would be carried out commercially to produce manufactured soil. Temperatures during composting reached 50 °C, or above, for 23 days when biosolids were included as a composting feedstock but temperatures barely reached 40 °C when green waste alone was composted. Addition of biosolids to the feedstock increased total N, EC, extractable NH(4), NO(3) and P but lowered pH, macroporosity, water holding capacity, microbial biomass C and basal respiration in composts. Additions of soil or ash/sand to the composts greatly increased the available water holding capacity of the materials. Principal component analysis (PCA) of PCR-DGGE 16S rDNA amplicons separated bacterial communities according to addition of soil to the compost. For fungal ITS-RNA amplicons, PCA separated communities based on the addition of biosolids. Bacterial species richness and Shannon's diversity index were greatest for composts where soil had been added but for fungal communities these parameters were greatest in the treatments where 50% biosolids had been included. These results were interpreted in relation to soil having an inoculation effect and biosolids having an acidifying effect thereby favouring a fungal community.
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Affiliation(s)
- O N Belyaeva
- School of Agriculture and Food Sciences/CRC CARE, The University of Queensland, St Lucia, Queensland 4072, Australia
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Magdich S, Jarboui R, Rouina BB, Boukhris M, Ammar E. A yearly spraying of olive mill wastewater on agricultural soil over six successive years: impact of different application rates on olive production, phenolic compounds, phytotoxicity and microbial counts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2012; 430:209-216. [PMID: 22647243 DOI: 10.1016/j.scitotenv.2012.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 04/11/2012] [Accepted: 05/01/2012] [Indexed: 06/01/2023]
Abstract
Olive mill wastewater (OMW) spraying effects onto olive-tree fields were investigated. Three OMW levels (50, 100 and 200 m(3)ha(-1)year(-1)) were applied over six successive years. Olive-crop yields, phenolic compounds progress, phytotoxicity and microbial counts were studied at different soil depths. Olive yield showed improvements with OMW level applied. Soil polyphenolic content increased progressively in relation to OMW levels in all the investigated layers. However, no significant difference was noted in lowest treatment rate compared to the control field. In the soil upper-layers (0-40 cm), five phenolic compounds were identified over six consecutive years of OMW-spraying. In all the soil-layers, the radish germination index exceeded 85%. However, tomato germination test values decreased with the applied OMW amount. For all treatments, microbial counts increased with OMW quantities and spraying frequency. Matrix correlation showed a strong relationship between soil polyphenol content and microorganisms, and a negative one to tomato germination index.
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Affiliation(s)
- Salwa Magdich
- UR Etude et Gestion des Environnements Urbains et Côtiers, Université de Sfax, Ecole Nationale d'Ingénieurs de Sfax, BP 1173-3038 Sfax, Tunisia
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Meng H, Li K, Nie M, Wan JR, Quan ZX, Fang CM, Chen JK, Gu JD, Li B. Responses of bacterial and fungal communities to an elevation gradient in a subtropical montane forest of China. Appl Microbiol Biotechnol 2012; 97:2219-30. [PMID: 22539023 DOI: 10.1007/s00253-012-4063-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 03/27/2012] [Accepted: 03/28/2012] [Indexed: 10/28/2022]
Abstract
Bacteria and fungi are ecologically important contributors to various functioning of forest ecosystems. In this study, we examined simultaneously the bacterial and fungal distributions in response to elevation changes of a forest. By using clone library analysis from genomic DNA extracted from forest humic clay soils, the composition and diversity of bacterial and fungal communities were determined across an elevation gradient from low via medium to high, in a subtropical forest in the Mountain Lushan, China. Our results showed that soil water content and nutrient availability, specifically total carbon, differed significantly with elevation changes. Although the soil acidity did not differ significantly among the three sites, low pH (around 4) could be an important selection factor selecting for acidophilic Acidobacteria and Alphaproteobacteria, which were the most abundant bacterial clones. As the majority of the fungi recovered, both Basidiomycota and Ascomycota, and their relative abundance were most closely associated with the total carbon. Based on the Shannon-Weaver diversity index and ∫-libshuff analysis, the soil at medium elevation contained the highest diversity of bacteria compared with those at high and low elevations. However, it is difficult to predict overall fungal diversity along elevation. The extreme high soil moisture content which may lead to the formation of anaerobic microhabitats in the forest soils potentially reduces the overall bacterial and fungal diversity.
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Affiliation(s)
- Han Meng
- School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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21
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Yadav S, Kaushik R, Saxena AK, Arora DK. Diversity and phylogeny of plant growth-promoting bacilli from moderately acidic soil. J Basic Microbiol 2010; 51:98-106. [DOI: 10.1002/jobm.201000098] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 06/21/2010] [Indexed: 11/10/2022]
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Simpson AJ, Simpson MJ, Smith E, Kelleher BP. Microbially derived inputs to soil organic matter: are current estimates too low? ENVIRONMENTAL SCIENCE & TECHNOLOGY 2007; 41:8070-6. [PMID: 18186339 DOI: 10.1021/es071217x] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Soil microbes are central to many soil processes, but due to the structural complexity of soil organic matter, the accurate quantification of microbial biomass contributions continues to pose a significant analytical challenge. In this study, microbes from a range of soils were cultured such that their molecular profile could be compared to that of soil organic matter and native vegetation. With the use of modern NMR spectroscopy, the contributions from microbial species can be discerned in soil organic matter and quantified. On the basis of these studies, the contributions of microbial biomass to soil organic matter appear to be much higher than the 1-5% reported by other researchers. In some soils, microbial biomass was found to contribute >50% of the extractable soil organic matter fractions and approximately 45% of the humin fraction and accounted for >80% of the soil nitrogen. These findings are significant because organic matter is intimately linked to nutrient release and transport in soils, nitrogen turnover rates, contaminant fate, soil quality, and fertility. Therefore, if in some cases soil organic matter and soil organic nitrogen are predominately of microbial origin, it is likely that this fraction, whether in the form of preserved material or living cells, plays an underestimated role in several soil processes.
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Affiliation(s)
- André J Simpson
- Department of Chemistry, University of Toronto, Scarborough College, 1265 Military Trail, Toronto, Ontario, Canada.
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Matthies C, Gössner A, Acker G, Schramm A, Drake HL. Lactovum miscens gen. nov., sp. nov., an aerotolerant, psychrotolerant, mixed-fermentative anaerobe from acidic forest soil. Res Microbiol 2004; 155:847-54. [PMID: 15567280 DOI: 10.1016/j.resmic.2004.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Accepted: 06/15/2004] [Indexed: 10/26/2022]
Abstract
An aerotolerant, psychrotolerant anaerobe, anNAG3, was isolated from an acidic forest floor solution (in situ pH of 4.5). Cells of anNAG3 stained Gram-positive did not form spores, and were not motile. Cells were ovoid, approximately 1 microm long and 0.7 microm wide, mostly in pairs, and contained a multi-layered cell wall and intracytoplasmic membranes. Growth was observed at pH 3.5-7.5 and 0-35 degrees C. Glucose, galactose, fructose, mannitol, glucosamine, N-acetylglucosamine, cellobiose, and maltose supported growth. Lactate, ethanol, formate, and acetate were end products. H(2) and CH(4) were not detected, and only very minor amounts of CO(2) were produced. The relative amount of a particular product was dependent on the substrate utilized, and product profiles indicated that (i) sugars were initially metabolized to pyruvate via glycolysis, and (ii) lactate dehydrogenase and pyruvate-formate lyase were responsible for the subsequent metabolism of pyruvate. O(2) was not significantly utilized and was not toxic to growth. anNAG3 did not contain detectable membranous or cytoplasmic cytochromes. Nitrate, sulfate, and Fe(III) were not dissimilated. Thus, anNAG3 was characterized as an aerotolerant, non-acetogenic chemoorganotroph with a mixed-fermentative metabolism. The G + C content of the DNA was 37.6 mol%. The similarity of the 16S rRNA gene sequence of anNAG3 to that of its closest phylogenetic relatives (which were in the genera Lactococcus and Streptococcus) approximated 88-89%, indicating that anNAG3 constitutes the type species of a new genus. Based on the collective properties of anNAG3, it is proposed that anNAG3 be termed Lactovum miscens.
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Affiliation(s)
- Carola Matthies
- Department of Ecological Microbiology, University of Bayreuth, 95440 Bayreuth, Germany
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Reith F, Drake HL, Küsel K. Anaerobic activities of bacteria and fungi in moderately acidic conifer and deciduous leaf litter. FEMS Microbiol Ecol 2002; 41:27-35. [DOI: 10.1111/j.1574-6941.2002.tb00963.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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