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Hu Z, Delgado-Baquerizo M, Fanin N, Chen X, Zhou Y, Du G, Hu F, Jiang L, Hu S, Liu M. Nutrient-induced acidification modulates soil biodiversity-function relationships. Nat Commun 2024; 15:2858. [PMID: 38570522 PMCID: PMC10991381 DOI: 10.1038/s41467-024-47323-3] [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: 08/18/2023] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Nutrient enrichment is a major global change component that often disrupts the relationship between aboveground biodiversity and ecosystem functions by promoting species dominance, altering trophic interactions, and reducing ecosystem stability. Emerging evidence indicates that nutrient enrichment also reduces soil biodiversity and weakens the relationship between belowground biodiversity and ecosystem functions, but the underlying mechanisms remain largely unclear. Here, we explore the effects of nutrient enrichment on soil properties, soil biodiversity, and multiple ecosystem functions through a 13-year field experiment. We show that soil acidification induced by nutrient enrichment, rather than changes in mineral nutrient and carbon (C) availability, is the primary factor negatively affecting the relationship between soil diversity and ecosystem multifunctionality. Nitrogen and phosphorus additions significantly reduce soil pH, diversity of bacteria, fungi and nematodes, as well as an array of ecosystem functions related to C and nutrient cycling. Effects of nutrient enrichment on microbial diversity also have negative consequences at higher trophic levels on the diversity of microbivorous nematodes. These results indicate that nutrient-induced acidification can cascade up its impacts along the soil food webs and influence ecosystem functioning, providing novel insight into the mechanisms through which nutrient enrichment influences soil community and ecosystem properties.
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Affiliation(s)
- Zhengkun Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro‑Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain
| | - Nicolas Fanin
- INRAE, Bordeaux Sciences Agro, UMR 1391 ISPA, Villenave-d'Ornon, France
| | - Xiaoyun Chen
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Zhou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guozhen Du
- College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Feng Hu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuijin Hu
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Manqiang Liu
- Centre for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro‑Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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Kumar V, Ameen F, Verma P. Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach. Front Microbiol 2024; 15:1350164. [PMID: 38529176 PMCID: PMC10961449 DOI: 10.3389/fmicb.2024.1350164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg-1) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.
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Affiliation(s)
- Vineet Kumar
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Pradeep Verma
- Bioprocess and Bioenergy Laboratory, Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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Béchade B, Cabuslay CS, Hu Y, Mendonca CM, Hassanpour B, Lin JY, Su Y, Fiers VJ, Anandarajan D, Lu R, Olson CJ, Duplais C, Rosen GL, Moreau CS, Aristilde L, Wertz JT, Russell JA. Physiological and evolutionary contexts of a new symbiotic species from the nitrogen-recycling gut community of turtle ants. THE ISME JOURNAL 2023; 17:1751-1764. [PMID: 37558860 PMCID: PMC10504363 DOI: 10.1038/s41396-023-01490-1] [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: 03/21/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023]
Abstract
While genome sequencing has expanded our knowledge of symbiosis, role assignment within multi-species microbiomes remains challenging due to genomic redundancy and the uncertainties of in vivo impacts. We address such questions, here, for a specialized nitrogen (N) recycling microbiome of turtle ants, describing a new genus and species of gut symbiont-Ischyrobacter davidsoniae (Betaproteobacteria: Burkholderiales: Alcaligenaceae)-and its in vivo physiological context. A re-analysis of amplicon sequencing data, with precisely assigned Ischyrobacter reads, revealed a seemingly ubiquitous distribution across the turtle ant genus Cephalotes, suggesting ≥50 million years since domestication. Through new genome sequencing, we also show that divergent I. davidsoniae lineages are conserved in their uricolytic and urea-generating capacities. With phylogenetically refined definitions of Ischyrobacter and separately domesticated Burkholderiales symbionts, our FISH microscopy revealed a distinct niche for I. davidsoniae, with dense populations at the anterior ileum. Being positioned at the site of host N-waste delivery, in vivo metatranscriptomics and metabolomics further implicate I. davidsoniae within a symbiont-autonomous N-recycling pathway. While encoding much of this pathway, I. davidsoniae expressed only a subset of the requisite steps in mature adult workers, including the penultimate step deriving urea from allantoate. The remaining steps were expressed by other specialized gut symbionts. Collectively, this assemblage converts inosine, made from midgut symbionts, into urea and ammonia in the hindgut. With urea supporting host amino acid budgets and cuticle synthesis, and with the ancient nature of other active N-recyclers discovered here, I. davidsoniae emerges as a central player in a conserved and impactful, multipartite symbiosis.
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Affiliation(s)
- Benoît Béchade
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA.
| | - Christian S Cabuslay
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Yi Hu
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875, Beijing, China
| | - Caroll M Mendonca
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Bahareh Hassanpour
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Jonathan Y Lin
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546-4402, USA
| | - Yangzhou Su
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546-4402, USA
| | - Valerie J Fiers
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Dharman Anandarajan
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Richard Lu
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Chandler J Olson
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
- Department of Biological Sciences, University of Alabama, 1325 Hackberry Ln, Tuscaloosa, AL, 35487, USA
| | - Christophe Duplais
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
| | - Gail L Rosen
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, 3141 Chestnut St., Philadelphia, PA, 19104, USA
| | - Corrie S Moreau
- Department of Entomology, Cornell University, Cornell AgriTech, Geneva, NY, 14456, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - John T Wertz
- Department of Biology, Calvin University, 1726 Knollcrest Circle SE, Grand Rapids, MI, 49546-4402, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
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Enespa, Chandra P. Tool and techniques study to plant microbiome current understanding and future needs: an overview. Commun Integr Biol 2022; 15:209-225. [PMID: 35967908 PMCID: PMC9367660 DOI: 10.1080/19420889.2022.2082736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.
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Affiliation(s)
- Enespa
- Department of Plant Pathology, School of Agriculture, SMPDC, University of Lucknow, Lucknow, India
| | - Prem Chandra
- Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar (A Central) University, Lucknow, India
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5
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Guergouri I, Guergouri M, Khouni S, Benhizia Y. Identification of cultivable bacterial strains producing biosurfactants/bioemulsifiers isolated from an Algerian oil refinery. Arch Microbiol 2022; 204:649. [PMID: 36171503 DOI: 10.1007/s00203-022-03265-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/02/2022]
Abstract
Algerian petrochemical industrial areas are usually running spills and leakages of hydrocarbons, which constitutes a major source of toxic compounds in soil such as aromatic hydrocarbons. In this paper, samples of crude oil-polluted soil were collected from Skikda's oil refinery and were subjected to mono and polyaromatic hydrocarbons threshold assessment. Soil physicochemical parameters were determined for each sample to examine their response to pollution. Amid 34 isolated bacteria, eleven strains were selected as best Biosurfactants (Bs)/Bioemulsifiers (Be) producers and were assigned to Firmicutes and Proteobacteria phyla based on molecular identification. Phylogenetic analysis of partial 16S rDNA gene sequences allowed the construction of evolutionary trees by means of the maximum likelihood method. Accordingly, strains were similar to Bacillus spp., Priesta spp., Pseudomonas spp., Enterobacter spp. and Kosakonia spp. with more than 95% similarity. These strains could be qualified candidates for an efficient bioremediation process of severally polluted soils.
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Affiliation(s)
- Ibtissem Guergouri
- Laboratory of Molecular and Cellular Biology, Department of Microbiology, Faculty of Nature and Life Sciences, Mentouri Brothers Constantine 1 University, Constantine, Algeria.
| | - Mounia Guergouri
- Laboratory of Materials Chemistry, Faculty of Exact Sciences, Department of Chemistry, Mentouri Brothers Constantine 1 University, Constantine, Algeria
| | - Sabra Khouni
- Laboratory of Molecular and Cellular Biology, Department of Microbiology, Faculty of Nature and Life Sciences, Mentouri Brothers Constantine 1 University, Constantine, Algeria
| | - Yacine Benhizia
- Laboratory of Molecular and Cellular Biology, Department of Microbiology, Faculty of Nature and Life Sciences, Mentouri Brothers Constantine 1 University, Constantine, Algeria
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6
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Wang S, Xu C, Song L, Zhang J. Anaerobic Digestion of Food Waste and Its Microbial Consortia: A Historical Review and Future Perspectives. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159519. [PMID: 35954875 PMCID: PMC9367938 DOI: 10.3390/ijerph19159519] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/04/2023]
Abstract
Renewable energy source, such as food waste (FW), has drawn great attention globally due to the energy crisis and the environmental problem. Anaerobic digestion (AD) mediated by novel microbial consortia is widely used to convert FW to clean energy. Despite of the considerable progress on food waste and FWAD optimization condition in recent years, a comprehensive and predictive understanding of FWAD microbial consortia is absent and therefore represents a major research challenge in FWAD. The review begins with a global view on the FWAD status and is followed by an overview of the role of AD key conditions’ association with microbial community variation during the three main energy substances (hydrogen, organic acids, and methane) production by FWAD. The following topic is the historical understanding of the FWAD microorganism through the development of molecular biotechnology, from classic strain isolation to low-throughput sequencing technologies, to high-throughput sequencing technologies, and to the combination of high-throughput sequencing and isotope tracing. Finally, the integration of multi-omics for better understanding of the microbial community activity and the synthetic biology for the manipulation of the functioning microbial consortia during the FWAD process are proposed. Understanding microbial consortia in FWAD helps us to better manage the global renewable energy source.
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Affiliation(s)
- Shuijing Wang
- School of Resources and Environmental Engineering, Anhui University, Hefei 230039, China;
| | - Chenming Xu
- College of Environment and Energy Engineering, Anhui Jianzhu University, Hefei 230601, China;
| | - Liyan Song
- School of Resources and Environmental Engineering, Anhui University, Hefei 230039, China;
- Correspondence: (L.S.); (J.Z.); Tel.: +86-55163861441 (L.S.); +86-55163828252 (J.Z.); Fax: +86-55163861724 (L.S.); +86-55163828252 (J.Z.)
| | - Jin Zhang
- College of Environment and Energy Engineering, Anhui Jianzhu University, Hefei 230601, China;
- Correspondence: (L.S.); (J.Z.); Tel.: +86-55163861441 (L.S.); +86-55163828252 (J.Z.); Fax: +86-55163861724 (L.S.); +86-55163828252 (J.Z.)
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7
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Saji N, Saito Y, Yamashita T, Murotani K, Tsuduki T, Hisada T, Sugimoto T, Niida S, Toba K, Sakurai T. Relationship Between Plasma Lipopolysaccharides, Gut Microbiota, and Dementia: A Cross-Sectional Study. J Alzheimers Dis 2022; 86:1947-1957. [PMID: 35213381 DOI: 10.3233/jad-215653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Previous studies have demonstrated associations between gut microbiota, microbial metabolites, and cognitive decline. However, relationships between these factors and lipopolysaccharides (LPS; molecules of the outer membrane of gram-negative bacteria) remain controversial. OBJECTIVE To evaluate associations between plasma LPS, gut microbiota, and cognitive function. METHODS We performed a cross-sectional sub-analysis of data of 127 participants (women: 58%, mean age: 76 years) from our prospective cohort study regarding the relationship between gut microbiota and cognitive function. We enrolled patients who visited our memory clinic and assessed demographics, dementia-related risk factors, cognitive function, brain imaging, gut microbiomes, and microbial metabolites. We evaluated relationships between cognitive decline and plasma LPS using multivariable logistic regression analyses. RESULTS Plasma LPS concentration increased with increasing degree of cognitive decline and total cerebral small vessel disease (SVD) score (Kruskal-Wallis test; p = 0.016 and 0.007, respectively). Participants with high plasma LPS concentrations tended to have lower concentrations of gut microbial metabolites, such as lactic acid and acetic acid, and were less likely to consume fish and shellfish (44.7% versus 69.6%, p = 0.027) than those with low plasma LPS concentrations. Multivariable analyses revealed that plasma LPS concentration was independently associated with the presence of mild cognitive impairment in participants without dementia (odds ratio: 2.09, 95% confidence interval: 1.14-3.84, p = 0.007). CONCLUSION In this preliminary study, plasma LPS concentration was associated with both cognitive decline and cerebral SVD and significantly correlated with beneficial gut microbial metabolites. Plasma LPS may be a risk factor for cognitive decline.
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Affiliation(s)
- Naoki Saji
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Yoshihiro Saito
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Tomoya Yamashita
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Kenta Murotani
- Biostatistics Center, Graduate School of Medicine, Kurume University, Fukuoka, Japan
| | - Tsuyoshi Tsuduki
- Laboratory of Food and Biomolecular Science, Department of Bioscience and Biotechnology for Future Bioindustries, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | | | - Taiki Sugimoto
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan.,Department of Prevention and Care Science, Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Shumpei Niida
- Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Kenji Toba
- Tokyo Metropolitan Geriatric Medical Center, Tokyo, Japan
| | - Takashi Sakurai
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan.,Department of Prevention and Care Science, Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan.,Department of Cognition and Behavioral Science, Nagoya University Graduate School of Medicine, Aichi, Japan
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8
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Gut Microbial Shifts Indicate Melanoma Presence and Bacterial Interactions in a Murine Model. Diagnostics (Basel) 2022; 12:diagnostics12040958. [PMID: 35454006 PMCID: PMC9029337 DOI: 10.3390/diagnostics12040958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 02/04/2023] Open
Abstract
Through a multitude of studies, the gut microbiota has been recognized as a significant influencer of both homeostasis and pathophysiology. Certain microbial taxa can even affect treatments such as cancer immunotherapies, including the immune checkpoint blockade. These taxa can impact such processes both individually as well as collectively through mechanisms from quorum sensing to metabolite production. Due to this overarching presence of the gut microbiota in many physiological processes distal to the GI tract, we hypothesized that mice bearing tumors at extraintestinal sites would display a distinct intestinal microbial signature from non-tumor-bearing mice, and that such a signature would involve taxa that collectively shift with tumor presence. Microbial OTUs were determined from 16S rRNA genes isolated from the fecal samples of C57BL/6 mice challenged with either B16-F10 melanoma cells or PBS control and analyzed using QIIME. Relative proportions of bacteria were determined for each mouse and, using machine-learning approaches, significantly altered taxa and co-occurrence patterns between tumor- and non-tumor-bearing mice were found. Mice with a tumor had elevated proportions of Ruminococcaceae, Peptococcaceae.g_rc4.4, and Christensenellaceae, as well as significant information gains and ReliefF weights for Bacteroidales.f__S24.7, Ruminococcaceae, Clostridiales, and Erysipelotrichaceae. Bacteroidales.f__S24.7, Ruminococcaceae, and Clostridiales were also implicated through shifting co-occurrences and PCA values. Using these seven taxa as a melanoma signature, a neural network reached an 80% tumor detection accuracy in a 10-fold stratified random sampling validation. These results indicated gut microbial proportions as a biosensor for tumor detection, and that shifting co-occurrences could be used to reveal relevant taxa.
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Saji N, Murotani K, Sato N, Tsuduki T, Hisada T, Shinohara M, Sugimoto T, Niida S, Toba K, Sakurai T. Relationship Between Plasma Neurofilament Light Chain, Gut Microbiota, and Dementia: A Cross-Sectional Study. J Alzheimers Dis 2022; 86:1323-1335. [PMID: 35180112 DOI: 10.3233/jad-215141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Previous studies have demonstrated associations between gut microbiota, microbial metabolites, and cognitive decline. However, relationships between these factors and neurofilament light chain (NfL; a disease-nonspecific biomarker of neural damage) remain controversial. OBJECTIVE To evaluate the associations between plasma NfL, gut microbiota, and cognitive function. METHODS We performed a cross-sectional sub-analysis of data from our prospective cohort study that was designed to investigate the relationship between gut microbiota and cognitive function. Patients who visited our memory clinic were enrolled and demographics, dementia-related risk factors, cognitive function, brain imaging, gut microbiomes, and microbial metabolites were assessed. We evaluated the relationships between the gut microbiome, microbial metabolites, and plasma NfL. Moreover, the relationships between plasma NfL and cognitive function were assessed using multivariable logistic regression analyses. RESULTS We analyzed 128 participants (women: 59%, mean age: 74 years). Participants with high (above the median) plasma NfL concentrations tended to be older, women, and hypertensive and have a history of stroke, chronic kidney disease, and dementia. Plasma NfL was also associated with cerebral small vessel disease. However, plasma NfL levels were not significantly correlated with gut microbial metabolites. Multivariable analyses revealed that a higher plasma NfL concentration was independently associated with the presence of dementia (odds ratio: 9.94, 95% confidence interval: 2.75-48.2, p < 0.001). CONCLUSION High plasma NfL concentration was independently associated with the presence of dementia as previously reported. However, plasma NfL levels were not significantly correlated with gut microbial metabolites in this preliminary study.
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Affiliation(s)
- Naoki Saji
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Kenta Murotani
- Biostatistics Center, Graduate School of Medicine, Kurume University, Fukuoka, Japan
| | - Naoyuki Sato
- Department of Aging Neurobiology, Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Tsuyoshi Tsuduki
- Laboratory of Food and Biomolecular Science, Department of Bioscience and Biotechnology for Future Bioindustries, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | | | - Mitsuru Shinohara
- Department of Aging Neurobiology, Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Taiki Sugimoto
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan.,Department of Prevention and Care Science, Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Shumpei Niida
- Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Kenji Toba
- Tokyo Metropolitan Geriatric Medical Center, Tokyo, Japan
| | - Takashi Sakurai
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan.,Department of Prevention and Care Science, Research Institute, National Center for Geriatrics and Gerontology, Aichi, Japan.,Department of Cognition and Behavioral Science, Nagoya University Graduate School of Medicine, Aichi, Japan
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10
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Takeda T, Chiba Y. Evaluation of a natural S-equol supplement in treating premenstrual symptoms and the effect of the gut microbiota: An open-label pilot study. Neuropsychopharmacol Rep 2022; 42:127-134. [PMID: 35128842 PMCID: PMC9216369 DOI: 10.1002/npr2.12234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 12/17/2022] Open
Abstract
AIM Premenstrual syndrome causes disturbances in many women's daily activities. Isoflavones might cause changes in the estrogen cycle by their selective estrogen receptor modulator-like activities. Equol, which is a metabolite of a soy isoflavone, has greater biological activity than other soy isoflavones. In this preliminary study, we aimed to examine the effect of a natural S-equol supplement (SE5-OH) on premenstrual symptoms. The gut microbiota has recently been suggested to play an important role in brain function in psychiatric disease, such as depression. Therefore, we further aimed to evaluate the relationship of the effect of SE5-OH and the gut microbiota at preintervention. METHODS Twenty women who showed premenstrual symptoms and were nonequol producers were enrolled in an open-label, single-arm, clinical study in which they received oral SE5-OH for two period cycles. The Daily Record of Severity of Problems (DRSP) total score was evaluated during the intervention cycles. Before taking SE5-OH, fecal samples were obtained and subjected to terminal restriction fragment length polymorphism analysis. RESULTS The response rate to treatment (≥50% reduction from baseline in the DRSP total score) was 10.5%. Post hoc analysis showed a significant improvement in the change in the DRSP total score (P = .008) and DRSP scores for four core premenstrual dysphoric disorder symptoms. Multiple regression analysis showed that the percentage improvement of the DRSP total score was positively related to Bifidobacterium and negatively related to Clostridium cluster IV. CONCLUSION SE5-OH supplementation may be an acceptable treatment for premenstrual symptoms. The intestinal microbiota may have an effect on SE5-OH.
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Affiliation(s)
- Takashi Takeda
- Division of Women's Health, Research Institute of Traditional Asian Medicine, Kindai University, Osaka-Sayama, Japan
| | - Yasutaka Chiba
- Clinical Research Center, Kindai University Hospital, Osaka-Sayama, Japan
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11
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Relationship between the Japanese-style diet, gut microbiota, and dementia: A cross-sectional study. Nutrition 2021; 94:111524. [PMID: 34952361 DOI: 10.1016/j.nut.2021.111524] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 09/16/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Previous studies have shown associations between the gut microbiota, microbial metabolites, and cognitive decline. However, the effect of the dietary composition on such associations has not been fully investigated. The aims of this study were to evaluate the relationships between adherence to a Japanese-style diet, the gut microbiota, and cognitive decline. Furthermore, we aimed to evaluate the three forms of the Japanese diet index (JDI; the conventional [JDI9], updated [JDI12], and a newly modified JDI) to determine which would show the closest relationships with cognition and the gut microbiota. METHODS We performed a cross-sectional subanalysis of data from a prospective hospital-based cohort study. We assessed the patients' demographic characteristics, dietary composition, risk factors, cognitive function, brain imaging, gut microbiome, and microbial metabolites. On the basis of previous studies, a nine-component traditional JDI (JDI9), a 12-component modern JDI (JDI12), and a 12-component revised JDI (rJDI12), were defined. We evaluated the relationships between the JDI scores, cognitive function, and the gut microbiome and microbial metabolites using multivariable logistic regression analyses. RESULTS We analyzed data from 85 eligible participants (61% women; mean age: 74.6 ± 7.4 y). Compared with participants who had dementia, those without dementia were more likely to consume foods in the JDI12, including fish and shellfish (64.5 versus 39.1%, P = 0.048), mushrooms (61.3 versus 30.4%, P = 0.015), soybeans and soybean-derived foods (62.9 versus 30.4%, P = 0.013), and coffee (71 versus 43.5%, P = 0.024). There were non-significant trends toward lower fecal concentrations of gut microbial metabolites in participants with a more traditional Japanese diet. Participants with dementia had lower JDI scores than those without dementia (dementia versus non-dementia, median JDI9 score: 5 versus 7, P = 0.049; JDI12: 7 versus 8, P = 0.017; and rJDI12: 7 versus 9, P = 0.006, respectively). CONCLUSIONS Adherence to a traditional Japanese diet was found to be inversely associated with cognitive decline and tended to be associated with lower concentrations of gut microbial metabolites.
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12
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Mainetti T, Palmisano M, Rezzonico F, Stres B, Kern S, Smits THM. Broad diversity of bacteria degrading 17ß-estradiol-3-sulfate isolated from river sediment and biofilm at a wastewater treatment plant discharge. Arch Microbiol 2021; 203:4209-4219. [PMID: 34080042 PMCID: PMC8360860 DOI: 10.1007/s00203-021-02409-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 10/31/2022]
Abstract
Conjugated estrogens, such as 17β-estradiol-3-sulfate (E2-3S), can be released into aquatic environments through wastewater treatment plants (WWTP). There, they are microbiologically degraded into free estrogens, which can have harmful effects on aquatic wildlife. Here, the degradation of E2-3S in environmental samples taken upstream, downstream and at the effluent of a WWTP was assessed. Sediment and biofilm samples were enriched for E2-3S-degrading microorganisms, yielding a broad diversity of bacterial isolates, including known and novel degraders of estrogens. Since E2-3S-degrading bacteria were also isolated in the sample upstream of the WWTP, the WWTP does not influence the ability of the microbial community to degrade E2-3S.
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Affiliation(s)
- Tamara Mainetti
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Marilena Palmisano
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Blaž Stres
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia.,Jozef Stefan Institute, Ljubljana, Slovenia
| | - Susanne Kern
- Environmental Analytics Group, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.
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13
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Jordan D, Mills D. Past, Present, and Future of DNA Typing for Analyzing Human and Non-Human Forensic Samples. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.646130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Forensic DNA analysis has vastly evolved since the first forensic samples were evaluated by restriction fragment length polymorphism (RFLP). Methodologies advanced from gel electrophoresis techniques to capillary electrophoresis and now to next generation sequencing (NGS). Capillary electrophoresis was and still is the standard method used in forensic analysis. However, dependent upon the information needed, there are several different techniques that can be used to type a DNA fragment. Short tandem repeat (STR) fragment analysis, Sanger sequencing, SNapShot, and capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) are a few of the techniques that have been used for the genetic analysis of DNA samples. NGS is the newest and most revolutionary technology and has the potential to be the next standard for genetic analysis. This review briefly encompasses many of the techniques and applications that have been utilized for the analysis of human and nonhuman DNA samples.
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14
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Westaway JAF, Huerlimann R, Miller CM, Kandasamy Y, Norton R, Rudd D. Methods for exploring the faecal microbiome of premature infants: a review. Matern Health Neonatol Perinatol 2021; 7:11. [PMID: 33685524 PMCID: PMC7941982 DOI: 10.1186/s40748-021-00131-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
The premature infant gut microbiome plays an important part in infant health and development, and recognition of the implications of microbial dysbiosis in premature infants has prompted significant research into these issues. The approaches to designing investigations into microbial populations are many and varied, each with its own benefits and limitations. The technique used can influence results, contributing to heterogeneity across studies. This review aimed to describe the most common techniques used in researching the preterm infant microbiome, detailing their various limitations. The objective was to provide those entering the field with a broad understanding of available methodologies, so that the likely effects of their use can be factored into literature interpretation and future study design. We found that although many techniques are used for characterising the premature infant microbiome, 16S rRNA short amplicon sequencing is the most common. 16S rRNA short amplicon sequencing has several benefits, including high accuracy, discoverability and high throughput capacity. However, this technique has limitations. Each stage of the protocol offers opportunities for the injection of bias. Bias can contribute to variability between studies using 16S rRNA high throughout sequencing. Thus, we recommend that the interpretation of previous results and future study design be given careful consideration.
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Affiliation(s)
- Jacob A F Westaway
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia.
| | - Roger Huerlimann
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
| | - Catherine M Miller
- James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia
| | - Yoga Kandasamy
- Townsville University Hospital, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Robert Norton
- Pathology Queensland, 100 Angus Smith Dr, Douglas, QLD, 4814, Australia
| | - Donna Rudd
- James Cook University, 1 James Cook Dr, Douglas, QLD, 4811, Australia
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15
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Qin J, Li M, Zhang H, Liu H, Zhao J, Yang D. Nitrogen Deposition Reduces the Diversity and Abundance of cbbL Gene-Containing CO 2-Fixing Microorganisms in the Soil of the Stipa baicalensis Steppe. Front Microbiol 2021; 12:570908. [PMID: 33737915 PMCID: PMC7961154 DOI: 10.3389/fmicb.2021.570908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/10/2021] [Indexed: 11/13/2022] Open
Abstract
CO2 fixation by autotrophic microbes has a significant effect on the carbon cycle in temperate grasslands. Nitrogen (N) deposition in soil has been steadily increasing for decades, which has consequences for soil microorganisms. However, the impact of this deposition on the diversity and abundance of CO2-fixing soil microorganisms remains unclear in temperate grasslands. In the present study, the cbbL gene, a key gene in the Calvin–Benson–Bassham cycle that encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, was used to study CO2-fixing microbes under different rates of N addition (0, 15, 30, 50, 100, and 150 kg N ha–1 yr–1) in a 9-year field experiment in a temperate grassland. The results showed that N addition led to significant reductions in cbbL gene abundance and genetic diversity and altered cbbL gene community composition. High N addition enhanced the relative abundances of Acidiferrobacterales and Rhizobiales but reduced those of Burkholderiales and Rhodobacterales. Structural equation modeling further revealed that N addition primarily reduced cbbL genetic diversity by increasing the soil NO3-N content and decreasing the soil pH. N addition indirectly reduced cbbL gene abundance, possibly by increasing the soil N/phosphorus (P) ratio and decreasing the soil pH. These findings suggest that N addition increases the soil available N and causes soil acidification, which may inhibit growth of CO2-fixing microbes to some extent.
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Affiliation(s)
- Jie Qin
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Ming Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Haifang Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Hongmei Liu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Jianning Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Dianlin Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
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16
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Saji N, Murotani K, Hisada T, Tsuduki T, Sugimoto T, Kimura A, Niida S, Toba K, Sakurai T. The Association between Cerebral Small Vessel Disease and the Gut Microbiome: A Cross-Sectional Analysis. J Stroke Cerebrovasc Dis 2021; 30:105568. [PMID: 33423868 DOI: 10.1016/j.jstrokecerebrovasdis.2020.105568] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Recent studies have demonstrated an association between the gut microbiome and cognitive function. However, the associations between the gut microbiome and brain parenchyma damage, and their underlying mechanisms, remain unclear. MATERIALS AND METHODS We performed a cross-sectional sub-analysis using data from our prospective cohort study to determine the association between the gut microbiome and cerebral small vessel disease (SVD). We assessed patient demographics, risk factors, cognitive function, brain imaging, voxel-based specific regional analysis system for Alzheimer's Disease (VSRAD, indicating brain atrophy), and the gut microbiome as indicated by enterotypes and faecal microbiome metabolites. We then analysed the associations between total SVD scores, cognitive function, and the gut microbiome. RESULTS We analysed data from 87 patients without dementia or a history of stroke, 64 of whom exhibited mild cognitive impairment. Higher total SVD scores were associated with cognitive decline and behavioural and psychological symptoms. Compared with all other patients, patients with enterotype I (Bacteroides >30%) were more likely to have cognitive decline (median scores: Mini-Mental State Examination, 25 vs. 27, P = 0.047; Clinical Dementia Rating-Sum of Boxes, 1.5 vs. 0.5, P = 0.002) and present with cerebral SVD and high VSRAD scores (1.01 vs. 0.57, P = 0.012). Furthermore, faecal metabolites were significantly higher in patients with higher total SVD scores compared with those with lower scores. Multivariable logistic regression analyses indicated that certain gut microbiomes may double the risk of white matter hyperintensity. CONCLUSIONS The gut microbiome is associated with cerebral SVD.
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Affiliation(s)
- Naoki Saji
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, 7-430 Morioka, Obu, Aichi 474-8511, Japan.
| | - Kenta Murotani
- Biostatistics Center, Graduate School of Medicine, Kurume University, 67 Asahi-cho, Kurume, Fukuoka 830-0011, Japan
| | - Takayoshi Hisada
- TechnoSuruga Laboratory Co., Ltd., 330 Nagasaki, Shimizu-ku, Shizuoka, Shizuoka 424-0065, Japan
| | - Tsuyoshi Tsuduki
- Laboratory of Food and Biomolecular Science, Department of Bioscience and Biotechnology for Future Bioindustries, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Taiki Sugimoto
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, 7-430 Morioka, Obu, Aichi 474-8511, Japan
| | - Ai Kimura
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, 7-430 Morioka, Obu, Aichi 474-8511, Japan
| | - Shumpei Niida
- Research Institute, National Center for Geriatrics and Gerontology, 7-430 Morioka, Obu, Aichi 474-8511, Japan
| | - Kenji Toba
- Tokyo Metropolitan Geriatric Medical Center, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan
| | - Takashi Sakurai
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, 7-430 Morioka, Obu, Aichi 474-8511, Japan; Department of Cognition and Behavioural Science, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
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17
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Schmautz Z, Espinal CA, Bohny AM, Rezzonico F, Junge R, Frossard E, Smits THM. Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments. BMC Microbiol 2021; 21:12. [PMID: 33407126 PMCID: PMC7789318 DOI: 10.1186/s12866-020-02075-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/17/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An aquaponic system couples cultivation of plants and fish in the same aqueous medium. The system consists of interconnected compartments for fish rearing and plant production, as well as for water filtration, with all compartments hosting diverse microbial communities, which interact within the system. Due to the design, function and operation mode of the individual compartments, each of them exhibits unique biotic and abiotic conditions. Elucidating how these conditions shape microbial communities is useful in understanding how these compartments may affect the quality of the water, in which plants and fish are cultured. RESULTS We investigated the possible relationships between microbial communities from biofilms and water quality parameters in different compartments of the aquaponic system. Biofilm samples were analyzed by total community profiling for bacterial and archaeal communities. The results implied that the oxygen levels could largely explain the main differences in abiotic parameters and microbial communities in each compartment of the system. Aerobic system compartments are highly biodiverse and work mostly as a nitrifying biofilter, whereas biofilms in the anaerobic compartments contain a less diverse community. Finally, the part of the system connecting the aerobic and anaerobic processes showed common conditions where both aerobic and anaerobic processes were observed. CONCLUSION Different predicted microbial activities for each compartment were found to be supported by the abiotic parameters, of which the oxygen saturation, total organic carbon and total nitrogen differentiated clearly between samples from the main aerobic loop and the anaerobic compartments. The latter was also confirmed using microbial community profile analysis.
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Affiliation(s)
- Zala Schmautz
- Ecological Engineering Centre, Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland.,Group of Plant Nutrition, Institute of Agricultural Sciences, ETH Zurich, Lindau, Switzerland
| | | | - Andrea M Bohny
- Group of Plant Nutrition, Institute of Agricultural Sciences, ETH Zurich, Lindau, Switzerland
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Ranka Junge
- Ecological Engineering Centre, Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Emmanuel Frossard
- Group of Plant Nutrition, Institute of Agricultural Sciences, ETH Zurich, Lindau, Switzerland
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland.
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18
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Phosphate-Solubilizing Fungi: Current Perspective and Future Need for Agricultural Sustainability. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60659-6_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Suárez-Moo P, Lamelas A, Garcia-Bautista I, Barahona-Pérez LF, Sandoval-Flores G, Valdes-Lozano D, Toledano-Thompson T, Polanco-Lugo E, Valdez-Ojeda R. Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico. PeerJ 2020; 8:e10339. [PMID: 33354414 PMCID: PMC7731659 DOI: 10.7717/peerj.10339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites. Methods The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation. Results We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.
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Affiliation(s)
- Pablo Suárez-Moo
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | - Araceli Lamelas
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | - Itza Garcia-Bautista
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
| | | | - Gloria Sandoval-Flores
- Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autonoma de Tamaulipas, Merida, Yucatan, Mexico
| | - David Valdes-Lozano
- Centro de Investigación y de Estudios Avanzados, Insituto Politecnico Nacional, Merida, Yucatan, Mexico
| | - Tanit Toledano-Thompson
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
| | - Erik Polanco-Lugo
- Campus de Ciencias Biológicas y Agropecuarias,, Universidad Autonoma de Yucatan, Merida, Yucatan, Mexico
| | - Ruby Valdez-Ojeda
- Unidad de Energia Renovable, Centro de Investigacion Cientifica de Yucatan, Merida, Yucatan, Mexico
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20
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Ballesté E, Demeter K, Masterson B, Timoneda N, Sala-Comorera L, Meijer WG. Implementation and integration of microbial source tracking in a river watershed monitoring plan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 736:139573. [PMID: 32474276 DOI: 10.1016/j.scitotenv.2020.139573] [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: 04/26/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 05/20/2023]
Abstract
Fecal pollution of water bodies poses a serious threat for public health and ecosystems. Microbial source tracking (MST) is used to track the source of this pollution facilitating better management of pollution at the source. In this study we tested 12 MST markers to track human, ruminant, sheep, horse, pig and gull pollution to assess their usefulness as an effective management tool of water quality. First, the potential of the selected markers to track the source was evaluated using fresh fecal samples. Subsequently, we evaluated their performance in a catchment with different impacts, considering land use and environmental conditions. All MST markers showed high sensitivity and specificity, although none achieved 100% for both. Although some of the MST markers were detected in hosts other than the intended ones, their abundance in the target group was always several orders of magnitude higher than in the non-target hosts, demonstrating their suitability to distinguish between sources of pollution. The MST analysis matched the land use in the watershed allowing an accurate assessment of the main sources of pollution, in this case mainly human and ruminant pollution. Correlating environmental parameters including temperature and rainfall with MST markers provided insight into the dynamics of the pollution in the catchment. The levels of the human marker showed a significant negative correlation with rainfall in human polluted areas suggesting a dilution of the pollution, whereas at agricultural areas the ruminant marker increased with rainfall. There were no seasonal differences in the levels of human marker, indicating human pollution as a constant pressure throughout the year, whereas the levels of the ruminant marker was influenced by the seasons, being more abundant in summer and autumn. MST analysis integrated with land use and environmental data can improve the management of fecal polluted areas and set up best practice.
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Affiliation(s)
- Elisenda Ballesté
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Katalin Demeter
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Bartholomew Masterson
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Natàlia Timoneda
- Computational Genomics Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, UCD Earth Institute, UCD Conway Institute, University College Dublin, Dublin, Ireland.
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21
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Relationship between dementia and gut microbiome-associated metabolites: a cross-sectional study in Japan. Sci Rep 2020; 10:8088. [PMID: 32424166 PMCID: PMC7235213 DOI: 10.1038/s41598-020-65196-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 04/30/2020] [Indexed: 12/16/2022] Open
Abstract
Dysregulation of the gut microbiome is associated with dementia. However, the relationship between microbiome-associated metabolites and dementia has yet to be identified. Outpatients visiting a memory clinic in Japan enrolled in this cross-sectional study; 107 subjects were eligible for the study, 25 of which had dementia. We collected demographics, activities of daily living, risk factors, cognitive function, and brain imaging data. The gut microbiome was assessed using terminal restriction fragment length polymorphism analysis. Concentrations of faecal metabolite were measured. We used multivariable logistic regression analyses to identify whether metabolites were independently related to dementia. The concentrations of metabolites were significantly different between subjects with and those without dementia. Every 1 standard deviation increment in faecal ammonia concentration was associated with around a 1.6-fold risk for the presence of dementia. A higher faecal lactic acid concentration was related to a lower risk of dementia, by around 60%. A combination of higher faecal ammonia and lactic acid concentrations was indicative of the presence of dementia, and had a similar predictive value as traditional biomarkers of dementia. Thus, faecal ammonia and lactic acid are related to dementia, independently of the other risk factors for dementia and dysregulation of the gut microbiome.
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22
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Ali S, Saldias S, Weerasuriya N, Delaney K, Kandasamy S, Lazarovits G. Corn microbial diversity and its relationship to yield. Can J Microbiol 2020; 66:457-473. [PMID: 32155347 DOI: 10.1139/cjm-2020-0002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study aimed to identify possible relationships between corn (Zea mays L.) productivity and its endosphere microbial community. Any insights would be used to develop testable hypotheses at the farm level. Sap was collected from 14 fields in 2014 and 10 fields in 2017, with a yield range of 10.1 to 21.7 tonnes per hectare (t/ha). The microbial sap communities were analyzed using terminal restriction fragment length polymorphism (TRFLP) and identified using an internal pure culture reference database and BLAST. This technique is rapid and inexpensive and is suitable for use at the grower level. Diversity, richness, and normalized abundances of each bacterial population in corn sap samples were evaluated to link the microbiome of a specific field to its yield. A negative trend was observed (r = -0.60), with higher-yielding fields having lower terminal restriction fragment (TRF) richness. A partial least square regression analysis of TRF intensity and binary data from 2014 identified 10 TRFs (bacterial genera) that positively, or negatively, correlated with corn yields, when either absent or present at certain levels or ratios. Using these observations, a model was developed that accommodated criteria for each of the 10 microbes and assigned a score for each field out of 10. Data collected in 2014 showed that sites with higher model scores were highly correlated with larger yields (r = 0.83). This correlation was also seen when the 2017 data set was used (r = 0.87). We were able to conclude that a positive significant effect was seen with the model score and yield (adjusted R2 = 0.67, F[1,22] = 46.7, p < 0.001) when combining 2014 and 2017 data. The results of this study are being expanded to identify the key microbes in the corn sap community that potentially impact corn yield, regardless of corn variety, geographic factors, or edaphic factors.
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Affiliation(s)
- Shimaila Ali
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada
| | - Soledad Saldias
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada
| | - Nimalka Weerasuriya
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada.,Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
| | - Kristen Delaney
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada
| | - Saveetha Kandasamy
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada
| | - George Lazarovits
- A&L Biologicals, Agroecological Research Services Centre, 2136 Jetstream Road, London, ON N5V 3P5, Canada.,Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A 3K7, Canada
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Pradhan S, Fan L, Roddick FA, Shahsavari E, Ball AS, Zhang X. A comparative study of biological activated carbon based treatments on two different types of municipal reverse osmosis concentrates. CHEMOSPHERE 2020; 240:124925. [PMID: 31563715 DOI: 10.1016/j.chemosphere.2019.124925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/05/2019] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
A study was conducted to understand the impact of reverse osmosis concentrate (ROC) characteristics on the efficacy of biological activated carbon (BAC) based treatments for removing organics and nutrients from two ROC streams (ROCa derived from municipal waste input with high salinity, and ROCb derived from domestic waste plus industrial trade waste with markedly lower salinity). Fluorescence excitation and emission matrix spectra and molecular weight analysis demonstrated that ROCa and ROCb had a significantly different composition of organic compounds due to the petrochemical processing and abattoir waste compounds in ROCb. Although the sequence of coagulation, UV/H2O2 and BAC gave the highest organic removal from the two ROCs (67% DOC for ROCa and 62% for ROCb), UV/H2O2 followed by BAC achieved satisfactory removal (>55%) for both ROC types. Sequential treatment involving coagulation gave better phosphorus removal (>90%) than any single treatment (<65%). Total nitrogen (TN) removal was fairly low (<50%) for all the treatment options and the salinity level had insignificant impact on nitrogen removal. Analysis of bacterial communities suggested that higher phosphorus removal and lower total nitrogen and nitrate removal from ROCb than ROCa was related to the presence of various denitrifying or phosphorus accumulating bacteria in the BAC.
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Affiliation(s)
| | - Linhua Fan
- School of Engineering, RMIT University, Australia
| | | | | | - Andrew S Ball
- School of Applied Sciences, RMIT University, Australia
| | - Xiaolei Zhang
- School of Engineering, RMIT University, Australia; School of Environmental and Chemical Engineering, Shanghai University, No. 99 Shangda Road, Shanghai, 200444, China.
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24
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Saji N, Murotani K, Hisada T, Tsuduki T, Sugimoto T, Kimura A, Niida S, Toba K, Sakurai T. The relationship between the gut microbiome and mild cognitive impairment in patients without dementia: a cross-sectional study conducted in Japan. Sci Rep 2019; 9:19227. [PMID: 31852995 PMCID: PMC6920432 DOI: 10.1038/s41598-019-55851-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Recent studies have revealed an association between the dysregulation of the gut microbiome and dementia. However, whether this dysregulation is associated with mild cognitive impairment (MCI), an early stage of cognitive decline, in patients without dementia remains unclear. We performed a cross-sectional analysis to determine the association between the gut microbiome and MCI. Data, including patient demographics, risk factors, cognitive function, and brain imaging, were collected. The gut microbiome was assessed through terminal restriction fragment length polymorphism analysis. Multivariable logistic regression models were used to identify factors independently associated with MCI. Graphical modelling was used to illustrate mutual associations between MCI and identified factors. We analysed 82 patients, 61 of whom exhibited MCI. Patients with MCI had a higher prevalence of Bacteroides. Furthermore, patients with more Bacteroides were more likely to present with white matter hyperintensity and high voxel-based specific regional analysis system for Alzheimer’s Disease (VSRAD) scores, indicating cortical and hippocampal atrophy. A multivariable logistic regression analysis revealed that a greater prevalence of Bacteroides was independently associated with MCI. Graphical modelling also showed a close association between Bacteroides and MCI. In conclusion, an increased prevalence of Bacteroides is independently associated with the presence of MCI in patients without dementia.
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Affiliation(s)
- Naoki Saji
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan.
| | - Kenta Murotani
- Biostatistics Center, Graduate School of Medicine, Kurume University, Fukuoka, Japan
| | | | - Tsuyoshi Tsuduki
- Laboratory of Food and Biomolecular Science, Department of Bioscience and Biotechnology for Future Bioindustries, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Taiki Sugimoto
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Ai Kimura
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Shumpei Niida
- Medical Genome Center, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Kenji Toba
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Takashi Sakurai
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan.,Department of Cognition and Behavioural Science, Nagoya University Graduate School of Medicine, Aichi, Japan
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25
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Chen J, Arafat Y, Ud Din I, Yang B, Zhou L, Wang J, Letuma P, Wu H, Qin X, Wu L, Lin S, Zhang Z, Lin W. Nitrogen Fertilizer Amendment Alter the Bacterial Community Structure in the Rhizosphere of Rice ( Oryza sativa L.) and Improve Crop Yield. Front Microbiol 2019; 10:2623. [PMID: 31798559 PMCID: PMC6868037 DOI: 10.3389/fmicb.2019.02623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 10/28/2019] [Indexed: 01/01/2023] Open
Abstract
Availability of nitrogen (N) in soil changes the composition and activities of microbial community, which is critical for the processing of soil organic matter and health of crop plants. Inappropriate application of N fertilizer can alter the rhizosphere microbial community and disturb the soil N homeostasis. The goal of this study was to assess the effect of different ratio of N fertilizer at various early to late growth stages of rice, while keeping the total N supply constant on rice growth performance, microbial community structure, and soil protein expression in rice rhizosphere. Two different N regimes were applied, i.e., traditional N application (NT) consists of three sessions including 60, 30 and 10% at pre-transplanting, tillering and panicle initiation stages, respectively, while efficient N application (NF) comprises of four sessions, i.e., 30, 30, 30, and 10%), where the fourth session was extended to anthesis stage. Soil metaproteomics combined with Terminal Restriction Fragment Length Polymorphism (T-RFLP) were used to determine the rhizosphere biological process. Under NF application, soil enzymes, nitrogen utilization efficiency and rice yield were significantly higher compared to NT application. T-RFLP and qPCR analysis revealed differences in rice rhizosphere bacterial diversity and structure. NF significantly decreased the specific microbes related to denitrification, but opposite result was observed for bacteria associated with nitrification. Furthermore, soil metaproteomics analysis showed that 88.28% of the soil proteins were derived from microbes, 5.74% from plants, and 6.25% from fauna. Specifically, most of the identified microbial proteins were involved in carbohydrate, amino acid and protein metabolisms. Our experiments revealed that NF positively regulates the functioning of the rhizosphere ecosystem and further enabled us to put new insight into microbial communities and soil protein expression in rice rhizosphere.
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Affiliation(s)
- Jun Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yasir Arafat
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Genetic Breeding and Comprehensive Utilization of the Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Israr Ud Din
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Bo Yang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liuting Zhou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juanying Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Puleng Letuma
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongmiao Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xianjin Qin
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Linkun Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhixing Zhang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiong Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, Fujian Agriculture and Forestry University, Fuzhou, China
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Holeva MC, Morán F, Scuderi G, González A, López MM, Llop P. Development of a real-time PCR method for the specific detection of the novel pear pathogen Erwinia uzenensis. PLoS One 2019; 14:e0219487. [PMID: 31291321 PMCID: PMC6619794 DOI: 10.1371/journal.pone.0219487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/25/2019] [Indexed: 11/24/2022] Open
Abstract
Erwinia uzenensis is a plant-pathogenic bacterium, recently described in Japan, which infects pear trees, causing the ‘bacterial black shoot disease of European pear’ (BBSDP). Like other Erwinia pear pathogens, E. uzenensis causes damp, black lesions on young shoots resembling those of E. amylovora, but not blossom blight, fruitlet blight or wilting of the shoot tip. The distribution of E. uzenensis seems restricted to the country where it was reported up to now, but it may spread to other countries and affect new hosts, as is the current situation with E. piriflorinigrans and E. pyrifoliae. Fast and accurate detection systems for this new pathogen are needed to study its biology and to identify it on pear or other hosts. We report here the development of a specific and sensitive detection protocol based on a real-time PCR with a TaqMan probe for E. uzenensis, and its evaluation. In sensitivity assays, the detection threshold of this protocol was 101 cfu ml-1 on pure bacterial cultures and 102–103 cfu ml-1 on spiked plant material. The specificity of the protocol was evaluated against E. uzenensis and 46 strains of pear-associated Erwinia species different to E. uzenensis. No cross-reaction with the non-target bacterial species or the loss of sensitivity were observed. This specific and sensitive diagnostic tool may reveal a wider distribution and host range of E. uzenensis initially considered restricted to a region and will expand our knowledge of the life cycle and environmental preferences of this pathogen.
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Affiliation(s)
- Maria C. Holeva
- Laboratory of Bacteriology, Department of Plant Pathology, Benaki Phytopathological Institute, Kifissia, Attica, Greece
| | - Félix Morán
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Giuseppe Scuderi
- Laboratory of Biotechnology, Department of Sustainable agriculture, biodiversity and food security, Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Asier González
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - María M. López
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
| | - Pablo Llop
- Laboratory of Bacteriology, Department of Plant Pathology, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, Spain
- * E-mail: ,
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Kandasamy S, Liu EYR, Patterson G, Saldias S, Ali S, Lazarovits G. Introducing key microbes from high productive soil transforms native soil microbial community of low productive soil. Microbiologyopen 2019; 8:e895. [PMID: 31250991 PMCID: PMC6813456 DOI: 10.1002/mbo3.895] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 11/11/2022] Open
Abstract
This study aimed to understand the changes in rhizosphere microbial structure and diversity of an average corn yielding field site soil with the introduced microbial candidates from a high‐yielding site. Soils used in this study were from two growers’ fields located in Dunnville, Ontario, Canada, where one of the farms has an exceptional high corn yield (G‐site soil; ca 20 tons/acre) and the other yields an average crop (H‐site soil; 12 tons/acre) (8 years of unpublished A & L data). In growth room experiments using wheat as the indicator crop, calcium alginate beads with microbes composed of Azospirillum lipoferum, Rhizobium leguminosarum, Burkholderia ambifaria, Burkholderia graminis, Burkholderia vietnamiensis, Pseudomonas lurida, Exiguobacterium acetylicum, Kosakonia cowanii, and Paenibacillus polymyxa was introduced into the soil at planting to the average‐yielding soil. These bacteria had been isolated from the high‐yielding farm soil. Among the nine microbial candidates tested, three (P. polymyxa, E. acetylicum and K. cowanii) significantly impacted the plant health and biometrics in addition to microbial richness and diversity, where the microbial profile became very similar to the high productive G‐site soil. One hundred and forty‐two bacterial terminal restriction fragments (TRFs) were involved in the community shift and 48 of them showed significant correlation to several interacting soil factors. This study indicates the potential of shifting microbial profiles of average‐yielding soils by introducing key candidates from highly productive soils to increase biological soil health.
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Affiliation(s)
- Saveetha Kandasamy
- A&L Biologicals, Agroecological Research Services Centre, London, Canada
| | - Elaine Yi Ran Liu
- A&L Biologicals, Agroecological Research Services Centre, London, Canada.,Department of Microbiology and Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Canada
| | - Greg Patterson
- A&L Biologicals, Agroecological Research Services Centre, London, Canada
| | - Soledad Saldias
- A&L Biologicals, Agroecological Research Services Centre, London, Canada
| | - Shimaila Ali
- A&L Biologicals, Agroecological Research Services Centre, London, Canada
| | - George Lazarovits
- A&L Biologicals, Agroecological Research Services Centre, London, Canada
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28
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Sun YQ, Wang J, Shen C, He JZ, Ge Y. Plant evenness modulates the effect of plant richness on soil bacterial diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 662:8-14. [PMID: 30682712 DOI: 10.1016/j.scitotenv.2019.01.211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Understanding the relationships between aboveground and belowground biodiversity will help to expand our knowledge on how ecological communities and processes are interactively determined, and thus provide new perspectives for the conservation of biodiversity. Despite the theoretical analyses generally predicting a positive relationship between plant richness and soil microbial diversity, the results from empirical studies have been mixed, probably due to the effect of plant evenness. To investigate this relationship, we conducted field experiments in two geographically distinct sites (Linhai and Shenmu, >1400km apart), by simultaneously manipulating plant richness (2, 4, and 8 species) and evenness (homogeneous versus non-homogeneous). After one year, the bacterial response to plant richness with different plant evenness levels was evaluated using terminal restriction fragment length polymorphism (T-RFLP) analysis. Our results showed that plant evenness modulated plant richness effects on bacterial community, as reflected by the more pronounced positive correlations between bacterial richness and plant richness in homogeneous plant community than in the non-homogeneous treatment. Additionally, plant community structure significantly affected bacterial communities only in the homogeneous treatment in Shenmu, but not in the non-homogeneous treatments. Our results demonstrate that plant evenness could regulate plant richness effects on bacterial alpha- and beta-diversity and thus provide valuable insights into the association between aboveground and belowground biodiversity.
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Affiliation(s)
- Yao-Qin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Wang
- School of Life Sciences, Taizhou University, Taizhou 318000, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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29
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Differences in Bacterial Diversity, Composition and Function due to Long-Term Agriculture in Soils in the Eastern Free State of South Africa. DIVERSITY 2019. [DOI: 10.3390/d11040061] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Land-use change from natural to managed agricultural ecosystems significantly impacts soil bacterial diversity and function. The Eastern Free State (EFS) is one of the most productive agricultural regions in South Africa. However, no studies aiming to understand the changes in bacterial diversity, composition and function due to land-use change in this area have been conducted. This study investigated, using high-throughput 16S rRNA gene amplicon sequencing, the effects of long-term agriculture on bacterial diversity, composition and putative function in the EFS by comparing microbiomes from lands that have been under agronomic activity for over 50 years to those from uncultivated land. Results indicate that agriculture increased bacterial diversity. Soil chemical analysis showed that land-use shifted soils from being oligotrophic to copiotrophic, which changed bacterial communities from being Actinobacteria dominated to Proteobacteria dominated. Predictive functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) suggested that agricultural soil was abundant in genes associated with plant fitness and plant growth promotion, while non-agricultural soil was abundant in genes related to organic matter degradation. Together, these results suggest that edaphic factors induced by long-term agriculture resulted in shifts in bacterial diversity and putative function in the EFS.
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30
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Luziatelli F, Ficca AG, Colla G, Baldassarre Švecová E, Ruzzi M. Foliar Application of Vegetal-Derived Bioactive Compounds Stimulates the Growth of Beneficial Bacteria and Enhances Microbiome Biodiversity in Lettuce. FRONTIERS IN PLANT SCIENCE 2019; 10:60. [PMID: 30804958 PMCID: PMC6370708 DOI: 10.3389/fpls.2019.00060] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 01/16/2019] [Indexed: 05/02/2023]
Abstract
Many studies on plant biostimulants and organic fertilizers have been focused on the ability of these products to increase crop productivity and ameliorate crop tolerance to abiotic stresses. However, little information is available on their effect on plant microbiota, whereas it is well known that microorganisms associated with plant play crucial roles on the health and productivity of their host. The aim of this study was to evaluate the effect of a vegetal-derived protein hydrolysate (PH), a vegetal-derived PH enriched with copper (Cu-PH), and a tropical plant extract enriched with micronutrients (PE) on shoot growth and the epiphytic bacterial population of lettuce plants and the ability of these products to enhance the growth of beneficial or harmful bacteria. The three plant-derived products enhanced shoot biomass of lettuce plants indicating a biostimulant effect of the products. Data obtained using culture-independent (Terminal Restriction Fragment Length Polymorphism and Next Generation Sequencing) and culture-dependent approaches indicated that foliar application of commercial products altered the composition of the microbial population and stimulated the growth of specific bacteria belonging to Pantoea, Pseudomonas, Acinetobacter, and Bacillus genus. Data presented in this work demonstrated that some of these strains exhibited potential plant growth-promoting properties and/or biocontrol activity against fungi and bacteria phytopathogens including Fusarium, Trichoderma, and Erwinia species. No indication of potential health risks associated to the enrichment of human or plant bacterial pathogens emerged by the analysis of the microbiota of treated and no-treated plants. Overall, the findings presented in this study indicate that the commercial organic-based products can enhance the growth of beneficial bacteria occurring in the plant microbiota and signals produced by these bacteria can act synergistically with the organic compounds to enhance plant growth and productivity.
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Affiliation(s)
- Francesca Luziatelli
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Anna Grazia Ficca
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
| | - Giuseppe Colla
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | | | - Maurizio Ruzzi
- Department for Innovation in Biological, Agrofood and Forest Systems, University of Tuscia, Viterbo, Italy
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31
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Saji N, Niida S, Murotani K, Hisada T, Tsuduki T, Sugimoto T, Kimura A, Toba K, Sakurai T. Analysis of the relationship between the gut microbiome and dementia: a cross-sectional study conducted in Japan. Sci Rep 2019; 9:1008. [PMID: 30700769 PMCID: PMC6353871 DOI: 10.1038/s41598-018-38218-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 12/18/2018] [Indexed: 11/20/2022] Open
Abstract
Dysregulation of the gut microbiome is associated with several life-threatening conditions and thus might represent a useful target for the prevention of dementia. However, the relationship between the gut microbial population and dementia has not yet been fully clarified. We recruited outpatients visiting our memory clinic to participate in this study. Information on patient demographics, risk factors, and activities of daily living was collected, and cognitive function was assessed using neuropsychological tests and brain magnetic resonance imaging scans. Faecal samples were obtained, and the gut microbiome was assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis, one of the most well-established and reliable 16S ribosomal RNA-based methods for classifying gut microbiota. Patients were divided into two groups, demented and non-demented. Multivariable logistic regression models were used to identify the variables independently associated with dementia. The T-RFLP analysis revealed differences in the composition of the gut microbiome: the number of Bacteroides (enterotype I) was lower and the number of ‘other’ bacteria (enterotype III) was higher in demented than non-demented patients. Multivariable analyses showed that the populations of enterotype I and enterotype III bacteria were strongly associated with dementia, independent of the traditional dementia biomarkers. Further studies of the metabolites of gut microbes are needed to determine the mechanism underlying this association.
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Affiliation(s)
- Naoki Saji
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan.
| | - Shumpei Niida
- Medical Genome Center, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Kenta Murotani
- Biostatistics Center, Graduate School of Medicine, Kurume University, Fukuoka, Japan
| | | | - Tsuyoshi Tsuduki
- Laboratory of Food and Biomolecular Science, Department of Bioscience and Biotechnology for Future Bioindustries, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Taiki Sugimoto
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Ai Kimura
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Kenji Toba
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan
| | - Takashi Sakurai
- Center for Comprehensive Care and Research on Memory Disorders, National Center for Geriatrics and Gerontology, Aichi, Japan.,Department of Cognition and Behavioural Science, Nagoya University Graduate School of Medicine, Aichi, Japan
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32
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Terraced Iron Formations: Biogeochemical Processes Contributing to Microbial Biomineralization and Microfossil Preservation. GEOSCIENCES 2018. [DOI: 10.3390/geosciences8120480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Terraced iron formations (TIFs) are laminated structures that cover square meter-size areas on the surface of weathered bench faces and tailings piles at the Mount Morgan mine, which is a non-operational open pit mine located in Queensland, Australia. Sampled TIFs were analyzed using molecular and microanalytical techniques to assess the bacterial communities that likely contributed to the development of these structures. The bacterial community from the TIFs was more diverse compared to the tailings on which the TIFs had formed. The detection of both chemolithotrophic iron-oxidizing bacteria, i.e., Acidithiobacillus ferrooxidans and Mariprofundus ferrooxydans, and iron-reducing bacteria, i.e., Acidobacterium capsulatum, suggests that iron oxidation/reduction are continuous processes occurring within the TIFs. Acidophilic, iron-oxidizing bacteria were enriched from the TIFs. High-resolution electron microscopy was used to characterize iron biomineralization, i.e., the association of cells with iron oxyhydroxide mineral precipitates, which served as an analog for identifying the structural microfossils of individual cells as well as biofilms within iron oxyhydroxide laminations—i.e., alternating layers containing schwertmannite (Fe16O16(OH)12(SO4)2) and goethite (FeO(OH)). Kinetic modeling estimated that it would take between 0.25–2.28 years to form approximately one gram of schwertmannite as a lamination over a one-m2 surface, thereby contributing to TIF development. This length of time could correspond with seasonable rainfall or greater than average annual rainfall. In either case, the presence of water is critical for sustaining microbial activity, and subsequently iron oxyhydroxide mineral precipitation. The TIFs from the Mount Morgan mine also contain laminations of gypsum (CaSO·2H2O) alternating with iron oxyhydroxide laminations. These gypsum laminations likely represented drier periods of the year, in which millimeter-size gypsum crystals presumably precipitated as water gradually evaporated. Interestingly, gypsum acted as a substrate for the attachment of cells and the growth of biofilms that eventually became mineralized within schwertmannite and goethite. The dissolution and reprecipitation of gypsum suggest that microenvironments with circumneutral pH conditions could exist within TIFs, thereby supporting iron oxidation under circumneutral pH conditions. In conclusion, this study highlights the relationship between microbes for the development of TIFs and also provides interpretations of biogeochemical processes contributing to the preservation of bacterial cells and entire biofilms under acidic conditions.
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33
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A Novel Target Pathogen Identification and Tracking System Using Capillary Electrophoresis-Random Amplified Polymorphic DNA. Sci Rep 2018; 8:15365. [PMID: 30337634 PMCID: PMC6193972 DOI: 10.1038/s41598-018-33702-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/20/2018] [Indexed: 02/07/2023] Open
Abstract
Rapid and accurate identification of pathogen is a major quarantine strategy for outbreak prevention. We used capillary electrophoresis-random amplified polymorphic DNA (CE-RAPD) to generate highly discriminatory pathogen profiles, reduced batch effects between profiles by novel normalization procedure and pattern of technical repeats, followed by target similarity evaluation using target identification score (TIS). A full target signature contains several patterns. TIS system was optimized by training set isolates that included three species, and validated using two hundred clinical Klebsiella pneumoniae isolates. Hierarchical clustering analysis showed CE-RAPD profiles arrange clusters according to the species or the source. Moreover, samples with similar profile may display similar antibiotic susceptibility. By using a signature of four patterns, the TIS system could accurately identify target among different isolates. The variation between isolates may be caused by small change in genome. TIS system provides a standardized tool for building of outbreak firewall and facilitate data exchange.
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Baker BH, Brooks JP, Deng DD, Smith RK, Kröger R, Prince Czarnecki JM. Effects of Low-Grade Weirs on Soil Microbial Communities in Agricultural Drainage Ditches. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1155-1162. [PMID: 30272767 DOI: 10.2134/jeq2017.12.0489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Agricultural fertilizer application throughout the Mississippi River basin has been identified as a major source of N pollution to the Gulf of Mexico. Using best management practices, such as low-grade weirs, has been identified as a potential solution to mitigate nutrient loads in agricultural runoff. This study assessed impacts of weir implementation in four agricultural drainage ditches (three with weirs and one control site) in the Mississippi Delta. Soil samples collected from field locations in spring 2013 were analyzed for denitrifier abundance using genes (16s ribosomal RNA [rRNA] genes, , , and ) via quantitative polymerase chain reaction (qPCR), microbial community profiles via terminal-restriction fragment length polymorphism (T-RFLP) of 16s rRNA genes, soil parameters (C, N, and moisture), and vegetation presence at sample locations. Gene quantification was successful, except for , which was found below detection limits (5000 gene copies g soil). Distance from weirs was negatively correlated with 16S rRNA genes and soil moisture, and soil moisture was positively correlated with 16s rRNA and S gene abundance. Results of empirical Bayesian kriging did not exhibit obvious patterns of microbial diversity in relation to weir proximity. Preliminary assessment of seasonal trends showed genes 16s rRNA and , soil N, and mean T-RF values to be greater in fall than in spring. Results highlight that weirs had no direct impact on microbial diversity or denitrification functional gene abundance. Correlations between microbial measures and environmental parameters suggest that adequate management of N runoff from agricultural landscapes will require ecological engineering beyond weirs to optimize N mitigation.
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Ren Q, Li C, Yang W, Song H, Ma P, Wang C, Schneider RL, Morreale SJ. Revegetation of the riparian zone of the Three Gorges Dam Reservoir leads to increased soil bacterial diversity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:23748-23763. [PMID: 29876849 DOI: 10.1007/s11356-018-2333-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
As one of the most active components in soil, bacteria can affect soil physicochemical properties, its biological characteristics, and even its quality and health. We characterized dynamics of the soil bacterial diversity in planted (with Taxodium distichum) and unplanted soil in the riparian zone of the Three Gorges Dam Reservoir (TGDR), in southwestern China, in order to accurately quantify the changes in long-term soil bacterial community structure after revegetation. Measurements were taken annually in situ in the TGDR over the course of 5 years, from 2012 to 2016. Soil chemical properties and bacterial diversity were analyzed in both the planted and unplanted soil. After revegetation, the soil chemical properties in planted soil were significantly different than in unplanted soil. The effects of treatment, time, and the interaction of both time and treatment had significant impacts on most diversity indices. Specifically, the bacterial community diversity indices in planted soil were significantly higher and more stable than that in unplanted soil. The correlation analyses indicated that the diversity indices correlated with the pH value, organic matter, and soil available nutrients. After revegetation in the riparian zone of the TGDR, the soil quality and health is closely related to the observed bacterial diversity, and a higher bacterial diversity avails the maintenance of soil functionality. Thus, more reforestation should be carried out in the riparian zone of the TGDR, so as to effectively mitigate the negative ecological impacts of the dam. Vegetating the reservoir banks with Taxodium distichum proved successful, but planting mixed stands of native tree species could promote even higher riparian soil biodiversity and improved levels of ecosystem functioning within the TGDR.
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Affiliation(s)
- Qingshui Ren
- Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region of the Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Changxiao Li
- Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region of the Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, People's Republic of China.
| | - Wenhang Yang
- Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region of the Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Hong Song
- Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region of the Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Peng Ma
- Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region of the Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chaoying Wang
- Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region of the Ministry of Education, School of Life Sciences, Southwest University, Chongqing, 400715, People's Republic of China
| | - Rebecca L Schneider
- Department of Natural Resources, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Stephen J Morreale
- Department of Natural Resources, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
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Progressive biogeochemical transformation of placer gold particles drives compositional changes in associated biofilm communities. FEMS Microbiol Ecol 2018; 94:4992300. [DOI: 10.1093/femsec/fiy080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/01/2018] [Indexed: 11/14/2022] Open
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Prather CM, Belovsky GE, Cantrell SA, González G. Tropical herbivorous phasmids, but not litter snails, alter decomposition rates by modifying litter bacteria. Ecology 2018; 99:782-791. [PMID: 29603190 DOI: 10.1002/ecy.2169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/01/2018] [Accepted: 01/04/2018] [Indexed: 11/08/2022]
Abstract
Consumers can alter decomposition rates through both feces and selective feeding in many ecosystems, but these combined effects have seldom been examined in tropical ecosystems. Members of the detrital food web (litter-feeders or microbivores) should presumably have greater effects on decomposition than herbivores, members of the green food web. Using litterbag experiments within a field enclosure experiment, we determined the relative effects of common litter snails (Megalomastoma croceum) and herbivorous walking sticks (Lamponius portoricensis) on litter composition, decomposition rates, and microbes in a Puerto Rican rainforest, and whether consumer effects were altered by canopy cover presence. Although canopy presence did not alter consumers' effects, focal organisms had unexpected influences on decomposition. Decomposition was not altered by litter snails, but herbivorous walking sticks reduced leaf decomposition by about 50% through reductions in high quality litter abundance and, consequently, lower bacterial richness and abundance. This relatively unexplored but potentially important link between tropical herbivores, detritus, and litter microbes in this forest demonstrates the need to consider autotrophic influences when examining rainforest ecosystem processes.
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Affiliation(s)
- Chelse M Prather
- Department of Biological Sciences, Galvin Life Sciences, University of Notre Dame, Notre Dame, Indiana, 46656, USA.,Luquillo Long-Term Ecological Research Site, Río Grande, PR 00745, Puerto Rico.,Department of Biology and Biochemistry, University of Houston, Houston, Texas, 77004, USA
| | - Gary E Belovsky
- Department of Biological Sciences, Galvin Life Sciences, University of Notre Dame, Notre Dame, Indiana, 46656, USA.,Luquillo Long-Term Ecological Research Site, Río Grande, PR 00745, Puerto Rico
| | - Sharon A Cantrell
- Luquillo Long-Term Ecological Research Site, Río Grande, PR 00745, Puerto Rico.,Department of Biology, Universidad del Turabo Gurabo, Gurabo, PR 00778, Puerto Rico
| | - Grizelle González
- Luquillo Long-Term Ecological Research Site, Río Grande, PR 00745, Puerto Rico.,USDA Forest Service, International Institute of Tropical Forestry, Jardín Botánico Sur, 1201 Calle Ceiba, Río Piedras, PR 00926, Puerto Rico
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38
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Spiesman BJ, Stapper AP, Inouye BD. Patch size, isolation, and matrix effects on biodiversity and ecosystem functioning in a landscape microcosm. Ecosphere 2018. [DOI: 10.1002/ecs2.2173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Brian J. Spiesman
- Department of Biological Science Florida State University Tallahassee Florida 32306 USA
| | - Andres P. Stapper
- Department of Otolaryngology Stanford University Stanford California 94304 USA
| | - Brian D. Inouye
- Department of Biological Science Florida State University Tallahassee Florida 32306 USA
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Bokulich NA, Bamforth CW, Mills DA. A Review of Molecular Methods for Microbial Community Profiling of Beer and Wine. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1094/asbcj-2012-0709-01] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nicholas A. Bokulich
- Department of Viticulture and Enology and Department of Food Science and Technology
| | | | - David A. Mills
- Department of Viticulture and Enology and Department of Food Science and Technology, University of California, Davis 95616
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Kanissery RG, Welsh A, Gomez A, Connor L, Sims GK. Identification of metolachlor mineralizing bacteria in aerobic and anaerobic soils using DNA-stable isotope probing. Biodegradation 2017; 29:117-128. [PMID: 29285669 DOI: 10.1007/s10532-017-9817-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 12/21/2017] [Indexed: 10/18/2022]
Abstract
The influence of soil environmental factors such as aeration on the ecology of microorganisms involved in the mineralization and degradation of the popular soil-applied pre-emergent herbicide, metolachlor is unknown. To address this knowledge gap, we utilized DNA-based stable isotope probing (SIP) where soil microcosms were incubated aerobically or anaerobically and received herbicide treatments with unlabeled metolachlor or 13C-metolachlor. Mineralization of metolachlor was confirmed as noted from the evolution of 14CO2 from 14C-metolachlor-treated microcosms and clearly demonstrated the efficient utilization of the herbicide as a carbon source. Terminal restriction fragment length polymorphisms (T-RFLP) bacterial community profiling performed on soil DNA extracts indicated that fragment 307 bp from aerobic soil and 212 bp from anaerobic soil were detected only in the herbicide-treated (both unlabeled metolachlor and 13C-metolachlor) soils when compared to the untreated control microcosms. T-RFLP profiles from the ultracentrifugation fractions illustrated that these individual fragments experienced an increase in relative abundance at a higher buoyant density (BD) in the labeled fractions when compared to the unlabeled herbicide amendment fractions. The shift in BD of individual T-RFLP fragments in the density-resolved fractions suggested the incorporation of 13C from labeled herbicide into the bacterial DNA and enabled the identification of organisms responsible for metolachlor uptake from the soil. Subsequent cloning and 16S rRNA gene sequencing of the 13C-enriched fractions implicated the role of organisms closely related to Bacillus spp. in aerobic mineralization and members of Acidobacteria phylum in anaerobic mineralization of metolachlor in soil.
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Affiliation(s)
- Ramdas G Kanissery
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, 1102 S. Goodwin Ave, Urbana, IL, 61801, USA. .,Southwest Florida Research & Education Center, University of Florida, 2685 SR 29 North, Immokalee, FL, 34142, USA.
| | - Allana Welsh
- Agricen Sciences, 801 Highway 377S, Pilot Point, TX, 76258, USA
| | - Andres Gomez
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1102 S. Goodwin Ave, Urbana, IL, 61801, USA.,University of Minnesota, 495D AnSc/VetMed, 1988 Fitch Avenue, St. Paul, MN, 55108, USA
| | - Lynn Connor
- USDA Global Change and Photosynthesis Unit, 1102 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Gerald K Sims
- Department of Entomology, Plant Pathology and Weed Sciences, New Mexico State University, Skeen Hall, Room N141, 945 College Avenue, Las Cruces, NM, 88003, USA
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Yoshikawa M, Zhang M, Kurisu F, Toyota K. Bacterial Degraders of Coexisting Dichloromethane, Benzene, and Toluene, Identified by Stable-Isotope Probing. WATER, AIR, AND SOIL POLLUTION 2017; 228:418. [PMID: 29104324 PMCID: PMC5653698 DOI: 10.1007/s11270-017-3604-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 10/11/2017] [Indexed: 06/07/2023]
Abstract
Most bioremediation studies on volatile organic compounds (VOCs) have focused on a single contaminant or its derived compounds and degraders have been identified under single contaminant conditions. Bioremediation of multiple contaminants remains a challenging issue. To identify a bacterial consortium that degrades multiple VOCs (dichloromethane (DCM), benzene, and toluene), we applied DNA-stable isotope probing. For individual tests, we combined a 13C-labeled VOC with other two unlabeled VOCs, and prepared three unlabeled VOCs as a reference. Over 11 days, DNA was periodically extracted from the consortia, and the bacterial community was evaluated by next-generation sequencing of bacterial 16S rRNA gene amplicons. Density gradient fractions of the DNA extracts were amplified by universal bacterial primers for the 16S rRNA gene sequences, and the amplicons were analyzed by terminal restriction fragment length polymorphism (T-RFLP) using restriction enzymes: HhaI and MspI. The T-RFLP fragments were identified by 16S rRNA gene cloning and sequencing. Under all test conditions, the consortia were dominated by Rhodanobacter, Bradyrhizobium/Afipia, Rhizobium, and Hyphomicrobium. DNA derived from Hyphomicrobium and Propioniferax shifted toward heavier fractions under the condition added with 13C-DCM and 13C-benzene, respectively, compared with the reference, but no shifts were induced by 13C-toluene addition. This implies that Hyphomicrobium and Propioniferax were the main DCM and benzene degraders, respectively, under the coexisting condition. The known benzene degrader Pseudomonas sp. was present but not actively involved in the degradation.
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Affiliation(s)
- Miho Yoshikawa
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567 Japan
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Koganei, Tokyo 184-8588 Japan
| | - Ming Zhang
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567 Japan
| | - Futoshi Kurisu
- Research Center for Water Environment Technology, The University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo, 113-8656 Japan
| | - Koki Toyota
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Koganei, Tokyo 184-8588 Japan
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Narr A, Nawaz A, Wick LY, Harms H, Chatzinotas A. Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD). Front Microbiol 2017; 8:1975. [PMID: 29067022 PMCID: PMC5641378 DOI: 10.3389/fmicb.2017.01975] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/25/2017] [Indexed: 11/13/2022] Open
Abstract
Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors.
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Affiliation(s)
- Anja Narr
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Ali Nawaz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research—UFZ, Halle/Saale, Germany
| | - Lukas Y. Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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43
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Bajury DM, Nashri SM, King Jie Hung P, Sarbini SR. Evaluation of potential prebiotics: a review. FOOD REVIEWS INTERNATIONAL 2017. [DOI: 10.1080/87559129.2017.1373287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Dayang Marshitah Bajury
- Department of Crop Science, Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Bintulu, Malaysia
| | - Siti Maisarah Nashri
- Department of Crop Science, Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Bintulu, Malaysia
| | - Patricia King Jie Hung
- Department of Crop Science, Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Bintulu, Malaysia
| | - Shahrul Razid Sarbini
- Department of Crop Science, Faculty of Agricultural and Food Sciences, Universiti Putra Malaysia Bintulu Campus, Bintulu, Malaysia
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Du C, Geng Z, Wang Q, Zhang T, He W, Hou L, Wang Y. Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest. J Microbiol 2017; 55:684-693. [PMID: 28865070 DOI: 10.1007/s12275-017-6466-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 03/13/2017] [Accepted: 07/05/2017] [Indexed: 01/16/2023]
Abstract
Microbial communities in subsurface soil are specialized for their environment, which is distinct from that of the surface communities. However, little is known about the microbial communities (bacteria and fungi) that exist in the deeper soil horizons. Vertical changes in microbial alpha-diversity (Chao1 and Shannon indices) and community composition were investigated at four soil depths (0-10, 10-20, 20-40, and 40-60 cm) in a natural secondary forest of Betula albosinensis by high-throughput sequencing of the 16S and internal transcribed spacer rDNA regions. The numbers of operational taxonomic units (OTUs), and the Chao1 and Shannon indices decreased in the deeper soil layers. Each soil layer contained both mutual and specific OTUs. In the 40-60 cm soil layer, 175 and 235 specific bacterial and fungal OTUs were identified, respectively. Acidobacteria was the most dominant bacterial group in all four soil layers, but reached its maximum at 40-60 cm (62.88%). In particular, the 40-60 cm soil layer typically showed the highest abundance of the fungal genus Inocybe (47.46%). The Chao1 and Shannon indices were significantly correlated with the soil organic carbon content. Redundancy analysis indicated that the bacterial communities were closely correlated with soil organic carbon content (P = 0.001). Collectively, these results indicate that soil nutrients alter the microbial diversity and relative abundance and affect the microbial composition.
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Affiliation(s)
- Can Du
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Zengchao Geng
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China.
| | - Qiang Wang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Tongtong Zhang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Wenxiang He
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Lin Hou
- College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
| | - Yueling Wang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, Yangling, College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi, 712100, P. R. China
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Fish K, Osborn AM, Boxall JB. Biofilm structures (EPS and bacterial communities) in drinking water distribution systems are conditioned by hydraulics and influence discolouration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 593-594:571-580. [PMID: 28360007 DOI: 10.1016/j.scitotenv.2017.03.176] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/13/2017] [Accepted: 03/19/2017] [Indexed: 06/07/2023]
Abstract
High-quality drinking water from treatment works is degraded during transport to customer taps through the Drinking Water Distribution System (DWDS). Interactions occurring at the pipe wall-water interface are central to this degradation and are often dominated by complex microbial biofilms that are not well understood. This study uses novel application of confocal microscopy techniques to quantify the composition of extracellular polymeric substances (EPS) and cells of DWDS biofilms together with concurrent evaluation of the bacterial community. An internationally unique, full-scale, experimental DWDS facility was used to investigate the impact of three different hydraulic patterns upon biofilms and subsequently assess their response to increases in shear stress, linking biofilms to water quality impacts such as discolouration. Greater flow variation during growth was associated with increased cell quantity but was inversely related to EPS-to-cell volume ratios and bacterial diversity. Discolouration was caused and EPS was mobilised during flushing of all conditions. Ultimately, biofilms developed under low-varied flow conditions had lowest amounts of biomass, the greatest EPS volumes per cell and the lowest discolouration response. This research shows that the interactions between hydraulics and biofilm physical and community structures are complex but critical to managing biofilms within ageing DWDS infrastructure to limit water quality degradation and protect public health.
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Affiliation(s)
- K Fish
- Pennine Water Group, Department of Civil and Structural Engineering, The University of Sheffield, Sheffield S1 3JD, UK; NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, Western Bank, Sheffield S10 2TN, UK.
| | - A M Osborn
- Biosciences and Food Technology Discipline, School of Science, RMIT University, PO Box 71, Bundoora, Melbourne VIC3083, Australia
| | - J B Boxall
- Pennine Water Group, Department of Civil and Structural Engineering, The University of Sheffield, Sheffield S1 3JD, UK
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Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum SP, Schlüter A, Goesmann A, Sczyrba A, Stoye J. Bioinformatics for NGS-based metagenomics and the application to biogas research. J Biotechnol 2017; 261:10-23. [PMID: 28823476 DOI: 10.1016/j.jbiotec.2017.08.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022]
Abstract
Metagenomics has proven to be one of the most important research fields for microbial ecology during the last decade. Starting from 16S rRNA marker gene analysis for the characterization of community compositions to whole metagenome shotgun sequencing which additionally allows for functional analysis, metagenomics has been applied in a wide spectrum of research areas. The cost reduction paired with the increase in the amount of data due to the advent of next-generation sequencing led to a rapidly growing demand for bioinformatic software in metagenomics. By now, a large number of tools that can be used to analyze metagenomic datasets has been developed. The Bielefeld-Gießen center for microbial bioinformatics as part of the German Network for Bioinformatics Infrastructure bundles and imparts expert knowledge in the analysis of metagenomic datasets, especially in research on microbial communities involved in anaerobic digestion residing in biogas reactors. In this review, we give an overview of the field of metagenomics, introduce into important bioinformatic tools and possible workflows, accompanied by application examples of biogas surveys successfully conducted at the Center for Biotechnology of Bielefeld University.
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Affiliation(s)
- Sebastian Jünemann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Faculty of Technology, Bielefeld University, Bielefeld, Germany.
| | - Nils Kleinbölting
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Sebastian Jaenicke
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Christian Henke
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Johanna Nelkner
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Yvonne Stolze
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Stefan P Albaum
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Jens Stoye
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany; Faculty of Technology, Bielefeld University, Bielefeld, Germany
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Peachey LE, Jenkins TP, Cantacessi C. This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth–Microbiota Interactions in Veterinary Species. Trends Parasitol 2017; 33:619-632. [DOI: 10.1016/j.pt.2017.04.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 01/25/2023]
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Grativol AD, Marchetti AA, Wetler-Tonini RM, Venancio TM, Gatts CE, Thompson FL, Rezende CE. Bacterial interactions and implications for oil biodegradation process in mangrove sediments. MARINE POLLUTION BULLETIN 2017; 118:221-228. [PMID: 28259419 DOI: 10.1016/j.marpolbul.2017.02.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 02/18/2017] [Accepted: 02/18/2017] [Indexed: 06/06/2023]
Abstract
Mangrove sediment harbors a unique microbiome and is a hospitable environment for a diverse group of bacteria capable of oil biodegradation. Our goal was to understand bacterial community dynamics from mangrove sediments contaminated with heavy-oil and to evaluate patterns potentially associated with oil biodegradation is such environments. We tested the previously proposed hypothesis of a two-phase pattern of petroleum biodegradation, under which key events in the degradation process take place in the first three weeks after contamination. Two sample sites with different oil pollution histories were compared through T-RFLP analyses and using a pragmatic approach based on the Microbial Resource Management Framework. Our data corroborated the already reported two-phase pattern of oil biodegradation, although the original proposed explanation related to the biophysical properties of the soil is questioned, opening the possibility to consider other plausible hypotheses of microbial interactions as the main drivers of this pattern.
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Affiliation(s)
- Adriana Daudt Grativol
- Centro de Biociências e Biotecnologia/Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil.
| | - Albany A Marchetti
- Centro de Biociências e Biotecnologia/Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Rita M Wetler-Tonini
- Centro de Biociências e Biotecnologia/Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Thiago M Venancio
- Centro de Biociências e Biotecnologia/Laboratório de Química e Funções de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Carlos En Gatts
- Centro de Ciências e Tecnologia/Laboratório de Ciências Físicas, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, CCS, Laboratório de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos E Rezende
- Centro de Biociências e Biotecnologia/Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
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49
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Chemical composition and antibacterial activity of the essential oil and various extracts from Cassia sophera L. against Bacillus sp. from soil. ARAB J CHEM 2017. [DOI: 10.1016/j.arabjc.2013.07.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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50
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Szemiako K, Śledzińska A, Krawczyk B. A new assay based on terminal restriction fragment length polymorphism of homocitrate synthase gene fragments for Candida species identification. J Appl Genet 2017; 58:409-414. [PMID: 28349380 PMCID: PMC5509809 DOI: 10.1007/s13353-017-0394-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/21/2017] [Accepted: 03/17/2017] [Indexed: 12/02/2022]
Abstract
Candida sp. have been responsible for an increasing number of infections, especially in patients with immunodeficiency. Species-specific differentiation of Candida sp. is difficult in routine diagnosis. This identification can have a highly significant association in therapy and prophylaxis. This work has shown a new application of the terminal restriction fragment length polymorphism (t-RFLP) method in the molecular identification of six species of Candida, which are the most common causes of fungal infections. Specific for fungi homocitrate synthase gene was chosen as a molecular target for amplification. The use of three restriction enzymes, DraI, RsaI, and BglII, for amplicon digestion can generate species-specific fluorescence labeled DNA fragment profiles, which can be used to determine the diagnostic algorithm. The designed method can be a cost-efficient high-throughput molecular technique for the identification of six clinically important Candida species.
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Affiliation(s)
- Kasjan Szemiako
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Anna Śledzińska
- Department of Therapy Monitoring and Pharmacogenetics, Medical University of Gdańsk, Gdańsk, Poland
| | - Beata Krawczyk
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12, 80-233, Gdańsk, Poland.
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