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Corral-García LS, Molina MC, Bautista LF, Simarro R, Espinosa CI, Gorines-Cordero G, González-Benítez N. Bacterial Diversity in Old Hydrocarbon Polluted Sediments of Ecuadorian Amazon River Basins. TOXICS 2024; 12:119. [PMID: 38393214 PMCID: PMC10892221 DOI: 10.3390/toxics12020119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024]
Abstract
The Ecuadorian Amazon rainforest stands out as one of the world's most biodiverse regions, yet faces significant threats due to oil extraction activities dating back to the 1970s in the northeastern provinces. This research investigates the environmental and societal consequences of prolonged petroleum exploitation and oil spills in Ecuador's Amazon. Conducted in June 2015, the study involved a comprehensive analysis of freshwater sediment samples from 24 locations in the Rio Aguarico and Napo basins. Parameters such as water and air temperature, conductivity, soil pH, and hydrocarbon concentrations were examined. Total petroleum hydrocarbon (TPH) concentrations ranged from 9.4 to 847.4 mg kg-1, with polycyclic aromatic hydrocarbon (PAH) levels varying from 10.15 to 711.1 mg kg-1. The pristane/phytane ratio indicated historic hydrocarbon pollution in 8 of the 15 chemically analyzed sediments. Using non-culturable techniques (Illumina), bacterial analyses identified over 350 ASV, with prominent families including Comamonadaceae, Chitinophagaceae, Anaeromyxobacteraceae, Sphingomonadaceae, and Xanthobacteraceae. Bacterial diversity, assessed in eight samples, exhibited a positive correlation with PAH concentrations. The study provides insights into how microbial communities respond to varying levels of hydrocarbon pollution, shedding light on the enduring impact of oil exploitation in the Amazonian region. Its objective is to deepen our understanding of the environmental and human well-being in the affected area, underscoring the pressing need for remedial actions in the face of ongoing ecological challenges.
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Affiliation(s)
- Lara S. Corral-García
- Centro de Investigación en Biodiversidad y Cambio Global, Department of Ecology, Universidad Autónoma de Madrid, C/Darwin, 2, 28049 Madrid, Spain
| | - María Carmen Molina
- Biodiversity and Conservation Unit, Department of Biology and Geology, Physics and Inorganic Chemistry, Instituto de Investigación en Cambio Global, Universidad Rey Juan Carlos, Tulipán s/n, Mostoles, 28933 Madrid, Spain; (M.C.M.); (N.G.-B.)
| | - Luis Fernando Bautista
- Department of Chemical and Environmental Technology, ESCET, Universidad Rey Juan Carlos, Tulipán s/n, Mostoles, 28933 Madrid, Spain;
| | - Raquel Simarro
- Plant Pathology Laboratory (DTEVL), INIA-CSIC, Ctra, de La Coruña, Km 7.5, 28040 Madrid, Spain;
| | - Carlos Iván Espinosa
- Department of Biological and Agricultural Sciences, Universidad Técnica Particular de Loja, San Cayetano alto s/n, Loja 1101608, Ecuador;
| | - Guillermo Gorines-Cordero
- Biodiversity and Conservation Unit, Department of Biology and Geology, Physics and Inorganic Chemistry, Instituto de Investigación en Cambio Global, Universidad Rey Juan Carlos, Tulipán s/n, Mostoles, 28933 Madrid, Spain; (M.C.M.); (N.G.-B.)
| | - Natalia González-Benítez
- Biodiversity and Conservation Unit, Department of Biology and Geology, Physics and Inorganic Chemistry, Instituto de Investigación en Cambio Global, Universidad Rey Juan Carlos, Tulipán s/n, Mostoles, 28933 Madrid, Spain; (M.C.M.); (N.G.-B.)
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Yang D, Kato H, Kawatsu K, Osada Y, Azuma T, Nagata Y, Kondoh M. Reconstruction of a Soil Microbial Network Induced by Stress Temperature. Microbiol Spectr 2022; 10:e0274822. [PMID: 35972265 PMCID: PMC9602341 DOI: 10.1128/spectrum.02748-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 01/04/2023] Open
Abstract
The microbial community is viewed as a network of diverse microorganisms connected by various interspecific interactions. While the stress gradient hypothesis (SGH) predicts that positive interactions are favored in more stressful environments, the prediction has been less explored in complex microbial communities due to the challenges of identifying interactions. Here, by applying a nonlinear time series analysis to the amplicon-based diversity time series data of the soil microbiota cultured under less stressful (30°C) or more stressful (37°C) temperature conditions, we show how the microbial network responds to temperature stress. While the genera that persisted only under the less stressful condition showed fewer positive effects, the genera that appeared only under the more stressful condition received more positive effects, in agreement with SGH. However, temperature difference also induced reconstruction of the community network, leading to an increased proportion of negative interactions at the whole-community level. The anti-SGH pattern can be explained by the stronger competition caused by increased metabolic rate and population densities. IMPORTANCE By combining amplicon-based diversity survey with recently developed nonlinear analytical tools, we successfully determined the interaction networks of more than 150 natural soil microbial genera under less or more temperature stress and explored the applicability of the stress gradient hypothesis to soil microbiota, shedding new light on the well-known hypothesis.
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Affiliation(s)
- Dailin Yang
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Kazutaka Kawatsu
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Yutaka Osada
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | - Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Michio Kondoh
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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Nguyen HT, Kim Y, Choi JW, Jeong S, Cho K. Soil microbial communities-mediated bioattenuation in simulated aquifer storage and recovery (ASR) condition: Long-term study. ENVIRONMENTAL RESEARCH 2021; 197:111069. [PMID: 33785325 DOI: 10.1016/j.envres.2021.111069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/24/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
This study evaluated the long-term organic removal performance and microbial community shift in simulated aquifer storage and recovery (ASR) conditions. For this purpose, anoxic soil box systems were operated at 15 °C for one year. The results showed that the assimilable organic carbon (AOC) concentration in the anoxic soil box systems was successfully decreased by 79.1%. The dissolved organic carbon (DOC) concentration increased during the initial operational periods; however, it subsequently decreased during long-term operation. Readily biodegradable organic fractions (i.e., low-molecular weight (LMW) neutrals and LMW acids) decreased along with time elapsed, whereas non-biodegradable fraction (i.e., humic substances) increased. Proteobacteria and Acidobacteriota were predominant in the anoxic box systems throughout the operational periods. Firmicutes and Bacteroidota suddenly increased during the initial operational period while Gemmatimonadota slightly increased during prolonged long-term operation. Interestingly, the microbial community structures were significantly shifted with respect to the operational periods while the effects of AOC/NO3- addition were negligible. Various bacterial species preferring low temperature or anoxic conditions were detected as predominant bacteria. Some denitrifying (i.e., Noviherbaspirillum denitrificans) and iron reducing bacteria (i.e., Geobacter spp.) appeared during the long-term operation; these bacterial communities also acted as organic degraders in the simulated ASR systems. The findings of this study suggest that the application of natural bioattenuation using indigenous soil microbial communities can be a promising option as an organic carbon management strategy in ASR systems.
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Affiliation(s)
- Hien Thi Nguyen
- Water Cycle Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Division of Energy & Environment Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea
| | - Youngjae Kim
- Water Cycle Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jae-Woo Choi
- Water Cycle Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Division of Energy & Environment Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea
| | - Seongpil Jeong
- Water Cycle Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Division of Energy & Environment Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea.
| | - Kyungjin Cho
- Water Cycle Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Division of Energy & Environment Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Republic of Korea.
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Wang M, Eyre AW, Thon MR, Oh Y, Dean RA. Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds. Front Microbiol 2020; 11:559728. [PMID: 33013792 PMCID: PMC7506108 DOI: 10.3389/fmicb.2020.559728] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/17/2020] [Indexed: 12/26/2022] Open
Abstract
Microbes form close associations with host plants including rice as both surface (epiphytes) and internal (endophytes) inhabitants. Yet despite rice being one of the most important cereal crops agriculturally and economically, knowledge of its microbiome, particularly core inhabitants and any functional properties bestowed is limited. In this study, the microbiome in rice seedlings derived directly from seeds was identified, characterized and compared to the microbiome of the seed. Rice seeds were sourced from two different locations in Arkansas, USA of two different rice genotypes (Katy, M202) from two different harvest years (2013, 2014). Seeds were planted in sterile media and bacterial as well as fungal communities were identified through 16S and ITS sequencing, respectively, for four seedling compartments (root surface, root endosphere, shoot surface, shoot endosphere). Overall, 966 bacterial and 280 fungal ASVs were found in seedlings. Greater abundance and diversity were detected for the microbiome associated with roots compared to shoots and with more epiphytes than endophytes. The seedling compartments were the driving factor for microbial community composition rather than other factors such as rice genotype, location and harvest year. Comparison with datasets from seeds revealed that 91 (out of 296) bacterial and 11 (out of 341) fungal ASVs were shared with seedlings with the majority being retained within root tissues. Core bacterial and fungal microbiome shared across seedling samples were identified. Core bacteria genera identified in this study such as Rhizobium, Pantoea, Sphingomonas, and Paenibacillus have been reported as plant growth promoting bacteria while core fungi such as Pleosporales, Alternaria and Occultifur have potential as biocontrol agents.
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Affiliation(s)
- Mengying Wang
- Fungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
| | - Alexander W Eyre
- Fungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
| | - Michael R Thon
- Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Villamayor, Spain
| | - Yeonyee Oh
- Fungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
| | - Ralph A Dean
- Fungal Genomics Laboratory, Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
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Suzuki S, Yamada T. Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication. PeerJ 2020; 8:e8722. [PMID: 32257635 PMCID: PMC7104724 DOI: 10.7717/peerj.8722] [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: 10/22/2019] [Accepted: 02/10/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND With the development of DNA sequencing technology, static omics profiling in microbial communities, such as taxonomic and functional gene composition determination, has become possible. Additionally, the recently proposed in situ growth rate estimation method allows the applicable range of current comparative metagenomics to be extended to dynamic profiling. However, with this method, the applicable target range is presently limited. Furthermore, the characteristics of coverage depth during replication have not been sufficiently investigated. RESULTS We developed a probabilistic model that mimics coverage depth dynamics. This statistical model explains the bias that occurs in the coverage depth due to DNA replication and errors that arise from coverage depth observation. Although our method requires a complete genome sequence, it involves a stable to low coverage depth (>0.01×). We also evaluated the estimation using real whole-genome sequence datasets and reproduced the growth dynamics observed in previous studies. By utilizing a circular distribution in the model, our method facilitates the quantification of unmeasured coverage depth features, including peakedness, skewness, and degree of density, around the replication origin. When we applied the model to time-series culture samples, the skewness parameter, which indicates the asymmetry, was stable over time; however, the peakedness and degree of density parameters, which indicate the concentration level at the replication origin, changed dynamically. Furthermore, we demonstrated the activity measurement of multiple replication origins in a single chromosome. CONCLUSIONS We devised a novel framework for quantifying coverage depth dynamics. Our study is expected to serve as a basis for replication activity estimation from a broader perspective using the statistical model.
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Affiliation(s)
- Shinya Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo, Japan
| | - Takuji Yamada
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo, Japan
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Kaminski MA, Sobczak A, Dziembowski A, Lipinski L. Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis. Genes (Basel) 2019; 10:E688. [PMID: 31500174 PMCID: PMC6771000 DOI: 10.3390/genes10090688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 11/29/2022] Open
Abstract
Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, Sphingopyxislindanitolerans, and compared it to the other available Sphingopyxis genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of lin genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other Sphingopyxis strains. Additional analysis of 44 Sphingopyxis representatives provides insights into the pangenome of Sphingopyxis and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome.
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Affiliation(s)
- Michal A Kaminski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
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Ogawa N, Kato H, Kishida K, Ichihashi E, Ishige T, Yoshikawa H, Nagata Y, Ohtsubo Y, Tsuda M. Suppression of substrate inhibition in phenanthrene-degrading Mycobacterium by co-cultivation with a non-degrading Burkholderia strain. MICROBIOLOGY-SGM 2019; 165:625-637. [PMID: 30994434 DOI: 10.1099/mic.0.000801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In natural environments contaminated by recalcitrant organic pollutants, efficient biodegradation of such pollutants has been suggested to occur through the cooperation of different bacterial species. A phenanthrene-degrading bacterial consortium, MixEPa4, from polluted soil was previously shown to include a phenanthrene-degrading strain, Mycobacterium sp. EPa45, and a non-polycyclic aromatic hydrocarbon (PAH)-degrading strain, Burkholderia sp. Bcrs1W. In this study, we show that addition of phenanthrene to rich liquid medium resulted in the transient growth arrest of EPa45 during its degradation of phenanthrene. RNA-sequencing analysis of the growth-arrested cells showed the phenanthrene-dependent induction of genes that were predicted to be involved in the catabolism of this compound, and many other cell systems, such as a ferric iron-uptake, were up-regulated, implying iron deficiency of the cells. This negative effect of phenanthrene became much more apparent when using phenanthrene-containing minimal agar medium; colony formation of EPa45 on such agar was significantly inhibited in the presence of phenanthrene and its intermediate degradation products. However, growth inhibition was suppressed by the co-residence of viable Bcrs1W cells. Various Gram-negative bacterial strains, including the three other strains from MixEPa4, also exhibited varying degrees of suppression of the growth inhibition effect on EPa45, strongly suggesting that this effect is not strain-specific. Growth inhibition of EPa45 was also observed by other PAHs, biphenyl and naphthalene, and these two compounds and phenanthrene also inhibited the growth of another mycobacterial strain, M. vanbaalenii PYR-1, that can use them as carbon sources. These phenomena of growth inhibition were also suppressed by Bcrs1W. Our findings suggest that, in natural environments, various non-PAH-degrading bacterial strains play potentially important roles in the facilitation of PAH degradation by the co-residing mycobacteria.
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Affiliation(s)
- Natsumi Ogawa
- 1 Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Hiromi Kato
- 1 Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Kouhei Kishida
- 1 Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Eikichi Ichihashi
- 1 Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Taichiro Ishige
- 2 Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- 2 Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Tokyo 156-8502, Japan
| | - Yuji Nagata
- 1 Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Yoshiyuki Ohtsubo
- 1 Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Masataka Tsuda
- 1 Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
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Liu XX, Hu X, Cao Y, Pang WJ, Huang JY, Guo P, Huang L. Biodegradation of Phenanthrene and Heavy Metal Removal by Acid-Tolerant Burkholderia fungorum FM-2. Front Microbiol 2019; 10:408. [PMID: 30930861 PMCID: PMC6427951 DOI: 10.3389/fmicb.2019.00408] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/18/2019] [Indexed: 11/13/2022] Open
Abstract
Phenanthrene (PHE) is a common pollutant of acidic and non-acidic environments that is recalcitrant to biodegradation. Herein, Burkholderia fungorum FM-2 (GenBank accession no. KM263605) was isolated from oil-contaminated soil in Xinjiang and characterized morphologically, physiologically, and phylogenetically. Environmental parameters including PHE concentration, pH, temperature, and salinity were optimized, and heavy metal tolerance was investigated. The MIC of strain FM-2 tolerant to Pb(II) and Cd(II) was 50 and 400 mg L−1, respectively, while the MIC of Zn(II) was >1,200 mg L−1. Atypically for a B. fungorum strain, FM-2 utilized PHE (300 mg L−1) as a sole carbon source over a wide pH range (between pH 3 and 9). PHE and heavy metal metabolism were assessed using gas chromatography (GC), inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), Fourier-transform infrared (FTIR) spectroscopy and ultraviolet (UV) absorption spectrometry. The effects of heavy metals on the bioremediation of PHE in soil were investigated, and the findings suggest that FM-2 has potential for combined bioremediation of soils co-contaminated with PHE and heavy metals.
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Affiliation(s)
- Xin-Xin Liu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Xin Hu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Yue Cao
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Wen-Jing Pang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Jin-Yu Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Peng Guo
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
| | - Lei Huang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, College of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, China
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Nishiyama E, Higashi K, Mori H, Suda K, Nakamura H, Omori S, Maruyama S, Hongoh Y, Kurokawa K. The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan. Front Bioeng Biotechnol 2018; 6:202. [PMID: 30619848 PMCID: PMC6306410 DOI: 10.3389/fbioe.2018.00202] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/10/2018] [Indexed: 12/02/2022] Open
Abstract
Diverse microorganisms specifically inhabit extreme environments, such as hot springs and deep-sea hydrothermal vents. To test the hypothesis that the microbial community structure is predictable based on environmental factors characteristic of such extreme environments, we conducted correlation analyses of microbial taxa/functions and environmental factors using metagenomic and 61 types of physicochemical data of water samples from nine hot springs in the Kirishima area (Kyusyu, Japan), where hot springs with diverse chemical properties are distributed in a relatively narrow area. Our metagenomic analysis revealed that the samples can be classified into two major types dominated by either phylum Crenarchaeota or phylum Aquificae. The correlation analysis showed that Crenarchaeota dominated in nutrient-rich environments with high concentrations of ions and total carbons, whereas Aquificae dominated in nutrient-poor environments with low ion concentrations. These environmental factors were also important explanatory variables in the generalized linear models constructed to predict the abundances of Crenarchaeota or Aquificae. Functional enrichment analysis of genes also revealed that the separation of the two major types is primarily attributable to genes involved in autotrophic carbon fixation, sulfate metabolism and nitrate reduction. Our results suggested that Aquificae and Crenarchaeota play a vital role in the Kirishima hot spring water ecosystem through their metabolic pathways adapted to each environment. Our findings provide a basis to predict microbial community structures in hot springs from environmental parameters, and also provide clues for the exploration of biological resources in extreme environments.
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Affiliation(s)
- Eri Nishiyama
- Biotechnological Research Support Division, FASMAC Co. Ltd, Kanagawa, Japan.,Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Koichi Higashi
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Hiroshi Mori
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
| | - Konomi Suda
- Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
| | - Hitomi Nakamura
- Department of Solid Earth Geochemistry, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Soichi Omori
- Faculty of Liberal Arts, The Open University of Japan, Chiba, Japan
| | - Shigenori Maruyama
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - Yuichi Hongoh
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ken Kurokawa
- Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
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10
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El Azhari N, Dermou E, Barnard RL, Storck V, Tourna M, Beguet J, Karas PA, Lucini L, Rouard N, Botteri L, Ferrari F, Trevisan M, Karpouzas DG, Martin-Laurent F. The dissipation and microbial ecotoxicity of tebuconazole and its transformation products in soil under standard laboratory and simulated winter conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:892-906. [PMID: 29763870 DOI: 10.1016/j.scitotenv.2018.05.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/30/2018] [Accepted: 05/07/2018] [Indexed: 06/08/2023]
Abstract
Tebuconazole (TBZ) is a widely used triazole fungicide at EU level on cereals and vines. It is relatively persistent in soil where it is transformed to various transformation products (TPs) which might be environmentally relevant. We assessed the dissipation of TBZ in soil under contrasting incubation conditions (standard vs winter simulated) that are relevant to its application scheme, determined its transformation pathway using advanced analytical tools and 14C-labeled TBZ and assessed its soil microbial toxicity. Mineralization of 14C-triazole-ring-labeled TBZ was negligible but up to 11% of 14C-penyl-ring-labeled TBZ evolved as 14CO2 within 150 days of incubation. TBZ persistence increased at higher dose rates (×10 compared to the recommended agronomical dose ×1) and under winter simulated conditions compared to standard incubation conditions (at ×1 dose rate DT50 of 202 and 88 days, respectively). Non-target suspect screening enabled the detection of 22 TPs of TBZ, among which 17 were unknown. Mass spectrometry analysis led to the identification of 1-(4-chlorophenyl) ethanone, a novel TP of TBZ, the formation of which and decay in soil was determined by gas chromatography mass spectrometry. Three hypothetical transformation pathways of TBZ, all converging to 1H-1,2,4-triazole are proposed based on suspect screening. The ecotoxicological effect of TBZ and of its TPs was assessed by measuring by qPCR the abundance of the total bacteria and the relative abundance of 11 prokaryotic taxa and 4 functional groups. A transient impact of TBZ on the relative abundance of all prokaryotic taxa (except α-proteobacteria and Bacteroidetes) and one functional microbial group (pcaH-carrying microorganisms) was observed. However the direction of the effect (positive or negative) varied, and in certain cases, depended on the incubation conditions. Proteobacteria was the most responsive phylum to TBZ with recovery observed 20 days after treatment. The ecotoxicological effects on the soil microorganisms were not correlated with 1-(4-chlorophenyl) ethanone.
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Affiliation(s)
- Najoi El Azhari
- AEIFORIA srl, Loc. Faggiola 12-16, 29027 Gariga di Podenzano, Italy; Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, 21000 Dijon, France; SATT Grand Est, 64A rue Sully, 21000 Dijon, France
| | - Eftychia Dermou
- AEIFORIA srl, Loc. Faggiola 12-16, 29027 Gariga di Podenzano, Italy; University of Patras, 2 Seferi str., 30100 Agrinio, Greece
| | - Romain L Barnard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Veronika Storck
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Maria Tourna
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis 41500, Larisa, Greece
| | - Jérémie Beguet
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Panagiotis A Karas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis 41500, Larisa, Greece
| | - Luigi Lucini
- Università Cattolica di Sacro Cuore, via Parmense 84, 29122 Piacenza, Italy
| | - Nadine Rouard
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Lucio Botteri
- AEIFORIA srl, Loc. Faggiola 12-16, 29027 Gariga di Podenzano, Italy
| | - Federico Ferrari
- AEIFORIA srl, Loc. Faggiola 12-16, 29027 Gariga di Podenzano, Italy
| | - Marco Trevisan
- Università Cattolica di Sacro Cuore, via Parmense 84, 29122 Piacenza, Italy
| | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, Viopolis 41500, Larisa, Greece
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11
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Higashi K, Suzuki S, Kurosawa S, Mori H, Kurokawa K. Latent environment allocation of microbial community data. PLoS Comput Biol 2018; 14:e1006143. [PMID: 29874232 PMCID: PMC6005635 DOI: 10.1371/journal.pcbi.1006143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 06/18/2018] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
As data for microbial community structures found in various environments has increased, studies have examined the relationship between environmental labels given to retrieved microbial samples and their community structures. However, because environments continuously change over time and space, mixed states of some environments and its effects on community formation should be considered, instead of evaluating effects of discrete environmental categories. Here we applied a hierarchical Bayesian model to paired datasets containing more than 30,000 samples of microbial community structures and sample description documents. From the training results, we extracted latent environmental topics that associate co-occurring microbes with co-occurring word sets among samples. Topics are the core elements of environmental mixtures and the visualization of topic-based samples clarifies the connections of various environments. Based on the model training results, we developed a web application, LEA (Latent Environment Allocation), which provides the way to evaluate typicality and heterogeneity of microbial communities in newly obtained samples without confining environmental categories to be compared. Because topics link words and microbes, LEA also enables to search samples semantically related to the query out of 30,000 microbiome samples. In the past decade, microbiomes from various natural and human symbiotic environments have been thoroughly studied. However, our knowledge is limited as to what types of environments affect the structure of a microbial community. In the first place, how can we define “environments”, in particular, the environmental entities that are often continuously varying and difficult to discretely categorize? We assumed that environments could be represented from microbiome data because the structure of microbial communities reflect the state of the environment. We applied a probabilistic topic model to a dataset containing taxonomic composition data and natural language sample descriptions of >30,000 microbiome samples and extracted “latent environments” of the microbial communities, which are core elements of environmental mixtures. Integrating the training results of the model, we developed a web application to explore the microbiome universe and to place new metagenomic data on this universe like a global positioning system. Our tool shows what kinds of the environment naturally exist and are similar to each other on the perspective of the structural patterns of microbiome, and provides the way to evaluate the commonality and the heterogeneity of users’ microbiome samples.
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Affiliation(s)
- Koichi Higashi
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Japan
| | - Shinya Suzuki
- Department of Biological Information, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
| | - Shin Kurosawa
- Department of Biological Information, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
| | - Hiroshi Mori
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Japan
| | - Ken Kurokawa
- Genome Evolution Laboratory, National Institute of Genetics, Mishima, Japan
- * E-mail:
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12
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Papadopoulou ES, Genitsaris S, Omirou M, Perruchon C, Stamatopoulou A, Ioannides I, Karpouzas DG. Bioaugmentation of thiabendazole-contaminated soils from a wastewater disposal site: Factors driving the efficacy of this strategy and the diversity of the indigenous soil bacterial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 233:16-25. [PMID: 29049942 DOI: 10.1016/j.envpol.2017.10.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/03/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
The application of the fungicide thiabendazole (TBZ) in fruit packaging plants (FPP) results in the production of effluents which are often disposed in adjacent field sites. These require remediation to prevent further environmental dispersal of TBZ. We assessed the bioaugmentation potential of a newly isolated TBZ-degrading bacterial consortium in a naturally contaminated soil (NCS) exhibiting a natural gradient of TBZ levels (12000, 400, 250 and 12 mg kg-1). The effect of aging on bioaugmentation efficacy was comparatively tested in a soil with similar physicochemical properties and soil microbiota, which was artificially, contaminated with the same TBZ levels (ACS). The impact of bioaugmentation and TBZ on the bacterial diversity in the NCS was explored via amplicon sequencing. Bioaugmentation effectively removed TBZ from both soils at levels up to 400 mg kg-1 but failed at the highest contamination level (12000 mg kg-1). Dissipation of TBZ in bioaugmented samples showed a concentration-dependent pattern, while aging of TBZ had a slight effect on bioaugmentation efficiency. Bioaugmentation had no impact on the soil bacterial diversity, in contrast to TBZ contamination. Soils from the hotspots of TBZ contamination (12000 mg kg-1) showed a drastically lower α-diversity driven by the dominance of β- and γ-proteobacteria at the expense of all other bacterial phyla, especially Actinobacteria. Overall, bioaugmentation with specialized microbial inocula could be an effective solution for the recovery of disposal sites contaminated with persistent chemicals like TBZ.
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Affiliation(s)
- Evangelia S Papadopoulou
- University of Thessaly, Department of Biochemistry and Biotechnology, Lab of Plant and Environmental Biotechnology, 41500 Larissa, Greece
| | - Savvas Genitsaris
- University of Thessaly, Department of Biochemistry and Biotechnology, Lab of Plant and Environmental Biotechnology, 41500 Larissa, Greece
| | | | - Chiara Perruchon
- University of Thessaly, Department of Biochemistry and Biotechnology, Lab of Plant and Environmental Biotechnology, 41500 Larissa, Greece
| | - Anastasia Stamatopoulou
- University of Thessaly, Department of Biochemistry and Biotechnology, Lab of Plant and Environmental Biotechnology, 41500 Larissa, Greece
| | | | - Dimitrios G Karpouzas
- University of Thessaly, Department of Biochemistry and Biotechnology, Lab of Plant and Environmental Biotechnology, 41500 Larissa, Greece.
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13
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Baksi KD, Kuntal BK, Mande SS. 'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data. Front Microbiol 2018; 9:36. [PMID: 29416530 PMCID: PMC5787560 DOI: 10.3389/fmicb.2018.00036] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/09/2018] [Indexed: 12/21/2022] Open
Abstract
Realization of the importance of microbiome studies, coupled with the decreasing sequencing cost, has led to the exponential growth of microbiome data. A number of these microbiome studies have focused on understanding changes in the microbial community over time. Such longitudinal microbiome studies have the potential to offer unique insights pertaining to the microbial social networks as well as their responses to perturbations. In this communication, we introduce a web based framework called 'TIME' (Temporal Insights into Microbial Ecology'), developed specifically to obtain meaningful insights from microbiome time series data. The TIME web-server is designed to accept a wide range of popular formats as input with options to preprocess and filter the data. Multiple samples, defined by a series of longitudinal time points along with their metadata information, can be compared in order to interactively visualize the temporal variations. In addition to standard microbiome data analytics, the web server implements popular time series analysis methods like Dynamic time warping, Granger causality and Dickey Fuller test to generate interactive layouts for facilitating easy biological inferences. Apart from this, a new metric for comparing metagenomic time series data has been introduced to effectively visualize the similarities/differences in the trends of the resident microbial groups. Augmenting the visualizations with the stationarity information pertaining to the microbial groups is utilized to predict the microbial competition as well as community structure. Additionally, the 'causality graph analysis' module incorporated in TIME allows predicting taxa that might have a higher influence on community structure in different conditions. TIME also allows users to easily identify potential taxonomic markers from a longitudinal microbiome analysis. We illustrate the utility of the web-server features on a few published time series microbiome data and demonstrate the ease with which it can be used to perform complex analysis.
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Affiliation(s)
- Krishanu D. Baksi
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Bhusan K. Kuntal
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
- Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory (NCL), Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sharmila S. Mande
- Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., Pune, India
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14
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Di Guardo A, Terzaghi E, Raspa G, Borin S, Mapelli F, Chouaia B, Zanardini E, Morosini C, Colombo A, Fattore E, Davoli E, Armiraglio S, Sale VM, Anelli S, Nastasio P. Differentiating current and past PCB and PCDD/F sources: The role of a large contaminated soil site in an industrialized city area. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 223:367-375. [PMID: 28118998 DOI: 10.1016/j.envpol.2017.01.033] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/13/2017] [Accepted: 01/15/2017] [Indexed: 05/18/2023]
Abstract
Cities and contaminated areas can be primary or secondary sources of polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and other chemicals, into air and soil and can influence the regional level of some of these pollutants. In a contaminated site, the evaluation of such emissions can be crucial in the choice of the remediation technology to be adopted. In the city of Brescia (Northern Italy), more than 100 ha of agricultural areas were contaminated with PCBs, PCDD/Fs and heavy metals, originating from the activities of a former PCB factory. In order to evaluate the current emissions of PCBs and PCDD/Fs from the contaminated site, in a location where other current sources are present, we compared measured and predicted air concentrations, resulting from chemical volatilization from soils as well as fingerprints of Brescia soils and of soils contaminated by specific sources. The results confirm that the contaminated area is still a current and important secondary source of PCBs to the air, and to a lesser extent of PCDFs (especially the more volatile), but not for PCDDs. PCBs in soils have fingerprints similar to highly chlorinated mixtures, indicating contamination by these mixtures and/or a long weathering process. PCB 209 is also present at important levels. PCDD fingerprints in soil cannot be related to current emission sources, while PCDFs are compatible to industrial and municipal waste incineration, although weathering and/or natural attenuation may have played a role in modifying such soil fingerprints. Finally, we combined chemical and microbiological analyses to provide an integrated approach to evaluate soil fingerprints and their variation in a wider perspective, which accounts for the mutual effects between contamination and soil microbiota, a pivotal hint for addressing in situ bioremediation activities.
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Affiliation(s)
| | - Elisa Terzaghi
- DiSAT, University of Insubria, Via Valleggio 11, Como, Italy
| | - Giuseppe Raspa
- DCEME, Sapienza University of Rome, Via Eudossiana 18, Rome, Italy
| | - Sara Borin
- DeFENS, University of Milan, Via Celoria 2, Milan, Italy
| | | | - Bessem Chouaia
- DeFENS, University of Milan, Via Celoria 2, Milan, Italy
| | | | | | - Andrea Colombo
- Department of Environmental Health Sciences, IRCCS-Istituto di Ricerche Farmacologiche ''Mario Negri'', Via La Masa 19, Milan, Italy
| | - Elena Fattore
- Department of Environmental Health Sciences, IRCCS-Istituto di Ricerche Farmacologiche ''Mario Negri'', Via La Masa 19, Milan, Italy
| | - Enrico Davoli
- Department of Environmental Health Sciences, IRCCS-Istituto di Ricerche Farmacologiche ''Mario Negri'', Via La Masa 19, Milan, Italy
| | - Stefano Armiraglio
- Municipality of Brescia - Museum of Natural Sciences, Via Ozanam 4, Brescia, Italy
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15
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Grazziotin AL, Koonin EV, Kristensen DM. Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res 2016; 45:D491-D498. [PMID: 27789703 PMCID: PMC5210652 DOI: 10.1093/nar/gkw975] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/08/2016] [Accepted: 10/21/2016] [Indexed: 11/13/2022] Open
Abstract
Viruses are the most abundant and diverse biological entities on earth, and while most of this diversity remains completely unexplored, advances in genome sequencing have provided unprecedented glimpses into the virosphere. The Prokaryotic Virus Orthologous Groups (pVOGs, formerly called Phage Orthologous Groups, POGs) resource has aided in this task over the past decade by using automated methods to keep pace with the rapid increase in genomic data. The uses of pVOGs include functional annotation of viral proteins, identification of genes and viruses in uncharacterized DNA samples, phylogenetic analysis, large-scale comparative genomics projects, and more. The pVOGs database represents a comprehensive set of orthologous gene families shared across multiple complete genomes of viruses that infect bacterial or archaeal hosts (viruses of eukaryotes will be added at a future date). The pVOGs are constructed within the Clusters of Orthologous Groups (COGs) framework that is widely used for orthology identification in prokaryotes. Since the previous release of the POGs, the size has tripled to nearly 3000 genomes and 300 000 proteins, and the number of conserved orthologous groups doubled to 9518. User-friendly webpages are available, including multiple sequence alignments and HMM profiles for each VOG. These changes provide major improvements to the pVOGs database, at a time of rapid advances in virus genomics. The pVOGs database is hosted jointly at the University of Iowa at http://dmk-brain.ecn.uiowa.edu/pVOGs and the NCBI at ftp://ftp.ncbi.nlm.nih.gov/pub/kristensen/pVOGs/home.html.
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Affiliation(s)
- Ana Laura Grazziotin
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA 52242, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - David M Kristensen
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA 52242, USA .,National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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16
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Czaplicki LM, Gunsch CK. Reflection on Molecular Approaches Influencing State-of-the-Art Bioremediation Design: Culturing to Microbial Community Fingerprinting to Omics. JOURNAL OF ENVIRONMENTAL ENGINEERING (NEW YORK, N.Y.) 2016; 142:10.1061/(ASCE)EE.1943-7870.0001141. [PMID: 28348455 PMCID: PMC5364726 DOI: 10.1061/(asce)ee.1943-7870.0001141] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 03/31/2016] [Indexed: 05/30/2023]
Abstract
Bioremediation is generally viewed as a cost effective and sustainable technology because it relies on microbes to transform pollutants into benign compounds. Advances in molecular biological analyses allow unprecedented microbial detection and are increasingly incorporated into bioremediation. Throughout history, state-of-the-art techniques have informed bioremediation strategies. However, the insights those techniques provided were not as in depth as those provided by recently developed omics tools. Advances in next generation sequencing (NGS) have now placed metagenomics and metatranscriptomics within reach of environmental engineers. As NGS costs decrease, metagenomics and metatranscriptomics have become increasingly feasible options to rapidly scan sites for specific degradative functions and identify microorganisms important in pollutant degradation. These omic techniques are capable of revolutionizing biological treatment in environmental engineering by allowing highly sensitive characterization of previously uncultured microorganisms. Omics enables the discovery of novel microorganisms for use in bioaugmentation and supports systematic optimization of biostimulation strategies. This review describes the omics journey from roots in biology and medicine to its current status in environmental engineering including potential future directions in commercial application.
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Affiliation(s)
- Lauren M. Czaplicki
- Ph.D. Candidate, Department of Civil & Environmental Engineering, Duke University, Durham, NC 27708-0287 USA
| | - Claudia K. Gunsch
- Associate Professor, Department of Civil & Environmental Engineering, Duke University, Durham, NC 27708-0287 USA
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17
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Lokmer A, Goedknegt MA, Thieltges DW, Fiorentino D, Kuenzel S, Baines JF, Wegner KM. Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales. Front Microbiol 2016; 7:1367. [PMID: 27630625 PMCID: PMC5006416 DOI: 10.3389/fmicb.2016.01367] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/18/2016] [Indexed: 01/09/2023] Open
Abstract
Unveiling the factors and processes that shape the dynamics of host associated microbial communities (microbiota) under natural conditions is an important part of understanding and predicting an organism's response to a changing environment. The microbiota is shaped by host (i.e., genetic) factors as well as by the biotic and abiotic environment. Studying natural variation of microbial community composition in multiple host genetic backgrounds across spatial as well as temporal scales represents a means to untangle this complex interplay. Here, we combined a spatially-stratified with a longitudinal sampling scheme within differentiated host genetic backgrounds by reciprocally transplanting Pacific oysters between two sites in the Wadden Sea (Sylt and Texel). To further differentiate contingent site from host genetic effects, we repeatedly sampled the same individuals over a summer season to examine structure, diversity and dynamics of individual hemolymph microbiota following experimental removal of resident microbiota by antibiotic treatment. While a large proportion of microbiome variation could be attributed to immediate environmental conditions, we observed persistent effects of antibiotic treatment and translocation suggesting that hemolymph microbial community dynamics is subject to within-microbiome interactions and host population specific factors. In addition, the analysis of spatial variation revealed that the within-site microenvironmental heterogeneity resulted in high small-scale variability, as opposed to large-scale (between-site) stability. Similarly, considerable within-individual temporal variability was in contrast with the overall temporal stability at the site level. Overall, our longitudinal, spatially-stratified sampling design revealed that variation in hemolymph microbiota is strongly influenced by site and immediate environmental conditions, whereas internal microbiome dynamics and oyster-related factors add to their long-term stability. The combination of small and large scale resolution of spatial and temporal observations therefore represents a crucial but underused tool to study host-associated microbiome dynamics.
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Affiliation(s)
- Ana Lokmer
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research List auf Sylt, Germany
| | - M Anouk Goedknegt
- Department of Coastal Systems, Royal Netherlands Institute for Sea Research, Utrecht University Texel, Netherlands
| | - David W Thieltges
- Department of Coastal Systems, Royal Netherlands Institute for Sea Research, Utrecht University Texel, Netherlands
| | - Dario Fiorentino
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research List auf Sylt, Germany
| | - Sven Kuenzel
- Max Planck Institute for Evolutionary Biology Plön, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary BiologyPlön, Germany; Institute for Experimental Medicine, Christian-Albrechts-Universität zu KielKiel, Germany
| | - K Mathias Wegner
- Coastal Ecology, Wadden Sea Station Sylt, Alfred Wegener Institute - Helmholtz Centre for Polar and Marine Research List auf Sylt, Germany
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18
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Tabata M, Ohhata S, Nikawadori Y, Kishida K, Sato T, Kawasumi T, Kato H, Ohtsubo Y, Tsuda M, Nagata Y. Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide. DNA Res 2016; 23:581-599. [PMID: 27581378 PMCID: PMC5144681 DOI: 10.1093/dnares/dsw041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/09/2016] [Indexed: 11/20/2022] Open
Abstract
γ-Hexachlorocyclohexane (γ-HCH) is a recalcitrant man-made chlorinated pesticide. Here, the complete genome sequences of four γ-HCH-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-HCH degrader, were compared. Together with several experimental data, we showed that (i) all the four strains carry almost identical linA to linE genes for the conversion of γ-HCH to maleylacetate (designated “specific” lin genes), (ii) considerably different genes are used for the metabolism of maleylacetate in one of the four strains, and (iii) the linKLMN genes for the putative ABC transporter necessary for γ-HCH utilization exhibit structural divergence, which reflects the phylogenetic relationship of their hosts. Replicon organization and location of the lin genes in the four genomes are significantly different with one another, and that most of the specific lin genes are located on multiple sphingomonad-unique plasmids. Copies of IS6100, the most abundant insertion sequence in the four strains, are often located in close proximity to the specific lin genes. Analysis of the footprints of target duplication upon IS6100 transposition and the experimental detection of IS6100 transposition strongly suggested that the IS6100 transposition has caused dynamic genome rearrangements and the diversification of lin-flanking regions in the four strains.
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Affiliation(s)
- Michiro Tabata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Satoshi Ohhata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Yuki Nikawadori
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Kouhei Kishida
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Takuya Sato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Toru Kawasumi
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Hiromi Kato
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Yoshiyuki Ohtsubo
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Masataka Tsuda
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai 980-8577, Japan
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19
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Han SI. Phylogenetic characteristics of bacterial populations and isolation of aromatic compounds utilizing bacteria from humus layer of oak forest. ACTA ACUST UNITED AC 2016. [DOI: 10.7845/kjm.2016.6028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Complete genome sequence of Burkholderia caribensis Bcrs1W (NBRC110739), a strain co-residing with phenanthrene degrader Mycobacterium sp. EPa45. J Biotechnol 2016; 228:67-68. [DOI: 10.1016/j.jbiotec.2016.04.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 11/20/2022]
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21
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Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities. Appl Microbiol Biotechnol 2016; 100:7263-79. [PMID: 27102130 DOI: 10.1007/s00253-016-7532-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/28/2016] [Accepted: 04/05/2016] [Indexed: 02/06/2023]
Abstract
We collected several biofilm samples from Japanese rivers and established a reproducible multi-species biofilm model that can be analyzed in laboratories. Bacterial abundance at the generic level was highly similar between the planktonic and biofilm communities, whereas comparative metatranscriptomic analysis revealed many upregulated and downregulated genes in the biofilm. Many genes involved in iron-sulfur metabolism, stress response, and cell envelope function were upregulated; biofilm formation is mediated by an iron-dependent signaling mechanism and the signal is relayed to stress-responsive and cell envelope function genes. Flagella-related gene expression was regulated depending upon the growth phase, indicating different roles of flagella during the adherence, maturation, and dispersal steps of biofilm formation. Downregulation of DNA repair genes was observed, indicating that spontaneous mutation frequency would be elevated within the biofilm and that the biofilm is a cradle for generating novel genetic traits. Although the significance remains unclear, genes for rRNA methyltransferase, chromosome partitioning, aminoacyl-tRNA synthase, and cysteine, methionine, leucine, thiamine, nucleotide, and fatty acid metabolism were found to be differentially regulated. These results indicate that planktonic and biofilm communities are in different dynamic states. Studies on biofilm and sessile cells, which have received less attention, are important for understanding microbial ecology and for designing tailor-made anti-biofilm drugs.
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22
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Complete Genome Sequence of a Phenanthrene Degrader, Burkholderia sp. HB-1 (NBRC 110738). GENOME ANNOUNCEMENTS 2015; 3:3/6/e01283-15. [PMID: 26543118 PMCID: PMC4645203 DOI: 10.1128/genomea.01283-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The phenanthrene-degrading Burkholderia sp. HB-1 was isolated from a phenanthrene-enrichment culture seeded with a pristine farm soil sample. We report the complete genome sequence of HB-1, which has been deposited to the stock culture (NBRC 110738) at Biological Resource Center, National Institute of Technology and Evaluation (NITE), Tokyo, Japan. The genome of strain HB-1 comprises two circular chromosomes of 4.1 Mb and 3.1 Mb. The finishing was facilitated by the computational tools GenoFinisher, AceFileViewer, and ShortReadManager.
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