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Cruz FVDS, Barbosa da Costa N, Juneau P. Non-pathogenic microbiome associated to aquatic plants and anthropogenic impacts on this interaction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174663. [PMID: 38992379 DOI: 10.1016/j.scitotenv.2024.174663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/22/2024] [Accepted: 07/07/2024] [Indexed: 07/13/2024]
Abstract
The microbiota associated with aquatic plants plays a crucial role in promoting plant growth and development. The structure of the plant microbiome is shaped by intricate interactions among hosts, microbes, and environmental factors. Consequently, anthropogenic pressures that disrupt these interactions can indirectly impact the ecosystem services provided by aquatic plants, such as CO2 fixation, provision of food resources, shelter to animals, nutrient cycling, and water purification. Presently, studies on plant-microbiota interactions primarily focus on terrestrial hosts and overlook aquatic environments with their unique microbiomes. Therefore, there is a pressing need for a comprehensive understanding of plant microbiomes in aquatic ecosystems. This review delves into the overall composition of the microbiota associated with aquatic plant, with a particular emphasis on bacterial communities, which have been more extensively studied. Subsequently, the functions provided by the microbiota to their aquatic plants hosts are explored, including the acquisition and mobilization of nutrients, production of auxin and related compounds, enhancement of photosynthesis, and protection against biotic and abiotic stresses. Additionally, the influence of anthropogenic stressors, such as climate change and aquatic contamination, on the interaction between microbiota and aquatic plants is discussed. Finally, knowledge gaps are highlighted and future directions in this field are suggested.
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Affiliation(s)
- Fernanda Vieira da Silva Cruz
- Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL, EcotoQ, TOXEN, Department of Biological Sciences, Université du Québec à Montréal, Montréal Succ. Centre-Ville, H3C 3P8 Montréal, QC, Canada
| | - Naíla Barbosa da Costa
- Institut national de la recherche scientifique - Centre Eau Terre Environnement, 490 Couronne St, Québec City, Québec G1K 9A9, Canada
| | - Philippe Juneau
- Ecotoxicology of Aquatic Microorganisms Laboratory, GRIL, EcotoQ, TOXEN, Department of Biological Sciences, Université du Québec à Montréal, Montréal Succ. Centre-Ville, H3C 3P8 Montréal, QC, Canada.
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Macey MC. Genome-resolved metagenomics identifies novel active microbes in biogeochemical cycling within methanol-enriched soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13246. [PMID: 38575138 PMCID: PMC10994693 DOI: 10.1111/1758-2229.13246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Abstract
Metagenome assembled genomes (MAGs), generated from sequenced 13C-labelled DNA from 13C-methanol enriched soils, were binned using an ensemble approach. This method produced a significantly larger number of higher-quality MAGs compared to direct binning approaches. These MAGs represent both the primary methanol utilizers and the secondary utilizers labelled via cross-feeding and predation on the labelled methylotrophs, including numerous uncultivated taxa. Analysis of these MAGs enabled the identification of multiple metabolic pathways within these active taxa that have climatic relevance relating to nitrogen, sulfur and trace gas metabolism. This includes denitrification, dissimilatory nitrate reduction to ammonium, ammonia oxidation and metabolism of organic sulfur species. The binning of viral sequence data also yielded extensive viral MAGs, identifying active viral replication by both lytic and lysogenic phages within the methanol-enriched soils. These MAGs represent a valuable resource for characterizing biogeochemical cycling within terrestrial environments.
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Affiliation(s)
- Michael C. Macey
- AstrobiologyOU, Earth, Environment and Ecosystem SciencesThe Open UniversityMilton KeynesUK
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Wei W, Shi X, Wang M, Zhou Z. Manure application maintained the CO 2 fixation activity of soil autotrophic bacteria but changed its ecological characteristics in an entisol of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169630. [PMID: 38154636 DOI: 10.1016/j.scitotenv.2023.169630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023]
Abstract
The response of soil autotrophs to anthropogenic activities has attracted increasing attention against the background of global change. Here, three entisol plots under different fertilizing regimes, including no fertilization (CK), manure (M), and a combined application of chemical fertilizer and manure (NPKM) were selected, and then the soil RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) activity and cbbl (gene encoding the large subunit of RubisCO) composition were measured to indicate the activity and community of autotrophic bacteria, respectively. The results revealed that the RubisCO activity of CK showed no difference from that of M but was significantly higher than that of NPKM. The CK and M had the lowest and highest soil cbbl abundance, respectively. The α-diversity of soil cbbl-carrying bacteria showed no significant difference among these treatments, whereas they showed significantly different community structures of cbbl-carrying bacteria. Meanwhile, compared with CK, M had significantly lower abundances of bacterial species with the functions of nitrogen fixation (Azoarcus sp.KH32C) or detoxification (Methylibium petroleiphilum), indicating that manure application might have an inhibiting potential to some beneficial autotrophic bacterial species in this entisol.
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Affiliation(s)
- Wanling Wei
- College of Resources and Environment, Southwest University, Chongqing 400715, China; Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing 400715, China; The National Monitoring Base for Purple Soil Fertility and Fertilizer Efficiency, Southwest University, Chongqing 400715, China
| | - Mingxia Wang
- College of Resources and Environment, Southwest University, Chongqing 400715, China
| | - Zhifeng Zhou
- College of Resources and Environment, Southwest University, Chongqing 400715, China.
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Lin WH, Tsai TS. Comparisons of the Oral Microbiota from Seven Species of Wild Venomous Snakes in Taiwan Using the High-Throughput Amplicon Sequencing of the Full-Length 16S rRNA Gene. BIOLOGY 2023; 12:1206. [PMID: 37759605 PMCID: PMC10525742 DOI: 10.3390/biology12091206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/26/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023]
Abstract
A venomous snake's oral cavity may harbor pathogenic microorganisms that cause secondary infection at the wound site after being bitten. We collected oral samples from 37 individuals belonging to seven species of wild venomous snakes in Taiwan, including Naja atra (Na), Bungarus multicinctus (Bm), Protobothrops mucrosquamatus (Pm), Trimeresurus stejnegeri (Ts), Daboia siamensis (Ds), Deinagkistrodon acutus (Da), and alpine Trimeresurus gracilis (Tg). Bacterial species were identified using full-length 16S rRNA amplicon sequencing analysis, and this is the first study using this technique to investigate the oral microbiota of multiple Taiwanese snake species. Up to 1064 bacterial species were identified from the snake's oral cavities, with 24 pathogenic and 24 non-pathogenic species among the most abundant ones. The most abundant oral bacterial species detected in our study were different from those found in previous studies, which varied by snake species, collection sites, sampling tissues, culture dependence, and analysis methods. Multivariate analysis revealed that the oral bacterial species compositions in Na, Bm, and Pm each were significantly different from the other species, whereas those among Ts, Ds, Da, and Tg showed fewer differences. Herein, we reveal the microbial diversity in multiple species of wild snakes and provide potential therapeutic implications regarding empiric antibiotic selection for wildlife medicine and snakebite management.
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Affiliation(s)
- Wen-Hao Lin
- Institute of Wildlife Conservation, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
| | - Tein-Shun Tsai
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
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Han L, Fang K, You X, Li Y, Wang X, Wang J. Earthworms synergize with indigenous soil functional microorganisms to accelerate the preferential degradation of the highly toxic S-enantiomer of the fungicide imazalil in soil. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131778. [PMID: 37290354 DOI: 10.1016/j.jhazmat.2023.131778] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/15/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
The roles of soil and earthworm gut microorganisms in the degradation of the chiral fungicide imazalil (IMA) enantiomers were systemically studied in soil-earthworm systems. S-IMA degraded slower than R-IMA in soil without earthworms. After the addition of earthworms, S-IMA degraded faster than R-IMA. Methylibium was the potential degradative bacterium likely related to the preferential degradation of R-IMA in soil. However, the addition of earthworms significantly decreased the relative abundance of Methylibium, especially in R-IMA-treated soil. Meanwhile, a new potential degradative bacterium Aeromonas first appeared in soil-earthworm systems. Compared with enantiomer-treated soil, the relative abundance of indigenous soil bacterium Kaistobacter significantly boomed in enantiomer-treated soil with earthworms. Interestingly, Kaistobacter in the earthworm gut also obviously increased after exposure to enantiomers, particularly in S-IMA-treated soil, which was associated with the significant increase in Kaistobacter in soil. More importantly, the relative abundances of Aeromonas and Kaistobacter in S-IMA-treated soil were obviously higher than those in R-IMA-treated soil after the addition of earthworms. Moreover, these two potential degradative bacteria were also potential bacterial hosts of the biodegradation genes p450 and bph. Collectively, gut microorganisms are important helpers in soil pollution remediation by participating in the preferential degradation of S-IMA mediated by indigenous soil microorganisms.
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Affiliation(s)
- Lingxi Han
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao 266109, PR China
| | - Kuan Fang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, PR China
| | - Xiangwei You
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, PR China
| | - Yiqiang Li
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, PR China
| | - Xiuguo Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences (CAAS), Qingdao 266101, PR China.
| | - Jun Wang
- College of Resources and Environment, Key Laboratory of Agricultural Environment, Shandong Agricultural University, Tai'an 271000, PR China
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Pensky J, Fisher AT, Gorski G, Schrad N, Bautista V, Saltikov C. Linking nitrate removal, carbon cycling, and mobilization of geogenic trace metals during infiltration for managed recharge. WATER RESEARCH 2023; 239:120045. [PMID: 37201373 DOI: 10.1016/j.watres.2023.120045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/14/2023] [Accepted: 05/02/2023] [Indexed: 05/20/2023]
Abstract
We present results from a series of laboratory column studies investigating the impacts of infiltration dynamics and the addition of a soil-carbon amendment (wood mulch or almond shells) on water quality during infiltration for flood-managed aquifer recharge (flood-MAR). Recent studies suggest that nitrate removal could be enhanced during infiltration for MAR through the application of a wood chip permeable reactive barrier (PRB). However, less is understood about how other readily available carbon sources, such as almond shells, could be used as a PRB material, and how carbon amendments could impact other solutes, such as trace metals. Here we show that the presence of a carbon amendment increases nitrate removal relative to native soil, and that there is greater nitrate removal in association with longer fluid retention times (slower infiltration rates). Almond shells promoted more efficient nitrate removal than wood mulch or native soil, but also promoted the mobilization of geogenic trace metals (Mn, Fe, and As) during experiments. Almond shells in a PRB likely enhanced nitrate removal and trace metal cycling by releasing labile carbon, promoting reducing conditions, and providing habitat for microbial communities, the composition of which shifted in response. These results suggest that limiting the amount of bioavailable carbon released by a carbon-rich PRB may be preferred where geogenic trace metals are common in soils. Given the dual threats to groundwater supplies and quality worldwide, incorporating a suitable carbon source into the soil for managed infiltration projects could help to generate co-benefits and avoid undesirable results.
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Affiliation(s)
- Jennifer Pensky
- Department of Earth and Planetary Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, United States.
| | - Andrew T Fisher
- Department of Earth and Planetary Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Galen Gorski
- Department of Earth and Planetary Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Nicole Schrad
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, United States
| | - Victor Bautista
- Department of Earth and Planetary Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Chad Saltikov
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, United States
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Genome-based taxonomic classification of the closest-to-Comamonadaceae group supports a new family Sphaerotilaceae fam. nov. and taxonomic revisions. Syst Appl Microbiol 2022; 45:126352. [DOI: 10.1016/j.syapm.2022.126352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/06/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022]
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Pensky J, Fisher AT, Gorski G, Schrad N, Dailey H, Beganskas S, Saltikov C. Enhanced cycling of nitrogen and metals during rapid infiltration: Implications for managed recharge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156439. [PMID: 35660593 DOI: 10.1016/j.scitotenv.2022.156439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/12/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
We present results from a series of plot-scale field experiments to quantify physical infiltration dynamics and the influence of adding a carbon-rich, permeable reactive barrier (PRB) for the cycling of nitrogen and associated trace metals during rapid infiltration for managed aquifer recharge (MAR). Recent studies suggest that adding a bio-available carbon source to soils can enhance denitrification rates and associated N load reduction during moderate-to-rapid infiltration (≤1 m/day). We examined the potential for N removal during faster infiltration (>1 m/day), through coarse and carbon-poor soils, and how adding a carbon-rich PRB (wood chips) affects subsurface redox conditions and trace metal mobilization. During rapid infiltration, plots amended with a carbon-rich PRB generally demonstrated modest increases in subsurface loads of dissolved organic carbon, nitrite, manganese and iron, decreases in loads of nitrate and ammonium, and variable changes in arsenic. These trends differed considerably from those seen during infiltration through native soil without a carbon-rich PRB. Use of a carbon-rich soil amendment increased the fraction of dissolved N species that was removed at equivalent inflowing N loads. There is evidence that N removal took place primarily via denitrification. Shifts in microbial ecology following infiltration in all of the plots included increases in the relative abundances of microbes in the families Comamonadaceae, Pseudomonadaceae, Methylophilaceae, Rhodocyclaceae and Sphingomonadaceae, all of which contain genera capable of carrying out denitrification. These results, in combination with studies that have tested other soil types, flow rates, and system scales, show how water quality can be improved during infiltration for managed recharge, even during rapid infiltration, with a carbon-rich soil amendment.
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Affiliation(s)
- Jennifer Pensky
- Department of Earth and Planetary Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, United States.
| | - Andrew T Fisher
- Department of Earth and Planetary Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Galen Gorski
- Department of Earth and Planetary Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Nicole Schrad
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, United States
| | - Hannah Dailey
- Department of Earth and Planetary Sciences, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Sarah Beganskas
- Water Resource Management, Delaware River Basin Commission, West Trenton, NJ 08628, United States
| | - Chad Saltikov
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA 95064, United States
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Rani V, Prasanna R, Kaushik R. Prospecting the significance of methane-utilizing bacteria in agriculture. World J Microbiol Biotechnol 2022; 38:176. [PMID: 35922575 DOI: 10.1007/s11274-022-03331-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
Microorganisms act as both the source and sink of methane, a potent greenhouse gas, thus making a significant contribution to the environment as an important driver of climate change. The rhizosphere and phyllosphere of plants growing in natural (mangroves) and artificial wetlands (flooded agricultural ecosystems) harbor methane-utilizing bacteria that oxidize methane at the source and reduce its net flux. For several decades, microorganisms have been used as biofertilizers to promote plant growth. However, now their role in reducing net methane flux, especially from flooded agricultural ecosystems is gaining momentum globally. Research in this context has mainly focused on taxonomic aspects related to methanotrophy among diverse bacterial genera, and environmental factors that govern methane utilization in natural and artificial wetland ecosystems. In the last few decades, concerted efforts have been made to develop multifunctional microbial inoculants that can oxidize methane and alleviate greenhouse gas emissions, as well as promote plant growth. In this context, combinations of taxonomic groups commonly found in rice paddies and those used as biofertilizers are being explored. This review deals with methanotrophy among diverse bacterial domains, factors influencing methane-utilizing ability, and explores the potential of novel methane-utilizing microbial consortia with plant growth-promoting traits in flooded ecosystems.
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Affiliation(s)
- Vijaya Rani
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Radha Prasanna
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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Zhang M, Zhou Z, Zhang J, Yu Y, Sun L, Lu T, Qian H. Metagenomic ecotoxicity assessment of trace difenoconazole on freshwater microbial community. CHEMOSPHERE 2022; 294:133742. [PMID: 35090847 DOI: 10.1016/j.chemosphere.2022.133742] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Difenoconazole, a typical triazole fungicide, inhibits the activity of cytochrome P450 enzyme in fungi, and is extensively used in protecting fruits, vegetables, and cereal crops. However, reports elucidating the effects of difenoconazole on aquatic microbial communities are limited. Our study showed that difenoconazole promoted microalgae growth at concentrations ranging from 0.1 to 5 μg/L, which was similar with its environmental residual concentrations. Metagenomic analysis revealed that the aquatic microbial structure could self-regulate to cope with difenoconazole-induced stress by accumulating bacteria exhibiting pollutant degrading abilities. In the short-term, several functional pathways related to xenobiotic biodegradation and analysis were upregulated to provide ability for aquatic microbial community to process xenobiotic stress. Moreover, most disturbed ecological functions were recovered due to the redundancy of microbial communities after prolonged exposure. Furthermore, the risks associated with the dissemination of antibiotic resistance genes were enhanced by difenoconazole in the short-term. Overall, our study contributes to a comprehensive understanding of the difenoconazole-induced ecological impacts and the behavior of aquatic microbial communities that are coping with xenobiotic stress.
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Affiliation(s)
- Mengwei Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China; Department of Jianhu, Zhejiang Industry Polytechnic College, Shaoxing, 312000, PR China
| | - Zhigao Zhou
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Jinfeng Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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Torres-Beltrán M, Vargas-Gastélum L, Magdaleno-Moncayo D, Riquelme M, Herguera-García JC, Prieto-Davó A, Lago-Lestón A. The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain. PeerJ 2021; 9:e12474. [PMID: 34993013 PMCID: PMC8679910 DOI: 10.7717/peerj.12474] [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: 07/15/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022] Open
Abstract
Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.
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Affiliation(s)
- Mónica Torres-Beltrán
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Lluvia Vargas-Gastélum
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Dante Magdaleno-Moncayo
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Meritxell Riquelme
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Juan Carlos Herguera-García
- Departamento de Ecología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Alejandra Prieto-Davó
- Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Asunción Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
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12
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Cui Y, Park CY, Kim SY, Wong SK, Lim AS, Oh HM, Chun SJ, Ahn CY. Aquariibacter albus gen. nov., sp. nov., a new member of the order Burkholderiales, isolated from a freshwater aquarium. Int J Syst Evol Microbiol 2021; 71. [PMID: 34596504 DOI: 10.1099/ijsem.0.005022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, strain SJAQ100T, was isolated from a freshwater aquarium and was characterized taxonomically and phylogenetically. Strain SJAQ100T was a Gram-stain-negative, aerobic, rod-shaped and non-motile bacterium. The strain grew optimally with 0 % NaCl and at 25-37 °C on Reasoner's 2A agar. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the strain SJAQ100T clustered with members of Burkholderiales incertae sedis in the order Burkholderiales, but sequence similarities to known species were less than 96.5 %. The genomic DNA G+C content of strain SJAQ100T was 71.2 mol%. Genomic comparisons of strain SJAQ100T with species in the order Burkholderiales were made using the Genome-to-Genome Distance Calculator, average nucleotide identity and average amino acid identity analyses (values indicated ≤22.1, ≤78.1, and ≤68.1 % respectively). Strain SJAQ100T contained C16 : 0 and C16 : 1 ω7c/C16 : 1 ω6c as major fatty acids and Q-8 as the major quinone. The major polyamines were putrescine and cadaverine. Strain SJAQ100T contained phosphatidylethanolamine and diphosphatidylglycerol as major polar lipids. Based on the genotypic, chemotaxonomic and phenotypic results, strain SJAQ100T represents a novel genus and species, Aquariibacter albus gen. nov., sp. nov., which belongs to order Burkholderiales and the class Betaproteobacteria. The type strain is SJAQ100T (=KCTC 72203T=CGMCC 1.18869T=MCC 4385T).
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Affiliation(s)
- Yingshun Cui
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Chan-Yeong Park
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Song-Yeon Kim
- Division of Applied Life Science, Gyeongsang National University, 501, Jinju-daero, Jinju 52828, Republic of Korea
| | - Shu-Kuan Wong
- National Institute of Polar Research, 10-3, Midori-cho, Tachikawa-shi, Tokyo 190-8518, Japan
| | - An Suk Lim
- Division of Applied Life Science, Gyeongsang National University, 501, Jinju-daero, Jinju 52828, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Seong-Jun Chun
- LMO research team, National Institute of Ecology, 1210, Geumgang-ro, Maseo-myeon, Seocheon, 33657, Republic of Korea
| | - Chi-Yong Ahn
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity. DIVERSITY 2020. [DOI: 10.3390/d12100392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive to land management. Dactylis glomerata L. samples were collected from grassland sites with contrasting land use intensities but comparable soil properties at three different timepoints. To assess the plant-associated bacterial community structure in the compartments rhizosphere, bulk soil and endosphere, a molecular barcoding approach based on high throughput 16S rRNA amplicon sequencing was used. A distinct composition of plant-associated core bacterial communities independent of land use intensity was identified. Pseudomonas, Rhizobium and Bradyrhizobium were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were Rhodoplanes, Methylibium, Kaistobacter and Bradyrhizobium. Due to the frequent occurrence of plant-promoting abilities in the genera found in the plant-associated core bacterial communities, our study helps to identify “healthy” plant-associated bacterial core communities. The variable part of the plant-associated microbiome, represented by the fluctuation of taxa at the different sampling timepoints, was increased under low land use intensity. This higher compositional variation in samples from plots with low land use intensity indicates a more selective recruitment of bacteria with traits required at different timepoints of plant development compared to samples from plots with high land use intensity.
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Mangse G, Werner D, Meynet P, Ogbaga CC. Microbial community responses to different volatile petroleum hydrocarbon class mixtures in an aerobic sandy soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 264:114738. [PMID: 32417579 DOI: 10.1016/j.envpol.2020.114738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 04/20/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Volatile Petroleum Hydrocarbon (VPH) class effects on soil microbial composition were investigated using two next-generation sequencing (NGS) techniques - 454 pyrosequencing and ion torrent sequencing. Microbial activity was stimulated by adding different VPH compound classes to the sandy soil in comparison with live controls without VPH addition. Microbial community structure was significantly affected by the various VPH classes. At the genus level, Rhodococcus, Desulfosporosinus, Polaromonas, Mesorhizobium and Methylibium had the highest relative abundances in the straight-chain alkane (str-alk) treated soil as compared to the control (p < 0.05, 2 sample t-tests) while Pseudomonas was more dominant in the cyclic alkane (cyc-alk) contaminated soil. Pseudonocardia was significantly higher in relative abundance in the aromatic hydrocarbon (aro-H) treated batches as compared to the control (p < 0.05, 2 sample t-tests). A non-metric multidimensional scaling (NMDS) of the Bray Curtis similarity between microbial communities in the batches revealed at least 60% similarity for each treatment and also showed that VPH class was a statistically significant factor in shaping the bacterial communities in the soil treatments (Global R = 0.861, p < 0.01). The NGS platforms (454 GS Junior and Ion torrent) compared in this study did not appear to affect the outcomes of the microbial community structure and composition analysis.
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Affiliation(s)
- George Mangse
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, England, UK; Department of Microbiology & Biotechnology, Nile University of Nigeria, Abuja, Nigeria.
| | - David Werner
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, England, UK
| | - Paola Meynet
- School of Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, England, UK
| | - Chukwuma C Ogbaga
- Department of Microbiology & Biotechnology, Nile University of Nigeria, Abuja, Nigeria; Department of Biological Sciences, Nile University of Nigeria, Abuja, Nigeria
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15
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Whittington HD, Singh M, Ta C, Azcárate-Peril MA, Bruno-Bárcena JM. Accelerated Biodegradation of the Agrochemical Ametoctradin by Soil-Derived Microbial Consortia. Front Microbiol 2020; 11:1898. [PMID: 32982997 PMCID: PMC7477900 DOI: 10.3389/fmicb.2020.01898] [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] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/20/2020] [Indexed: 01/25/2023] Open
Abstract
Pesticide-resistant plant pathogens are an increasing threat to the global food supply and have generated a need for novel, efficacious agrochemicals. The current regulatory process for approving new agrochemicals is a tedious but necessary process. One way to accelerate the safety evaluation process is to utilize in vitro systems to demonstrate pesticide degradation by soil microbes prior to ex vivo soil evaluations. This approach may have the capability to generate metabolic profiles free of inhibitory substances, such as humic acids, commonly present in ex vivo soil systems. In this study, we used a packed-bed microbial bioreactor to assess the role of the natural soil microbial community during biodegradation of the triazolopyrimidine fungicide, ametoctradin. Metabolite profiles produced during in vitro ametoctradin degradation were similar to the metabolite profiles obtained during environmental fate studies and demonstrated the degradation of 81% of the parent compound in 72 h compared to a half-life of 2 weeks when ametoctradin was left in the soil. The microbial communities of four different soil locations and the bioreactor microbiome were compared using high throughput sequencing. It was found that biodegradation of ametoctradin in both ex vivo soils and in vitro in the bioreactor correlated with an increase in the relative abundance of Burkholderiales, well characterized microbial degraders of xenobiotic compounds.
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Affiliation(s)
- Hunter D Whittington
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Mahatam Singh
- BASF Corporation, Research Triangle Park, NC, United States
| | - Chanh Ta
- BASF Corporation, Research Triangle Park, NC, United States
| | - M Andrea Azcárate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - José M Bruno-Bárcena
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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16
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Gorski G, Dailey H, Fisher AT, Schrad N, Saltikov C. Denitrification during infiltration for managed aquifer recharge: Infiltration rate controls and microbial response. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138642. [PMID: 32334223 DOI: 10.1016/j.scitotenv.2020.138642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Managed aquifer recharge (MAR) systems can be designed and operated to improve water supply and quality simultaneously by creating favorable conditions for contaminant removal during infiltration through shallow soils. We present results from laboratory flow-through column experiments, using intact soil cores from two MAR sites, elucidating conditions that are favorable to nitrate (NO3) removal via microbial denitrification during infiltration. Experiments focused on quantitative relations between infiltration rate and the presence or absence of a carbon-rich permeable reactive barrier (PRB) on both amounts and rates of nitrate removal during infiltration and associated shifts in microbial ecology. Experiments were conducted using a range of infiltration rates relevant to MAR (0.3-1.4 m/day), with PRBs made of native soil (NS), woodchips (WC) and a 50:50 mixture of woodchips and native soil (MIX). The latter two (carbon-rich) PRB treatments led to statistically significant increases in the amount of nitrate removed by increasing zero-order denitrification rates, both within the PRB materials and in the underlying soil. The highest fraction of nitrate removal occurred at the lowest infiltration rates for all treatments. However, the highest nitrogen mass removal (∆NL) was observed at 0.4-0.7 m/day for both the WC and MIX treatments. In contrast, the maximum ∆NL for the NS treatment was observed at the lowest infiltration rates measured (~0.3 m/day). Further, both carbon-rich PRBs had a substantial impact on the soil microbial ecology in the underlying soil, with lower overall diversity and a greater relative abundance of groups known to degrade carbon and metabolize nitrogen. These results demonstrate that infiltration rates and carbon availability can combine to create favorable conditions for denitrification during infiltration for MAR and show how these factors shape and sustain the microbial community structures responsible for nutrient cycling in associated soils.
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Affiliation(s)
- Galen Gorski
- Department of Earth and Planetary Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States.
| | - Hannah Dailey
- Department of Earth and Planetary Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Andrew T Fisher
- Department of Earth and Planetary Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Nicole Schrad
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
| | - Chad Saltikov
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, United States
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17
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Boada E, Santos-Clotas E, Bertran S, Cabrera-Codony A, Martín MJ, Bañeras L, Gich F. Potential use of Methylibium sp. as a biodegradation tool in organosilicon and volatile compounds removal for biogas upgrading. CHEMOSPHERE 2020; 240:124908. [PMID: 31726596 DOI: 10.1016/j.chemosphere.2019.124908] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Organosilicon compounds are the most undesirable compounds for the energy recovery of biogas. These compounds are still resistant to biodegradation when biotechnologies are considered for biogas purification. Herein we isolated 52 bacterial species from anaerobic batch enrichment cultures (BEC) saturated with D4 and from an anaerobic lab-scale biotrickling filter (BTF) fed with a gas flow containing D4 as unique carbon source. Among those Methylibium sp. and Pseudomonas aeruginosa showed the highest capacity to remove D4 (53.04% ± 0.03 and 24.42% ± 0.02, respectively). Contrarily, co-culture evaluation treatment for the biodegradation of siloxanes together with volatile organic compounds removed a lower concentration of D4 compared to toluene and limonene, which were completely removed. Remarkably, the siloxane D5 proved to be more biodegradable than D4. Substrates removal values achieved by Methylibium sp. suggested that this bacterial isolate could be used in biological removal technologies of siloxanes.
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Affiliation(s)
- Ellana Boada
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, Campus Montilivi, Maria Aurèlia Capmany 40, E-17003, Girona, Catalonia, Spain
| | - Eric Santos-Clotas
- LEQUIA. Institute of Environment. University of Girona, Campus Montilivi, Maria Aurèlia Capmany 69, E-17003, Girona, Catalonia, Spain
| | - Salvador Bertran
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, Campus Montilivi, Maria Aurèlia Capmany 40, E-17003, Girona, Catalonia, Spain
| | - Alba Cabrera-Codony
- LEQUIA. Institute of Environment. University of Girona, Campus Montilivi, Maria Aurèlia Capmany 69, E-17003, Girona, Catalonia, Spain
| | - Maria J Martín
- LEQUIA. Institute of Environment. University of Girona, Campus Montilivi, Maria Aurèlia Capmany 69, E-17003, Girona, Catalonia, Spain
| | - Lluís Bañeras
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, Campus Montilivi, Maria Aurèlia Capmany 40, E-17003, Girona, Catalonia, Spain
| | - Frederic Gich
- Molecular Microbial Ecology Group (gEMM-IEA), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, Campus Montilivi, Maria Aurèlia Capmany 40, E-17003, Girona, Catalonia, Spain.
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18
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Zhou XK, Li QQ, Dong LM, Yang DQ, Liu L, Fang BZ, Jeon CO, Li WJ, Duan YQ. Pseudorivibacter rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere soil of Camellia sinensis (L.) O. Ktze and emended description of the genus Rivibacter. Int J Syst Evol Microbiol 2019; 70:1071-1078. [PMID: 31755854 DOI: 10.1099/ijsem.0.003878] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, facultative anaerobic, motile and straight rod-shaped bacterium, designated strain C1-9T, was isolated from rhizosphere soil of Camellia sinensis (L.) O. Ktze collected from a tea garden in Huize, south-western PR China. Cells were oxidase-positive and catalase-negative. Growth occurred at 20-40 °C and pH 6.0-10.0, with an optimal growth at 30 °C and pH 7.0. The respiratory quinone was detected as ubiquinone-8 (Q-8). The major fatty acids were identified as summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c or C18 : 1ω6c). The cellular polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids, two unidentified lipids, one unidentified aminophospholipid and one unidentified aminolipid. The polyamine types were detected as 1,8-diaminooctane and 2-hydroxyputrescine. The genomic DNA G+C content was 68.6 mol%. Based on the results of 16S rRNA gene sequence analysis, strain C1-9T (MF687442) showed highest sequence similarity to Rivibacter subsaxonicus DSM 19570T (97.1 %). The phylogenetic tree based on 16S rRNA gene sequences showed that strain C1-9T clustered close to R. subsaxonicus DSM 19570T, Methylibium petroleiphilum CCTCC AB 2014193T and species belonging to the genera Rhizobacter and Piscinibacter. The phylogenomic tree indicated that strain C1-9T formed a clade with R. subsaxonicus. The average nucleotide identity value was 76.0 % between strain C1-9T and R. subsaxonicus DSM 19570T, which is lower than the prokaryotic species delineation threshold of 95.0-96.0 %. The polyphasic taxonomic characteristics indicated that strain C1-9T represents a novel species of a new genus within the order Burkholderiales, for which the name Pseudorivibacter rhizosphaerae gen. nov., sp. nov. (type strain C1-9T = KCTC 62325T=CGMCC 1.13864T) is proposed.
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Affiliation(s)
- Xing-Kui Zhou
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, PR China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, PR China
| | - Qing-Qing Li
- Life Science College, Southwest Forestry University, Kunming 650224, PR China.,Key Laboratory for Conserving Wildlife with Small Populations in Yunnan (Southwest Forestry University), Kunming 650224, PR China
| | - Li-Min Dong
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, PR China
| | - Deng-Qiang Yang
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, PR China
| | - Lan Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Yan-Qing Duan
- China Tobacco Yunnan Industrial Co. Ltd., Kunming, 650231, PR China
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19
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Pelomicrobium methylotrophicum gen. nov., sp. nov. a moderately thermophilic, facultatively anaerobic, lithoautotrophic and methylotrophic bacterium isolated from a terrestrial mud volcano. Extremophiles 2019; 24:177-185. [PMID: 31705207 DOI: 10.1007/s00792-019-01145-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
A novel moderately thermophilic, bacterium, strain SM250T, was isolated from a terrestrial mud volcano, Taman peninsula, Krasnodar region, Russia. Cells of strain SM250T were Gram-negative non-spore forming motile straight rods. Growth was observed at temperatures 30-63 °C (optimum at 50 °C), pH 6.5-10.0 (optimum at pH 8.5) and NaCl concentrations 0-4.5% (w/v) (optimum at 1.0-1.5% (w/v)). The novel isolate grows by aerobic respiration or anaerobic respiration with nitrate as the terminal electron acceptor. Strain SM250T grows by the utilization of methanol, formate and a number of other organic compounds or lithoautotrophically with hydrogen, elemental sulfur or thiosulfate as electron donors. The total size of the genome of the novel isolate was 3,327,116 bp and a genomic DNA G + C content was 64.8 mol%. Analysis of the 16S rRNA gene sequences revealed that strain SM250T belongs to the class Hydrogenophilia within the phylum Proteobacteria, with less than 91% of 16S rRNA gene sequence similarity to any species with validly published name. We propose to assign strain SM250T to a new species of a novel genus Pelomicrobium methylotrophicum gen. nov., sp. nov. The type strain is SM250T (= KCTC 62861T = VKM B-3274T).
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20
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Kucharzyk KH, Rectanus HV, Bartling CM, Rosansky S, Minard-Smith A, Mullins LA, Neil K. Use of omic tools to assess methyl tert-butyl ether (MTBE) degradation in groundwater. JOURNAL OF HAZARDOUS MATERIALS 2019; 378:120618. [PMID: 31301927 DOI: 10.1016/j.jhazmat.2019.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/03/2019] [Accepted: 05/05/2019] [Indexed: 06/10/2023]
Abstract
This study employed innovative technologies to evaluate multiple lines of evidence for natural attenuation (NA) of methyl tertiary-butyl ether (MTBE) in groundwater at the 22 Area of Marine Corps Base (MCB) Camp Pendleton after decommissioning of a biobarrier system. For comparison, data from the 13 Area Gas Station where active treatment of MTBE is occurring was used to evaluate the effectiveness of omic techniques in assessing biodegradation. Overall, the 22 Area Gas Station appeared to be anoxic. MTBE was detected in large portion of the plume. In comparison, concentrations of MTBE at the 13 Area Gas Station were much higher (42,000 μg/L to 2800 μg/L); however, none of the oxygenates were detected. Metagenomic analysis of the indigenous groundwater microbial community revealed the presence of bacterial strains known to aerobically and anaerobically degrade MTBE at both sites. While proteomic analysis at the 22 Area Gas Station showed the presence of proteins of MTBE degrading microorganisms, the MTBE degradative proteins were only found at the 13 Area Gas Station. Taken together, these results provide evidence for previous NA of MTBE in the groundwater at 22 Area Gas Station and demonstrate the effectiveness of innovative-omic technologies to assist monitored NA assessments.
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Affiliation(s)
| | | | | | - Steve Rosansky
- Battelle Memorial Institute, Columbus, OH, United States
| | | | | | - Kenda Neil
- Naval Facilities Engineering Command (NAVFAC) Engineering and Expeditionary Warfare Center (EXWC), Port Huaneme, CA, United States
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21
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Wang Q, Yang M, Song X, Tang S, Yu L. Aerobic and Anaerobic Biodegradation of 1,2-Dibromoethane by a Microbial Consortium under Simulated Groundwater Conditions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16193775. [PMID: 31597267 PMCID: PMC6802363 DOI: 10.3390/ijerph16193775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/24/2019] [Accepted: 09/28/2019] [Indexed: 11/16/2022]
Abstract
This study was conducted to explore the potential for 1,2-Dibromoethane (EDB) biodegradation by an acclimated microbial consortium under simulated dynamic groundwater conditions. The enriched EDB-degrading consortium consisted of anaerobic bacteria Desulfovibrio, facultative anaerobe Chromobacterium, and other potential EDB degraders. The results showed that the biodegradation efficiency of EDB was more than 61% at 15 °C, and the EDB biodegradation can be best described by the apparent pseudo-first-order kinetics. EDB biodegradation occurred at a relatively broad range of initial dissolved oxygen (DO) from 1.2 to 5.1 mg/L, indicating that the microbial consortium had a strong ability to adapt. The addition of 40 mg/L of rhamnolipid and 0.3 mM of sodium lactate increased the biodegradation. A two-phase biodegradation scheme was proposed for the EDB biodegradation in this study: an aerobic biodegradation to carbon dioxide and an anaerobic biodegradation via a two-electron transfer pathway of dihaloelimination. To our knowledge, this is the first study that reported EDB biodegradation by an acclimated consortium under both aerobic and anaerobic conditions, a dynamic DO condition often encountered during enhanced biodegradation of EDB in the field.
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Affiliation(s)
- Qing Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China.
| | - Miaoyan Yang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xin Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China.
| | - Shiyue Tang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lei Yu
- Department of Environmental Engineering, Nanjing Forestry University, Nanjing 210037, China.
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Lee TH, Cao WZ, Tsang DCW, Sheu YT, Shia KF, Kao CM. Emulsified polycolloid substrate biobarrier for benzene and petroleum-hydrocarbon plume containment and migration control - A field-scale study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 666:839-848. [PMID: 30818208 DOI: 10.1016/j.scitotenv.2019.02.160] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/10/2019] [Accepted: 02/10/2019] [Indexed: 05/06/2023]
Abstract
The objective of this field-scale study was to assess the effectiveness of applying an emulsified polycolloid substrate (EPS; containing cane molasses, soybean oil, and surfactants) biobarrier in the control and remediation of a petroleum-hydrocarbon plume in natural waters. An abandoned petrochemical manufacturing facility site was contaminated by benzene and other petroleum products due to a leakage from a storage tank. Because benzene is a petroleum hydrocarbon with a high migration ability, it was used as the target compound in the field-scale study. Batch partition and sorption experiment results indicated that the EPS to water partition coefficient for benzene was 232 mg/mg at 25 °C. This suggests that benzene had a higher sorption affinity to EPS, which decreased the benzene concentrations in groundwater. The EPS solution was pressure-injected into three remediation wells (RWs; 150 L EPS in 800 L groundwater). Groundwater samples were collected from an upgradient background well, two downgradient monitor wells (MWs), and the three RWs for analyses. EPS injection increased total organic carbon (TOC) concentrations (up to 786 mg/L) in groundwater, which also resulted in the formation of anaerobic conditions. An abrupt drop in benzene concentration (from 6.9 to below 0.04 mg/L) was observed after EPS supplementation in the RWs due to both sorption and biodegradation mechanisms. Results show that the EPS supplement increased total viable bacteria and enhanced bioremediation efficiency, which accounted for the observed decrease in benzene concentration. The first-order decay rate in RW1 increased from 0.003 to 0.023 d-1 after EPS application. Injection of EPS resulted in significant growth of indigenous bacteria, and 23 petroleum-hydrocarbon-degrading bacterial species were detected, which enhanced the in situ benzene biodegradation efficiency. Results demonstrate that the EPS biobarrier can effectively contain a petroleum-hydrocarbon plume and prevent its migration to downgradient areas, which reduces the immediate risk presented to downgradient receptors.
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Affiliation(s)
- T H Lee
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - W Z Cao
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - D C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Y T Sheu
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - K F Shia
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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23
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Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries. Genes (Basel) 2019; 10:genes10040299. [PMID: 31013797 PMCID: PMC6523138 DOI: 10.3390/genes10040299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022] Open
Abstract
The concept of the human oral microbiome was applied to understand health and disease, lifestyles, and dietary habits throughout part of human history. In the present study, we augment the understanding of ancient oral microbiomes by characterizing human dental calculus samples recovered from the ancient Abbey of Badia Pozzeveri (central Italy), with differences in socioeconomic status, time period, burial type, and sex. Samples dating from the Middle Ages (11th century) to the Industrial Revolution era (19th century) were characterized using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Consistent with previous studies, individuals from Badia Pozzeveri possessed commensal oral bacteria that resembled modern oral microbiomes. These results suggest that members of the oral microbiome are ubiquitous despite differences in geographical regions, time period, sex, and socioeconomic status. The presence of fecal bacteria could be in agreement with poor hygiene practices, consistent with the time period. Respiratory tract, nosocomial, and other rare pathogens detected in the dental calculus samples are intriguing and could suggest subject-specific comorbidities that could be reflected in the oral microbiome.
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24
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Lee TH, Tsang DCW, Chen WH, Verpoort F, Sheu YT, Kao CM. Application of an emulsified polycolloid substrate biobarrier to remediate petroleum-hydrocarbon contaminated groundwater. CHEMOSPHERE 2019; 219:444-455. [PMID: 30551111 DOI: 10.1016/j.chemosphere.2018.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Emulsified polycolloid substrate (EPS) was developed and applied in situ to form a biobarrier for the containment and enhanced bioremediation of a petroleum-hydrocarbon plume. EPS had a negative zeta potential (-35.7 mv), which promoted its even distribution after injection. Batch and column experiments were performed to evaluate the effectiveness of EPS on toluene containment and biodegradation. The EPS-to-water partition coefficient for toluene (target compound) was 943. Thus, toluene had a significant sorption affinity to EPS, which caused reduced toluene concentration in water phase in the EPS/water system. Groundwater containing toluene (18 mg/L) was pumped into the three-column system at a flow rate of 0.28 mL/min, while EPS was injected into the second column to form a biobarrier. A significant reduction of toluene concentration to 0.1 mg/L was observed immediately after EPS injection. This indicates that EPS could effectively contain toluene plume and prevent its further migration to farther downgradient zone. Approximately 99% of toluene was removed after 296 PVs of operation via sorption, natural attenuation, and EPS-enhanced biodegradation. Increase in total organic carbon and bacteria were also observed after EPS supplement. Supplement of EPS resulted in a growth of petroleum-hydrocarbon degrading bacteria, which enhanced the toluene biodegradation.
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Affiliation(s)
- T H Lee
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - D C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - W H Chen
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - F Verpoort
- Department of Applied Chemistry, Wuhan University of Technology, Wuhan, China
| | - Y T Sheu
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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Rhizosphere Microbial Response to Multiple Metal(loid)s in Different Contaminated Arable Soils Indicates Crop-Specific Metal-Microbe Interactions. Appl Environ Microbiol 2018; 84:AEM.00701-18. [PMID: 30291123 DOI: 10.1128/aem.00701-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/01/2018] [Indexed: 02/01/2023] Open
Abstract
In this study, we sampled rhizosphere soils from seven different agricultural fields adjacent to mining areas and cultivated with different crops (corn, rice, or soybean), to study the interactions among the innate microbiota, soil chemical properties, plants, and metal contamination. The rhizosphere bacterial communities were characterized by Illumina sequencing of the 16S rRNA genes, and their interactions with the local environments, including biotic and abiotic factors, were analyzed. Overall, these soils were heavily contaminated with multiple metal(loid)s, including V, Cr, Cu, Sb, Pb, Cd, and As. The interactions between environmental parameters and microbial communities were identified using multivariate regression tree analysis, canonical correspondence analysis, and network analysis. Notably, metal-microbe interactions were observed to be crop specific. The rhizosphere communities were strongly correlated with V and Cr levels, although these sites were contaminated from Sb and Zn/Pb mining, suggesting that these two less-addressed metals may play important roles in shaping the rhizosphere microbiota. Members of Gaiellaceae cooccurred with other bacterial taxa (biotic interactions) and several metal(loid)s, suggesting potential metal(loid) resistance or cycling involving this less-well-known taxon.IMPORTANCE The rhizosphere is the "hub" for plant-microbe interactions and an active region for exchange of nutrients and energy between soil and plants. In arable soils contaminated by mining activities, the rhizosphere may be an important barrier resisting metal uptake. Therefore, the responses of the rhizosphere microbiota to metal contamination involve important biogeochemical processes, which can affect metal bioavailability and thus impact food safety. However, understanding these processes remains a challenge. The current study illustrates that metal-microbe interactions may be crop specific and some less-addressed metals, such as V and Cr, may play important roles in shaping bacterial communities. The current study provides new insights into metal-microbe interactions and contributes to future implementation and monitoring efforts in contaminated arable soils.
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Cousins CR, Fogel M, Bowden R, Crawford I, Boyce A, Cockell C, Gunn M. Biogeochemical probing of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland. GEOBIOLOGY 2018; 16:507-521. [PMID: 29856116 DOI: 10.1111/gbi.12291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
We investigated bacterial and archaeal communities along an ice-fed surficial hot spring at Kverkfjöll volcano-a partially ice-covered basaltic volcano at Vatnajökull glacier, Iceland, using biomolecular (16S rRNA, apsA, mcrA, amoA, nifH genes) and stable isotope techniques. The hot spring environment is characterized by high temperatures and low dissolved oxygen concentrations at the source (68°C and <1 mg/L (±0.1%)) changing to lower temperatures and higher dissolved oxygen downstream (34.7°C and 5.9 mg/L), with sulfate the dominant anion (225 mg/L at the source). Sediments are comprised of detrital basalt, low-temperature alteration phases and pyrite, with <0.4 wt. % total organic carbon (TOC). 16S rRNA gene profiles reveal that organisms affiliated with Hydrogenobaculum (54%-87% bacterial population) and Thermoproteales (35%-63% archaeal population) dominate the micro-oxic hot spring source, while sulfur-oxidizing archaea (Sulfolobales, 57%-82%), and putative sulfur-oxidizing and heterotrophic bacterial groups dominate oxic downstream environments. The δ13 Corg (‰ V-PDB) values for sediment TOC and microbial biomass range from -9.4‰ at the spring's source decreasing to -12.6‰ downstream. A reverse effect isotope fractionation of ~3‰ between sediment sulfide (δ34 S ~0‰) and dissolved water sulfate (δ34 S +3.2‰), and δ18 O values of ~ -5.3‰ suggest pyrite forms abiogenically from volcanic sulfide, followed by abiogenic and microbial oxidation. These environments represent an unexplored surficial geothermal environment analogous to transient volcanogenic habitats during putative "snowball Earth" scenarios and volcano-ice geothermal environments on Mars.
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Affiliation(s)
- Claire R Cousins
- School of Earth and Environmental Science, University of St Andrews, St Andrews, UK
| | - Marilyn Fogel
- Department of Earth Sciences, University of California Riverside, Riverside, California
| | - Roxane Bowden
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, District of Columbia
| | | | | | - Charles Cockell
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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Kou S, Vincent G, Gonzalez E, Pitre FE, Labrecque M, Brereton NJB. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial. Front Microbiol 2018; 9:366. [PMID: 29545788 PMCID: PMC5838024 DOI: 10.3389/fmicb.2018.00366] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/16/2018] [Indexed: 11/27/2022] Open
Abstract
Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.
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Affiliation(s)
- Shumeng Kou
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Gilles Vincent
- Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
| | - Frederic E. Pitre
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de Recherche en Biologie Végétale, Montreal Botanical Garden, Montréal, QC, Canada
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Lee KH, Ab Samad LS, Lwin PM, Riedel SF, Magin A, Bashir M, Vaishampayan PA, Lin WJ. On the Rocks: Microbiological Quality and Microbial Diversity of Packaged Ice in Southern California. J Food Prot 2017; 80:1041-1049. [PMID: 28517954 DOI: 10.4315/0362-028x.jfp-16-295] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ice is defined as a food and is frequently used in direct contact with food and beverages. Packaged ice is commercially produced and can be easily found in grocery and convenience stores. However, the quality and safety of packaged ice products is not consistent. The Packaged Ice Quality Control Standards manual (PIQCS) published by the International Packaged Ice Association provides the quality and processing standards for packaged ice produced by its members. Packaged ice produced on the premise of stores (on-site packaged ice) is not required to be in compliance with these standards. In this study, packaged ice produced by manufacturing plants or by in-store bagger (ISB) machines and on-site packaged ice were compared for their microbiological quality and microbial diversity. Our results revealed that 19% of the 120 on-site packaged ice samples did not meet the PIQCS microbial limit of 500 CFU/mL (or g) and also the absence of coliforms and Escherichia coli . Staphylococci were found in 34% of the on-site packaged ice samples, most likely through contamination from the packaging workers. None of the ISB and manufactured packaged ice samples had unacceptable microbial levels, and all were devoid of staphylococci. Salmonella was absent in all samples analyzed in this study. Microbial community analysis of ice based on 16S/18S rRNA targeted sequencing revealed a much higher microbial diversity and abundance in the on-site packaged ice than in the ISB ice. Proteobacteria, especially Alphaproteobacteria and Betaproteobacteria, were the dominant bacterial groups in all samples tested. Most of these bacteria were oligotrophic; however, a few opportunistic or potential pathogens were found at low levels in the on-site packaged ice but not in the ISB packaged ice. The types of microbes identified may provide information needed to investigate potential sources of contamination. Our data also suggest a need for enforcement of processing standards during the on-site packaging of ice.
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Affiliation(s)
- Kun Ho Lee
- 1 Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, USA (ORCID; http://orcid.org/0000-0003-0001-3488 [W.-J.L.])
| | - Liana S Ab Samad
- 1 Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, USA (ORCID; http://orcid.org/0000-0003-0001-3488 [W.-J.L.])
| | - Phillip M Lwin
- 1 Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, USA (ORCID; http://orcid.org/0000-0003-0001-3488 [W.-J.L.])
| | - Stefan F Riedel
- 1 Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, USA (ORCID; http://orcid.org/0000-0003-0001-3488 [W.-J.L.])
| | - Ashley Magin
- 1 Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, USA (ORCID; http://orcid.org/0000-0003-0001-3488 [W.-J.L.])
| | - Mina Bashir
- 2 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, USA.,3 Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
| | - Parag A Vaishampayan
- 2 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, USA
| | - Wei-Jen Lin
- 1 Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, USA (ORCID; http://orcid.org/0000-0003-0001-3488 [W.-J.L.])
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Röthig T, Yum LK, Kremb SG, Roik A, Voolstra CR. Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment. Sci Rep 2017; 7:44714. [PMID: 28303925 PMCID: PMC5356181 DOI: 10.1038/srep44714] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/13/2017] [Indexed: 11/16/2022] Open
Abstract
Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L-1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment.
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Affiliation(s)
- Till Röthig
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Lauren K. Yum
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Stephan G. Kremb
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Anna Roik
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Christian R. Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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30
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Kasai D, Imai S, Asano S, Tabata M, Iijima S, Kamimura N, Masai E, Fukuda M. Identification of natural rubber degradation gene in Rhizobacter gummiphilus NS21. Biosci Biotechnol Biochem 2017; 81:614-620. [DOI: 10.1080/09168451.2016.1263147] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
A Gram-negative rubber-degrading bacterium, Rhizobacter gummiphilus NS21 grew and produced aldehyde metabolites on a deproteinized natural rubber (DPNR)-overlay agar medium forming a clearing zone. A transposon-insertion mutant, which had lost the ability to degrade DPNR, was isolated to identify the rubber degradation genes. Sequencing analysis indicated that the transposon was inserted into a putative oxygenase gene, latA. The deduced amino acid sequence of latA has 36% identity with that of roxA, which encodes a rubber oxygenase of Xanthomonas sp. strain 35Y. Phylogenetic analysis revealed that LatA constitutes a distinct group from RoxA. Heterologous expression in a Methylibium host and deletion analysis of latA indicated that the latA product is responsible for the depolymerization of DPNR. The quantitative reverse transcription-PCR analysis indicated that the transcription of latA is induced during the growth on DPNR. These results strongly suggest that latA is directly involved in the degradation of rubber in NS21.
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Affiliation(s)
- Daisuke Kasai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Shunsuke Imai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Shota Asano
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Michiro Tabata
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - So Iijima
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Masao Fukuda
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
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31
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Agafonova NV, Doronina NV, Kaparullina EN, Fedorov DN, Gafarov AB, Sazonova OI, Sokolov SL, Trotsenko YA. A novel Delftia plant symbiont capable of autotrophic methylotrophy. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717010039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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32
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Sheu SY, Li YS, Chen WM. Piscinibacterium candidicorallinum gen. nov., sp. nov., a member of the order Burkholderiales isolated from a fish pond. Int J Syst Evol Microbiol 2016; 66:5260-5267. [PMID: 27665758 DOI: 10.1099/ijsem.0.001505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated LYH-15T was isolated from a freshwater fish pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of LYH-15T were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, poly-β-hydroxybutyrate-containing, non-spore forming, straight rods and formed light-coral-colored colonies. Growth occurred at 15-40 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and with 0-0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that LYH-15T forms a distinct phyletic line within the order Burkholderiales, with less than 94 % sequence similarity to its closest relatives with validly published names. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8 and the DNA G+C content was 63.8 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized lipids. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of the genotypic and phenotypic data, LYH-15T represents a novel species of a new genus in the order Burkholderiales, for which the name Piscinibacterium candidicorallinum gen. nov., sp. nov. is proposed. The type strain is LYH-15T (=BCRC 80969T=LMG 29480T=KCTC 52168T).
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Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Yi-Shu Li
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142, Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
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Alfonso-Gordillo G, Cristiani-Urbina E, Flores-Ortiz CM, Peralta H, Cancino-Díaz JC, Cruz-Maya JA, Jan-Roblero J. Stenotrophomonas maltophilia isolated from gasoline-contaminated soil is capable of degrading methyl tert-butyl ether. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Joshi G, Schmidt R, Scow KM, Denison MS, Hristova KR. Effect of benzene and ethylbenzene on the transcription of methyl-tert-butyl ether degradation genes of Methylibium petroleiphilum PM1. MICROBIOLOGY-SGM 2016; 162:1563-1571. [PMID: 27450417 DOI: 10.1099/mic.0.000338] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Methyl-tert-butyl ether (MTBE) and its degradation by-product, tert-butyl alcohol (TBA), are widespread contaminants detected frequently in groundwater in California. Since MTBE was used as a fuel oxygenate for almost two decades, leaking underground fuel storage tanks are an important source of contamination. Gasoline components such as BTEX (benzene, toluene, ethylbenzene and xylenes) are often present in mixtures with MTBE and TBA. Investigations of interactions between BTEX and MTBE degradation have not yielded consistent trends, and the molecular mechanisms of BTEX compounds' impact on MTBE degradation are not well understood. We investigated trends in transcription of biodegradation genes in the MTBE-degrading bacterium, Methylibium petroleiphilum PM1 upon exposure to MTBE, TBA, ethylbenzene and benzene as individual compounds or in mixtures. We designed real-time quantitative PCR assays to target functional genes of strain PM1 and provide evidence for induction of genes mdpA (MTBE monooxygenase), mdpJ (TBA hydroxylase) and bmoA (benzene monooxygenase) in response to MTBE, TBA and benzene, respectively. Delayed induction of mdpA and mdpJ transcription occurred with mixtures of benzene and MTBE or TBA, respectively. bmoA transcription was similar in the presence of MTBE or TBA with benzene as in their absence. Our results also indicate that ethylbenzene, previously proposed as an inhibitor of MTBE degradation in some bacteria, inhibits transcription of mdpA, mdpJ and bmoAgenes in strain PM1.
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Affiliation(s)
- Geetika Joshi
- Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Radomir Schmidt
- Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Kate M Scow
- Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Michael S Denison
- Department of Environmental Toxicology, One Shields Avenue, University of California, Davis, CA 95616, USA
| | - Krassimira R Hristova
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.,Department of Land, Air and Water Resources, One Shields Avenue, University of California, Davis, CA 95616, USA
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Rime T, Hartmann M, Frey B. Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier. THE ISME JOURNAL 2016; 10:1625-41. [PMID: 26771926 PMCID: PMC4918445 DOI: 10.1038/ismej.2015.238] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/09/2015] [Accepted: 11/08/2015] [Indexed: 11/09/2022]
Abstract
Rapid disintegration of alpine glaciers has led to the formation of new terrain consisting of mineral debris colonized by microorganisms. Despite the importance of microbial pioneers in triggering the formation of terrestrial ecosystems, their sources (endogenous versus exogenous) and identities remain elusive. We used 454-pyrosequencing to characterize the bacterial and fungal communities in endogenous glacier habitats (ice, sub-, supraglacial sediments and glacier stream leaving the glacier forefront) and in atmospheric deposition (snow, rain and aeolian dust). We compared these microbial communities with those occurring in recently deglaciated barren soils before and after snow melt (snow-covered soil and barren soil). Atmospheric bacteria and fungi were dominated by plant-epiphytic organisms and differed from endogenous glacier habitats and soils indicating that atmospheric input of microorganisms is not a major source of microbial pioneers in newly formed soils. We found, however, that bacterial communities in newly exposed soils resembled those of endogenous habitats, which suggests that bacterial pioneers originating from sub- and supraglacial sediments contributed to the colonization of newly exposed soils. Conversely, fungal communities differed between habitats suggesting a lower dispersal capability than bacteria. Yeasts putatively adapted to cold habitats characteristic of snow and supraglacial sediments were similar, despite the fact that these habitats were not spatially connected. These findings suggest that environmental filtering selects particular fungi in cold habitats. Atmospheric deposition provided important sources of dissolved organic C, nitrate and ammonium. Overall, microbial colonizers triggering soil development in alpine environments mainly originate from endogenous glacier habitats, whereas atmospheric deposition contributes to the establishment of microbial communities by providing sources of C and N.
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Affiliation(s)
- Thomas Rime
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Martin Hartmann
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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36
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Chakraborty S, Britton M, Martínez-García PJ, Dandekar AM. Deep RNA-Seq profile reveals biodiversity, plant-microbe interactions and a large family of NBS-LRR resistance genes in walnut (Juglans regia) tissues. AMB Express 2016; 6:12. [PMID: 26883051 PMCID: PMC4755957 DOI: 10.1186/s13568-016-0182-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/29/2016] [Indexed: 11/10/2022] Open
Abstract
Deep RNA-Seq profiling, a revolutionary method used for quantifying transcriptional levels, often includes non-specific transcripts from other co-existing organisms in spite of stringent protocols. Using the recently published walnut genome sequence as a filter, we present a broad analysis of the RNA-Seq derived transcriptome profiles obtained from twenty different tissues to extract the biodiversity and possible plant-microbe interactions in the walnut ecosystem in California. Since the residual nature of the transcripts being analyzed does not provide sufficient information to identify the exact strain, inferences made are constrained to the genus level. The presence of the pathogenic oomycete Phytophthora was detected in the root through the presence of a glyceraldehyde-3-phosphate dehydrogenase. Cryptococcus, the causal agent of cryptococcosis, was found in the catkins and vegetative buds, corroborating previous work indicating that the plant surface supported the sexual cycle of this human pathogen. The RNA-Seq profile revealed several species of the endophytic nitrogen fixing Actinobacteria. Another bacterial species implicated in aerobic biodegradation of methyl tert-butyl ether (Methylibium petroleiphilum) is also found in the root. RNA encoding proteins from the pea aphid were found in the leaves and vegetative buds, while a serine protease from mosquito with significant homology to a female reproductive tract protease from Drosophila mojavensis in the vegetative bud suggests egg-laying activities. The comprehensive analysis of RNA-seq data present also unraveled detailed, tissue-specific information of ~400 transcripts encoded by the largest family of resistance (R) genes (NBS-LRR), which possibly rationalizes the resistance of the specific walnut plant to the pathogens detected. Thus, we elucidate the biodiversity and possible plant-microbe interactions in several walnut (Juglans regia) tissues in California using deep RNA-Seq profiling.
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Affiliation(s)
| | - Monica Britton
- />UC Davis Genome Center Bioinformatics Core Facility, Davis, CA 95616 USA
| | | | - Abhaya M. Dandekar
- />Plant Sciences Department, University of California, Davis, CA 95616 USA
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Alcaraz LD, Martínez-Sánchez S, Torres I, Ibarra-Laclette E, Herrera-Estrella L. The Metagenome of Utricularia gibba's Traps: Into the Microbial Input to a Carnivorous Plant. PLoS One 2016; 11:e0148979. [PMID: 26859489 PMCID: PMC4747601 DOI: 10.1371/journal.pone.0148979] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/26/2016] [Indexed: 02/01/2023] Open
Abstract
The genome and transcriptome sequences of the aquatic, rootless, and carnivorous plant Utricularia gibba L. (Lentibulariaceae), were recently determined. Traps are necessary for U. gibba because they help the plant to survive in nutrient-deprived environments. The U. gibba's traps (Ugt) are specialized structures that have been proposed to selectively filter microbial inhabitants. To determine whether the traps indeed have a microbiome that differs, in composition or abundance, from the microbiome in the surrounding environment, we used whole-genome shotgun (WGS) metagenomics to describe both the taxonomic and functional diversity of the Ugt microbiome. We collected U. gibba plants from their natural habitat and directly sequenced the metagenome of the Ugt microbiome and its surrounding water. The total predicted number of species in the Ugt was more than 1,100. Using pan-genome fragment recruitment analysis, we were able to identify to the species level of some key Ugt players, such as Pseudomonas monteilii. Functional analysis of the Ugt metagenome suggests that the trap microbiome plays an important role in nutrient scavenging and assimilation while complementing the hydrolytic functions of the plant.
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Affiliation(s)
- Luis David Alcaraz
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70–275, 04510, Ciudad Universitaria, Ciudad de México, México
| | - Shamayim Martínez-Sánchez
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70–275, 04510, Ciudad Universitaria, Ciudad de México, México
| | - Ignacio Torres
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, 58190, Morelia, Michoacán, México
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología, A.C, 91070, Carretera antigua a Coatepec 351, El Haya Xalapa, Veracruz, México
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Km 9.6 Carretera Irapuato-León, 36821, Irapuato, Guanajuato, México
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Km 9.6 Carretera Irapuato-León, 36821, Irapuato, Guanajuato, México
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Leung HTC, Maas KR, Wilhelm RC, Mohn WW. Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils. THE ISME JOURNAL 2016; 10:363-75. [PMID: 26274049 PMCID: PMC4737928 DOI: 10.1038/ismej.2015.118] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/09/2022]
Abstract
Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here, we investigated the effects of three timber-harvesting methods, varying in the degree of organic matter removal, on putatively hemicellulolytic bacterial and fungal populations 10 or more years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated (13)C from labeled hemicellulose, analyzing (13)C-enriched phospholipid fatty acids, bacterial 16 S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, whereas distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears resilient.
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Affiliation(s)
- Hilary T C Leung
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kendra R Maas
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Roland C Wilhelm
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
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Yilmaz P, Yarza P, Rapp JZ, Glöckner FO. Expanding the World of Marine Bacterial and Archaeal Clades. Front Microbiol 2016; 6:1524. [PMID: 26779174 PMCID: PMC4705458 DOI: 10.3389/fmicb.2015.01524] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/18/2015] [Indexed: 12/18/2022] Open
Abstract
Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.
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Affiliation(s)
- Pelin Yilmaz
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology Bremen, Germany
| | | | - Josephine Z Rapp
- HGF-MPG Joint Research Group for Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen and the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven, Germany
| | - Frank O Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine MicrobiologyBremen, Germany; Life Sciences and Chemistry, Jacobs UniversityBremen, Germany
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Fu LY, Wu CY, Zhou YX, Zuo JE, Ding Y. Treatment of petrochemical secondary effluent by an up-flow biological aerated filter (BAF). WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 73:2031-2038. [PMID: 27120658 DOI: 10.2166/wst.2016.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this study, petrochemical secondary effluent was treated by a 55 cm diameter pilot-scale biological aerated filter (BAF) with a media depth of 220 cm. Volcanic rock grains were filled as the BAF media. Median removal efficiency of chemical oxygen demand (COD) and ammonia nitrogen (NH3-N) was 29.35 and 57.98%, respectively. Moreover, the removal profile of the COD, NH3-N, total nitrogen and total organic carbon demonstrated that the filter height of 140 cm made up to 90% of the total removal efficiency of the final effluent. By gas chromatography-mass spectrometry, removal efficiencies of 2-chloromethyl-1,3-dioxolane, and benzonitrile, indene and naphthalene were obtained, ranging from 30.12 to 63.01%. The biomass and microbial activity of the microorganisms on the filter media were in general reduced with increasing filter height, which is consistent with the removal profile of the contaminants. The detected genera Defluviicoccus, Betaproteobacteria_unclassified and the Blastocatella constituted 1.86-6.75% of the identified gene, enhancing the COD and nitrogen removal in BAF for treating petrochemical secondary effluent.
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Affiliation(s)
- L Y Fu
- School of Environment, Tsinghua University, Beijing 100084, China; Research Center of Water Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - C Y Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China E-mail: ; Research Center of Water Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Y X Zhou
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China E-mail: ; Research Center of Water Pollution Control Technology, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - J E Zuo
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Y Ding
- College of Architecture and Civil Engineering, Beijing University of Technology, Beijing 100124, China
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Szabó Z, Gyula P, Robotka H, Bató E, Gálik B, Pach P, Pekker P, Papp I, Bihari Z. Draft genome sequence of Methylibium sp. strain T29, a novel fuel oxygenate-degrading bacterial isolate from Hungary. Stand Genomic Sci 2015. [PMID: 26221420 PMCID: PMC4517660 DOI: 10.1186/s40793-015-0023-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Methylibium sp. strain T29 was isolated from a gasoline-contaminated aquifer and proved to have excellent capabilities in degrading some common fuel oxygenates like methyl tert-butyl ether, tert-amyl methyl ether and tert-butyl alcohol along with other organic compounds. Here, we report the draft genome sequence of M. sp. strain T29 together with the description of the genome properties and its annotation. The draft genome consists of 608 contigs with a total size of 4,449,424 bp and an average coverage of 150×. The genome exhibits an average G + C content of 68.7 %, and contains 4754 protein coding and 52 RNA genes, including 48 tRNA genes. 71 % of the protein coding genes could be assigned to COG (Clusters of Orthologous Groups) categories. A formerly unknown circular plasmid designated as pT29A was isolated and sequenced separately and found to be 86,856 bp long.
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Affiliation(s)
- Zsolt Szabó
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Péter Gyula
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Hermina Robotka
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Emese Bató
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Bence Gálik
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Péter Pach
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Péter Pekker
- Materials Science Research Group, Hungarian Academy of Sciences-University of Miskolc, Miskolc, Hungary
| | - Ildikó Papp
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
| | - Zoltán Bihari
- Bay Zoltán Nonprofit Ltd. for Applied Research, Budapest, Hungary
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Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway. Appl Environ Microbiol 2015; 81:6241-52. [PMID: 26150458 DOI: 10.1128/aem.01822-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/26/2015] [Indexed: 11/20/2022] Open
Abstract
In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs.
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Metagenomic Sequencing Unravels Gene Fragments with Phylogenetic Signatures of O2-Tolerant NiFe Membrane-Bound Hydrogenases in Lacustrine Sediment. Curr Microbiol 2015; 71:296-302. [PMID: 26044993 PMCID: PMC4486115 DOI: 10.1007/s00284-015-0846-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/19/2015] [Indexed: 11/13/2022]
Abstract
Many promising hydrogen technologies utilising hydrogenase enzymes have been slowed by the fact that most hydrogenases are extremely sensitive to O2. Within the group 1 membrane-bound NiFe hydrogenase, naturally occurring tolerant enzymes do exist, and O2 tolerance has been largely attributed to changes in iron–sulphur clusters coordinated by different numbers of cysteine residues in the enzyme’s small subunit. Indeed, previous work has provided a robust phylogenetic signature of O2 tolerance [1], which when combined with new sequencing technologies makes bio prospecting in nature a far more viable endeavour. However, making sense of such a vast diversity is still challenging and could be simplified if known species with O2-tolerant enzymes were annotated with information on metabolism and natural environments. Here, we utilised a bioinformatics approach to compare O2-tolerant and sensitive membrane-bound NiFe hydrogenases from 177 bacterial species with fully sequenced genomes for differences in their taxonomy, O2 requirements, and natural environment. Following this, we interrogated a metagenome from lacustrine surface sediment for novel hydrogenases via high-throughput shotgun DNA sequencing using the Illumina™ MiSeq platform. We found 44 new NiFe group 1 membrane-bound hydrogenase sequence fragments, five of which segregated with the tolerant group on the phylogenetic tree of the enzyme’s small subunit, and four with the large subunit, indicating de novo O2-tolerant protein sequences that could help engineer more efficient hydrogenases.
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Careghini A, Saponaro S, Sezenna E, Daghio M, Franzetti A, Gandolfi I, Bestetti G. Lab-scale tests and numerical simulations for in situ treatment of polluted groundwater. JOURNAL OF HAZARDOUS MATERIALS 2015; 287:162-170. [PMID: 25644032 DOI: 10.1016/j.jhazmat.2015.01.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 12/23/2014] [Accepted: 01/11/2015] [Indexed: 06/04/2023]
Abstract
Methyl tert-butyl ether (MTBE) is used at significant percentages as an additive of unleaded gasoline. The physical-chemical properties of the substance (water solubility, soil organic carbon-water partition coefficient) cause high mobility and high concentrations in groundwater. Laboratory scale batch and column tests and mathematical modeling were performed to study the feasibility of a biobarrier (BB), that is an in situ permeable biological barrier with or without inoculation, for the remediation of MTBE and other gasoline-derived pollutants (benzene, toluene, ethylbenzene, o-xylene and m+p-xylenes, BTEXs) polluted groundwater and to estimate kinetic constants. The experimental results showed simultaneous biodegradation of MTBE and BTEXs, with similar removals in the uninoculated and the inoculated systems. Ranges for the first order kinetic removal were obtained for MTBE ((0.18±0.02)/(0.28±0.11d(-1))), B ((0.39±0.12)/(0.56±0.12d(-1))), T ((0.51±0.03)/(0.78±0.15d(-1))), E ((0.46±0.18)/(1.57±0.21d(-1))), o-X ((0.24±0.08)/(0.64±0.09d(-1))) and m+p-X ((0.20±0.04)/(1.21±0.04d(-1))). The results of the laboratory tests allowed to improve mathematical modeling in order to design a full-scale BB at a gasoline-contaminated site.
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Affiliation(s)
- A Careghini
- Politecnico di Milano, DICA Sez. Ambientale, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - S Saponaro
- Politecnico di Milano, DICA Sez. Ambientale, Piazza Leonardo da Vinci 32, 20133 Milano, Italy.
| | - E Sezenna
- Politecnico di Milano, DICA Sez. Ambientale, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - M Daghio
- Università degli Studi Milano-Bicocca, Dipartimento di Scienze dell'Ambiente e del Territorio, Piazza della Scienza 1, 20126 Milano, Italy
| | - A Franzetti
- Università degli Studi Milano-Bicocca, Dipartimento di Scienze dell'Ambiente e del Territorio, Piazza della Scienza 1, 20126 Milano, Italy
| | - I Gandolfi
- Università degli Studi Milano-Bicocca, Dipartimento di Scienze dell'Ambiente e del Territorio, Piazza della Scienza 1, 20126 Milano, Italy
| | - G Bestetti
- Università degli Studi Milano-Bicocca, Dipartimento di Scienze dell'Ambiente e del Territorio, Piazza della Scienza 1, 20126 Milano, Italy
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Good NM, Lamb A, Beck DAC, Martinez-Gomez NC, Kalyuzhnaya MG. C₁-Pathways in Methyloversatilis universalis FAM5: Genome Wide Gene Expression and Mutagenesis Studies. Microorganisms 2015; 3:175-97. [PMID: 27682085 PMCID: PMC5023235 DOI: 10.3390/microorganisms3020175] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/17/2015] [Accepted: 03/26/2015] [Indexed: 11/25/2022] Open
Abstract
Methyloversatilis universalis FAM5 utilizes single carbon compounds such as methanol or methylamine as a sole source of carbon and energy. Expression profiling reveals distinct sets of genes altered during growth on methylamine vs methanol. As expected, all genes for the N-methylglutamate pathway were induced during growth on methylamine. Among other functions responding to the aminated source of C1-carbon, are a heme-containing amine dehydrogenase (Qhp), a distant homologue of formaldehyde activating enzyme (Fae3), molybdenum-containing formate dehydrogenase, ferredoxin reductase, a set of homologues to urea/ammonium transporters and amino-acid permeases. Mutants lacking one of the functional subunits of the amine dehydrogenase (ΔqhpA) or Δfae3 showed no growth defect on C1-compounds. M. universalis FAM5 strains with a lesion in the H4-folate pathway were not able to use any C1-compound, methanol or methylamine. Genes essential for C1-assimilation (the serine cycle and glyoxylate shunt) and H4MTP-pathway for formaldehyde oxidation showed similar levels of expression on both C1-carbon sources. M. universalis FAM5 possesses three homologs of the formaldehyde activating enzyme, a key enzyme of the H4MTP-pathway. Strains lacking the canonical Fae (fae1) lost the ability to grow on both C1-compounds. However, upon incubation on methylamine the fae1-mutant produced revertants (Δfae1R), which regained the ability to grow on methylamine. Double and triple mutants (Δfae1RΔfae3, or Δfae1RΔfae2 or Δfae1RΔfae2Δfae3) constructed in the revertant strain background showed growth similar to the Δfae1R phenotype. The metabolic pathways for utilization of methanol and methylamine in Methyloversatilis universalis FAM5 are reconstructed based on these gene expression and phenotypic data.
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Affiliation(s)
- Nathan M. Good
- Department of Microbiology, University of Washington, Seattle, WA 98195-1700, USA; E-Mails: (N.M.G.); (A.L.)
| | - Andrew Lamb
- Department of Microbiology, University of Washington, Seattle, WA 98195-1700, USA; E-Mails: (N.M.G.); (A.L.)
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-7735, USA; E-Mails: (D.A.C.B.); (N.C.M.G.)
| | - David A. C. Beck
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-7735, USA; E-Mails: (D.A.C.B.); (N.C.M.G.)
- eScience Institute, University of Washington, Seattle, WA 98195-1570, USA
| | - N. Cecilia Martinez-Gomez
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195-7735, USA; E-Mails: (D.A.C.B.); (N.C.M.G.)
| | - Marina G. Kalyuzhnaya
- Department of Microbiology, University of Washington, Seattle, WA 98195-1700, USA; E-Mails: (N.M.G.); (A.L.)
- Biology Department, San Diego State University, North Life Science Room 401, San Diego, CA 92182-4614, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-619-594-5626
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46
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Nayak DD, Marx CJ. Experimental Horizontal Gene Transfer of Methylamine Dehydrogenase Mimics Prevalent Exchange in Nature and Overcomes the Methylamine Growth Constraints Posed by the Sub-Optimal N-Methylglutamate Pathway. Microorganisms 2015; 3:60-79. [PMID: 27682079 PMCID: PMC5023228 DOI: 10.3390/microorganisms3010060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/16/2015] [Accepted: 02/16/2015] [Indexed: 12/14/2022] Open
Abstract
Methylamine plays an important role in the global carbon and nitrogen budget; microorganisms that grow on reduced single carbon compounds, methylotrophs, serve as a major biological sink for methylamine in aerobic environments. Two non-orthologous, functionally degenerate routes for methylamine oxidation have been studied in methylotrophic Proteobacteria: Methylamine dehydrogenase and the N-methylglutamate pathway. Recent work suggests the N-methylglutamate (NMG) pathway may be more common in nature than the well-studied methylamine dehydrogenase (MaDH, encoded by the mau gene cluster). However, the distribution of these pathways across methylotrophs has never been analyzed. Furthermore, even though horizontal gene transfer (HGT) is commonly invoked as a means to transfer these pathways between strains, the physiological barriers to doing so have not been investigated. We found that the NMG pathway is both more abundant and more universally distributed across methylotrophic Proteobacteria compared to MaDH, which displays a patchy distribution and has clearly been transmitted by HGT even amongst very closely related strains. This trend was especially prominent in well-characterized strains of the Methylobacterium extroquens species, which also display significant phenotypic variability during methylamine growth. Strains like Methylobacterium extorquens PA1 that only encode the NMG pathway grew on methylamine at least five-fold slower than strains like Methylobacterium extorquens AM1 that also possess the mau gene cluster. By mimicking a HGT event through the introduction of the M. extorquens AM1 mau gene cluster into the PA1 genome, the resulting strain instantaneously achieved a 4.5-fold increase in growth rate on methylamine and a 11-fold increase in fitness on methylamine, which even surpassed the fitness of M. extorquens AM1. In contrast, when three replicate populations of wild type M. extorquens PA1 were evolved on methylamine as the sole carbon and energy source for 150 generations neither fitness nor growth rate improved. These results suggest that the NMG pathway permits slow growth on methylamine and is widely distributed in methylotrophs; however, rapid growth on methylamine can be achieved quite readily through acquisition of the mau cluster by HGT.
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Affiliation(s)
- Dipti D Nayak
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
| | - Christopher J Marx
- Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
- Biological Sciences, University of Idaho, Moscow, ID 83844, USA.
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA.
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Joshi G, Schmidt R, Scow KM, Denison MS, Hristova KR. Gene mdpC plays a regulatory role in the methyl-tert-butyl ether degradation pathway of Methylibium petroleiphilum strain PM1. FEMS Microbiol Lett 2015; 362:fnv029. [PMID: 25724531 DOI: 10.1093/femsle/fnv029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Among the few bacteria known to utilize methyl tert-butyl ether (MTBE) as a sole carbon source, Methylibium petroleiphilum PM1 is a well-characterized organism with a sequenced genome; however, knowledge of the genetic regulation of its MTBE degradation pathway is limited. We investigated the role of a putative transcriptional activator gene, mdpC, in the induction of MTBE-degradation genes mdpA (encoding MTBE monooxygenase) and mdpJ (encoding tert-butyl alcohol hydroxylase) of strain PM1 in a gene-knockout mutant mdpC(-). We also utilized quantitative reverse transcriptase PCR assays targeting genes mdpA, mdpJ and mdpC to determine the effects of the mutation on transcription of these genes. Our results indicate that gene mdpC is involved in the induction of both mdpA and mdpJ in response to MTBE and tert-butyl alcohol (TBA) exposure in PM1. An additional independent mechanism may be involved in the induction of mdpJ in the presence of TBA.
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Affiliation(s)
- Geetika Joshi
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Radomir Schmidt
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Kate M Scow
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA
| | - Michael S Denison
- Department of Environmental Toxicology, University of California, Davis, CA 95616, USA
| | - Krassimira R Hristova
- Department of Land, Air and Water Resources, University of California, Davis, CA 95616, USA Biological Sciences Department, Marquette University, Milwaukee, WI 53201, USA
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Purkamo L, Bomberg M, Nyyssönen M, Kukkonen I, Ahonen L, Itävaara M. Heterotrophic communities supplied by ancient organic carbon predominate in deep fennoscandian bedrock fluids. MICROBIAL ECOLOGY 2015; 69:319-332. [PMID: 25260922 DOI: 10.1007/s00248-014-0490-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/29/2014] [Indexed: 06/03/2023]
Abstract
The deep subsurface hosts diverse life, but the mechanisms that sustain this diversity remain elusive. Here, we studied microbial communities involved in carbon cycling in deep, dark biosphere and identified anaerobic microbial energy production mechanisms from groundwater of Fennoscandian crystalline bedrock sampled from a deep drill hole in Outokumpu, Finland, by using molecular biological analyses. Carbon cycling pathways, such as carbon assimilation, methane production and methane consumption, were studied with cbbM, rbcL, acsB, accC, mcrA and pmoA marker genes, respectively. Energy sources, i.e. the terminal electron accepting processes of sulphate-reducing and nitrate-reducing communities, were assessed with detection of marker genes dsrB and narG, respectively. While organic carbon is scarce in deep subsurface, the main carbon source for microbes has been hypothesized to be inorganic carbon dioxide. However, our results demonstrate that carbon assimilation is performed throughout the Outokumpu deep scientific drill hole water column by mainly heterotrophic microorganisms such as Clostridia. The source of carbon for the heterotrophic microbial metabolism is likely the Outokumpu bedrock, mainly composed of serpentinites and metasediments with black schist interlayers. In addition to organotrophic metabolism, nitrate and sulphate are other possible energy sources. Methanogenic and methanotrophic microorganisms are scarce, but our analyses suggest that the Outokumpu deep biosphere provides niches for these organisms; however, they are not very abundant.
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Affiliation(s)
- Lotta Purkamo
- VTT Technical Research Centre of Finland, PL1000, 02044, Espoo, Finland,
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Phyllosphere bacterial community of floating macrophytes in paddy soil environments as revealed by illumina high-throughput sequencing. Appl Environ Microbiol 2014; 81:522-32. [PMID: 25362067 DOI: 10.1128/aem.03191-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.
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50
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Abstract
Glacial comminution of bedrock generates fresh mineral surfaces capable of sustaining chemotrophic microbial communities under the dark conditions that pervade subglacial habitats. Geochemical and isotopic evidence suggests that pyrite oxidation is a dominant weathering process generating protons that drive mineral dissolution in many subglacial systems. Here, we provide evidence correlating pyrite oxidation with chemosynthetic primary productivity and carbonate dissolution in subglacial sediments sampled from Robertson Glacier (RG), Alberta, Canada. Quantification and sequencing of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) transcripts suggest that populations closely affiliated with Sideroxydans lithotrophicus, an iron sulfide-oxidizing autotrophic bacterium, are abundant constituents of microbial communities at RG. Microcosm experiments indicate sulfate production during biological assimilation of radiolabeled bicarbonate. Geochemical analyses of subglacial meltwater indicate that increases in sulfate levels are associated with increased calcite and dolomite dissolution. Collectively, these data suggest a role for biological pyrite oxidation in driving primary productivity and mineral dissolution in a subglacial environment and provide the first rate estimate for bicarbonate assimilation in these ecosystems. Evidence for lithotrophic primary production in this contemporary subglacial environment provides a plausible mechanism to explain how subglacial communities could be sustained in near-isolation from the atmosphere during glacial-interglacial cycles.
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