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Kashani M, Engle MA, Kent DB, Gregston T, Cozzarelli IM, Mumford AC, Varonka MS, Harris CR, Akob DM. Illegal dumping of oil and gas wastewater alters arid soil microbial communities. Appl Environ Microbiol 2024; 90:e0149023. [PMID: 38294246 PMCID: PMC10880632 DOI: 10.1128/aem.01490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/27/2023] [Indexed: 02/01/2024] Open
Abstract
The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.
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Affiliation(s)
- Mitra Kashani
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Mark A Engle
- Department of Earth, Environmental and Resource Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Douglas B Kent
- U.S. Geological Survey, Earth Systems Processes Division, Menlo Park, California, USA
| | | | - Isabelle M Cozzarelli
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Adam C Mumford
- U.S. Geological Survey, Maryland-Delaware-D.C. Water Science Center, Baltimore, Maryland, USA
| | - Matthew S Varonka
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Cassandra R Harris
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
| | - Denise M Akob
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, Virginia, USA
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2
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Muratova A, Golubev S, Romanova V, Sungurtseva I, Nurzhanova A. Effect of Heavy-Metal-Resistant PGPR Inoculants on Growth, Rhizosphere Microbiome and Remediation Potential of Miscanthus × giganteus in Zinc-Contaminated Soil. Microorganisms 2023; 11:1516. [PMID: 37375018 DOI: 10.3390/microorganisms11061516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Microbial-assisted phytoremediation is considered a more effective approach to soil rehabilitation than the sole use of plants. Mycolicibacterium sp. Pb113 and Chitinophaga sp. Zn19, heavy-metal-resistant PGPR strains originally isolated from the rhizosphere of Miscanthus × giganteus, were used as inoculants of the host plant grown in control and zinc-contaminated (1650 mg/kg) soil in a 4-month pot experiment. The diversity and taxonomic structure of the rhizosphere microbiomes, assessed with metagenomic analysis of rhizosphere samples for the 16S rRNA gene, were studied. Principal coordinate analysis showed differences in the formation of the microbiomes, which was affected by zinc rather than by the inoculants. Bacterial taxa affected by zinc and the inoculants, and the taxa potentially involved in the promotion of plant growth as well as in assisted phytoremediation, were identified. Both inoculants promoted miscanthus growth, but only Chitinophaga sp. Zn19 contributed to significant Zn accumulation in the aboveground part of the plant. In this study, the positive effect of miscanthus inoculation with Mycolicibacterium spp. and Chitinophaga spp. was demonstrated for the first time. On the basis of our data, the bacterial strains studied may be recommended to improve the efficiency of M. × giganteus phytoremediation of zinc-contaminated soil.
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Affiliation(s)
- Anna Muratova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Sergey Golubev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Valeria Romanova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420021 Kazan, Russia
| | - Irina Sungurtseva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 410049 Saratov, Russia
| | - Asil Nurzhanova
- Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan
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3
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Sinninghe Damsté JS, Rijpstra WIC, Huber KJ, Albuquerque L, Egas C, Bale NJ. Dominance of mixed ether/ester, intact polar membrane lipids in five species of the order Rubrobacterales: Another group of bacteria not obeying the "lipid divide". Syst Appl Microbiol 2023; 46:126404. [PMID: 36868099 DOI: 10.1016/j.syapm.2023.126404] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/26/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023]
Abstract
The composition of the core lipids and intact polar lipids (IPLs) of five Rubrobacter species was examined. Methylated (ω-4) fatty acids (FAs) characterized the core lipids of Rubrobacter radiotolerans, R. xylanophilus and R. bracarensis. In contrast, R. calidifluminis and R. naiadicus lacked ω-4 methyl FAs but instead contained abundant (i.e., 34-41 % of the core lipids) ω-cyclohexyl FAs not reported before in the order Rubrobacterales. Their genomes contained an almost complete operon encoding proteins enabling production of cyclohexane carboxylic acid CoA thioester, which acts as a building block for ω-cyclohexyl FAs in other bacteria. Hence, the most plausible explanation for the biosynthesis of these cyclic FAs in R. calidifluminis and R. naiadicus is a recent acquisition of this operon. All strains contained 1-O-alkyl glycerol ether lipids in abundance (up to 46 % of the core lipids), in line with the dominance (>90 %) of mixed ether/ester IPLs with a variety of polar headgroups. The IPL head group distribution of R. calidifluminis and R. naiadicus differed, e.g. they lacked a novel IPL tentatively assigned as phosphothreoninol. The genomes of all five Rubrobacter species contained a putative operon encoding the synthesis of the 1-O-alkyl glycerol phosphate, the presumed building block of mixed ether/ester IPLs, which shows some resemblance with an operon enabling ether lipid production in various other aerobic bacteria but requires more study. The uncommon dominance of mixed ether/ester IPLs in Rubrobacter species exemplifies our recent growing awareness that the lipid divide between archaea and bacteria/eukaryotes is not as clear cut as previously thought.
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Affiliation(s)
- Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, the Netherlands; Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, the Netherlands.
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, the Netherlands
| | - Katharina J Huber
- Department of Microorganisms, Leibniz-Institute DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, D-38124 Braunschweig, Germany
| | - Luciana Albuquerque
- CNC - Center for Neuroscience and Cell Biology, UC-Biotech, Biocant Park, 3060-197, Cantanhede, Portugal
| | - Conceição Egas
- CNC - Center for Neuroscience and Cell Biology, UC-Biotech, Biocant Park, 3060-197, Cantanhede, Portugal; BIOCANT - Transfer Technology Association, Biocant Park, 3060-197 Cantanhede, Portugal
| | - Nicole J Bale
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Texel, the Netherlands
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Cho C, Lee D, Jeong D, Kim S, Kim MK, Srinivasan S. Characterization of radiation-resistance mechanism in Spirosoma montaniterrae DY10 T in terms of transcriptional regulatory system. Sci Rep 2023; 13:4739. [PMID: 36959250 PMCID: PMC10036542 DOI: 10.1038/s41598-023-31509-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/13/2023] [Indexed: 03/25/2023] Open
Abstract
To respond to the external environmental changes for survival, bacteria regulates expression of a number of genes including transcription factors (TFs). To characterize complex biological phenomena, a biological system-level approach is necessary. Here we utilized six computational biology methods to infer regulatory network and to characterize underlying biologically mechanisms relevant to radiation-resistance. In particular, we inferred gene regulatory network (GRN) and operons of radiation-resistance bacterium Spirosoma montaniterrae DY10[Formula: see text] and identified the major regulators for radiation-resistance. Our results showed that DNA repair and reactive oxygen species (ROS) scavenging mechanisms are key processes and Crp/Fnr family transcriptional regulator works as a master regulatory TF in early response to radiation.
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Affiliation(s)
- Changyun Cho
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dohoon Lee
- Bioinformatics Institute, Seoul National University, Seoul, 08826, Republic of Korea
- BK21 FOUR Intelligence Computing, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dabin Jeong
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
| | - Sathiyaraj Srinivasan
- Department of Bio & Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 01797, Republic of Korea.
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Liu H, Li FY, Liu J, Shi C, Tang K, Yang Q, Liu Y, Fu Q, Gao X, Wang N, Guo W. The reciprocal changes in dominant species with complete metabolic functions explain the decoupling phenomenon of microbial taxonomic and functional composition in a grassland. Front Microbiol 2023; 14:1113157. [PMID: 37007478 PMCID: PMC10060659 DOI: 10.3389/fmicb.2023.1113157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/22/2023] [Indexed: 03/18/2023] Open
Abstract
The decoupling of microbial functional and taxonomic components refers to the phenomenon that a drastic change in microbial taxonomic composition leads to no or only a gentle change in functional composition. Although many studies have identified this phenomenon, the mechanisms underlying it are still unclear. Here we demonstrate, using metagenomics data from a steppe grassland soil under different grazing and phosphorus addition treatments, that there is no “decoupling” in the variation of taxonomic and metabolic functional composition of the microbial community within functional groups at species level. In contrast, the high consistency and complementarity between the abundance and functional gene diversity of two dominant species made metabolic functions unaffected by grazing and phosphorus addition. This complementarity between the two dominant species shapes a bistability pattern that differs from functional redundancy in that only two species cannot form observable redundancy in a large microbial community. In other words, the “monopoly” of metabolic functions by the two most abundant species leads to the disappearance of functional redundancy. Our findings imply that for soil microbial communities, the impact of species identity on metabolic functions is much greater than that of species diversity, and it is more important to monitor the dynamics of key dominant microorganisms for accurately predicting the changes in the metabolic functions of the ecosystems.
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Affiliation(s)
- Huaiqiang Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
- Collaborative Innovation Center for Grassland Ecological Security, Ministry of Education of China, Hohhot, China
- *Correspondence: Frank Yonghong Li,
| | - Jiayue Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Chunjun Shi
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Kuanyan Tang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qianhui Yang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Yu Liu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Qiang Fu
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Xiaotian Gao
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Ning Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wei Guo
- Ministry of Education Key Laboratory of Ecology and Resource Use on the Mongolian Plateau and Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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6
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A Multi-Analytical Approach to Infer Mineral–Microbial Interactions Applied to Petroglyph Sites in the Negev Desert of Israel. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12146936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Petroglyph sites exist all over the world. They are one of the earliest forms of mankind’s expression and a precursor to art. Despite their outstanding value, comprehensive research on conservation and preservation of rock art is minimal, especially as related to biodeterioration. For this reason, the main objective of this study was to explore the factors involved in the degradation of petroglyph sites in the Negev desert of Israel, with a focus on biodegradation processes. Through the use of culture-independent microbiological methods (metagenomics), we characterized the microbiomes of the samples, finding they were dominated by bacterial communities, in particular taxa of Actinobacteria and Cyanobacteria, with resistance to radiation and desiccation. By means of XRF and Raman spectroscopies, we defined the composition of the stone (calcite and quartz) and the dark crust (clay minerals with Mn and Fe oxides), unveiling the presence of carotenoids, indicative of biological colonization. Optical microscopy and SEM–EDX analyses on thin sections highlighted patterns of weathering, possibly connected to the presence of biodeteriorative microorganisms that leach the calcareous matrix from the bedrock and mobilize metal cations from the black varnish for metabolic processes, slowly weathering it.
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Rojas-Gätjens D, Valverde-Madrigal KS, Rojas-Jimenez K, Pereira R, Avey-Arroyo J, Chavarría M. Antibiotic-producing Micrococcales govern the microbiome that inhabits the fur of two- and three-toed sloths. Environ Microbiol 2022; 24:3148-3163. [PMID: 35621042 DOI: 10.1111/1462-2920.16082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022]
Abstract
Sloths have a dense coat on which insects, algae, and fungi coexist in a symbiotic relationship. This complex ecosystem requires different levels of control, however, most of these mechanisms remain unknown. We investigated the bacterial communities inhabiting the hair of two- (Choloepus Hoffmani) and three-toed (Bradypus variegatus) sloths and evaluated their potential for producing antibiotic molecules capable of exerting control over the hair microbiota. The analysis of 16S rRNA amplicon sequence variants (ASVs) revealed that the communities in both host species are dominated by Actinobacteriota and Firmicutes. The most abundant genera were Brevibacterium, Kocuria/Rothia, Staphylococcus, Rubrobacter, Nesterenkonia, and Janibacter. Furthermore, we isolated nine strains of Brevibacterium and Rothia capable of producing substances that inhibited the growth of common mammalian pathogens. The analysis of the biosynthetic gene clusters (BCGs) of these nine isolates suggests that the pathogen-inhibitory activity could be mediated by the presence of siderophores, terpenes, beta-lactones, Type III polyketide synthases (T3PKS), ribosomally synthesized, and post-translationally modified peptides (RiPPs), non-alpha poly-amino acids (NAPAA) like e-Polylysin, ectoine or nonribosomal peptides (NRPs). Our data suggest that Micrococcales that inhabit sloth hair could have a role in controlling microbial populations in that habitat, improving our understanding of this highly complex ecosystem. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Keilor Rojas-Jimenez
- Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Reinaldo Pereira
- Laboratorio Nacional de Nanotecnología (LANOTEC), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | | | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
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Liu D, Bhople P, Keiblinger KM, Wang B, An S, Yang N, Chater CCC, Yu F. Soil Rehabilitation Promotes Resilient Microbiome with Enriched Keystone Taxa than Agricultural Infestation in Barren Soils on the Loess Plateau. BIOLOGY 2021; 10:biology10121261. [PMID: 34943176 PMCID: PMC8698737 DOI: 10.3390/biology10121261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022]
Abstract
Drylands provide crucial ecosystem and economic services across the globe. In barren drylands, keystone taxa drive microbial structure and functioning in soil environments. In the current study, the Chinese Loess plateau’s agricultural (AL) and twenty-year-old rehabilitated lands (RL) provided a unique opportunity to investigate land-use-mediated effects on barren soil keystone bacterial and fungal taxa. Therefore, soils from eighteen sites were collected for metagenomic sequencing of bacteria specific 16S rRNA and fungi specific ITS2 regions, respectively, and to conduct molecular ecological networks and construct microbial OTU-based correlation matrices. In RL soils we found a more complex bacterial network represented by a higher number of nodes and links, with a link percentage of 77%, and a lower number of nodes and links for OTU-based fungal networks compared to the AL soils. A higher number of keystone taxa was observed in the RL (66) than in the AL (49) soils, and microbial network connectivity was positively influenced by soil total nitrogen and microbial biomass carbon contents. Our results indicate that plant restoration and the reduced human interventions in RL soils could guide the development of a better-connected microbial network and ensure sufficient nutrient circulation in barren soils on the Loess plateau.
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Affiliation(s)
- Dong Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Northwest A&F University, Xianyang 712100, China; (B.W.); (S.A.)
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Correspondence: (D.L.); (F.Y.)
| | - Parag Bhople
- Department of Biological Sciences, Faculty of Science and Engineering, University of Limerick, V94 T9PX Limerick, Ireland;
| | - Katharina Maria Keiblinger
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life-Sciences, 1190 Vienna, Austria;
| | - Baorong Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Northwest A&F University, Xianyang 712100, China; (B.W.); (S.A.)
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Northwest A&F University, Xianyang 712100, China; (B.W.); (S.A.)
| | - Nan Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China;
| | | | - Fuqiang Yu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Correspondence: (D.L.); (F.Y.)
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9
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Huang T, Liu W, Long XE, Jia Y, Wang X, Chen Y. Different Responses of Soil Bacterial Communities to Nitrogen Addition in Moss Crust. Front Microbiol 2021; 12:665975. [PMID: 34566900 PMCID: PMC8460773 DOI: 10.3389/fmicb.2021.665975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/16/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial communities in soil serve an important role in controlling terrestrial biogeochemical cycles and ecosystem processes. Increased nitrogen (N) deposition in Northwest China is generating quantifiable changes in many elements of the desert environment, but the impacts of N deposition, as well as seasonal variations, on soil bacterial community composition and structure are poorly understood. We used high-throughput sequencing of bacterial 16S rRNA genes from Gurbantünggüt Desert moss crust soils to study the impacts of N addition on soil bacterial communities in March, May, and November. In November, we discovered that the OTU richness and diversity of soil bacterial community dropped linearly with increasing N input. In November and March, the diversity of the soil bacterial community decreased significantly in the medium-N and high-N treatments. In May, N addition caused a substantial change in the makeup of the soil bacterial composition, while the impacts were far less apparent in November and March. Furthermore, the relative abundance of major bacterial phyla reacted non-linearly to N addition, with high-N additions decreasing the relative richness of Proteobacteria, Bacteroidetes, and Acidobacteria while increasing the relative abundance of Actinobacteria and Chloroflexi. We also discovered that seasonality, as characterized by changes in soil moisture, pH, SOC, and AK content, had a significant impact on soil bacterial communities. Significant variations in the makeup of the community were discovered at the phylum and genus levels throughout the various months. In May, the variety of soil bacterial community was at its peak. Further investigation showed that the decrease in soil bacterial diversity was mostly attributed to a drop in soil pH. These results indicated that the impact of N deposition on the soil bacterial community was seasonally dependent, suggesting that future research should evaluate more than one sample season at the same time.
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Affiliation(s)
- Tingwen Huang
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Weiguo Liu
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Xi-En Long
- School of Geographic Sciences, Nantong University, Nantong, China
| | - Yangyang Jia
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Xiyuan Wang
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Yinguang Chen
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
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10
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Mishra S, Kota S, Chaudhary R, Misra HS. Guanine quadruplexes and their roles in molecular processes. Crit Rev Biochem Mol Biol 2021; 56:482-499. [PMID: 34162300 DOI: 10.1080/10409238.2021.1926417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The role of guanine quadruplexes (G4) in fundamental biological processes like DNA replication, transcription, translation and telomere maintenance is recognized. G4 structure dynamics is regulated by G4 structure binding proteins and is thought to be crucial for the maintenance of genome integrity in both prokaryotic and eukaryotic cells. Growing research over the last decade has expanded the existing knowledge of the functional diversity of G4 (DNA and RNA) structures across the working models. The control of G4 structure dynamics using G4 binding drugs has been suggested as the putative targets in the control of cancer and bacterial pathogenesis. This review has brought forth the collections of recent information that indicate G4 (mostly G4 DNA) roles in microbial pathogenesis, DNA damaging stress response in bacteria and mammalian cells. Studies in mitochondrial gene function regulation by G4s have also been underscored. Finally, the interdependence of G4s and epigenetic modifications and their speculated medical implications through G4 interacting proteins has been discussed.
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Affiliation(s)
- Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| | - Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
| | - H S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
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Abstract
Concrete is an extreme but common environment and is home to microbial communities adapted to alkaline, saline, and oligotrophic conditions. Microbes inside the concrete that makes up buildings or roads have received little attention despite their ubiquity and capacity to interact with the concrete. Because concrete is a composite of materials which have their own microbial communities, we hypothesized that the microbial communities of concrete reflect those of the concrete components and that these communities change as the concrete ages. Here, we used a 16S amplicon study to show how microbial communities change over 2 years of outdoor weathering in two sets of concrete cylinders, one prone to the concrete-degrading alkali-silica reaction (ASR) and the other having the risk of the ASR mitigated. After identifying and removing taxa that were likely laboratory or reagent contaminants, we found that precursor materials, particularly the large aggregate (gravel), were the probable source of ∼50 to 60% of the bacteria observed in the first cylinders from each series. Overall, community diversity decreased over 2 years, with temporarily increased diversity in warmer summer months. We found that most of the concrete microbiome was composed of Proteobacteria, Firmicutes, and Actinobacteria, although community composition changed seasonally and over multiyear time scales and was likely influenced by environmental deposition. Although the community composition between the two series was not significantly different overall, several taxa, including Arcobacter, Modestobacter, Salinicoccus, Rheinheimera, Lawsonella, and Bryobacter, appear to be associated with ASR. IMPORTANCE Concrete is the most-used building material in the world and a biologically extreme environment, with a microbiome composed of bacteria that likely come from concrete precursor materials, aerosols, and environmental deposition. These microbes, though seeded from a variety of materials, are all subject to desiccation, heating, starvation, high salinity, and very high pH. Microbes that survive and even thrive under these conditions can potentially either degrade concrete or contribute to its repair. Thus, understanding which microbes survive in concrete, under what conditions, and for how long has potential implications for biorepair of concrete. Further, methodological pipelines for analyzing concrete microbial communities can be applied to concrete from a variety of structures or with different types of damage to identify bioindicator species that can be used for structural health monitoring and service life prediction.
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Bacterial and Archaeal Structural Diversity in Several Biodeterioration Patterns on the Limestone Walls of the Old Cathedral of Coimbra. Microorganisms 2021; 9:microorganisms9040709. [PMID: 33808176 PMCID: PMC8065406 DOI: 10.3390/microorganisms9040709] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 11/25/2022] Open
Abstract
The “University of Coimbra-Alta and Sofia” area was awarded the UNESCO World Heritage Site distinction in 2013. The Old Cathedral of Coimbra, a 12th-century limestone monument located in this area, has been significantly impacted during the last 800 years by physical, chemical, and biological processes. This led to the significant deterioration of some of its structures and carvings, with loss of aesthetical, cultural, and historical values. For this work, deteriorated spots of the walls of three semi-open chapels from the cloister of the Cathedral were sampled to ascertain their bacterial and archaeal structural diversity. Based on Next-Generation Sequencing (NGS) result analysis, we report the presence of microbial populations that are well adapted to an ecosystem with harsh conditions and that can establish a diverse biofilm in most cases. While it was possible to determine dominant phylogenetic groups in Archaea and Bacteria domains, there was no clear connection between specific core microbiomes and the different deterioration patterns analyzed. The distribution of these archaeal and bacterial communities within the analyzed biodeterioration spots suggests they are more influenced by abiotic factors (i.e., water availability, salinity, etc.), although they influence (and are influenced by) the algal and fungal population composition in this ecosystem. This work provides valuable information that can assist in establishing future guidelines for the preservation and conservation of this kind of historic stone monuments.
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13
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A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils. Int J Mol Sci 2021; 22:ijms22073438. [PMID: 33810508 PMCID: PMC8036350 DOI: 10.3390/ijms22073438] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.
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14
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George SF, Fierer N, Levy JS, Adams B. Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity. Front Microbiol 2021; 12:616730. [PMID: 33584618 PMCID: PMC7873294 DOI: 10.3389/fmicb.2021.616730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Abstract
Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.
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Affiliation(s)
- Scott F George
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States
| | - Joseph S Levy
- Department of Geology, Colgate University, Hamilton, NY, United States
| | - Byron Adams
- Department of Biology, Brigham Young University, Provo, UT, United States.,Monte L. Bean Museum, Brigham Young University, Provo, UT, United States
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15
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Meier DV, Imminger S, Gillor O, Woebken D. Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community. mSystems 2021; 6:e00786-20. [PMID: 33436509 PMCID: PMC7901476 DOI: 10.1128/msystems.00786-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
Desert surface soils devoid of plant cover are populated by a variety of microorganisms, many with yet unresolved physiologies and lifestyles. Nevertheless, a common feature vital for these microorganisms inhabiting arid soils is their ability to survive long drought periods and reactivate rapidly in rare incidents of rain. Chemolithotrophic processes such as oxidation of atmospheric hydrogen and carbon monoxide are suggested to be a widespread energy source to support dormancy and resuscitation in desert soil microorganisms. Here, we assessed the distribution of chemolithotrophic, phototrophic, and desiccation-related metabolic potential among microbial populations in arid biological soil crusts (BSCs) from the Negev Desert, Israel, via population-resolved metagenomic analysis. While the potential to utilize light and atmospheric hydrogen as additional energy sources was widespread, carbon monoxide oxidation was less common than expected. The ability to utilize continuously available energy sources might decrease the dependency of mixotrophic populations on organic storage compounds and carbon provided by the BSC-founding cyanobacteria. Several populations from five different phyla besides the cyanobacteria encoded CO2 fixation potential, indicating further potential independence from photoautotrophs. However, we also found population genomes with a strictly heterotrophic genetic repertoire. The highly abundant Rubrobacteraceae (Actinobacteriota) genomes showed particular specialization for this extreme habitat, different from their closest cultured relatives. Besides the ability to use light and hydrogen as energy sources, they encoded extensive O2 stress protection and unique DNA repair potential. The uncovered differences in metabolic potential between individual, co-occurring microbial populations enable predictions of their ecological niches and generation of hypotheses on the dynamics and interactions among them.IMPORTANCE This study represents a comprehensive community-wide genome-centered metagenome analysis of biological soil crust (BSC) communities in arid environments, providing insights into the distribution of genes encoding different energy generation mechanisms, as well as survival strategies, among populations in an arid soil ecosystem. It reveals the metabolic potential of several uncultured and previously unsequenced microbial genera, families, and orders, as well as differences in the metabolic potential between the most abundant BSC populations and their cultured relatives, highlighting once more the danger of inferring function on the basis of taxonomy. Assigning functional potential to individual populations allows for the generation of hypotheses on trophic interactions and activity patterns in arid soil microbial communities and represents the basis for future resuscitation and activity studies of the system, e.g., involving metatranscriptomics.
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Affiliation(s)
- Dimitri V Meier
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stefanie Imminger
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Dagmar Woebken
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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16
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Jeong SW, Choi YJ. Extremophilic Microorganisms for the Treatment of Toxic Pollutants in the Environment. Molecules 2020; 25:E4916. [PMID: 33114255 PMCID: PMC7660605 DOI: 10.3390/molecules25214916] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/13/2022] Open
Abstract
As concerns about the substantial effect of various hazardous toxic pollutants on the environment and public health are increasing, the development of effective and sustainable treatment methods is urgently needed. In particular, the remediation of toxic components such as radioactive waste, toxic heavy metals, and other harmful substances under extreme conditions is quite difficult due to their restricted accessibility. Thus, novel treatment methods for the removal of toxic pollutants using extremophilic microorganisms that can thrive under extreme conditions have been investigated during the past several decades. In this review, recent trends in bioremediation using extremophilic microorganisms and related approaches to develop them are reviewed, with relevant examples and perspectives.
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Affiliation(s)
| | - Yong Jun Choi
- School of Environmental Engineering, University of Seoul, Seoul 02504, Korea;
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17
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Miralles I, Lázaro R, Sánchez-Marañón M, Soriano M, Ortega R. Biocrust cover and successional stages influence soil bacterial composition and diversity in semiarid ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:134654. [PMID: 31905575 DOI: 10.1016/j.scitotenv.2019.134654] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Biocrusts are an important drylands landscape component, which enriches the upper millimeters of the soil with organic matter and initiates biogeochemical cycles. However, little is known about the influence of biocrusts on soil bacterial community structure and diversity. Different biocrust types representing a successional gradient were studied. This gradient, from the earliest to the latest successional stages, consisted of an incipient cyanobacterial biocrust < mature cyanobacterial biocrusts < biocrust dominated by the Squamarina lentigera and Diploschistes diacapsis lichens < Biocrust characterized by the Lepraria isidiata lichen. Moreover, in each biocrust type, four different percentages of biocrust cover were also selected. Soil diversity gradually increased with biocrust successional stage and percentage of biocrust cover. The biocrust cover had an important role in the total abundance of bacteria, generally increasing in soils colonized by the highest percentages of cover. Biocrust successional stage was the most important factor, significantly influencing 108 soil bacteria genera, whereas biocrust cover showed significant differences in only 10 genera. Principal Component Analysis showed contrasting microbial composition across the biocrust successional gradient. Some bacterial taxa were dominant in the soil colonized by different biocrust types. Thus, Leptolyngbya, Rubrobacter, Solirubrobacter, Geodermatophilus, etc., were more abundant in incipient cyanobacteria; Nostocales, Chroococcidiopsaceae, Coleofasciculaceae etc., under mature cyanobacterial biocrusts; Truepera, Sphingobacteriaceae, Actinophytocola, Kribella, etc., below the S. lentigera and D. diacapsis community, and Bryobacter, Ohtaekwangia, Opitutus, Pedosphaeraceae, etc., in soils colonized by L. isidiata. Several soil bacteria taxa showed significant correlations (p < 0.05) with chemical soil properties (pH, total nitrogen, total organic carbon, available phosphorous and electrical conductivity). We discuss the role of biocrusts influencing these chemical soil parameters, including the presence of certain metabolites secreted by biocrusts, and also their effects on soil moisture and several physical soil features, as well as their association with different microclimates, all of which could favor a more selective environment for certain bacteria.
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Affiliation(s)
- I Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain.
| | - R Lázaro
- Experimental Station of Arid Zones (CSIC), Almería, Spain
| | - M Sánchez-Marañón
- Department of Soil Science and Chemical Agriculture, University of Granada, 18071 Granada, Spain
| | - M Soriano
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
| | - R Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120, Almería, Spain
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18
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Iuliano A, Nowacka M, Rybak K, Rzepna M. The effects of electron beam radiation on material properties and degradation of commercial PBAT/PLA blend. J Appl Polym Sci 2020. [DOI: 10.1002/app.48462] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- A. Iuliano
- Faculty of ChemistryWarsaw University of Technology Noakowskiego 3, 00‐664 Warsaw Poland
- Department of Chemistry, Faculty of Food SciencesWarsaw University of Life Sciences—SGGW Nowoursynowska 159c, 02‐776 Warsaw Poland
| | - M. Nowacka
- Department of Food Engineering and Process Management, Faculty of Food SciencesWarsaw University of Life Sciences—SGGW Nowoursynowska st. 159c, 02‐776 Warsaw Poland
| | - K. Rybak
- Department of Food Engineering and Process Management, Faculty of Food SciencesWarsaw University of Life Sciences—SGGW Nowoursynowska st. 159c, 02‐776 Warsaw Poland
| | - M. Rzepna
- Institute of Nuclear Chemistry and Technology Dorodna 16 Warsaw 03‐195 Poland
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19
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Complete Genome Sequence of Rubrobacter xylanophilus Strain AA3-22, Isolated from Arima Onsen in Japan. Microbiol Resour Announc 2019; 8:8/34/e00818-19. [PMID: 31439702 PMCID: PMC6706694 DOI: 10.1128/mra.00818-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rubrobacter xylanophilus strain AA3-22, belonging to the phylum Actinobacteria, was isolated from nonvolcanic Arima Onsen (hot spring) in Japan. Here, we report the complete genome sequence of this organism, which was obtained by combining Oxford Nanopore long-read and Illumina short-read sequencing data. Rubrobacter xylanophilus strain AA3-22, belonging to the phylum Actinobacteria, was isolated from nonvolcanic Arima Onsen (hot spring) in Japan. Here, we report the complete genome sequence of this organism, which was obtained by combining Oxford Nanopore long-read and Illumina short-read sequencing data.
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20
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New genus-specific primers for PCR identification of Rubrobacter strains. Antonie Van Leeuwenhoek 2019; 112:1863-1874. [PMID: 31407134 PMCID: PMC6834744 DOI: 10.1007/s10482-019-01314-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/01/2019] [Indexed: 12/02/2022]
Abstract
A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. Amplification of DNA bands of about 267 nucleotides were generated from environmental DNA extracted from soil samples taken from two locations in the Atacama Desert. Sequencing of a DNA library prepared from the bands showed that all of the clones fell within the evolutionary radiation occupied by the genus Rubrobacter. Most of the clones were assigned to two lineages that were well separated from phyletic lines composed of Rubrobacter type strains. It can be concluded that primers Rubro223f and Rubro454r are specific for the genus Rubrobacter and can be used to detect the presence and abundance of members of this genus in the Atacama Desert and other biomes.
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21
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Tripathi BM, Kim HM, Jung JY, Nam S, Ju HT, Kim M, Lee YK. Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska. Front Microbiol 2019; 10:1442. [PMID: 31316487 PMCID: PMC6610311 DOI: 10.3389/fmicb.2019.01442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Permafrost-underlain tundra soils in Northern Hemisphere are one of the largest reservoirs of terrestrial carbon, which are highly sensitive to microbial decomposition due to climate warming. However, knowledge about the taxonomy and functions of microbiome residing in different horizons of permafrost-underlain tundra soils is still limited. Here we compared the taxonomic and functional composition of microbiome between different horizons of soil cores from a moist tussock tundra ecosystem in Council, Alaska, using 16S rRNA gene and shotgun metagenomic sequencing. The composition, diversity, and functions of microbiome varied significantly between soil horizons, with top soil horizon harboring more diverse communities than sub-soil horizons. The vertical gradient in soil physico-chemical parameters were strongly associated with composition of microbial communities across permafrost soil horizons; however, a large fraction of the variation in microbial communities remained unexplained. The genes associated with carbon mineralization were more abundant in top soil horizon, while genes involved in acetogenesis, fermentation, methane metabolism (methanogenesis and methanotrophy), and N cycling were dominant in sub-soil horizons. The results of phylogenetic null modeling analysis showed that stochastic processes strongly influenced the composition of the microbiome in different soil horizons, except the bacterial community composition in top soil horizon, which was largely governed by homogeneous selection. Our study expands the knowledge on the structure and functional potential of microbiome associated with different horizons of permafrost soil, which could be useful in understanding the effects of environmental change on microbial responses in tundra ecosystems.
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Affiliation(s)
| | - Hye Min Kim
- Environmental Safety Research Institute, NeoEnBiz, Bucheon, South Korea
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon, South Korea
| | - Sungjin Nam
- Korea Polar Research Institute, Incheon, South Korea
| | - Hyeon Tae Ju
- Korea Polar Research Institute, Incheon, South Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, South Korea
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22
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Whole-Genome Sequence of the Novel Rubrobacter taiwanensis Strain Yellowstone, Isolated from Yellowstone National Park. Microbiol Resour Announc 2019; 8:8/16/e00287-19. [PMID: 31000556 PMCID: PMC6473150 DOI: 10.1128/mra.00287-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The family Rubrobacteraceae is often represented by its thermophilic and radiotolerant species. Rubrobacter radiotolerans and Rubrobacter xylanophilus have been extensively studied, contributing to defining the characteristics of the family. The family Rubrobacteraceae is often represented by its thermophilic and radiotolerant species. Rubrobacter radiotolerans and Rubrobacter xylanophilus have been extensively studied, contributing to defining the characteristics of the family. We have now sequenced the genome of a Rubrobacter taiwanensis strain, isolated from Yellowstone National Park, to further characterize the family.
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23
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Shuryak I. Review of microbial resistance to chronic ionizing radiation exposure under environmental conditions. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2019; 196:50-63. [PMID: 30388428 DOI: 10.1016/j.jenvrad.2018.10.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 10/21/2018] [Indexed: 06/08/2023]
Abstract
Ionizing radiation (IR) produces multiple types of damage to nucleic acids, proteins and other crucial cellular components. Nevertheless, various microorganisms from phylogenetically distant taxa (bacteria, archaea, fungi) can resist IR levels many orders of magnitude above natural background. This intriguing phenomenon of radioresistance probably arose independently many times throughout evolution as a byproduct of selective pressures from other stresses (e.g. desiccation, UV radiation, chemical oxidants). Most of the literature on microbial radioresistance is based on acute γ-irradiation experiments performed in the laboratory, typically involving pure cultures grown under near-optimal conditions. There is much less information about the upper limits of radioresistance in the field, such as in radioactively-contaminated areas, where several radiation types (e.g. α and β, as well as γ) and other stressors (e.g. non-optimal temperature and nutrient levels, toxic chemicals, interspecific competition) act over multiple generations. Here we discuss several examples of radioresistant microbes isolated from extremely radioactive locations (e.g. Chernobyl and Mayak nuclear plant sites) and estimate the radiation dose rates they were able to tolerate. Some of these organisms (e.g. the fungus Cladosporium cladosporioides, the cyanobacterium Geitlerinema amphibium) are widely-distributed and colonize a variety of habitats. These examples suggest that resistance to chronic IR and chemical contamination is not limited to rare specialized strains from extreme environments, but can occur among common microbial taxa, perhaps due to overlap between mechanisms of resistance to IR and other stressors.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University, 630 West 168(th) street, VC-11-234/5, New York, NY, 10032, USA.
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24
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West NJ, Parrot D, Fayet C, Grube M, Tomasi S, Suzuki MT. Marine cyanolichens from different littoral zones are associated with distinct bacterial communities. PeerJ 2018; 6:e5208. [PMID: 30038864 PMCID: PMC6054067 DOI: 10.7717/peerj.5208] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/20/2018] [Indexed: 11/20/2022] Open
Abstract
The microbial diversity and function of terrestrial lichens have been well studied, but knowledge about the non-photosynthetic bacteria associated with marine lichens is still scarce. 16S rRNA gene Illumina sequencing was used to assess the culture-independent bacterial diversity in the strictly marine cyanolichen species Lichina pygmaea and Lichina confinis, and the maritime chlorolichen species Xanthoria aureola which occupy different areas on the littoral zone. Inland terrestrial cyanolichens from Austria were also analysed as for the marine lichens to examine further the impact of habitat/lichen species on the associated bacterial communities. The L. confinis and L. pygmaea communities were significantly different from those of the maritime Xanthoria aureola lichen found higher up on the littoral zone and these latter communities were more similar to those of the inland terrestrial lichens. The strictly marine lichens were dominated by the Bacteroidetes phylum accounting for 50% of the sequences, whereas Alphaproteobacteria, notably Sphingomonas, dominated the maritime and the inland terrestrial lichens. Bacterial communities associated with the two Lichina species were significantly different sharing only 33 core OTUs, half of which were affiliated to the Bacteroidetes genera Rubricoccus, Tunicatimonas and Lewinella, suggesting an important role of these species in the marine Lichina lichen symbiosis. Marine cyanolichens showed a higher abundance of OTUs likely affiliated to moderately thermophilic and/or radiation resistant bacteria belonging to the Phyla Chloroflexi, Thermi, and the families Rhodothermaceae and Rubrobacteraceae when compared to those of inland terrestrial lichens. This most likely reflects the exposed and highly variable conditions to which they are subjected daily.
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Affiliation(s)
- Nyree J. West
- Observatoire Océanologique de Banyuls sur mer, Sorbonne Université, CNRS, Banyuls sur mer, France
| | - Delphine Parrot
- Univ Rennes, CNRS, ISCR—UMR 6226, Rennes, France
- Current address: GEOMAR Helmholtz Centre for Ocean Research Kiel, Research Unit Marine Natural Products Chemistry, GEOMAR Centre for Marine Biotechnology, Kiel, Germany
| | - Claire Fayet
- Observatoire Océanologique de Banyuls sur mer, Sorbonne Université, CNRS, Banyuls sur mer, France
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Graz, Austria
| | | | - Marcelino T. Suzuki
- Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Sorbonne Université, CNRS, Banyuls sur mer, France
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25
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Kimbrel JA, Ballor N, Wu YW, David MM, Hazen TC, Simmons BA, Singer SW, Jansson JK. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Front Microbiol 2018; 9:1492. [PMID: 30042744 PMCID: PMC6048260 DOI: 10.3389/fmicb.2018.01492] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/15/2018] [Indexed: 11/13/2022] Open
Abstract
Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.
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Affiliation(s)
- Jeffrey A Kimbrel
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas Ballor
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yu-Wei Wu
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maude M David
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Terry C Hazen
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Blake A Simmons
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Steven W Singer
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Janet K Jansson
- Microbial Communities Group, Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA, United States.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
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Park M, Song J, Nam GG, Joung Y, Zhao L, Kim MK, Cho JC. Deinococcus lacus sp. nov., a gamma radiation-resistant bacterium isolated from an artificial freshwater pond. Int J Syst Evol Microbiol 2018; 68:1372-1377. [PMID: 29504923 DOI: 10.1099/ijsem.0.002683] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A Gram-stain-negative, pink-coloured, non-motile and gamma radiation-resistant bacterium, designated strain IMCC1711T, was isolated from a freshwater sample collected from an artificial pond (Inkyong Pond). The 16S rRNA gene sequence analysis showed that strain IMCC1711T was most closely related to Deinococcus piscis 3axT (94.2 %) and formed a robust phylogenetic clade with other species of the genus Deinococcus. Optimal growth of strain MCC1711T was observed at 25 °C and pH 7.0 without NaCl. Strain IMCC1711T exhibited high resistance to gamma radiation. The DNA G+C content of strain IMCC1711T was 59.1 mol% and MK-8 was the predominant isoprenoid quinone. Major fatty acid constituents of the strain were C17 : 1ω8c, C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C15 : 1ω6c. The major polar lipids constituted phosphatidylethanolamine, one unidentified phosphoglycolipid and two unidentified glycolipids. On the basis of taxonomic data obtained in this study, it was concluded that strain IMCC1711T represented a novel species of the genus Deinococcus, for which the name Deinococcus lacus sp. nov. is proposed. The type strain of Deinococcus lacus is IMCC1711T (KCTC 52494T=KACC 18979T=NBRC 112440T).
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Affiliation(s)
- Miri Park
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Jaeho Song
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Gi Gyun Nam
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Yochan Joung
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
| | - Lei Zhao
- Research Division for Biotechnology, Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea
| | - Min-Kyu Kim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute (KAERI), Jeongeup 56212, Republic of Korea
| | - Jang-Cheon Cho
- Department of Biological Sciences, Inha University, Incheon 22212, Republic of Korea
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Across the tree of life, radiation resistance is governed by antioxidant Mn 2+, gauged by paramagnetic resonance. Proc Natl Acad Sci U S A 2017; 114:E9253-E9260. [PMID: 29042516 PMCID: PMC5676931 DOI: 10.1073/pnas.1713608114] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Despite concerted functional genomic efforts to understand the complex phenotype of ionizing radiation (IR) resistance, a genome sequence cannot predict whether a cell is IR-resistant or not. Instead, we report that absorption-display electron paramagnetic resonance (EPR) spectroscopy of nonirradiated cells is highly diagnostic of IR survival and repair efficiency of DNA double-strand breaks (DSBs) caused by exposure to gamma radiation across archaea, bacteria, and eukaryotes, including fungi and human cells. IR-resistant cells, which are efficient at DSB repair, contain a high cellular content of manganous ions (Mn2+) in high-symmetry (H) antioxidant complexes with small metabolites (e.g., orthophosphate, peptides), which exhibit narrow EPR signals (small zero-field splitting). In contrast, Mn2+ ions in IR-sensitive cells, which are inefficient at DSB repair, exist largely as low-symmetry (L) complexes with substantially broadened spectra seen with enzymes and strongly chelating ligands. The fraction of cellular Mn2+ present as H-complexes (H-Mn2+), as measured by EPR of live, nonirradiated Mn-replete cells, is now the strongest known gauge of biological IR resistance between and within organisms representing all three domains of life: Antioxidant H-Mn2+ complexes, not antioxidant enzymes (e.g., Mn superoxide dismutase), govern IR survival. As the pool of intracellular metabolites needed to form H-Mn2+ complexes depends on the nutritional status of the cell, we conclude that IR resistance is predominantly a metabolic phenomenon. In a cross-kingdom analysis, the vast differences in taxonomic classification, genome size, and radioresistance between cell types studied here support that IR resistance is not controlled by the repertoire of DNA repair and antioxidant enzymes.
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Cheptsov VS, Vorobyova EA, Manucharova NA, Gorlenko MV, Pavlov AK, Vdovina MA, Lomasov VN, Bulat SA. 100 kGy gamma-affected microbial communities within the ancient Arctic permafrost under simulated Martian conditions. Extremophiles 2017; 21:1057-1067. [DOI: 10.1007/s00792-017-0966-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/21/2017] [Indexed: 11/28/2022]
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Jung KW, Lim S, Bahn YS. Microbial radiation-resistance mechanisms. J Microbiol 2017; 55:499-507. [PMID: 28664512 DOI: 10.1007/s12275-017-7242-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 06/19/2017] [Indexed: 11/28/2022]
Abstract
Organisms living in extreme environments have evolved a wide range of survival strategies by changing biochemical and physiological features depending on their biological niches. Interestingly, organisms exhibiting high radiation resistance have been discovered in the three domains of life (Bacteria, Archaea, and Eukarya), even though a naturally radiationintensive environment has not been found. To counteract the deleterious effects caused by radiation exposure, radiation- resistant organisms employ a series of defensive systems, such as changes in intracellular cation concentration, excellent DNA repair systems, and efficient enzymatic and non-enzymatic antioxidant systems. Here, we overview past and recent findings about radiation-resistance mechanisms in the three domains of life for potential usage of such radiationresistant microbes in the biotechnology industry.
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Affiliation(s)
- Kwang-Woo Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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31
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Gat D, Mazar Y, Cytryn E, Rudich Y. Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:6709-6718. [PMID: 28422476 DOI: 10.1021/acs.est.7b00362] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microorganisms carried by dust storms are transported through the atmosphere and may affect human health and the functionality of microbial communities in various environments. Characterizing the dust-borne microbiome in dust storms of different origins or that followed different trajectories provides valuable data to improve our understanding of global health and environmental impacts. We present a comparative study on the diversity of dust-borne bacterial communities in dust storms from three distinct origins (North Africa, Syria and Saudi Arabia) and compare them with local bacterial communities sampled on clear days, all collected at a single location: Rehovot, Israel. Storms from different dust origins exhibited distinct bacterial communities, with signature bacterial taxa. Dust storms were characterized by a lower abundance of selected antibiotic resistance genes (ARGs) compared with ambient dust, asserting that the origin of these genes is local and possibly anthropogenic. With the progression of the storm, the storm-borne bacterial community showed increasing resemblance to ambient dust, suggesting mixing with local dust. These results show, for the first time, that dust storms from different sources display distinct bacterial communities, suggesting possible diverse effects on the environment and public health.
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Affiliation(s)
- Daniella Gat
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Yinon Mazar
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agriculture Research Organization , Rishon Lezion 7528809, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 7610001, Israel
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32
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Ranawat P, Rawat S. Radiation resistance in thermophiles: mechanisms and applications. World J Microbiol Biotechnol 2017; 33:112. [DOI: 10.1007/s11274-017-2279-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/26/2017] [Indexed: 12/28/2022]
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33
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Jurburg SD, Nunes I, Stegen JC, Le Roux X, Priemé A, Sørensen SJ, Salles JF. Autogenic succession and deterministic recovery following disturbance in soil bacterial communities. Sci Rep 2017; 7:45691. [PMID: 28383027 PMCID: PMC5382530 DOI: 10.1038/srep45691] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 03/03/2017] [Indexed: 01/23/2023] Open
Abstract
The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.
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Affiliation(s)
- Stephanie D Jurburg
- Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands
| | - Inês Nunes
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - James C Stegen
- Earth and Biological Sciences, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xavier Le Roux
- Microbial Ecology Center, INRA (UMR 1418), CNRS, Université Lyon1, Université de Lyon, 69622 Villeurbanne, France
| | - Anders Priemé
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - Joana Falcão Salles
- Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands
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Etemadifar Z, Gholami M, Derikvand P. UV-Resistant Bacteria with Multiple-Stress Tolerance Isolated from Desert Areas in Iran. GEOMICROBIOLOGY JOURNAL 2016; 33:1-7. [DOI: 10.1080/01490451.2015.1063025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 06/01/2015] [Indexed: 07/30/2023]
Affiliation(s)
- Zahra Etemadifar
- Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Mahmoud Gholami
- Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Peyman Derikvand
- Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
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35
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Domagal-Goldman SD, Wright KE, Adamala K, Arina de la Rubia L, Bond J, Dartnell LR, Goldman AD, Lynch K, Naud ME, Paulino-Lima IG, Singer K, Walther-Antonio M, Abrevaya XC, Anderson R, Arney G, Atri D, Azúa-Bustos A, Bowman JS, Brazelton WJ, Brennecka GA, Carns R, Chopra A, Colangelo-Lillis J, Crockett CJ, DeMarines J, Frank EA, Frantz C, de la Fuente E, Galante D, Glass J, Gleeson D, Glein CR, Goldblatt C, Horak R, Horodyskyj L, Kaçar B, Kereszturi A, Knowles E, Mayeur P, McGlynn S, Miguel Y, Montgomery M, Neish C, Noack L, Rugheimer S, Stüeken EE, Tamez-Hidalgo P, Imari Walker S, Wong T. The Astrobiology Primer v2.0. ASTROBIOLOGY 2016; 16:561-653. [PMID: 27532777 PMCID: PMC5008114 DOI: 10.1089/ast.2015.1460] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/06/2016] [Indexed: 05/09/2023]
Affiliation(s)
- Shawn D Domagal-Goldman
- 1 NASA Goddard Space Flight Center , Greenbelt, Maryland, USA
- 2 Virtual Planetary Laboratory , Seattle, Washington, USA
| | - Katherine E Wright
- 3 University of Colorado at Boulder , Colorado, USA
- 4 Present address: UK Space Agency, UK
| | - Katarzyna Adamala
- 5 Department of Genetics, Cell Biology and Development, University of Minnesota , Minneapolis, Minnesota, USA
| | | | - Jade Bond
- 7 Department of Physics, University of New South Wales , Sydney, Australia
| | | | | | - Kennda Lynch
- 10 Division of Biological Sciences, University of Montana , Missoula, Montana, USA
| | - Marie-Eve Naud
- 11 Institute for research on exoplanets (iREx) , Université de Montréal, Montréal, Canada
| | - Ivan G Paulino-Lima
- 12 Universities Space Research Association , Mountain View, California, USA
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | - Kelsi Singer
- 14 Southwest Research Institute , Boulder, Colorado, USA
| | | | - Ximena C Abrevaya
- 16 Instituto de Astronomía y Física del Espacio (IAFE) , UBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rika Anderson
- 17 Department of Biology, Carleton College , Northfield, Minnesota, USA
| | - Giada Arney
- 18 University of Washington Astronomy Department and Astrobiology Program , Seattle, Washington, USA
| | - Dimitra Atri
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Jeff S Bowman
- 19 Lamont-Doherty Earth Observatory, Columbia University , Palisades, New York, USA
| | | | | | - Regina Carns
- 22 Polar Science Center, Applied Physics Laboratory, University of Washington , Seattle, Washington, USA
| | - Aditya Chopra
- 23 Planetary Science Institute, Research School of Earth Sciences, Research School of Astronomy and Astrophysics, The Australian National University , Canberra, Australia
| | - Jesse Colangelo-Lillis
- 24 Earth and Planetary Science, McGill University , and the McGill Space Institute, Montréal, Canada
| | | | - Julia DeMarines
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Carie Frantz
- 27 Department of Geosciences, Weber State University , Ogden, Utah, USA
| | - Eduardo de la Fuente
- 28 IAM-Departamento de Fisica, CUCEI , Universidad de Guadalajara, Guadalajara, México
| | - Douglas Galante
- 29 Brazilian Synchrotron Light Laboratory , Campinas, Brazil
| | - Jennifer Glass
- 30 School of Earth and Atmospheric Sciences, Georgia Institute of Technology , Atlanta, Georgia , USA
| | | | | | - Colin Goldblatt
- 33 School of Earth and Ocean Sciences, University of Victoria , Victoria, Canada
| | - Rachel Horak
- 34 American Society for Microbiology , Washington, DC, USA
| | | | - Betül Kaçar
- 36 Harvard University , Organismic and Evolutionary Biology, Cambridge, Massachusetts, USA
| | - Akos Kereszturi
- 37 Research Centre for Astronomy and Earth Sciences , Hungarian Academy of Sciences, Budapest, Hungary
| | - Emily Knowles
- 38 Johnson & Wales University , Denver, Colorado, USA
| | - Paul Mayeur
- 39 Rensselaer Polytechnic Institute , Troy, New York, USA
| | - Shawn McGlynn
- 40 Earth Life Science Institute, Tokyo Institute of Technology , Tokyo, Japan
| | - Yamila Miguel
- 41 Laboratoire Lagrange, UMR 7293, Université Nice Sophia Antipolis , CNRS, Observatoire de la Côte d'Azur, Nice, France
| | | | - Catherine Neish
- 43 Department of Earth Sciences, The University of Western Ontario , London, Canada
| | - Lena Noack
- 44 Royal Observatory of Belgium , Brussels, Belgium
| | - Sarah Rugheimer
- 45 Department of Astronomy, Harvard University , Cambridge, Massachusetts, USA
- 46 University of St. Andrews , St. Andrews, UK
| | - Eva E Stüeken
- 47 University of Washington , Seattle, Washington, USA
- 48 University of California , Riverside, California, USA
| | | | - Sara Imari Walker
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
- 50 School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science, Arizona State University , Tempe, Arizona, USA
| | - Teresa Wong
- 51 Department of Earth and Planetary Sciences, Washington University in St. Louis , St. Louis, Missouri, USA
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36
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Goordial J, Davila A, Greer CW, Cannam R, DiRuggiero J, McKay CP, Whyte LG. Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert. Environ Microbiol 2016; 19:443-458. [DOI: 10.1111/1462-2920.13353] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Rebecca Cannam
- McGill University Macdonald Campus; Ste-Anne-de-Bellevue Quebec Canada
| | | | | | - Lyle G. Whyte
- McGill University Macdonald Campus; Ste-Anne-de-Bellevue Quebec Canada
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Rao S, Chan OW, Lacap-Bugler DC, Pointing SB. Radiation-Tolerant Bacteria Isolated from High Altitude Soil in Tibet. Indian J Microbiol 2016; 56:508-512. [PMID: 27784950 DOI: 10.1007/s12088-016-0604-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/27/2016] [Indexed: 12/24/2022] Open
Abstract
This study reports the identification of ionising radiation tolerant bacteria from a high elevation arid region of central Tibet. Nineteen isolates were isolated from soil exposed to ionising radiation at doses from 0 to 15 kGy. Isolates were phylogenetically characterised using 16S rRNA gene sequences. Most isolates comprised taxa from the Actinobacteria, Cyanobacteria, Firmicutes and proteobacteria and these survived doses up to 5 kGy. The Firmicutes and Deinococci also survived doses up to 10 kGy, and the highest dose of 15 kGy was survived only by the Deinococci. No altitude-related pattern was discernible within the range 4638-5240 m, instead culturable bacterial estimates for irradiated soil were strongly influenced by the abundance of Deinococci. We conclude that the relatively high UV exposure in Tibet has contributed to the high diversity of radiation tolerant soil bacteria. In addition, the strong association between desiccation-tolerance and radiation tolerance pathways suggests the arid environment may also have selected in favour of radiation tolerant taxa.
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Affiliation(s)
- Subramanya Rao
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, China ; Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1010 New Zealand
| | - Olivia W Chan
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1010 New Zealand
| | - Donnabella C Lacap-Bugler
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1010 New Zealand
| | - Stephen B Pointing
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1010 New Zealand ; Institute of Nature and Environmental Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192 Japan
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38
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Draft Genome Sequence of Kocuria rhizophila RF, a Radiation-Resistant Soil Isolate. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00095-16. [PMID: 26966202 PMCID: PMC4786658 DOI: 10.1128/genomea.00095-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Kocuria rhizophila RF, a soil isolate from Iran, is a radiation-resistant bacterium. Only a limited amount of genomic information for radiation-resistant bacteria is currently available. Here, we report the draft genome sequence of this bacterium, providing knowledge to aid in the discovery of the genomic basis of its resistance to radiation.
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Musilova M, Wright G, Ward JM, Dartnell LR. Isolation of Radiation-Resistant Bacteria from Mars Analog Antarctic Dry Valleys by Preselection, and the Correlation between Radiation and Desiccation Resistance. ASTROBIOLOGY 2015; 15:1076-1090. [PMID: 26684506 PMCID: PMC4683558 DOI: 10.1089/ast.2014.1278] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 10/08/2015] [Indexed: 05/31/2023]
Abstract
UNLABELLED Extreme radiation-resistant microorganisms can survive doses of ionizing radiation far greater than are present in the natural environment. Radiation resistance is believed to be an incidental adaptation to desiccation resistance, as both hazards cause similar cellular damage. Desert soils are, therefore, promising targets to prospect for new radiation-resistant strains. This is the first study to isolate radiation-resistant microbes by using gamma-ray exposure preselection from the extreme cold desert of the Antarctic Dry Valleys (a martian surface analogue). Halomonads, identified by 16S rRNA gene sequencing, were the most numerous survivors of the highest irradiation exposures. They were studied here for the first time for both their desiccation and irradiation survival characteristics. In addition, the association between desiccation and radiation resistance has not been investigated quantitatively before for a broad diversity of microorganisms. Thus, a meta-analysis of scientific literature was conducted to gather a larger data set. A strong correlation was found between desiccation and radiation resistance, indicating that an increase in the desiccation resistance of 5 days corresponds to an increase in the room-temperature irradiation survival of 1 kGy. Irradiation at -79°C (representative of average martian surface temperatures) increases the microbial radiation resistance 9-fold. Consequently, the survival of the cold-, desiccation-, and radiation-resistant organisms isolated here has implications for the potential habitability of dormant or cryopreserved life on Mars. KEY WORDS Extremophiles-Halomonas sp.-Antarctica-Mars-Ionizing radiation-Cosmic rays.
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Affiliation(s)
| | - Gary Wright
- Department of Engineering and Applied Science, Cranfield University, Shrivenham, Swindon, UK
| | - John M. Ward
- Department of Biochemical Engineering, University College London, London, UK
| | - Lewis R. Dartnell
- UCL Institute for Origins, University College London, London, UK
- The Centre for Planetary Sciences at UCL/Birkbeck, Earth Sciences, University College London, London, UK
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40
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Morozova D, Moeller R, Rettberg P, Wagner D. Enhanced Radiation Resistance of Methanosarcina soligelidi SMA-21, a New Methanogenic Archaeon Isolated from a Siberian Permafrost-Affected Soil in Direct Comparison to Methanosarcina barkeri. ASTROBIOLOGY 2015; 15:951-960. [PMID: 26544020 DOI: 10.1089/ast.2015.1319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
UNLABELLED Permafrost-affected soils are characterized by a high abundance and diversity of methanogenic communities, which are considered suitable model organisms for potential life on Mars. Methanogens from Siberian permafrost have been proven to be highly resistant against divers stress conditions such as subzero temperatures, desiccation, and simulated thermophysical martian conditions. Here, we studied the radiation resistance of the currently described new species Methanosarcina soligelidi SMA-21, which was isolated from a Siberian permafrost-affected soil, in comparison to Methanosarcina barkeri, which is used as a reference organism from a nonpermafrost soil environment. Both strains were exposed to solar UV and ionizing radiation to assess their limits of survival. Methanosarcina soligelidi exhibit an increase in radiation resistance to UV (2.5- to 13.8-fold) and ionizing radiation (46.6-fold) compared to M. barkeri. The F10 (UVC) and D10 (X-rays) values of M. soligelidi are comparable to values for the well-known, highly radioresistant species Deinococcus radiodurans. In contrast, the radiation response of M. barkeri was highly sensitive to UV and ionizing radiation comparably to Escherichia coli and other radiosensitive microorganisms. This study showed that species of the same genus respond differently to UV and ionizing radiation, which might reflect the adaptation of Methanosarcina soligelidi SMA-21 to the harsh environmental conditions of the permafrost habitat. KEY WORDS Methanogenic archaea-Environmental UV-Ionizing radiation-Permafrost-Radiation resistance-Mars.
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Affiliation(s)
- Daria Morozova
- 1 GFZ German Research Centre for Geosciences , Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
| | - Ralf Moeller
- 2 German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Research Group Astrobiology, Köln, Germany
| | - Petra Rettberg
- 2 German Aerospace Center (DLR e.V.), Institute of Aerospace Medicine , Radiation Biology Department, Research Group Astrobiology, Köln, Germany
| | - Dirk Wagner
- 1 GFZ German Research Centre for Geosciences , Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, Potsdam, Germany
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Shivlata L, Satyanarayana T. Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Front Microbiol 2015; 6:1014. [PMID: 26441937 PMCID: PMC4585250 DOI: 10.3389/fmicb.2015.01014] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.
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42
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Rao S, Chan Y, Bugler-Lacap DC, Bhatnagar A, Bhatnagar M, Pointing SB. Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India. Indian J Microbiol 2015; 56:35-45. [PMID: 26843695 DOI: 10.1007/s12088-015-0549-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/14/2015] [Indexed: 11/24/2022] Open
Abstract
A culture-independent diversity assessment of archaea, bacteria and fungi in the Thar Desert in India was made. Six locations in Ajmer, Jaisalmer, Jaipur and Jodhupur included semi-arid soils, arid soils, arid sand dunes, plus arid cryptoendolithic substrates. A real-time quantitative PCR approach revealed that bacteria dominated soils and cryptoendoliths, whilst fungi dominated sand dunes. The archaea formed a minor component of all communities. Comparison of rRNA-defined community structure revealed that substrate and climate rather than location were the most parsimonious predictors. Sequence-based identification of 1240 phylotypes revealed that most taxa were common desert microorganisms. Semi-arid soils were dominated by actinobacteria and alpha proteobacteria, arid soils by chloroflexi and alpha proteobacteria, sand dunes by ascomycete fungi and cryptoendoliths by cyanobacteria. Climatic variables that best explained this distribution were mean annual rainfall and maximum annual temperature. Substrate variables that contributed most to observed diversity patterns were conductivity, soluble salts, Ca(2+) and pH. This represents an important addition to the inventory of desert microbiota, novel insight into the abiotic drivers of community assembly, and the first report of biodiversity in a monsoon desert system.
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Affiliation(s)
- Subramanya Rao
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1142 New Zealand
| | - Yuki Chan
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1142 New Zealand
| | - Donnabella C Bugler-Lacap
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1142 New Zealand
| | - Ashish Bhatnagar
- Department of Microbiology, Maharshi Dayanand Saraswathi University, Ajmer, Rajasthan India
| | - Monica Bhatnagar
- Department of Microbiology, Maharshi Dayanand Saraswathi University, Ajmer, Rajasthan India
| | - Stephen B Pointing
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1142 New Zealand
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Liu J, Hua ZS, Chen LX, Kuang JL, Li SJ, Shu WS, Huang LN. Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings. Appl Environ Microbiol 2014; 80:3677-86. [PMID: 24727268 PMCID: PMC4054149 DOI: 10.1128/aem.00294-14] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 04/02/2014] [Indexed: 11/20/2022] Open
Abstract
Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.
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Albuquerque L, Johnson MM, Schumann P, Rainey FA, da Costa MS. Description of two new thermophilic species of the genus Rubrobacter, Rubrobacter calidifluminis sp. nov. and Rubrobacter naiadicus sp. nov., and emended description of the genus Rubrobacter and the species Rubrobacter bracarensis. Syst Appl Microbiol 2014; 37:235-43. [PMID: 24780859 DOI: 10.1016/j.syapm.2014.03.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 03/11/2014] [Accepted: 03/14/2014] [Indexed: 11/25/2022]
Abstract
Four isolates, designated, RG-1(T), RG-3(T), RG-6 and RG-8 with optimum growth temperatures around 60°C were recovered from a hot stream near Ribeira Grande on the Island of São Miguel in the Azores. These strains were strictly aerobic, catalase and oxidase positive. The organisms could be divided into two groups; one comprising strains RG-1(T) and RG-6, the other formed by strains RG-3(T) and RG-8, with distinctive phenotypic and chemotaxonomic characteristics. Major fatty acids varied between the groups, but all contained iso-branched components such as iso-C16:0 10-methyl and iso-C17:0 10-methyl. Analysis of the 16S rRNA gene shows the strains to cluster with species of the genus Rubrobacter, specifically with Rubrobacter xylanophilus to which they have pairwise sequence similarity in the range of 98.4-98.6%. The DNA-DNA hybridization result show that strains RG-1(T) and RG-3(T) share 72% reassociation. Strains RG-1(T) and RG-3(T) displayed extreme tolerance to desiccation when compared to other species of the genus. Based on genotypic, physiological and biochemical characteristics we describe two new species: Rubrobacter calidifluminis sp. nov., represented by strain RG-1(T) (=CECT 8308(T) =JCM 19154(T)) and Rubrobacter naiadicus sp. nov. represented by strain RG-3(T) (=CECT 8310(T)=JCM 19155(T)). The description of the species Rubrobacter bracarensis[16] is emended to correct the fatty acid composition of these organisms. The discovery of new fatty acids in these species requires emendation of the description of the genus Rubrobacter.
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Affiliation(s)
- Luciana Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal.
| | - Megan M Johnson
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
| | - Peter Schumann
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen, D-38124 Braunschweig, Germany
| | - Fred A Rainey
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
| | - Milton S da Costa
- Department of Life Sciences, University of Coimbra, 3001-401 Coimbra, Portugal; Microbiology Unit, BIOCANT Biotechnological Park, 3060-197 Cantanhede, Portugal
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Zheleva A, Karamalakova Y, Nikolova G, Kumar R, Sharma R, Gadjeva V. A New Antioxidant with Natural Origin Characterized by Electron Paramagnetic Resonance Spectroscopy Methods. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/50yrtimb.2011.0027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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46
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Egas C, Barroso C, Froufe HJC, Pacheco J, Albuquerque L, da Costa MS. Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. Stand Genomic Sci 2014; 9:1062-75. [PMID: 25197483 PMCID: PMC4148983 DOI: 10.4056/sigs.5661021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the phylum “Actinobacteria” isolated from a hot spring in São Pedro do Sul, Portugal. This aerobic and halotolerant bacterium is also extremely resistant to gamma and UV radiation, which are the main reasons for the interest in sequencing its genome. Here, we present the complete genome sequence of strain RSPS-4 as well as its assembly and annotation. We also compare the gene sequence of this organism with that of the type strain of the species R. radiotolerans isolated from a hot spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of 2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp, 149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA genes and a single rRNA operon.
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Affiliation(s)
- C Egas
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - C Barroso
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - H J C Froufe
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - J Pacheco
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - L Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - M S da Costa
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Barba M, Dutoit R, Legrain C, Labedan B. Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism. BMC SYSTEMS BIOLOGY 2013; 7:99. [PMID: 24093154 PMCID: PMC4016543 DOI: 10.1186/1752-0509-7-99] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/25/2013] [Indexed: 01/18/2023]
Abstract
BACKGROUND Enzymes belonging to mechanistically diverse superfamilies often display similar catalytic mechanisms. We previously observed such an association in the case of the cyclic amidohydrolase superfamily whose members play a role in related steps of purine and pyrimidine metabolic pathways. To establish a possible link between enzyme homology and chemical similarity, we investigated further the neighbouring steps in the respective pathways. RESULTS We identified that successive reactions of the purine and pyrimidine pathways display similar chemistry. These mechanistically-related reactions are often catalyzed by homologous enzymes. Detection of series of similar catalysis made by succeeding enzyme families suggested some modularity in the architecture of the central metabolism. Accordingly, we introduce the concept of a reaction module to define at least two successive steps catalyzed by homologous enzymes in pathways alignable by similar chemical reactions. Applying such a concept allowed us to propose new function for misannotated paralogues. In particular, we discovered a putative ureidoglycine carbamoyltransferase (UGTCase) activity. Finally, we present experimental data supporting the conclusion that this UGTCase is likely to be involved in a new route in purine catabolism. CONCLUSIONS Using the reaction module concept should be of great value. It will help us to trace how the primordial promiscuous enzymes were assembled progressively in functional modules, as the present pathways diverged from ancestral pathways to give birth to the present-day mechanistically diversified superfamilies. In addition, the concept allows the determination of the actual function of misannotated proteins.
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Affiliation(s)
- Matthieu Barba
- Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris Sud, Bâtiment 400, 91405, Orsay Cedex, France
- present address: Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, 69622, Villeurbanne Cedex, France
| | - Raphaël Dutoit
- Institut de Recherches Microbiologiques J.-M. Wiame IRMW, Campus CERIA, Av. E. Gryson 1, 1070, Brussels, Belgium
| | - Christianne Legrain
- Institut de Recherches Microbiologiques J.-M. Wiame IRMW, Campus CERIA, Av. E. Gryson 1, 1070, Brussels, Belgium
| | - Bernard Labedan
- Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris Sud, Bâtiment 400, 91405, Orsay Cedex, France
- present address: Bioinformatique, Laboratoire de Recherche en Informatique, CNRS UMR 8623, Université Paris Sud, Bâtiment 650, 91405, Orsay Cedex, France
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Bhave SV, Shanbhag PV, Sonawane SK, Parab RR, Mahajan GB. Isolation and characterization of halotolerant Streptomyces radiopugnans from Antarctica soil. Lett Appl Microbiol 2013; 56:348-55. [PMID: 23384241 DOI: 10.1111/lam.12054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 01/30/2012] [Accepted: 01/30/2012] [Indexed: 11/30/2022]
Abstract
An actinomycete wild strain PM0626271 (= MTCC 5447), producing novel antibacterial compounds, was isolated from soil collected from Antarctica. The taxonomic status of the isolate was established by polyphasic approach. Scanning electron microscopy observations and the presence of LL-Diaminopimelic acid in the cell wall hydrolysate confirmed the genus Streptomyces. Analysis of 16S rRNA gene sequence showed highest sequence similarity to Streptomyces radiopugnans (99%). The phylogenetic tree constructed using near complete 16S rRNA gene sequences of the isolate and closely related strains revealed that although the isolate fell within the S. radiopugnans gene subclade, it was allocated a different branch in the phylogenetic tree, separating it from the majority of the radiopugnans strains. Similar to type strain, S. radiopugnans R97(T) , the Antarctica isolate displayed thermo tolerance as well as resistance to (60) Co gamma radiation, up to the dose of 15 kGy. However, media and salt tolerance studies revealed that, unlike the type strain, this isolate needed higher salinity for its growth. This is the first report of S. radiopugnans isolated from the Antarctica region. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of Streptomyces radiopugnans MTCC 5447 is JQ723477.
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Affiliation(s)
- S V Bhave
- Department of Natural Products, Piramal Enterprises Ltd., Mumbai, India.
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49
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There are more small amino acids and fewer aromatic rings in proteins of ionizing radiation-resistant bacteria. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0612-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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50
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A new bacterial hydrolase specific for the compatible solutes α-d-mannopyranosyl-(1→2)-d-glycerate and α-d-glucopyranosyl-(1→2)-d-glycerate. Enzyme Microb Technol 2013; 52:77-83. [DOI: 10.1016/j.enzmictec.2012.10.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 10/19/2012] [Accepted: 10/23/2012] [Indexed: 11/21/2022]
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