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Mei C, Shi Y, Wang Y, Qiu Z, Yang H. Termitidicoccus mucosus gen. nov. sp. nov. a novel Verrucomicrobiota species isolated from Reticulitermes chinensis gives insights of high adaptability of symbiotic bacteria to termite gut ecosystem. Res Microbiol 2024; 175:104173. [PMID: 38157920 DOI: 10.1016/j.resmic.2023.104173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 10/27/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
Verrucomicrobiota is widely distributed in various habitats including insect guts. It was found to be prevalent in almost all investigated termite guts, whereas their physiological functions are not very clear. In this study we characterized the physiological and genomic properties of Verrucomicrobiota strain TSB47T isolated from Reticulitermes chinensis. The cells of strain TSB47T were Gram-stain-negative, non-motile, and non-spore-forming coccoid with one or more warts. 16S rRNA gene analysis showed that the closest relatives of strain TSB47T were Opitutaceae strain TAV1 and Ereboglobus luteus Ho45T (98.3% and 95.4% sequence similarity, respectively). Whole genome analysis revealed that there are a large number of glycoside hydrolase genes, amino acid metabolism genes, complete Mo-Fe nitrogenase and Fe-Fe nitrogenase gene clusters, as well as cbb3-type cytochrome oxidase gene in the genome of strain TSB47T. Strain TSB47T grows well under anaerobic and microaerophilic conditions with a strong tolerance to oxygen. Physiological and genomic characters of strain TSB47T indicated its high adaptability to termite gut ecosystem. Based on phenotypic and phylogenetic evidence, we suggest strain TSB47T as the type species of a novel genus in the family Opitutaceae, for which the name Termitidicoccus mucosus sp. nov. is proposed. The type strain is TSB47T (CCTCC AB2022447T; KCTC 102044T).
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Affiliation(s)
- Cheng Mei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yu Shi
- College of Food and Biotechnology, Wuhan Institute of Design and Sciences, Wuhan 430079, PR China
| | - Yu Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Zhengyong Qiu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Hong Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
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Ouyang MY, Wang S, Nie WH, Wang PH, Liao WX, Liu XH, Lin SS, Lin RP, Chen GY, Zhu B, Shen J. Methylomonas defluvii sp. nov., a type I methane-oxidizing bacterium from a secondary sedimentation tank of a wastewater treatment plant. Int J Syst Evol Microbiol 2024; 74. [PMID: 38607367 DOI: 10.1099/ijsem.0.006321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
An aerobic methanotroph was isolated from a secondary sedimentation tank of a wastewater treatment plant and designated strain OY6T. Cells of OY6T were Gram-stain-negative, pink-pigmented, motile rods and contained an intracytoplasmic membrane structure typical of type I methanotrophs. OY6T could grow at a pH range of 4.5-7.5 (optimum pH 6.5) and at temperatures ranging from 20 °C to 37 °C (optimum 30 °C). The major cellular fatty acids were C14 : 0, C16 : 1ω7c/C16 : 1ω6c and C16 : 1ω5c; the predominant respiratory quinone was MQ-8. The genome size was 5.41 Mbp with a DNA G+C content of 51.7 mol%. OY6T represents a member of the family Methylococcaceae of the class Gammaproteobacteria and displayed 95.74-99.64 % 16S rRNA gene sequence similarity to the type strains of species of the genus Methylomonas. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) confirmed that OY6T should be classified as representing a novel species. The most closely related type strain was Methylomonas fluvii EbBT, with 16S rRNA gene sequence similarity, ANI by blast (ANIb), ANI by MUMmer (ANIm) and dDDH values of 99.64, 90.46, 91.92 and 44.5 %, respectively. OY6T possessed genes encoding both the particulate methane monooxygenase enzyme and the soluble methane monooxygenase enzyme. It grew only on methane or methanol as carbon sources. On the basis of phenotypic, genetic and phylogenetic data, strain OY6T represents a novel species within the genus Methylomonas for which the name Methylomonas defluvii sp. nov. is proposed, with strain OY6T (=GDMCC 1.4114T=KCTC 8159T=LMG 33371T) as the type strain.
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Affiliation(s)
- Ming-Yan Ouyang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Sai Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Wen-Han Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Pei-Hong Wang
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Wei-Xue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xiao-Hui Liu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Si-Si Lin
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Rong-Peng Lin
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Gong-You Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Jian Shen
- People's Hospital, Hangzhou 310014, Zhejiang, PR China
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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Podosokorskaya OA, Elcheninov AG, Novikov AA, Merkel AY, Kublanov IV. Fontisphaera persica gen. nov., sp. nov., a thermophilic hydrolytic bacterium from a hot spring of Baikal lake region, and proposal of Fontisphaeraceae fam. nov., and Limisphaeraceae fam. nov. within the Limisphaerales ord. nov. (Verrucomicrobiota). Syst Appl Microbiol 2023; 46:126438. [PMID: 37263084 DOI: 10.1016/j.syapm.2023.126438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/25/2023] [Accepted: 05/24/2023] [Indexed: 06/03/2023]
Abstract
A novel facultatively anaerobic moderately thermophilic bacterium, strain B-154 T, was isolated from a terrestrial hot spring in the Baikal lake region (Russian Federation). Gram-negative, motile, spherical cells were present singly, in pairs, or aggregates, and reproduced by binary fission. The strain grew at 30-57 °C and within a pH range of 5.1-8.4 with the optimum at 50 °C and pH 6.8-7.1. Strain B-154 T was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (xylan, starch, galactan, galactomannan, glucomannan, xyloglucan, pullulan, arabinan, lichenan, beta-glucan, pachyman, locust bean gum, xanthan gum). It did not require sodium chloride or yeast extract for growth. Major cellular fatty acids were anteiso-C15:0, iso-C16:0 and iso-C14:0. The respiratory quinone was MK-7. The complete genome of strain B-154 T was 4.73 Mbp in size; its G + C content was 61%. According to the phylogenomic analysis strain B-154 T forms a separate family-level phylogenetic lineage. Moreover, together with Limisphaera ngatamarikiensis and "Pedosphaera parvula" this strain forms a separate order-level phylogenetic lineage within Verrucomicrobiae class. Hence, we propose a novel order, Limisphaerales ord. nov., with two families Limisphaeraceae fam. nov. and Fontisphaeraceae fam. nov., and a novel genus and species Fontisphaera persica gen. nov., sp. nov. with type strain B-154 T. Ecogenomic analysis showed that representatives of the Limisphaerales are widespread in various environments. Although some of them were detected in hot springs the majority of Limisphaerales (54% of the studied metagenome-assembled genomes) were found in marine habitats. This study allowed a better understanding of physiology and ecology of Verrucomicrobiota - a rather understudied bacterial phylum.
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Affiliation(s)
- Olga A Podosokorskaya
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia.
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Andrei A Novikov
- Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology RAS, 7/2 Prospekt 60-letiya Oktyabrya, 117312 Moscow, Russia
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Kapinusova G, Lopez Marin MA, Uhlik O. Reaching unreachables: Obstacles and successes of microbial cultivation and their reasons. Front Microbiol 2023; 14:1089630. [PMID: 36960281 PMCID: PMC10027941 DOI: 10.3389/fmicb.2023.1089630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/10/2023] [Indexed: 03/09/2023] Open
Abstract
In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.
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Affiliation(s)
| | | | - Ondrej Uhlik
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
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Zhang JJ, Nie C, Fu WL, Cheng FL, Chen P, Gao ZF, Wu Y, Shen Y. Photoresponsive DNA-Modified Magnetic Bead-Assisted Rolling Circle Amplification-Driven Visual Photothermal Sensing of Escherichia coli. Anal Chem 2022; 94:16796-16802. [DOI: 10.1021/acs.analchem.2c03714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Jing Jing Zhang
- Advanced Materials Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan250014, China
| | - Chao Nie
- School of Food and Biological Engineering, Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei230009, China
| | - Wen Long Fu
- Advanced Materials Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan250014, China
| | - Feng Li Cheng
- Advanced Materials Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan250014, China
| | - Pu Chen
- Advanced Materials Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan250014, China
| | - Zhong Feng Gao
- Advanced Materials Institute, Qilu University of Technology, Shandong Academy of Sciences, Jinan250014, China
- Key Laboratory of Interfacial Reaction and Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan250022, China
| | - Yongning Wu
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing100022, China
| | - Yizhong Shen
- School of Food and Biological Engineering, Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei230009, China
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Galitskaya P, Biktasheva L, Blagodatsky S, Selivanovskaya S. Response of bacterial and fungal communities to high petroleum pollution in different soils. Sci Rep 2021; 11:164. [PMID: 33420266 PMCID: PMC7794381 DOI: 10.1038/s41598-020-80631-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023] Open
Abstract
Petroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1-5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4-7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.
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Affiliation(s)
- Polina Galitskaya
- grid.77268.3c0000 0004 0543 9688Institute of Environmental Sciences, Kazan Federal University, Kazan, 420008 Russia
| | - Liliya Biktasheva
- grid.77268.3c0000 0004 0543 9688Institute of Environmental Sciences, Kazan Federal University, Kazan, 420008 Russia
| | - Sergey Blagodatsky
- grid.9464.f0000 0001 2290 1502Institute of Plant Production and Agroecology in the Tropics and Subtropics, University of Hohenheim, 70599 Stuttgart, Germany ,grid.451005.5Institute of Physico-Chemical and Biological Problems of Soil Science, Pushchino, 142290 Russia
| | - Svetlana Selivanovskaya
- grid.77268.3c0000 0004 0543 9688Institute of Environmental Sciences, Kazan Federal University, Kazan, 420008 Russia
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Shan Y, Guo J, Fan W, Li H, Wu H, Song Y, Jalleh G, Wu W, Zhang G. Modern urbanization has reshaped the bacterial microbiome profiles of house dust in domestic environments. World Allergy Organ J 2020; 13:100452. [PMID: 32884612 PMCID: PMC7451671 DOI: 10.1016/j.waojou.2020.100452] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 07/17/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023] Open
Abstract
Background The prevalence of allergy and other common chronic diseases is higher in developed than developing countries, and higher in urban than rural regions. Urbanization through its modification of environmental microbiomes may play a predominant role in the development of these conditions. However, no studies have been conducted to compare the microbiome in house dust among areas with different urbanization levels. Methods House dust from Xinxiang rural area (XR, n = 74), Xinxiang urban area (XU, n = 33), and Zhengzhou urban area (ZU, n = 32) in central China, and from Australia (AU, n = 58 [with pets AUP, n = 15, without pets AUNP, n = 43]) were collected during a summer season in China and Australia. High-throughput sequencing of 16S rDNA was employed to profile house dust bacterial communities. Results Settled dust collected in China was dominant with 2 bacterial phyla: Proteobacteria and Actinobacteria, while floor dust collected in Australia had a higher proportion of phylum Proteobacteria, Firmicutes, and Actinobacteria. XR dust samples presented higher bacterial richness and diversity compared with XU or ZU samples. Urbanization level (r2 = 0.741 P < 0.001) had a significant correlation with the distribution of house dust bacterial community. At the genus level, there was a positive correlation (r coefficient > 0.5) between urbanization level and bacterial genera Streptococcus, Bartonella, Staphylococcus, Pseudomonas, Acinetobacter, Bacteroides, Corynebacterium_1,and Enhydrobacter and a negative correlation (r coefficient < −0.5) with Rhodanobacter. Conclusion There was a significant difference in house dust microbiota among different urbanization areas. The areas with a lower urbanization level presented higher dust-borne bacterial richness and diversity. Modern urbanization has a significant influence on the bacterial microbiome profiles of indoor dust.
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Affiliation(s)
- Yifan Shan
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province, 4353003, P.R. China
- Henan International Laboratory for Air Pollution Health Effects and Intervention, Xinxiang, Henan Province, 4353003, P.R. China
- School of Public Health, Curtin University, Perth, WA, Australia
- Department of Public Health, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, Japan
| | - Jing Guo
- School of Public Health, Curtin University, Perth, WA, Australia
| | - Wei Fan
- Henan Center for Disease Control and Prevention, Zhengzhou, Henan, 450000, P.R. China
| | - Huijun Li
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province, 4353003, P.R. China
- Henan International Laboratory for Air Pollution Health Effects and Intervention, Xinxiang, Henan Province, 4353003, P.R. China
| | - Hui Wu
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province, 4353003, P.R. China
- School of Public Health, Tianjin Medical University, Tianjin, 300070, P.R. China
- Henan Province General Medical Educations and Research Center, Xinxiang, Henan, 453003, P.R. China
| | - Yong Song
- School of Public Health, Curtin University, Perth, WA, Australia
| | - Geoffrey Jalleh
- School of Public Health, Curtin University, Perth, WA, Australia
| | - Weidong Wu
- School of Public Health, Xinxiang Medical University, Xinxiang, Henan Province, 4353003, P.R. China
- Henan International Laboratory for Air Pollution Health Effects and Intervention, Xinxiang, Henan Province, 4353003, P.R. China
- Corresponding author. School of Public Health, Xinxiang Medical University, 601 Jinsui Street, Xinxiang, Henan Province, 453003, P.R. China.
| | - Guicheng Zhang
- School of Public Health, Curtin University, Perth, WA, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA, 6102, Australia
- Corresponding author. School of Public Health, Curtin University of Technology, Kent St, Bentley, Western Australia, 6102, Australia.
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Perez-Mon C, Frey B, Frossard A. Functional and Structural Responses of Arctic and Alpine Soil Prokaryotic and Fungal Communities Under Freeze-Thaw Cycles of Different Frequencies. Front Microbiol 2020; 11:982. [PMID: 32523565 PMCID: PMC7261861 DOI: 10.3389/fmicb.2020.00982] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Ongoing climate change involves increasing snow scarcity, which results in more frequent freeze-thaw cycles (FTCs) in polar and alpine soils. Although repeated FTCs have been shown to alter the structure and functions of soil microbial communities, a thorough understanding on the influence of FTCs frequency on polar and especially alpine soil microbiomes is still elusive. Here, we investigated the impact of repeated weekly vs. daily FTC frequencies on the structure and functions of prokaryotic and fungal communities from north- and south-exposed soils from two mountain ridges, one in the Arctic and one in the High-Alps. FTCs affected prokaryotic communities more strongly than fungal communities, where mainly cold-tolerant and opportunistic fungi (e.g., Mrakia, Mortierella) were responsive. Prokaryotic communities were more affected by weekly FTCs than by daily FTCs. Daily FTCs favored fast-growing bacteria (e.g., Arthrobacter), while oligotrophic and largely uncultured taxa (e.g., Verrucomicrobia) benefited from weekly FTCs. FTCs negatively affected microbial respiration but had minor impacts on C-, N- and P-acquiring enzymatic activities. Plausible pre-adaptation of the microbial communities to naturally occurring frequent FTCs at their site of origin did not show a clear influence on the microbial responses to the tested FTCs. Altogether, our study provides an integrative overview on potential structural and functional changes of soil microbial communities in polar and alpine regions in response to the projected increase in FTCs; therefore advancing our understanding on the impact of climate change in these rapidly changing ecosystems.
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Affiliation(s)
- Carla Perez-Mon
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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O'Brien AM, Yu ZH, Luo DY, Laurich J, Passeport E, Frederickson ME. Resilience to multiple stressors in an aquatic plant and its microbiome. AMERICAN JOURNAL OF BOTANY 2020; 107:273-285. [PMID: 31879950 DOI: 10.1002/ajb2.1404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/09/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Outcomes of species interactions, especially mutualisms, are notoriously dependent on environmental context, and environments are changing rapidly. Studies have investigated how mutualisms respond to or ameliorate anthropogenic environmental changes, but most have focused on nutrient pollution or climate change and tested stressors one at a time. Relatively little is known about how mutualisms may be altered by or buffer the effects of multiple chemical contaminants, which differ fundamentally from nutrient or climate stressors and are especially widespread in aquatic habitats. METHODS We investigated the impacts of two contaminants on interactions between the duckweed Lemna minor and its microbiome. Sodium chloride (salt) and benzotriazole (a corrosion inhibitor) often co-occur in runoff to water bodies where duckweeds reside. We tested three L. minor genotypes with and without the culturable portion of their microbiome across field-realistic gradients of salt (3 levels) and benzotriazole (4 levels) in a fully factorial experiment (24 treatments, tested on each genotype) and measured plant and microbial growth. RESULTS Stressors had conditional effects. Salt decreased both plant and microbial growth and decreased plant survival more as benzotriazole concentrations increased. In contrast, benzotriazole did not affect microbial abundance and even benefited plants when salt and microbes were absent, perhaps due to biotransformation into growth-promoting compounds. Microbes did not ameliorate duckweed stressors; microbial inoculation increased plant growth, but not at high salt concentrations. CONCLUSIONS Our results suggest that multiple stressors matter when predicting responses of mutualisms to global change and that beneficial microbes may not always buffer hosts against stress.
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Affiliation(s)
- Anna M O'Brien
- Department of Ecology and Evolutionary Biology, University of Toronto
| | - Zhu Hao Yu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto
| | - Dian-Ya Luo
- Department of Ecology and Evolutionary Biology, University of Toronto
| | - Jason Laurich
- Department of Ecology and Evolutionary Biology, University of Toronto
| | - Elodie Passeport
- Department of Chemical Engineering and Applied Chemistry, University of Toronto
- Department of Civil and Mineral Engineering, University of Toronto
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Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface. mSphere 2019; 4:4/6/e00613-19. [PMID: 31852806 PMCID: PMC6920513 DOI: 10.1128/msphere.00613-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Verrucomicrobia phylum of bacteria is widespread in many different ecosystems; however, its role in microbial communities remains poorly understood. Verrucomicrobia are often low-abundance community members, yet previous research suggests they play a major role in organic carbon degradation. While Verrucomicrobia remain poorly represented in culture collections, numerous genomes have been reconstructed from metagenomic data sets in recent years. The study of genomes from across the phylum allows for an extensive assessment of their potential ecosystem roles. The significance of this work is (i) the recovery of a novel genus of Verrucomicrobia from 2.3 km in the subsurface with the ability to withstand the extreme conditions that characterize this environment, and (ii) the most extensive assessment of ecophysiological traits encoded by Verrucomicrobia genomes to date. We show that members of this phylum are specialist organic polymer degraders that can withstand a wider range of environmental conditions than previously thought. Bacteria of the phylum Verrucomicrobia are prevalent and are particularly common in soil and freshwater environments. Their cosmopolitan distribution and reported capacity for polysaccharide degradation suggests members of Verrucomicrobia are important contributors to carbon cycling across Earth’s ecosystems. Despite their prevalence, the Verrucomicrobia are underrepresented in isolate collections and genome databases; consequently, their ecophysiological roles may not be fully realized. Here, we expand genomic sampling of the Verrucomicrobia phylum by describing a novel genus, “Candidatus Marcellius,” belonging to the order Opitutales. “Ca. Marcellius” was recovered from a shale-derived produced fluid metagenome collected 313 days after hydraulic fracturing, the deepest environment from which a member of the Verrucomicrobia has been recovered to date. We uncover genomic attributes that may explain the capacity of this organism to inhabit a shale gas well, including the potential for utilization of organic polymers common in hydraulic fracturing fluids, nitrogen fixation, adaptation to high salinities, and adaptive immunity via CRISPR-Cas. To illuminate the phylogenetic and environmental distribution of these metabolic and adaptive traits across the Verrucomicrobia phylum, we performed a comparative genomic analysis of 31 publicly available, nearly complete Verrucomicrobia genomes. Our genomic findings extend the environmental distribution of the Verrucomicrobia 2.3 kilometers into the terrestrial subsurface. Moreover, we reveal traits widely encoded across members of the Verrucomicrobia, including the capacity to degrade hemicellulose and to adapt to physical and biological environmental perturbations, thereby contributing to the expansive habitat range reported for this phylum. IMPORTANCE The Verrucomicrobia phylum of bacteria is widespread in many different ecosystems; however, its role in microbial communities remains poorly understood. Verrucomicrobia are often low-abundance community members, yet previous research suggests they play a major role in organic carbon degradation. While Verrucomicrobia remain poorly represented in culture collections, numerous genomes have been reconstructed from metagenomic data sets in recent years. The study of genomes from across the phylum allows for an extensive assessment of their potential ecosystem roles. The significance of this work is (i) the recovery of a novel genus of Verrucomicrobia from 2.3 km in the subsurface with the ability to withstand the extreme conditions that characterize this environment, and (ii) the most extensive assessment of ecophysiological traits encoded by Verrucomicrobia genomes to date. We show that members of this phylum are specialist organic polymer degraders that can withstand a wider range of environmental conditions than previously thought.
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Yan H, Yang F, Gao J, Peng Z, Chen W. Subsoil microbial community responses to air exposure and legume growth depend on soil properties across different depths. Sci Rep 2019; 9:18536. [PMID: 31811223 PMCID: PMC6898284 DOI: 10.1038/s41598-019-55089-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/18/2019] [Indexed: 11/09/2022] Open
Abstract
Anthropogenic disturbance, such as agricultural and architectural activities, can greatly influence belowground soil microbes, and thus soil formation and nutrient cycling. The objective of this study was to investigate microbial community variation in deep soils affected by strong disturbances. In present study, twelve soil samples were collected from different depths (0–300 cm) and placed onto the surface. We investigated the structure variation of the microbial community down through the soil profiles in response to disturbance originated by legume plants (robinia and clover) cultivation vs. plant-free controls. The high-throughput sequencing of 16S rRNA genes showed that microbial α-diversity decreased with depth, and that growing both plants significantly impacted the diversity in the topsoil. The soil profile was clustered into three layers: I (0–40 cm), II (40–120 cm), and III (120–300 cm); with significantly different taxa found among them. Soil properties explained a large amount of the variation (23.5%) in the microbial community, and distinct factors affected microbial assembly in the different layers, e.g., available potassium in layer I, pH and total nitrogen in layer II, pH and organic matter in layer III. The prediction of metabolic functions and oxygen requirements indicated that the number of aerobic bacteria increased with more air exposure, which may further accelerate the transformation of nitrogen, sulfur, carbon, and pesticides in the soil. The diversity of soil microorganisms followed a depth-decay pattern, but became higher following legume growth and air exposure, with notable abundance variation of several important bacterial species, mainly belonging to Nitrospira, Verrucomicrobia, and Planctomycetes, and soil properties occurring across the soil profiles.
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Affiliation(s)
- Hongmei Yan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Fan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Jiamin Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Ziheng Peng
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, P.R. China.
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Kang MS, Hur M, Park SJ. Rhizocompartments and environmental factors affect microbial composition and variation in native plants. J Microbiol 2019; 57:550-561. [DOI: 10.1007/s12275-019-8646-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/24/2019] [Accepted: 01/30/2019] [Indexed: 11/27/2022]
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Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments. mSphere 2019; 4:4/3/e00631-18. [PMID: 31167950 PMCID: PMC6553558 DOI: 10.1128/msphere.00631-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions. Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named “Methylotetracoccus oryzae” C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems. IMPORTANCE Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.
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Ren B, Li C, Zhang X, Zhang Z. Fe(II)-dosed ceramic membrane bioreactor for wastewater treatment: Nutrient removal, microbial community and membrane fouling analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:116-126. [PMID: 30739846 DOI: 10.1016/j.scitotenv.2019.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
Ferrous dosing is used to reduce phosphorus concentration and alleviate polymeric membrane fouling in membrane bioreactor (MBR). However, limited studies have been conducted to investigate the impacts of ferrous dosing on ceramic membrane fouling, nutrient removal efficiency and microbial community. Accordingly, the aim of this study was to investigate the effect of intermittent ferrous dosing with Fe/P molar ratios of 2 and 1 (with a dosing frequency of every two days) on the overall nutrient removal, functional microbial changes and membrane fouling in ceramic membrane bioreactors (CMBR) in treatment of wastewater. TP concentration of 10 mg/L in influent decreased to 1.94 ± 0.62 mg/L (control), 0.38 ± 0.22 mg/L (Fe/P = 1) and 0.31 ± 0.18 mg/L (Fe/P = 2) in the effluent, respectively. Meanwhile, the effluent total nitrogen (TN) concentrations with Fe/P = 1 treatment (6.80 ± 2.02 mg/L) and Fe/P = 2 treatment (5.12 ± 2.28 mg/L) were lower than that of the control (7.72 ± 2.36 mg/L). Compared to Fe/P = 1, the TN removal performance was better for Fe/P = 2 mainly due to the increased abundance of denitrifying bacteria (Zoogloea and Acinetobacter). In addition, excess iron dose might have toxic effects on bacterial physiology, however the Fe concentrations that cause cell damage vary for different bacteria. The relative abundance of Zoogloea (aerobic denitrifying bacteria) continuously increased with ferrous addition (Fe/P = 2), while other bacteria including Dechloromonas, Hyphomicrobium and Thauera (anoxic denitrifying bacteria), Nitrospira (nitrifying bacteria) and Candidatus Accumulibacter (phosphorus accumulating organism) decreased sharply. Furthermore, membrane fouling was effectively moderated by ferrous dosing and Fe/P = 1 treatment showed improved membrane fouling mitigation than Fe/P = 2. Overall, intermittent ferrous addition in CMBR with Fe/P molar ratio of 1 was beneficial to the removal of nutrients (TP, TN and organics), enhanced succession of microbial community and membrane fouling mitigation.
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Affiliation(s)
- Baoyu Ren
- Research Institute of Environmental Engineering & Nano-Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, Guangdong, China; Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, Guangdong, China; School of Environment, Tsinghua University, Beijing 100084, China
| | - Chengyue Li
- Research Institute of Environmental Engineering & Nano-Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, Guangdong, China; Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, Guangdong, China; School of Environment, Tsinghua University, Beijing 100084, China
| | - Xihui Zhang
- Research Institute of Environmental Engineering & Nano-Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, Guangdong, China; Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, Guangdong, China; School of Environment, Tsinghua University, Beijing 100084, China; Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518055, Guangdong, China
| | - Zhenghua Zhang
- Research Institute of Environmental Engineering & Nano-Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, Guangdong, China; Guangdong Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, Guangdong, China; School of Environment, Tsinghua University, Beijing 100084, China.
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Singh JP, Ojinnaka EU, Krumins JA, Goodey NM. Abiotic factors determine functional outcomes of microbial inoculation of soils from a metal contaminated brownfield. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 168:450-456. [PMID: 30415167 DOI: 10.1016/j.ecoenv.2018.10.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 10/12/2018] [Accepted: 10/30/2018] [Indexed: 05/20/2023]
Abstract
Whole community microbial inoculation can improve soil function in contaminated environments. Here we conducted a case study to investigate whether biotic factors (inoculum) or abiotic factors (soil base) have more impact on the extracellular enzymatic activities in a whole community microbial inoculation. To this end, we cross-inoculated microbial communities between two heavy metal-contaminated soils, with high and low extracellular enzyme activities, respectively. We measured extracellular phosphatase activity, a proxy for soil function, after self- and cross-inoculation of microbial communities into sterilized soils, and all activities were normalized to non-inoculated controls. We found that inoculation increased phosphatase activity in the soils. For soils treated with different inocula, we found significant differences in the microbial community compositions but no significant differences in the extracellular phosphatase activities normalized to their respective sterilized, non-inoculated controls (4.7 ± 1.8 and 3.3 ± 0.5 for soils inoculated with microbial communities from 146 to 43, respectively). On the other hand, normalized phosphatase activities between the two soil bases were significantly different (4.1 ± 0.12 and 1.9 ± 0.12 for soil bases 146 and 43, respectively) regardless of the source of the inoculum that did not vary between soil bases. The results indicate that the abiotic properties of the soils were a significant predictor for phosphatase activity but not for the end-point composition of the microbial community. The findings suggest that targeted microbial inocula from metal contaminated soils can increase phosphatase activity, and likely soil functioning in general, but the degree to which this happens depends on the abiotic environment, in this case, metal contamination.
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Affiliation(s)
- Jay Prakash Singh
- Department of Earth and Environmental Science, Montclair State University, Montclair, NJ, USA
| | - Eleanor U Ojinnaka
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA
| | | | - Nina M Goodey
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, USA.
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Hahn MW, Koll U, Schmidt J. Isolation and Cultivation of Bacteria. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2019. [DOI: 10.1007/978-3-030-16775-2_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Chernov TI, Zhelezova AD, Kutovaya OV, Makeev AO, Tkhakakhova AK, Bgazhba NA, Kurbanova FG, Rusakov AV, Puzanova TA, Khokhlova OS. Comparative Analysis of the Structure of Buried and Surface Soils by Analysis of Microbial DNA. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718060073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Zhang S, Tsementzi D, Hatt JK, Bivins A, Khelurkar N, Brown J, Tripathi SN, Konstantinidis KT. Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics. Environ Microbiol 2018; 21:182-196. [DOI: 10.1111/1462-2920.14439] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Si‐Yu Zhang
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building Atlanta GA, 30332 USA
| | - Despina Tsementzi
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building Atlanta GA, 30332 USA
| | - Janet K. Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building Atlanta GA, 30332 USA
| | - Aaron Bivins
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building Atlanta GA, 30332 USA
| | - Nikunj Khelurkar
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building Atlanta GA, 30332 USA
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building Atlanta GA, 30332 USA
| | - Sachchida Nand Tripathi
- Department of Civil Engineering Indian Institute of Technology Kanpur UP, 208016 India
- Center for Environmental Science and Engineering Indian Institute of Technology Kanpur UP, 208016 India
| | - Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science & Technology Building Atlanta GA, 30332 USA
- School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences & Technology Building Atlanta Georgia, 30332 USA
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Isolation of Previously Uncultured Slow-Growing Bacteria by Using a Simple Modification in the Preparation of Agar Media. Appl Environ Microbiol 2018; 84:AEM.00807-18. [PMID: 30030229 DOI: 10.1128/aem.00807-18] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/29/2018] [Indexed: 12/26/2022] Open
Abstract
Most microorganisms living in the environment have yet to be cultured, owing at least in part to their slow and poor propagation properties and susceptibility to oxidative stress. Our previous studies demonstrated that a simple modification in the preparation of agar media, i.e., autoclaving the phosphate and agar separately (termed "PS" medium), can greatly improve the culturability of microorganisms by mitigating oxidative stress compared with the use of "PT" medium (autoclaving the phosphate and agar together). Here, we attempted to isolate phylogenetically novel bacteria by combining PS medium with prolonged cultivation. After inoculation with forest soil or pond sediment samples, significantly more colonies appeared on PS medium than on PT medium. A total of 98 and 74 colonies that emerged after more than 7 days of cultivation were isolated as slow growers from PS and PT media, respectively. Sequencing analysis of their 16S rRNA genes revealed that the slow growers recovered from PS medium included more phylogenetically novel bacteria than those from PT medium, including a strain that could be classified into a novel order in the class Alphaproteobacteria Further physiological analysis of representative strains showed that they were actually slow and poor growers and formed small but visible colonies only on PS medium. This study demonstrates that the culturability of previously uncultured bacteria can be improved by using an isolation strategy that combines a simple modification in medium preparation with an extended incubation time.IMPORTANCE Most microbial species inhabiting natural environments have not yet been isolated. One of the serious issues preventing their isolation is intrinsically slow and/or poor growth. Moreover, these slow and/or poor growers are likely to be highly sensitive to environmental stresses, especially oxidative stress. We reported previously that interaction between agar and phosphate during autoclave sterilization generates hydrogen peroxide, which adversely affects the culturability of environmental microorganisms, in particular, slow-growing organisms vulnerable to oxidative stress. In this study, we successfully isolated many slow-growing bacterial strains with phylogenetic novelty by simply modifying their cultivation on agar plates, i.e., autoclaving the phosphate and agar separately. The current limited repertoire of culture techniques still has room for improvement in the isolation of microorganisms previously considered unculturable.
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Pershina EV, Ivanova EA, Korvigo IO, Chirak EL, Sergaliev NH, Abakumov EV, Provorov NA, Andronov EE. Investigation of the core microbiome in main soil types from the East European plain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 631-632:1421-1430. [PMID: 29727966 DOI: 10.1016/j.scitotenv.2018.03.136] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 05/12/2023]
Abstract
The main goal of modern microbial ecology is to determine the key factors influencing the global diversity of microorganisms. Because of their complexity, soil communities are largely underexplored in this context. We studied soil genesis (combination of various soil-forming processes, specific to a particular soil type) that is driven by microbial activity. To investigate the interrelation between soil type and microbial diversity, we analyzed six soil types that are common in Russia, the Crimea, and Kazakhstan using 16S rDNA pyrosequencing. Soils of different types varied in the taxonomic composition of microbial communities. Their core microbiomes comprised 47 taxa within the orders Solirubrobacteriales and Hyphomicrobiaceae and the Gaiellaceae family. Two species from Bradyrhizobiaceae and Solirubrobactriaceae were present in all samples, whereas most other taxa were soil-type specific. Multiple resampling analysis revealed that two random soil samples from the same soil type shared more taxa than two samples from different types. The differences in community composition were mostly affected by the variation in pH values and exchangeable potassium content. The results show that data on the soil microbiome could be used for soil identification and clarification of their taxonomic position.
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Affiliation(s)
- Elizaveta V Pershina
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia; Department of Microbiology, Saint-Petersburg State University, Saint-Petersburg, Russia.
| | - Ekaterina A Ivanova
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia; Laboratory of Biology and Biochemistry of Soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
| | - Ilia O Korvigo
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny L Chirak
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Nurlan H Sergaliev
- West Kazakhstan Agrarian Technical University, Zhangir Khan, Uralsk, Kazakhstan
| | | | - Nikolai A Provorov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny E Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia; Laboratory of Biology and Biochemistry of Soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
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Chiang E, Schmidt ML, Berry MA, Biddanda BA, Burtner A, Johengen TH, Palladino D, Denef VJ. Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PLoS One 2018; 13:e0195112. [PMID: 29590198 PMCID: PMC5874073 DOI: 10.1371/journal.pone.0195112] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/17/2018] [Indexed: 01/10/2023] Open
Abstract
The bacterial phylum Verrucomicrobia was formally described two decades ago and originally believed to be a minor member of many ecosystems; however, it is now recognized as ubiquitous and abundant in both soil and aquatic systems. Nevertheless, knowledge of the drivers of its relative abundance and within-phylum habitat preferences remains sparse, especially in lake systems. Here, we documented the distribution of Verrucomicrobia in 12 inland lakes in Southeastern Michigan, a Laurentian Great Lake (Lake Michigan), and a freshwater estuary, which span a gradient in lake sizes, depths, residence times, and trophic states. A wide range of physical and geochemical parameters was covered by sampling seasonally from the surface and bottom of each lake, and by separating samples into particle-associated and free-living fractions. On average, Verrucomicrobia was the 4th most abundant phylum (range 1.7–41.7%). Fraction, season, station, and depth explained up to 70% of the variance in Verrucomicrobia community composition and preference for these habitats was phylogenetically conserved at the class-level. When relative abundance was linearly modeled against environmental data, Verrucomicrobia and non-Verrucomicrobia bacterial community composition correlated to similar quantitative environmental parameters, although there were lake system-dependent differences and > 55% of the variance remained unexplained. A majority of the phylum exhibited preference for the particle-associated fraction and two classes (Opitutae and Verrucomicrobiae) were identified to be more abundant during the spring season. This study highlights the high relative abundance of Verrucomicrobia in north temperate lake systems and expands insights into drivers of within-phylum habitat preferences of the Verrucomicrobia.
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Affiliation(s)
- Edna Chiang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Marian L. Schmidt
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Michelle A. Berry
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
| | - Bopaiah A. Biddanda
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI, United States of America
| | - Ashley Burtner
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Thomas H. Johengen
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Danna Palladino
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, United States of America
| | - Vincent J. Denef
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States of America
- * E-mail:
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Rivas-Marín E, Devos DP. The Paradigms They Are a-Changin': past, present and future of PVC bacteria research. Antonie van Leeuwenhoek 2017; 111:785-799. [PMID: 29058138 PMCID: PMC5945725 DOI: 10.1007/s10482-017-0962-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022]
Abstract
These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.
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Affiliation(s)
- Elena Rivas-Marín
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain.
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He S, Stevens SLR, Chan LK, Bertilsson S, Glavina del Rio T, Tringe SG, Malmstrom RR, McMahon KD. Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes. mSphere 2017; 2:e00277-17. [PMID: 28959738 PMCID: PMC5615132 DOI: 10.1128/msphere.00277-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/05/2017] [Indexed: 11/20/2022] Open
Abstract
Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called "Planctomycete-specific" cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called "Planctomycete-specific" cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.
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Affiliation(s)
- Shaomei He
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Geoscience, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Sarah L. R. Stevens
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | - Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
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25
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Samad MS, Johns C, Richards KG, Lanigan GJ, de Klein CAM, Clough TJ, Morales SE. Response to nitrogen addition reveals metabolic and ecological strategies of soil bacteria. Mol Ecol 2017; 26:5500-5514. [DOI: 10.1111/mec.14275] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/22/2017] [Accepted: 07/24/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Md Sainur Samad
- Department of Microbiology and Immunology; Otago School of Medical Sciences; University of Otago; Dunedin New Zealand
| | - Charlotte Johns
- Department of Soil and Physical Sciences; Lincoln University; Lincoln New Zealand
| | | | | | | | - Timothy J. Clough
- Department of Soil and Physical Sciences; Lincoln University; Lincoln New Zealand
| | - Sergio E. Morales
- Department of Microbiology and Immunology; Otago School of Medical Sciences; University of Otago; Dunedin New Zealand
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26
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Tanaka Y, Matsuzawa H, Tamaki H, Tagawa M, Toyama T, Kamagata Y, Mori K. Isolation of Novel Bacteria Including Rarely Cultivated Phyla, Acidobacteria and Verrucomicrobia, from the Roots of Emergent Plants by Simple Culturing Method. Microbes Environ 2017; 32:288-292. [PMID: 28740039 PMCID: PMC5606700 DOI: 10.1264/jsme2.me17027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A number of novel bacteria including members of rarely cultivated phyla, Acidobacteria and Verrucomicrobia, were successfully isolated from the roots of two emergent plants, Iris pseudacorus and Scirpus juncoides, by a simple culturing method. A total of 47.1% (66 strains) for I. pseudacorus and 42.1% (59 strains) for S. juncoides of all isolates (140 strains from each sample) were phylogenetically novel. Furthermore, Acidobacteria and Verrucomicrobia occupied 10.7% (15 strains) and 2.9% (4 strains) of I. pseudacorus isolates, and 2.1% (3 strains) and 3.6% (5 strains) of S. juncoides isolates, respectively, indicating that plant roots are attractive sources for isolating rarely cultivated microbes.
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Affiliation(s)
- Yasuhiro Tanaka
- Department of Environmental Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi
| | - Hiroaki Matsuzawa
- International Research Centre for River Basin Environment, University of Yamanashi
| | | | | | - Tadashi Toyama
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi
| | | | - Kazuhiro Mori
- Department of Civil and Environmental Engineering, Faculty of Engineering, University of Yamanashi
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27
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Cernava T, Erlacher A, Aschenbrenner IA, Krug L, Lassek C, Riedel K, Grube M, Berg G. Deciphering functional diversification within the lichen microbiota by meta-omics. MICROBIOME 2017; 5:82. [PMID: 28724401 PMCID: PMC5518139 DOI: 10.1186/s40168-017-0303-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/06/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. RESULTS The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders-Sphingomonadales, Rhodospirillales, Myxococcales, Chthoniobacterales, and Sphingobacteriales-harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols. CONCLUSIONS Functions that facilitate the persistence of Lobaria pulmonaria under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like Chthoniobacterales (Verrucomicrobia) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.
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Affiliation(s)
- Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnolgy GmbH, Petersgasse 14, 8010 Graz, Austria
| | - Armin Erlacher
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Ines Aline Aschenbrenner
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Lisa Krug
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Christian Lassek
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig-Jahn Strasse 15, 17489 Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig-Jahn Strasse 15, 17489 Greifswald, Germany
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
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28
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Barber NA, Chantos-Davidson KM, Amel Peralta R, Sherwood JP, Swingley WD. Soil microbial community composition in tallgrass prairie restorations converge with remnants across a 27-year chronosequence. Environ Microbiol 2017; 19:3118-3131. [PMID: 28474391 DOI: 10.1111/1462-2920.13785] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 04/21/2017] [Accepted: 04/28/2017] [Indexed: 11/30/2022]
Abstract
Restoration and management of natural ecosystems is a critical strategy in mitigating global biodiversity loss. This is exemplified in the American Midwest by efforts aimed at reclaiming historical grasslands lost to high-yield agriculture. While restorations traditionally take the form of plant reintroduction and management, advances in microbial analyses suggest that soil communities could be indicators restoration success. However, current understanding of key microbial taxa and functional activities in both natural and restored ecosystems is limited. Here, we investigated the impact of nearly 30 years of carefully managed restoration on soil microbial communities at the Nachusa Grasslands in northern Illinois, USA. We characterized bacterial and archaeal communities in a chronosequence of restored tallgrass prairies ranging from 1 to 27 years old across a growing season and compared them to communities in pre-restoration agricultural fields and remnant prairies. Results indicate that older restorations harboured communities statistically distinct from newer restorations. These communities converged toward those in local prairie remnants, suggesting that plant-focussed restoration has yielded soil bacterial communities reflective of a successful restoration. Recovery of microbial clades within the Verrucomicrobia and Acidobacteria are an important feature of this convergence, and these groups could be targeted for future soil-focussed, bottom-up restoration studies.
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Affiliation(s)
- Nicholas A Barber
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA.,Institute for the Study of the Environment, Sustainability, and Energy, Northern Illinois University, DeKalb, IL, USA
| | | | | | | | - Wesley D Swingley
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA.,Institute for the Study of the Environment, Sustainability, and Energy, Northern Illinois University, DeKalb, IL, USA
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29
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Zhou Y, Zhu H, Fu S, Yao Q. Variation in Soil Microbial Community Structure Associated with Different Legume Species Is Greater than that Associated with Different Grass Species. Front Microbiol 2017; 8:1007. [PMID: 28620371 PMCID: PMC5449475 DOI: 10.3389/fmicb.2017.01007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 05/19/2017] [Indexed: 11/13/2022] Open
Abstract
Plants are the essential factors shaping soil microbial community (SMC) structure. When most studies focus on the difference in the SMC structure associated different plant species, the variation in the SMC structure associated with phylogenetically close species is less investigated. Legume (Fabaceae) and grass (Poaceae) are functionally important plant groups; however, their influences on the SMC structure are seldom compared, and the variation in the SMC structure among legume or grass species is largely unknown. In this study, we grew three legume species vs. three grass species in mesocosms, and monitored the soil chemical property, quantified the abundance of bacteria and fungi. The SMC structure was also characterized using PCR-DGGE and Miseq sequencing. Results showed that legume and grass differentially affected soil pH, dissolved organic C, total N content, and available P content, and that legume enriched fungi more greatly than grass. Both DGGE profiling and Miseq-sequencing indicated that the bacterial diversity associated with legume was higher than that associated with grass. When legume increased the abundance of Verrucomicrobia, grass decreased it, and furthermore, linear discriminant analysis identified some group-specific microbial taxa as potential biomarkers of legume or grass. These data suggest that legume and grass differentially select for the SMC. More importantly, clustering analysis based on both DGGE profiling and Miseq-sequencing demonstrated that the variation in the SMC structure associated with three legume species was greater than that associated with three grass species.
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Affiliation(s)
- Yang Zhou
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass ScienceGuangzhou, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of MicrobiologyGuangzhou, China
| | - Shenglei Fu
- College of Environment and Planning, Henan UniversityKaifeng, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Litchi, Guangdong Engineering Research Center for Grass ScienceGuangzhou, China
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30
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Van Nevel S, Koetzsch S, Proctor CR, Besmer MD, Prest EI, Vrouwenvelder JS, Knezev A, Boon N, Hammes F. Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring. WATER RESEARCH 2017; 113:191-206. [PMID: 28214393 DOI: 10.1016/j.watres.2017.01.065] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
Drinking water utilities and researchers continue to rely on the century-old heterotrophic plate counts (HPC) method for routine assessment of general microbiological water quality. Bacterial cell counting with flow cytometry (FCM) is one of a number of alternative methods that challenge this status quo and provide an opportunity for improved water quality monitoring. After more than a decade of application in drinking water research, FCM methodology is optimised and established for routine application, supported by a considerable amount of data from multiple full-scale studies. Bacterial cell concentrations obtained by FCM enable quantification of the entire bacterial community instead of the minute fraction of cultivable bacteria detected with HPC (typically < 1% of all bacteria). FCM measurements are reproducible with relative standard deviations below 3% and can be available within 15 min of samples arriving in the laboratory. High throughput sample processing and complete automation are feasible and FCM analysis is arguably less expensive than HPC when measuring more than 15 water samples per day, depending on the laboratory and selected staining procedure(s). Moreover, many studies have shown FCM total (TCC) and intact (ICC) cell concentrations to be reliable and robust process variables, responsive to changes in the bacterial abundance and relevant for characterising and monitoring drinking water treatment and distribution systems. The purpose of this critical review is to initiate a constructive discussion on whether FCM could replace HPC in routine water quality monitoring. We argue that FCM provides a faster, more descriptive and more representative quantification of bacterial abundance in drinking water.
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Affiliation(s)
- S Van Nevel
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - S Koetzsch
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - C R Proctor
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - M D Besmer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - E I Prest
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - J S Vrouwenvelder
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands; Wetsus, Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands; King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Division of Biological and Environmental Science and Engineering (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - A Knezev
- Het Waterlaboratorium, J.W. Lucasweg 2, 2031 BE, Haarlem, The Netherlands
| | - N Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - F Hammes
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.
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Parulekar NN, Kolekar P, Jenkins A, Kleiven S, Utkilen H, Johansen A, Sawant S, Kulkarni-Kale U, Kale M, Sæbø M. Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis. PLoS One 2017; 12:e0173408. [PMID: 28282404 PMCID: PMC5345797 DOI: 10.1371/journal.pone.0173408] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/19/2017] [Indexed: 11/19/2022] Open
Abstract
Interactions between different phytoplankton taxa and heterotrophic bacterial communities within aquatic environments can differentially support growth of various heterotrophic bacterial species. In this study, phytoplankton diversity was studied using traditional microscopic techniques and the bacterial communities associated with phytoplankton bloom were studied using High Throughput Sequencing (HTS) analysis of 16S rRNA gene amplicons from the V1-V3 and V3-V4 hypervariable regions. Samples were collected from Lake Akersvannet, a eutrophic lake in South Norway, during the growth season from June to August 2013. Microscopic examination revealed that the phytoplankton community was mostly represented by Cyanobacteria and the dinoflagellate Ceratium hirundinella. The HTS results revealed that Proteobacteria (Alpha, Beta, and Gamma), Bacteriodetes, Cyanobacteria, Actinobacteria and Verrucomicrobia dominated the bacterial community, with varying relative abundances throughout the sampling season. Species level identification of Cyanobacteria showed a mixed population of Aphanizomenon flos-aquae, Microcystis aeruginosa and Woronichinia naegeliana. A significant proportion of the microbial community was composed of unclassified taxa which might represent locally adapted freshwater bacterial groups. Comparison of cyanobacterial species composition from HTS and microscopy revealed quantitative discrepancies, indicating a need for cross validation of results. To our knowledge, this is the first study that uses HTS methods for studying the bacterial community associated with phytoplankton blooms in a Norwegian lake. The study demonstrates the value of considering results from multiple methods when studying bacterial communities.
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MESH Headings
- Bacteria/genetics
- Bacteria/isolation & purification
- Bacteria/metabolism
- Cyanobacteria/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Bacterial/metabolism
- Enzyme-Linked Immunosorbent Assay
- High-Throughput Nucleotide Sequencing
- Lakes/microbiology
- Microcystins/analysis
- Microcystis/genetics
- Microcystis/metabolism
- Norway
- Phytoplankton/genetics
- Phytoplankton/growth & development
- Proteobacteria/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- Sequence Analysis, DNA
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Affiliation(s)
- Niranjan Nitin Parulekar
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
- * E-mail:
| | - Pandurang Kolekar
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Andrew Jenkins
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Synne Kleiven
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Hans Utkilen
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Anette Johansen
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
| | - Sangeeta Sawant
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Mohan Kale
- Department of Statistics, Savitribai Phule Pune University (formerly University of Pune), Pune, India
| | - Mona Sæbø
- Department of Natural Sciences and Environmental Health, Faculty of Technology, Natural Sciences and Maritime Sciences, University College of Southeast Norway, Bø i Telemark, Norway
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32
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Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios. Appl Environ Microbiol 2017; 83:AEM.02533-16. [PMID: 27913414 DOI: 10.1128/aem.02533-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/20/2022] Open
Abstract
Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient-poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CO2 to CH4 produced. After [13C]cellobiose amendment, the mesotrophic fen produced equal amounts of CH4 and CO2 The oligotrophic fen had lower CH4 production but produced 3 to 59 times more CO2 than CH4 RNA stable-isotope probing revealed that in the mesotrophic fen with higher CH4 production, cellobiose-derived carbon was mainly assimilated by various recognized fermenters of Firmicutes and by Proteobacteria The oligotrophic peat with excess CO2 production revealed a wider variety of cellobiose-C consumers, including Firmicutes and Proteobacteria, but also more unconventional degraders, such as Telmatobacter-related Acidobacteria and subphylum 3 of Verrucomicrobia Prominent and potentially fermentative Planctomycetes and Chloroflexi did not appear to process cellobiose-C. Our results show that anaerobic degradation resulting in different levels of CH4 production can involve distinct sets of bacterial degraders. By distinguishing cellobiose degraders from the total community, this study contributes to defining anaerobic bacteria that process cellulose-derived carbon in peat. Several of the identified degraders, particularly fermenters and potential Fe(III) or humic substance reducers in the oligotrophic peat, represent promising candidates for resolving the origin of excess CO2 production in peatlands. IMPORTANCE Peatlands are major sources of the greenhouse gas methane (CH4), yet in many peatlands, CO2 production from unresolved anaerobic processes exceeds CH4 production. Anaerobic degradation produces the precursors of CH4 production but also represents competing processes. We show that anaerobic degradation leading to high or low CH4 production involved distinct sets of bacteria. Well-known fermenters dominated in a peatland with high CH4 production, while novel and unconventional degraders could be identified in a site where CO2 production greatly exceeds CH4 production. Our results help identify and assign functions to uncharacterized bacteria that promote or inhibit CH4 production and reveal bacteria potentially producing the excess CO2 in acidic peat. This study contributes to understanding the microbiological basis for different levels of CH4 emission from peatlands.
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33
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Schang C, Lintern A, Cook PLM, Osborne C, McKinley A, Schmidt J, Coleman R, Rooney G, Henry R, Deletic A, McCarthy D. Presence and survival of culturable Campylobacter spp. and Escherichia coli in a temperate urban estuary. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 569-570:1201-1211. [PMID: 27395075 DOI: 10.1016/j.scitotenv.2016.06.195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 06/24/2016] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
Urban estuaries throughout the world typically contain elevated levels of faecal contamination, the extent of which is generally assessed using faecal indicator organisms (FIO) such as Escherichia coli. This study assesses whether the bacterial FIO, E. coli is a suitable surrogate for Campylobacter spp., in estuaries. The presence and survival dynamics of culturable E. coli and Campylobacter spp. are compared in the water column, bank sediments and bed sediments of the Yarra River estuary (located in Melbourne, Australia). The presence of E. coli did not necessarily indicate detectable levels of Campylobacter spp. in the water column, bed and bank sediments, but the inactivation rates of the two bacteria were similar in the water column. A key finding of the study is that E. coli and Campylobacter spp. can survive for up to 14days in the water column and up to 21days in the bed and bank sediments of the estuary. Preliminary data presented in this study also suggests that the inactivation rates of the two bacteria may be similar in bed and bank sediments. This undermines previous hypotheses that Campylobacter spp. cannot survive outside of its host and indicates that public health risks can persist in aquatic systems for up to three weeks after the initial contamination event.
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Affiliation(s)
- Christelle Schang
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Department of Civil Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia
| | - Anna Lintern
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Department of Civil Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia
| | - Perran L M Cook
- School of Chemistry, Monash University, Wellington Rd, Clayton 3800, Victoria, Australia
| | | | - Anand McKinley
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Department of Civil Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia
| | - Jonathon Schmidt
- ALS Environmental, Dalmore Drive, Scoresby 3179, Victoria, Australia
| | - Rhys Coleman
- Melbourne Water Corporation, La Trobe Street, Docklands 3008, Australia
| | - Graham Rooney
- Melbourne Water Corporation, La Trobe Street, Docklands 3008, Australia
| | - Rebekah Henry
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Department of Civil Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia
| | - Ana Deletic
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Department of Civil Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia
| | - David McCarthy
- Environmental and Public Health Microbiology Laboratory (EPHM Lab), Department of Civil Engineering, Monash University, Wellington Road, Clayton 3800, Victoria, Australia.
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Balmonte JP, Arnosti C, Underwood S, McKee BA, Teske A. Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia. Front Microbiol 2016; 7:1441. [PMID: 27695444 PMCID: PMC5023673 DOI: 10.3389/fmicb.2016.01441] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/30/2016] [Indexed: 12/16/2022] Open
Abstract
Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities, and illustrate the response of temperate riverine bacteria on fine taxonomic scales to a disturbance.
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Affiliation(s)
- John Paul Balmonte
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Carol Arnosti
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Sarah Underwood
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Brent A McKee
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Andreas Teske
- Department of Marine Sciences, The University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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Pinos S, Pontarotti P, Raoult D, Baudoin JP, Pagnier I. Compartmentalization in PVC super-phylum: evolution and impact. Biol Direct 2016; 11:38. [PMID: 27507008 PMCID: PMC4977879 DOI: 10.1186/s13062-016-0144-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/02/2016] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The PVC super-phylum gathers bacteria from seven phyla (Planctomycetes, Verrucomicrobiae, Chlamydiae, Lentisphaera, Poribacteria, OP3, WWE2) presenting different lifestyles, cell plans and environments. Planctomyces and several Verrucomicrobiae exhibit a complex cell plan, with an intracytoplasmic membrane inducing the compartmentalization of the cytoplasm into two regions (pirellulosome and paryphoplasm). The evolution and function of this cell plan is still subject to debate. In this work, we hypothesized that it could play a role in protection of the bacterial DNA, especially against Horizontal Genes Transfers (HGT). Therefore, 64 bacterial genomes belonging to seven different phyla (whose four PVC phyla) were studied. We reconstructed the evolution of the cell plan as precisely as possible, thanks to information obtained by bibliographic study and electronic microscopy. We used a strategy based on comparative phylogenomic in order to determine the part occupied by the horizontal transfers for each studied genomes. RESULTS Our results show that the bacteria Simkania negevensis (Chlamydiae) and Coraliomargarita akajimensis (Verrucomicrobiae), whose cell plan were unknown before, are compartmentalized, as we can see on the micrographies. This is one of the first indication of the presence of an intracytoplasmic membrane in a Chlamydiae. The proportion of HGT does not seems to be related to the cell plan of bacteria, suggesting that compartmentalization does not induce a protection of bacterial DNA against HGT. Conversely, lifestyle of bacteria seems to impact the ability of bacteria to exchange genes. CONCLUSIONS Our study allows a best reconstruction of the evolution of intracytoplasmic membrane, but this structure seems to have no impact on HGT occurrences. REVIEWERS This article was reviewed by Mircea Podar and Olivier Tenaillon.
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Affiliation(s)
- Sandrine Pinos
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 13385 Marseille, Cedex 5, France
| | - Pierre Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Evolution Biologique et Modélisation, 13385 Marseille, Cedex 5, France
| | - Didier Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Jean Pierre Baudoin
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
| | - Isabelle Pagnier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
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De Santi C, Willassen NP, Williamson A. Biochemical Characterization of a Family 15 Carbohydrate Esterase from a Bacterial Marine Arctic Metagenome. PLoS One 2016; 11:e0159345. [PMID: 27433797 PMCID: PMC4951047 DOI: 10.1371/journal.pone.0159345] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/30/2016] [Indexed: 12/20/2022] Open
Abstract
Background The glucuronoyl esterase enzymes of wood-degrading fungi (Carbohydrate Esterase family 15; CE15) form part of the hemicellulolytic and cellulolytic enzyme systems that break down plant biomass, and have possible applications in biotechnology. Homologous enzymes are predicted in the genomes of several bacteria, however these have been much less studied than their fungal counterparts. Here we describe the recombinant production and biochemical characterization of a bacterial CE15 enzyme denoted MZ0003, which was identified by in silico screening of a prokaryotic metagenome library derived from marine Arctic sediment. MZ0003 has high similarity to several uncharacterized gene products of polysaccharide-degrading bacterial species, and phylogenetic analysis indicates a deep evolutionary split between these CE15s and fungal homologs. Results MZ0003 appears to differ from previously-studied CE15s in some aspects. Some glucuronoyl esterase activity could be measured by qualitative thin-layer chromatography which confirms its assignment as a CE15, however MZ0003 can also hydrolyze a range of other esters, including p-nitrophenyl acetate, which is not acted upon by some fungal homologs. The structure of MZ0003 also appears to differ as it is predicted to have several large loop regions that are absent in previously studied CE15s, and a combination of homology-based modelling and site-directed mutagenesis indicate its catalytic residues deviate from the conserved Ser-His-Glu triad of many fungal CE15s. Taken together, these results indicate that potentially unexplored diversity exists among bacterial CE15s, and this may be accessed by investigation of the microbial metagenome. The combination of low activity on typical glucuronoyl esterase substrates, and the lack of glucuronic acid esters in the marine environment suggest that the physiological substrate of MZ0003 and its homologs is likely to be different from that of related fungal enzymes.
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Affiliation(s)
- Concetta De Santi
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Nils Peder Willassen
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Adele Williamson
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT—The Arctic University of Norway, Tromsø, Norway
- * E-mail:
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Gupta RS. Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification. FEMS Microbiol Rev 2016; 40:520-53. [PMID: 27279642 DOI: 10.1093/femsre/fuw011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2016] [Indexed: 12/24/2022] Open
Abstract
Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
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38
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Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility. Antonie van Leeuwenhoek 2015; 108:741-52. [PMID: 26184407 PMCID: PMC4525199 DOI: 10.1007/s10482-015-0530-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/07/2015] [Indexed: 12/18/2022]
Abstract
Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I (“Slash-and-burn deforestation”) the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II (“Management practices for sugarcane”) disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.
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Distribution and isolation of strains belonging to the order Solirubrobacterales. J Antibiot (Tokyo) 2015; 68:763-6. [PMID: 26126741 DOI: 10.1038/ja.2015.67] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/15/2015] [Accepted: 05/20/2015] [Indexed: 11/09/2022]
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40
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Effects of Misgurnus anguillicaudatus and Cipangopaludina cathayensis on Pollutant Removal and Microbial Community in Constructed Wetlands. WATER 2015. [DOI: 10.3390/w7052422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Anders H, Power JF, MacKenzie AD, Lagutin K, Vyssotski M, Hanssen E, Moreau JW, Stott MB. Limisphaera ngatamarikiensis gen. nov., sp. nov., a thermophilic, pink-pigmented coccus isolated from subaqueous mud of a geothermal hotspring. Int J Syst Evol Microbiol 2015; 65:1114-1121. [DOI: 10.1099/ijs.0.000063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, NGM72.4T, was isolated from a hot spring in the Ngatamariki geothermal field, New Zealand. Phylogenetic analysis based on 16S rRNA gene sequences grouped it into the phylum
Verrucomicrobia
and class level group 3 (also known as OPB35 soil group). NGM72.4T stained Gram-negative, and was catalase- and oxidase-positive. Cells were small cocci, 0.5–0.8 µm in diameter, which were motile by means of single flagella. Transmission electron micrograph (TEM) imaging showed an unusual pirellulosome-like intracytoplasmic membrane. The peptidoglycan content was very small with only trace levels of diaminopimelic acid detected. No peptidoglycan structure was visible in TEM imaging. The predominant isoprenoid quinone was MK-7 (92 %). The major fatty acids (>15 %) were C16 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Major phospholipids were phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME) and cardiolipin (CL), and a novel analogous series of phospholipids where diacylglycerol was replaced with diacylserinol (sPE, sPMME, sCL). The DNA G+C content was 65.6 mol%. Cells displayed an oxidative chemoheterotrophic metabolism. NGM72.4T is a strictly aerobic thermophile (growth optimum 60–65 °C), has a slightly alkaliphilic pH growth optimum (optimum pH 8.1–8.4) and has a NaCl tolerance of up to 8 g l−1. Colonies were small, circular and pigmented pale pink. The distinct phylogenetic position and phenotypic traits of strain NGM72.4T distinguish it from all other described species of the phylum
Verrucomicrobia
and, therefore, it is considered to represent a novel species in a new genus for which we propose the name Limisphaera ngatamarikiensis gen. nov., sp. nov. The type strain is NGM72.4T ( = ICMP 20182T = DSM 27329T).
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Affiliation(s)
- Heike Anders
- Lehrstuhl für Tierhygiene, Technische Universität München, Weihenstephaner Berg 3 0D-85354, Freising, Germany
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | - Jean F. Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
| | | | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | | | - Eric Hanssen
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - John W. Moreau
- University of Melbourne, 30 Flemington Road, Victoria 3010, Australia
| | - Matthew B. Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupō 3352, New Zealand
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Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon. Appl Environ Microbiol 2015; 81:2244-53. [PMID: 25616793 DOI: 10.1128/aem.03209-14] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH4, which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with (13)CO2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with (13)C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (∼20%) than did those in the rhizosphere (∼4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment.
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Gonzalez-Martinez A, Rodriguez-Sanchez A, Muñoz-Palazon B, Garcia-Ruiz MJ, Osorio F, van Loosdrecht MCM, Gonzalez-Lopez J. Microbial community analysis of a full-scale DEMON bioreactor. Bioprocess Biosyst Eng 2014; 38:499-508. [PMID: 25245398 DOI: 10.1007/s00449-014-1289-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/16/2014] [Indexed: 12/28/2022]
Abstract
Full-scale applications of autotrophic nitrogen removal technologies for the treatment of digested sludge liquor have proliferated during the last decade. Among these technologies, the aerobic/anoxic deammonification process (DEMON) is one of the major applied processes. This technology achieves nitrogen removal from wastewater through anammox metabolism inside a single bioreactor due to alternating cycles of aeration. To date, microbial community composition of full-scale DEMON bioreactors have never been reported. In this study, bacterial community structure of a full-scale DEMON bioreactor located at the Apeldoorn wastewater treatment plant was analyzed using pyrosequencing. This technique provided a higher-resolution study of the bacterial assemblage of the system compared to other techniques used in lab-scale DEMON bioreactors. Results showed that the DEMON bioreactor was a complex ecosystem where ammonium oxidizing bacteria, anammox bacteria and many other bacterial phylotypes coexist. The potential ecological role of all phylotypes found was discussed. Thus, metagenomic analysis through pyrosequencing offered new perspectives over the functioning of the DEMON bioreactor by exhaustive identification of microorganisms, which play a key role in the performance of bioreactors. In this way, pyrosequencing has been proven as a helpful tool for the in-depth investigation of the functioning of bioreactors at microbiological scale.
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Richards MA, Cassen V, Heavner BD, Ajami NE, Herrmann A, Simeonidis E, Price ND. MediaDB: a database of microbial growth conditions in defined media. PLoS One 2014; 9:e103548. [PMID: 25098325 PMCID: PMC4123892 DOI: 10.1371/journal.pone.0103548] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 06/30/2014] [Indexed: 01/24/2023] Open
Abstract
Isolating pure microbial cultures and cultivating them in the laboratory on defined media is used to more fully characterize the metabolism and physiology of organisms. However, identifying an appropriate growth medium for a novel isolate remains a challenging task. Even organisms with sequenced and annotated genomes can be difficult to grow, despite our ability to build genome-scale metabolic networks that connect genomic data with metabolic function. The scientific literature is scattered with information about defined growth media used successfully for cultivating a wide variety of organisms, but to date there exists no centralized repository to inform efforts to cultivate less characterized organisms by bridging the gap between genomic data and compound composition for growth media. Here we present MediaDB, a manually curated database of defined media that have been used for cultivating organisms with sequenced genomes, with an emphasis on organisms with metabolic network models. The database is accessible online, can be queried by keyword searches or downloaded in its entirety, and can generate exportable individual media formulation files. The data assembled in MediaDB facilitate comparative studies of organism growth media, serve as a starting point for formulating novel growth media, and contribute to formulating media for in silico investigation of metabolic networks. MediaDB is freely available for public use at https://mediadb.systemsbiology.net.
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Affiliation(s)
- Matthew A. Richards
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Victor Cassen
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Benjamin D. Heavner
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Nassim E. Ajami
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Andrea Herrmann
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Evangelos Simeonidis
- Institute for Systems Biology, Seattle, Washington, United States of America
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nathan D. Price
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail:
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Tandogan N, Abadian PN, Epstein S, Aoi Y, Goluch ED. Isolation of microorganisms using sub-micrometer constrictions. PLoS One 2014; 9:e101429. [PMID: 24978477 PMCID: PMC4076310 DOI: 10.1371/journal.pone.0101429] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/06/2014] [Indexed: 12/30/2022] Open
Abstract
We present an automated method for isolating pure bacterial cultures from samples containing multiple species that exploits the cell's own physiology to perform the separation. Cells compete to reach a chamber containing nutrients via a constriction whose cross-sectional area only permits a single cell to enter, thereby blocking the opening and preventing other cells from entering. The winning cell divides across the constriction and its progeny populate the chamber. The devices are passive and require no user interaction to perform their function. Device fabrication begins with the creation of a master mold that contains the desired constriction and chamber features. Replica molding is used to create patterned polymer chips from the master, which are bonded to glass microscope cover slips to create the constrictions. We tested constriction geometries ranging from 500 nanometers to 5 micrometers in width, 600 to 950 nanometers in height, and 10 to 40 micrometers in length. The devices were used to successfully isolate a pure Pseudomonas aeruginosa culture from a mixture that also contained Escherichia coli. We demonstrated that individual strains of the same species can be separated out from mixtures using red and green fluorescently-labeled E. coli. We also used the devices to isolate individual environmental species. Roseobacter sp. was separated from another marine species, Psychroserpens sp.
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Affiliation(s)
- Nil Tandogan
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Pegah N. Abadian
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Slava Epstein
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail: (EDG); (SE); (YA)
| | - Yoshiteru Aoi
- Department of Biology, Northeastern University, Boston, Massachusetts, United States of America
- Institute for Sustainable Science and Development, Hiroshima University, Hiroshima, Japan
- * E-mail: (EDG); (SE); (YA)
| | - Edgar D. Goluch
- Department of Chemical Engineering, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail: (EDG); (SE); (YA)
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Terrimicrobium sacchariphilum gen. nov., sp. nov., an anaerobic bacterium of the class ‘Spartobacteria’ in the phylum Verrucomicrobia, isolated from a rice paddy field. Int J Syst Evol Microbiol 2014; 64:1718-1723. [DOI: 10.1099/ijs.0.060244-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, mesophilic, carbohydrate-fermenting bacterium, designated NM-5T, was isolated from a rice paddy field. Cells of strain NM-5T were Gram-stain-negative, non-motile, non-spore-forming, short rods (0.5–0.7 µm×0.6–1.2 µm). The strain grew optimally at 37 °C (growth range 20–40 °C) and pH 7.0 (pH 5.5–8.0). The strain could grow fermentatively on arabinose, xylose, fructose, galactose, glucose, ribose, mannose, cellobiose, lactose, maltose and sucrose. The main end-products of glucose fermentation were acetate and propionate. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required but stimulated the growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The DNA G+C content was 46.3 mol%. The major cellular fatty acids were iso-C14 : 0, C18 : 0 and C16 : 0. 16S rRNA gene sequence analysis revealed that strain NM-5T belongs to the class ‘S
partobacteria’, subdivision 2 of the bacterial phylum
Verrucomicrobia
. Phylogenetically, the closest species was ‘Chthoniobacter flavus’ (89.6 % similarity in 16S rRNA gene sequence). A novel genus and species, Terrimicrobium sacchariphilum gen. nov., sp. nov., is proposed. The type strain of the type species is NM-5T ( = JCM 17479T = CGMCC 1.5168T).
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Verrucomicrobia are candidates for polysaccharide-degrading bacterioplankton in an arctic fjord of Svalbard. Appl Environ Microbiol 2014; 80:3749-56. [PMID: 24727271 DOI: 10.1128/aem.00899-14] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Arctic marine bacterial communities, members of the phylum Verrucomicrobia are consistently detected, although not typically abundant, in 16S rRNA gene clone libraries and pyrotag surveys of the marine water column and in sediments. In an Arctic fjord (Smeerenburgfjord) of Svalbard, members of the Verrucomicrobia, together with Flavobacteria and smaller proportions of Alpha- and Gammaproteobacteria, constituted the most frequently detected bacterioplankton community members in 16S rRNA gene-based clone library analyses of the water column. Parallel measurements in the water column of the activities of six endo-acting polysaccharide hydrolases showed that chondroitin sulfate, laminarin, and xylan hydrolysis accounted for most of the activity. Several Verrucomicrobia water column phylotypes were affiliated with previously sequenced, glycoside hydrolase-rich genomes of individual Verrucomicrobia cells that bound fluorescently labeled laminarin and xylan and therefore constituted candidates for laminarin and xylan hydrolysis. In sediments, the bacterial community was dominated by different lineages of Verrucomicrobia, Bacteroidetes, and Proteobacteria but also included members of multiple phylum-level lineages not observed in the water column. This community hydrolyzed laminarin, xylan, chondroitin sulfate, and three additional polysaccharide substrates at high rates. Comparisons with data from the same fjord in the previous summer showed that the bacterial community in Smeerenburgfjord changed in composition, most conspicuously in the changing detection frequency of Verrucomicrobia in the water column. Nonetheless, in both years the community hydrolyzed the same polysaccharide substrates.
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Ansola G, Arroyo P, Sáenz de Miera LE. Characterisation of the soil bacterial community structure and composition of natural and constructed wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 473-474:63-71. [PMID: 24361449 DOI: 10.1016/j.scitotenv.2013.11.125] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/25/2013] [Accepted: 11/27/2013] [Indexed: 05/20/2023]
Abstract
In the present study, the pyrosequencing of 16S ribosomal DNA was used to characterise the soil bacterial community composition of a constructed wetland receiving municipal wastewater and a nearby natural wetland. Soil samples were taken from different locations in each wetland (lagoon, zone with T. latifolia, zone with S. atrocinerea). Moreover, the water quality parameters were evaluated (pH, Tª, conductivity, dissolved oxygen, redox potential, nutrients and suspended solids), revealing that the organic matter and nutrient contents were significantly higher in the constructed wetland than in the natural one. In general, the bacterial communities of the natural wetland were more diverse than those of the constructed wetland. The major phylogenic groups of all soils included Proteobacteria, Verrucomicrobia and Chloroflexi, with Proteobacteria being the majority of the community composition. The Verrucomicrobia and Chloroflexi phyla were more abundant in the natural wetland than the constructed wetland; in contrast, the Proteobacteria phylum was more abundant in the constructed wetland than the natural wetland. Beta diversity analyses reveal that the soil bacterial communities in the natural wetland were less dissimilar to each other than to those of the constructed wetland.
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Affiliation(s)
- Gemma Ansola
- Departamento de Biodiversidad y Gestión Ambiental, Universidad de León. Campus de Vegazana s/n, CP: 24071, León, Spain.
| | - Paula Arroyo
- Instituto de Medioambiente, Recursos Naturales y Biodiversidad, Universidad de León. Calle La Serna, no. 56, CP: 24071, León, Spain.
| | - Luis E Sáenz de Miera
- Departamento de Biología Molecular, Universidad de León. Campus de Vegazana s/n, CP: 24071, León, Spain.
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Tsitko I, Lusa M, Lehto J, Parviainen L, Ikonen ATK, Lahdenperä AM, Bomberg M. The Variation of Microbial Communities in a Depth Profile of an Acidic, Nutrient-Poor Boreal Bog in Southwestern Finland. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/oje.2014.413071] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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