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Han D, Park KT, Kim H, Kim TH, Jeong MK, Nam SI. Interaction between phytoplankton and heterotrophic bacteria in Arctic fjords during the glacial melting season as revealed by eDNA metabarcoding. FEMS Microbiol Ecol 2024; 100:fiae059. [PMID: 38621717 PMCID: PMC11067963 DOI: 10.1093/femsec/fiae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/07/2024] [Accepted: 04/13/2024] [Indexed: 04/17/2024] Open
Abstract
The hydrographic variability in the fjords of Svalbard significantly influences water mass properties, causing distinct patterns of microbial diversity and community composition between surface and subsurface layers. However, surveys on the phytoplankton-associated bacterial communities, pivotal to ecosystem functioning in Arctic fjords, are limited. This study investigated the interactions between phytoplankton and heterotrophic bacterial communities in Svalbard fjord waters through comprehensive eDNA metabarcoding with 16S and 18S rRNA genes. The 16S rRNA sequencing results revealed a homogenous community composition including a few dominant heterotrophic bacteria across fjord waters, whereas 18S rRNA results suggested a spatially diverse eukaryotic plankton distribution. The relative abundances of heterotrophic bacteria showed a depth-wise distribution. By contrast, the dominant phytoplankton populations exhibited variable distributions in surface waters. In the network model, the linkage of phytoplankton (Prasinophytae and Dinophyceae) to heterotrophic bacteria, particularly Actinobacteria, suggested the direct or indirect influence of bacterial contributions on the fate of phytoplankton-derived organic matter. Our prediction of the metabolic pathways for bacterial activity related to phytoplankton-derived organic matter suggested competitive advantages and symbiotic relationships between phytoplankton and heterotrophic bacteria. Our findings provide valuable insights into the response of phytoplankton-bacterial interactions to environmental changes in Arctic fjords.
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Affiliation(s)
- Dukki Han
- Department of Marine Molecular Bioscience, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Ki-Tae Park
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Environmental Sciences and Biotechnology, Hallym University, Chuncheon 24252, Republic of Korea
| | - Haryun Kim
- East Sea Research Institute, Korea Institute of Ocean Science & Technology, Uljin 36315, Republic of Korea
| | - Tae-Hoon Kim
- Department of Oceanography, Faculty of Earth Systems and Environmental Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Man-Ki Jeong
- Department of Smart Fisheries Resources Management, Chonnam National University, Yeosu 59626, Republic of Korea
| | - Seung-Il Nam
- Korea Polar Research Institute, Incheon 21990, Republic of Korea
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2
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Wu X, Almatari AL, Cyr WA, Williams DE, Pfiffner SM, Rivkina EM, Lloyd KG, Vishnivetskaya TA. Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics. ENVIRONMENTAL MICROBIOME 2023; 18:33. [PMID: 37055869 PMCID: PMC10103415 DOI: 10.1186/s40793-023-00487-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1-0.2 ppt and brackish 0.3-1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10-100 kyr old), MP (105-120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.
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Affiliation(s)
- Xiaofen Wu
- Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996-1605, USA
| | - Abraham L Almatari
- Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996-1605, USA
| | - Wyatt A Cyr
- Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996-1605, USA
| | - Daniel E Williams
- Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996-1605, USA
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996-1605, USA
| | - Elizaveta M Rivkina
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia, 142290
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tatiana A Vishnivetskaya
- Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996-1605, USA.
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia, 142290.
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA.
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3
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El-Sayed MR, Emam AM, Osman AE, Abd El-Galil MAEAA, Sayed HH. Detection and description of a novel Psychrobacter glacincola infection in some Red Sea marine fishes in Hurghada, Egypt. BMC Vet Res 2023; 19:23. [PMID: 36717850 PMCID: PMC9885648 DOI: 10.1186/s12917-022-03542-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/05/2022] [Indexed: 01/31/2023] Open
Abstract
An important food-producing sector in Egypt is aquaculture and fisheries; however, several pathogenic microorganisms lead to high mortalities and significant economic losses. The occurrence of Psychrobacter glacincola infection among 180 wild marine fishes collected from the Red sea at Hurghada, Egypt were investigated in the present study. The disease prevalence rate was 6.7%. The recovered isolates were subjected to biochemical and molecular identification. The study also investigated pathogenicity and the antibiogram profile of the recovered isolates. The clinical examination of the infected fish revealed various signs that included lethargy and sluggish movement, hemorrhages and ulcers on the body and the operculum, scale loss, and fin congestion and rot, especially at the tail fin. Furthermore, during postmortem examination, congestion of the liver, spleen, and kidney was observed. Interestingly, 12 isolates were recovered and were homogenous bacteriologically and biochemically. The phylogenetic analysis based on 16S rRNA gene confirmed that MRB62 identified strain was closely related the genus Psychrobacter and identified as P. glacincola and was pathogenic to Rhabdosargus haffara fish, causing 23.3% mortality combined with reporting a series of clinical signs similar to that found in naturally infected fishes. The present study also showed that P. glacincola isolates were sensitive to all antibiotics used for sensitivity testing. Our findings add to the body of knowledge regarding the occurrence of pathogenic P. glacincola infection in Egyptian marine fishes and its potential effects on fish. Future large-scale surveys exploring this bacterium among other freshwater and marine fishes in Egypt would be helpful for the implementation of effective strategies for the prevention and control of this infection are warranted.
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Affiliation(s)
- Mohamed Raafat El-Sayed
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Sohag University, Sohag, Egypt.
| | - Arafah M Emam
- National Institute of Oceanography and Fisheries, NIOF, Cairo, Egypt
| | - Ahmed Elsayed Osman
- Department of Biochemistry, Faculty of Veterinary Medicine, Sohag University, Sohag, Egypt
| | | | - Haitham Helmy Sayed
- Department of Microbiology, Faculty of Veterinary Medicine, Sohag University, Sohag, Egypt
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Matsui K, Miki T. Microbial community composition and function in an urban waterway with combined sewer overflows before and after implementation of a stormwater storage pipe. PeerJ 2023; 11:e14684. [PMID: 36650829 PMCID: PMC9840855 DOI: 10.7717/peerj.14684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/13/2022] [Indexed: 01/15/2023] Open
Abstract
When the wastewater volume exceeds the sewer pipe capacity during extreme rainfall events, untreated sewage discharges directly into rivers as combined sewer overflow (CSO). To compare the impacts of CSOs and stormwater on urban waterways, we assessed physicochemical water quality, the 16S rRNA gene-based bacterial community structure, and EcoPlate-based microbial functions during rainfall periods in an urban waterway before and after a stormwater storage pipe was commissioned. A temporal variation analysis showed that CSOs have significant impacts on microbial function and bacterial community structure, while their contributions to physicochemical parameters, bacterial abundance, and chlorophyll a were not confirmed. Heat map analysis showed that the impact of CSO on the waterway bacterial community structure was temporal and the bacterial community composition in CSO is distinct from that in sewers. Hierarchical clustering analysis revealed that the waterway physicochemical water qualities, bacterial community composition, and microbial community function were distinguishable from the upper reach of the river, rather than between CSO and stormwater. Changes in the relative abundance of tetracycline resistance (tet) genes-especially tet(M)-were observed after CSOs but did not coincide with changes in the microbial community composition, suggesting that the parameters affecting the microbial community composition and relative abundance of tet genes differ. After pipe implementation, however, stormwater did not contribute to the abundance of tet genes in the waterway. These results indicate that CSO-induced acute microbial disturbances in the urban waterway were alleviated by the implementation of a stormwater storage pipe and will support the efficiency of storage pipe operation for waterway management in urban areas.
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Affiliation(s)
- Kazuaki Matsui
- Department of Civil and Environmental Engineering, Kindai University, Higashiosaka, Japan
| | - Takeshi Miki
- Faculty of Advanced Science and Technology, Ryukoku University, Otsu, Shiga, Japan
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5
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Leclaire S, Pineaux M, Blanchard P, White J, Hatch SA. Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird. Mol Ecol 2022; 32:2115-2133. [PMID: 35152516 DOI: 10.1111/mec.16398] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/03/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022]
Abstract
The microbiota is suggested to be a fundamental contributor to host reproduction and survival, but associations between microbiota and fitness are rare, especially for wild animals. Here, we tested the association between microbiota and two proxies of breeding performance in multiple body sites of the black-legged kittiwake, a seabird species. First we found that, in females, nonbreeders (i.e., birds that did not lay eggs) hosted different microbiota composition to that of breeders in neck and flank feathers, in the choanae, in the outer-bill and in the cloacae, but not in preen feathers and tracheae. These differences in microbiota might reflect variations in age or individual quality between breeders and nonbreeders. Second, we found that better female breeders (i.e., with higher body condition, earlier laying date, heavier eggs, larger clutch, and higher hatching success) had lower abundance of several Corynebacteriaceae in cloaca than poorer female breeders, suggesting that these bacteria might be pathogenic. Third, in females, better breeders had different microbiota composition and lower microbiota diversity in feathers, especially in preen feathers. They had also reduced dispersion in microbiota composition across body sites. These results might suggest that good breeding females are able to control their feather microbiota-potentially through preen secretions-more tightly than poor breeding females. We did not find strong evidence for an association between reproductive outcome and microbiota in males. Our results are consistent with the hypothesis that natural variation in the microbiota is associated with differences in host fitness in wild animals, but the causal relationships remain to be investigated.
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Affiliation(s)
- Sarah Leclaire
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Maxime Pineaux
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Pierrick Blanchard
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Joël White
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
- ENSFEA Castanet‐Tolosan France
| | - Scott A Hatch
- Institute for Seabird Research and Conservation Anchorage AK 99516 USA
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6
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Marian M, Licciardello G, Vicelli B, Pertot I, Perazzolli M. Ecology and potential functions of plant-associated microbial communities in cold environments. FEMS Microbiol Ecol 2022; 98:fiab161. [PMID: 34910139 PMCID: PMC8769928 DOI: 10.1093/femsec/fiab161] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Complex microbial communities are associated with plants and can improve their resilience under harsh environmental conditions. In particular, plants and their associated communities have developed complex adaptation strategies against cold stress. Although changes in plant-associated microbial community structure have been analysed in different cold regions, scarce information is available on possible common taxonomic and functional features of microbial communities across cold environments. In this review, we discuss recent advances in taxonomic and functional characterization of plant-associated microbial communities in three main cold regions, such as alpine, Arctic and Antarctica environments. Culture-independent and culture-dependent approaches are analysed, in order to highlight the main factors affecting the taxonomic structure of plant-associated communities in cold environments. Moreover, biotechnological applications of plant-associated microorganisms from cold environments are proposed for agriculture, industry and medicine, according to biological functions and cold adaptation strategies of bacteria and fungi. Although further functional studies may improve our knowledge, the existing literature suggest that plants growing in cold environments harbor complex, host-specific and cold-adapted microbial communities, which may play key functional roles in plant growth and survival under cold conditions.
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Affiliation(s)
- Malek Marian
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Giorgio Licciardello
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Bianca Vicelli
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Ilaria Pertot
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Michele Perazzolli
- Center Agriculture Food Environment (C3A), University of Trento, via E. Mach 1, 38098 San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
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7
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Abreu ACDS, Carazzolle MF, Crippa BL, Barboza GR, Mores Rall VL, de Oliveira Rocha L, Silva NCC. Bacterial diversity in organic and conventional Minas Frescal cheese production using targeted 16S rRNA sequencing. Int Dairy J 2021. [DOI: 10.1016/j.idairyj.2021.105139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Komura T, Takada Y. NADP + -dependent isocitrate dehydrogenase isozymes from a psychrotrophic bacterium, Psychrobacter sp. strain 13A. J Basic Microbiol 2021; 61:612-626. [PMID: 34101864 DOI: 10.1002/jobm.202000720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 11/08/2022]
Abstract
The genes encoding dimeric and monomeric isocitrate dehydrogenase (IDH) isozymes from a psychrotrophic bacterium, strain 13A (13AIDH-D and 13AIDH-M, respectively), were cloned and sequenced. The deduced amino acid sequences of these two IDHs showed high degrees of identity with those of bacteria of genus Psychrobacter. Analysis of the 16S ribosomal RNA gene of the strain 13A revealed that this bacterium is classified to genus Psychrobacter. The optimum temperatures for activities of 13AIDH-D and 13AIDH-M were 55°C and 45°C, respectively, indicating that they are mesophilic. On the contrary, 13AIDH-D maintained 90% of its maximum activity after incubation for 10 min at 50°C, while the 13AIDH-M activity was completely lost under the same condition. In addition, 13AIDH-D showed much higher specific activity than 13AIDH-M. From northern and western blot analyses, the 13AIDH-D gene was found to be not transcribed under the growth conditions tested in this study. However, the catalytic ability of the mesophilic 13AIDH-M was concluded to be enough to sustain the growth of strain 13A at low temperatures. Therefore, a novel pattern of the contribution of IDH isozymes in cold-living bacteria to their growth at low temperatures was confirmed in strain 13A.
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Affiliation(s)
- Tatsuhiko Komura
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yasuhiro Takada
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
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9
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Smitienko OA, Feldman TB, Petrovskaya LE, Nekrasova OV, Yakovleva MA, Shelaev IV, Gostev FE, Cherepanov DA, Kolchugina IB, Dolgikh DA, Nadtochenko VA, Kirpichnikov MP, Ostrovsky MA. Comparative Femtosecond Spectroscopy of Primary Photoreactions of Exiguobacterium sibiricum Rhodopsin and Halobacterium salinarum Bacteriorhodopsin. J Phys Chem B 2021; 125:995-1008. [PMID: 33475375 DOI: 10.1021/acs.jpcb.0c07763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The primary stages of the Exiguobacterium sibiricum rhodopsin (ESR) photocycle were investigated by femtosecond absorption laser spectroscopy in the spectral range of 400-900 nm with a time resolution of 25 fs. The dynamics of the ESR photoreaction were compared with the reactions of bacteriorhodopsin (bR) in purple membranes (bRPM) and in recombinant form (bRrec). The primary intermediates of the ESR photocycle were similar to intermediates I, J, and K in bacteriorhodopsin photoconversion. The CONTIN program was applied to analyze the characteristic times of the observed processes and to clarify the reaction scheme. A similar photoreaction pattern was observed for all studied retinal proteins, including two consecutive dynamic Stokes shift phases lasting ∼0.05 and ∼0.15 ps. The excited state decays through a femtosecond reactive pathway, leading to retinal isomerization and formation of product J, and a picosecond nonreactive pathway that leads only to the initial state. Retinal photoisomerization in ESR takes 0.69 ps, compared with 0.48 ps in bRPM and 0.74 ps in bRrec. The nonreactive excited state decay takes 5 ps in ESR and ∼3 ps in bR. We discuss the similarity of the primary reactions of ESR and other retinal proteins.
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Affiliation(s)
| | - Tatiana B Feldman
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Oksana V Nekrasova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | | | - Ivan V Shelaev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | - Fedor E Gostev
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia
| | | | - Irina B Kolchugina
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A Dolgikh
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Victor A Nadtochenko
- Semenov Federal Research Center of Chemical Physics, Moscow 119991, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Mikhail P Kirpichnikov
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Mikhail A Ostrovsky
- Emanuel Institute of Biochemical Physics, Moscow 119334, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
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Jarvis KG, Hsu CK, Pettengill JB, Ihrie J, Karathia H, Hasan NA, Grim CJ. Microbiome Population Dynamics of Cold-Smoked Sockeye Salmon during Refrigerated Storage and after Culture Enrichment. J Food Prot 2021; 85:238-253. [PMID: 34614175 DOI: 10.4315/jfp-21-228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/05/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Cold-smoked salmon is a ready-to-eat seafood product of high commercial importance. The processing and storage steps facilitate the introduction, growth, and persistence of foodborne pathogens and spoilage bacteria. The growth of commensal bacteria during storage and once the product is opened also influence the quality and safety of cold-smoked salmon. Here we investigated the microbial community through targeted 16S rRNA gene and shotgun metagenomic sequencing as means to better understand the interactions among bacteria in cold-smoked salmon. Cold-smoked salmon samples were tested over 30 days of aerobic storage at 4°C and cultured at each time point in a buffered Listeria enrichment broth (BLEB) commonly used to detect Listeria in foods. The microbiomes were composed of Firmicutes and Proteobacteria, namely, Carnobacterium, Brochothrix, Pseudomonas, Serratia, and Psychrobacter. Pseudomonas species were the most diverse species, with 181 taxa identified. In addition, we identified potential homologs to 10 classes of bacteriocins in microbiomes of cold-smoked salmon stored at 4°C and corresponding BLEB culture enrichments. The findings presented here contribute to our understanding of microbiome population dynamics in cold-smoked salmon, including changes in bacterial taxa during aerobic cold storage and after culture enrichment. This may facilitate improvements to pathogen detection and quality preservation of this food. HIGHLIGHTS
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Affiliation(s)
- Karen G Jarvis
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland 20708
| | - Chiun-Kang Hsu
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland 20708
| | - James B Pettengill
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20742
| | - John Ihrie
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland 20742
| | - Hiren Karathia
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Nur A Hasan
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742, USA
| | - Christopher J Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland 20708
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11
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Bacterial and archaeal community structure in benthic sediments from glacial lakes at the Múlajökull Glacier, central Iceland. Polar Biol 2020. [DOI: 10.1007/s00300-020-02770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Elmassry MM, Ray N, Sorge S, Webster J, Merry K, Caserio A, Vecellio DJ, Kruczek C, Dowd S, Ardon-Dryer K, Vanos J, San Francisco MJ. Investigating the culturable atmospheric fungal and bacterial microbiome in West Texas: implication of dust storms and origins of the air parcels. FEMS MICROBES 2020; 1:xtaa009. [PMID: 37333960 PMCID: PMC10117434 DOI: 10.1093/femsmc/xtaa009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/21/2020] [Indexed: 11/10/2023] Open
Abstract
Individuals often experience ailments such as allergies, asthma and respiratory tract infections throughout the year. Weather reports often include estimations of common allergens that can affect these individuals. To describe the local 'atmospheric microbiome' in Lubbock, Texas, USA, we examined the culturable fungal and bacterial microbiome present in the air on calm and dust storm days using internal transcribed spacer (ITS)-1 and 16S rRNA amplicon sequencing, respectively. While some types of airborne fungi were frequently present throughout the year, distinct differences were also observed between calm and dust storm days. We also observed the influence of the origin of air parcels and wind elevation of the air trajectory. The most abundant genera of fungi identified during the study period were Cryptococcus, Aureobasidium, Alternaria, Cladosporium and Filobasidium. This observation was not surprising considering the agricultural intensive environment of West Texas. Interestingly, Cladosporium, a common allergenic mold, was increased during days with dust storm events. The predominant bacterial genera observed were Bacillus, Pseudomonas, Psychrobacter, Massilia and Exiguobacterium. The relative abundance of the psychrophiles, Psychrobacter and Exiguobacterium, was surprising, given the semi-aridity of West Texas. Coupling our observations with back trajectories of the wind (Hybrid Single-Particle Lagrangian Integrated Trajectory models) demonstrated that dust storms, regional anthropogenic activity and origin of air parcels are important influences on the diversity and temporal presence of the atmospheric microbiome.
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Affiliation(s)
- Moamen M Elmassry
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Nandini Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Sara Sorge
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jennifer Webster
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Kyle Merry
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Angelica Caserio
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Daniel J Vecellio
- Department of Geography, Texas A&M University, College Station, TX 77843, USA
| | - Cassandra Kruczek
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Scot Dowd
- Molecular Research LP, Clovis Road, Shallowater, TX 79363, USA
| | - Karin Ardon-Dryer
- Department of Geosciences, Atmospheric Science Group, Texas Tech University, Lubbock, TX 79409, USA
| | - Jennifer Vanos
- School of Sustainability, Arizona State University, Tempe, AZ 85281, USA
| | - Michael J San Francisco
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
- Honors College, Texas Tech University, Lubbock, TX 79410, USA
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13
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Hanaoka Y, Kimoto H, Yoshimume K, Hara I, Matsuyama H, Yumoto I. Relationship Between Main Channel Structure of Catalases and the Evolutionary Direction in Cold-Adapted Hydrogen Peroxide-Tolerant Exiguobacteium and Psychrobacter. Indian J Microbiol 2020; 60:353-362. [PMID: 32647394 DOI: 10.1007/s12088-020-00878-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
Catalase has crucial role in adaptive response to H2O2. Main channel structure responsible for substrate selectivity was estimated to understand the relationship between the evolutionary direction of catalases from Exiguobacterium oxidotolerans and Psychrobacter piscatorii which survive in cold and high concentration of hydrogen peroxide, and their catalytic property. E. oxidotolerans catalase (EKTA) exhibited a higher ratio of compound I formation rate using peracetic acid (a substrate lager than H2O2)/catalase activity using H2O2 as the substrate than P. piscatori catalase (PKTA). It was considered that the ratio was attributed to the size of the amino acid residues locating at the bottle neck structure in the main channel. The differences in the ratio of the compound I formation rate with peracetic acid to catalase activity with H2O2 between the deeper branches in the phylogenetic tree in both EKTA and PKTA were large. This indicates that catalases from the hydrogen peroxide-tolerant bacteria have evolved in different directions, exhibiting effective catalytic activity and allowing broader substrates size or H2O2-specific substrate acceptability in EKTA and PKTA, respectively. It is considered that the main channel structure reflected the difference in the evolutionary direction of clade 1 and clade 3 catalases.
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Affiliation(s)
- Yoshiko Hanaoka
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan
| | - Hideyuki Kimoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan.,School of Biological Science and Engineering, Tokai University, Sapporo, Japan
| | | | | | - Hidetoshi Matsuyama
- School of Biological Science and Engineering, Tokai University, Sapporo, Japan
| | - Isao Yumoto
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukisamu-Higashi, Toyohira-ku, Sapporo, 062-8517 Japan
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14
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Teider Junior PI, Ribeiro Júnior JC, Ossugui EH, Tamanini R, Ribeiro J, Santos GA, Alfieri AA, Beloti V. Pseudomonas spp. and other psychrotrophic microorganisms in inspected and non-inspected Brazilian Minas Frescal cheese: proteolytic, lipolytic and AprX production potential. PESQUISA VETERINÁRIA BRASILEIRA 2019. [DOI: 10.1590/1678-5150-pvb-6037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ABSTRACT: The most consumed cheese in Brazil, Minas Frescal cheese (MFC) is highly susceptible to microbial contamination and clandestine production and commercialization can pose a risk to consumer health. The storage of this fresh product under refrigeration, although more appropriate, may favor the growth of spoilage psychrotrophic bacteria. The objective of this study was to quantify and compare Pseudomonas spp. and other psychrotrophic bacteria in inspected and non-inspected MFC samples, evaluate their lipolytic and proteolytic activities and their metalloprotease production potentials. Twenty MFC samples were evaluated: 10 inspected and 10 non-inspected. Counts of psychrotrophic bacteria and Pseudomonas spp., evaluation of the proteolytic and lipolytic potential of the isolates, and identification of potential producers of alkaline metalloprotease (AprX) were assessed. The mean total psychrotrophic counts were 1.07 (±2.18) × 109CFU/g in the inspected samples and 4.5 (±5.86) × 108CFU/g in the non-inspected, with no significant difference (p=0.37). The average score of Pseudomonas spp. was 6.86 (±18.6) × 105 and 2.08 (±3.65) × 106 CFU/g for the inspected and non-inspected MFC samples, respectively, with no significant difference (p=0.1). Pseudomonas spp. represented 0.06% and 0.004% of psychrotrophic bacteria found in inspected and non-inspected MFC samples, respectively. Collectively, 694 psychrotrophic strains and 47Pseudomonas spp. were isolated, of which 59.9% and 68.1% were simultaneously proteolytic and lipolytic, respectively. Of the 470 psychrotrophs isolated from inspected and 224 from non-inspected cheese samples, 5.74% and 2.23% contained aprX, respectively, while 100 and 86.96% of the Pseudomonas spp. isolates in inspected and non-inspected cheese samples contained the gene. The production potential of AprX did not, however, determine the proteolytic activity on plates of these isolates under the conditions evaluated in this study. Of total, 65.63% of the psychrotrophs that contained aprX gene were confirmed as Pseudomonas spp., using genus-specific PCR. Phylogenetic analysis of the 16S rRNA gene of the other psychrotrophs that were potential producers of AprX identified them as Serratia spp. (n=7), Raoultella ornithinolytica (n=1), and Acinetobacter schindleri (n=1) in the inspected samples and Psychrobacter sanguinis (n=1) and Leuconostoc mesenteroides (n=1) in the non-inspected samples. The production conditions of Brazilian MFC of these samples, while meeting the legal determinations, are not sufficient to control Pseudomonas and other spoilage-related psychrotrophs. Thus, stricter hygienic measures are required during the formal production of this type of cheese.
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15
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Benefits and Drawbacks of Harboring Plasmid pP32BP2, Identified in Arctic Psychrophilic Bacterium Psychrobacter sp. DAB_AL32B. Int J Mol Sci 2019; 20:ijms20082015. [PMID: 31022896 PMCID: PMC6514802 DOI: 10.3390/ijms20082015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 12/18/2022] Open
Abstract
Psychrobacter sp. DAB_AL32B, originating from Spitsbergen island (Arctic), carries the large plasmid pP32BP2 (54,438 bp). Analysis of the pP32BP2 nucleotide sequence revealed the presence of three predicted phenotypic modules that comprise nearly 30% of the plasmid genome. These modules appear to be involved in fimbriae synthesis via the chaperone-usher pathway (FIM module) and the aerobic and anaerobic metabolism of carnitine (CAR and CAI modules, respectively). The FIM module was found to be functional in diverse hosts since it facilitated the attachment of bacterial cells to abiotic surfaces, enhancing biofilm formation. The CAI module did not show measurable activity in any of the tested strains. Interestingly, the CAR module enabled the enzymatic breakdown of carnitine, but this led to the formation of the toxic by-product trimethylamine, which inhibited bacterial growth. Thus, on the one hand, pP32BP2 can enhance biofilm formation, a highly advantageous feature in cold environments, while on the other, it may prevent bacterial growth under certain environmental conditions. The detrimental effect of harboring pP32BP2 (and its CAR module) seems to be conditional, since this replicon may also confer the ability to use carnitine as an alternative carbon source, although a pathway to utilize trimethylamine is most probably necessary to make this beneficial. Therefore, the phenotype determined by this CAR-containing plasmid depends on the metabolic background of the host strain.
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16
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Leclaire S, Strandh M, Dell'Ariccia G, Gabirot M, Westerdahl H, Bonadonna F. Plumage microbiota covaries with the major histocompatibility complex in blue petrels. Mol Ecol 2019; 28:833-846. [PMID: 30582649 DOI: 10.1111/mec.14993] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/05/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023]
Abstract
To increase fitness, a wide range of vertebrates preferentially mate with partners that are dissimilar at the major histocompatibility complex (MHC) or that have high MHC diversity. Although MHC often can be assessed through olfactory cues, the mechanism by which MHC genes influence odour remains largely unclear. MHC class IIB molecules, which enable recognition and elimination of extracellular bacteria, have been suggested to influence odour indirectly by shaping odour-producing microbiota, i.e. bacterial communities. However, there is little evidence of the predicted covariation between an animal's MHC genotype and its bacterial communities in scent-producing body surfaces. Here, using high-throughput sequencing, we tested the covariation between MHC class IIB genotypes and feather microbiota in the blue petrel (Halobaena caerulea), a seabird with highly developed olfaction that has been suggested to rely on oduor cues during an MHC-based mate choice. First, we show that individuals with similar MHC class IIB profiles also have similar bacterial assemblages in their feathers. Then, we show that individuals with high MHC diversity have less diverse feather microbiota and also a reduced abundance of a bacterium of the genus Arsenophonus, a genus in which some species are symbionts of avian ectoparasites. Our results, showing that feather microbiota covary with MHC, are consistent with the hypothesis that individual MHC genotype may shape the semiochemical-producing microbiota in birds.
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Affiliation(s)
- Sarah Leclaire
- Laboratoire Evolution & Diversité Biologique, UMR 5174 (CNRS, Université Paul Sabatier, ENFA), Toulouse, France.,Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| | - Maria Strandh
- Molecular Ecology and Evolution Lab, Lund University, Lund, Sweden
| | - Gaia Dell'Ariccia
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| | - Marianne Gabirot
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
| | | | - Francesco Bonadonna
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS-CEFE, Montpellier, France
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17
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Dias LM, Folador ARC, Oliveira AM, Ramos RTJ, Silva A, Baraúna RA. Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome. Genome Biol Evol 2018; 10:731-741. [PMID: 29438502 PMCID: PMC5833320 DOI: 10.1093/gbe/evy029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2018] [Indexed: 11/12/2022] Open
Abstract
Exiguobacterium and Psychrobacter are bacterial genera with several cold-adapted species. These extremophiles are commonly isolated from the same habitats in Earth's cryosphere and have great ecological and biotechnological relevance. Thus, through comparative genomic analyses, it was possible to understand the functional diversity of these psychrotrophic and psychrophilic species and present new insights into the microbial adaptation to cold. The nucleotide identity between Exiguobacterium genomes was >90%. Three genomic islands were identified in the E. antarcticum B7 genome. These islands contained genes involved in flagella biosynthesis and chemotaxis, as well as enzymes for carotenoid biosynthesis. Clustering of cold shock proteins by Ka/Ks ratio suggests the occurrence of a positive selection over these genes. Neighbor-joining clustering of complete genomes showed that the E. sibiricum was the most closely related to E. antarcticum. A total of 92 genes were shared between Exiguobacterium and Psychrobacter. A reduction in the genomic content of E. antarcticum B7 was observed. It presented the smallest genome size of its genus and a lower number of genes because of the loss of many gene families compared with the other genomes. In our study, eight genomes of Exiguobacterium and Psychrobacter were compared and analysed. Psychrobacter showed higher genomic plasticity and E. antarcticum B7 presented a large decrease in genomic content without changing its ability to grow in cold environments.
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Affiliation(s)
- Larissa M Dias
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Adriana R C Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Amanda M Oliveira
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Rommel T J Ramos
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Rafael A Baraúna
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
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18
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Diversity and characterization of spoilage-associated psychrotrophs in food in cold chain. Int J Food Microbiol 2018; 290:86-95. [PMID: 30317110 DOI: 10.1016/j.ijfoodmicro.2018.09.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 01/24/2023]
Abstract
In this work, psychrotrophs known to cause food spoilage were isolated from commercial food products. Further, temperature sensitivities and volatile organic compounds of the representative strains were characterized to evaluate the population heterogeneity. A total of 490 isolates belonging to 38 genera of 20 families were identified from 30 psychrotroph-positive samples, among which Gram-negative bacteria occurred frequently. The genus Pseudomonas exhibited a clear predominance, especially Pseudomonas fragi, followed by Psychrobacter, Brochothrix, Serratia, and Stenotrophomonas, with the dominant bacteria varying with origin. Aquatic products related to Hafnia and quick-frozen food corresponding to Stenotrophomonas, as well as livestock products were shown to be good ecological niches for growth of psychrotrophs. The genus Pantoea was shown to have an intimate relationship with fruits. While in bean, cereal grain and dairy products, only Pseudomonas was present. The fits of the growth curves demonstrated good adaptability and tolerance of the tested strains under 4 °C, and multifarious growth also reflected intra-species differences and phenotypic diversity. Various kinds of esters, aromatic compounds, alcohols, and ketones were frequently detected by GC-MS. High alcohols were seen in Psychrobacter, but hydrocarbons and ethers were more often found in Pseudomonas. In particular, since high amounts of isophorone were only discovered in bacteria samples, it is speculated to be the characteristic substance of psychrotrophs.
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19
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Amelia TSM, Amirul AAA, Saidin J, Bhubalan K. Identification of Cultivable Bacteria from Tropical Marine Sponges and Their Biotechnological Potentials. Trop Life Sci Res 2018; 29:187-199. [PMID: 30112149 PMCID: PMC6072720 DOI: 10.21315/tlsr2018.29.2.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Marine sponges are acknowledged as bacterial hotspots in the oceanic biome. Aquatic bacteria are being investigated comprehensively for bioactive complexes and secondary metabolites. Cultivable bacteria associated with different species of sea sponges in South China Sea waters adjacent to Bidong Island, Terengganu were identified. Molecular identification was accomplished using 16S rRNA gene cloning and sequencing. Fourteen bacterial species were identified and their phylogenetic relationships were analysed by constructing a neighbour-joining tree with Molecular Evolutionary Genetics Analysis 6. The identified species encompassed four bacterial classes that were Firmicutes, Actinobacteria, Alphaproteobacteria and Gammaproteobacteria known to have been associated with sponges. The potential biotechnological applications of the identified bacteria were compared and reviewed based on relevant past studies. The biotechnological functions of the 14 cultivable isolates have been previously reported, hence reinforcing that bacteria associated with sponges are an abundant resource of scientifically essential compounds. Resilience of psychrotolerant bacteria, Psychrobacter celer, in warm tropical waters holds notable prospects for future research.
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Affiliation(s)
- Tan Suet May Amelia
- School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Al-Ashraf Abdullah Amirul
- School of Biological Sciences, Universiti Sains Malaysia, 11800 USM Pulau Pinang, Malaysia
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia (NIBM), Ministry of Science, Technology and Innovation, 11700 Gelugor, Pulau Pinang, Malaysia
- Centre of Chemical Biology, Universiti Sains Malaysia, 11900 Bayan Lepas, Pulau Pinang, Malaysia
| | - Jasnizat Saidin
- School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Kesaven Bhubalan
- School of Marine and Environmental Sciences, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia (NIBM), Ministry of Science, Technology and Innovation, 11700 Gelugor, Pulau Pinang, Malaysia
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
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20
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Bakermans C. Adaptations to marine versus terrestrial low temperature environments as revealed by comparative genomic analyses of the genus Psychrobacter. FEMS Microbiol Ecol 2018; 94:5032373. [DOI: 10.1093/femsec/fiy102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/27/2018] [Indexed: 12/13/2022] Open
Affiliation(s)
- Corien Bakermans
- Division of Mathematics and Natural Sciences, Penn State Altoona, United States
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21
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Genome content, metabolic pathways and biotechnological potential of the psychrophilic Arctic bacterium Psychrobacter sp. DAB_AL43B, a source and a host of novel Psychrobacter-specific vectors. J Biotechnol 2017; 263:64-74. [PMID: 28919459 DOI: 10.1016/j.jbiotec.2017.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/10/2017] [Accepted: 09/14/2017] [Indexed: 01/06/2023]
Abstract
Psychrobacter sp. DAB_AL43B, isolated from ornithogenic soil collected on the Arctic island of Spitsbergen, is a newly sequenced psychrophilic strain susceptible to conjugation and electrotransformation. Its genome consists of a circular chromosome (3.3 Mb) and four plasmids (4.4-6.4kb). In silico genome mining and microarray-based phenotypic analysis were performed to describe the metabolic potential of this strain and identify possible biotechnological applications. Metabolic reconstruction indicated that DAB_AL43B prefers low-molecular-weight carboxylates and amino acids as carbon and energy sources. Genetic determinants of heavy-metal resistance, anthracene degradation and possible aerobic denitrification were also identified. Comparative analyses revealed a relatively close relationship between DAB_AL43B and other sequenced Psychrobacter species. In addition, the plasmids of this strain were used as the basis for the construction of Escherichia coli-Psychrobacter spp. shuttle vectors. Taken together, the results of this work suggest that DAB_AL43B is a promising candidate as a new model strain for studies on Psychrobacter spp.
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22
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Lasa A, Romalde JL. Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation. GENOMICS DATA 2017; 12:7-10. [PMID: 28229046 PMCID: PMC5312645 DOI: 10.1016/j.gdata.2017.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/03/2017] [Accepted: 01/25/2017] [Indexed: 11/04/2022]
Abstract
To date, the genus Psychrobacter consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three Psychrobacter-like strains (C 20.9, Cmf 22.2 and Rd 27.2) isolated from reared clams in Galicia (Spain) are described. The sequenced genomes resulted in an assembly size of 3,143,782 bp for C 20.9 isolate, 3,168,467 bp for Cmf 22.2 isolate and 3,028,386 bp for Rd 27.2 isolate. Among the identified coding sequences of the genomes, mercury detoxification and biogeochemistry genes were found, as well as genes related to heavy metals and antibiotic resistance. Also virulence-related features were identified such as the siderophore vibrioferrin or an aerobactin-like siderophore. The phylogenetic analysis of the 16S rRNA gene suggested that these strains may represent novel species of the Psychrobacter genus. The genome sequences of the Psychrobacter sp. strains have been deposited at DDBJ/EMBL/GenBank under the accession numbers MRYA00000000 (Cmf 22.2), MRYB00000000 (Rd 27.2) and MRYC00000000 (C 20.9), and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858.
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Affiliation(s)
- Aide Lasa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología. Universidade de Santiago de Compostela, Campus Vida s/n. 15782, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología. Universidade de Santiago de Compostela, Campus Vida s/n. 15782, Santiago de Compostela, Spain
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23
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Franco DC, Signori CN, Duarte RTD, Nakayama CR, Campos LS, Pellizari VH. High Prevalence of Gammaproteobacteria in the Sediments of Admiralty Bay and North Bransfield Basin, Northwestern Antarctic Peninsula. Front Microbiol 2017; 8:153. [PMID: 28210255 PMCID: PMC5288382 DOI: 10.3389/fmicb.2017.00153] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/20/2017] [Indexed: 11/15/2022] Open
Abstract
Microorganisms dominate most Antarctic marine ecosystems, in terms of biomass and taxonomic diversity, and play crucial role in ecosystem functioning due to their high metabolic plasticity. Admiralty Bay is the largest bay on King George Island (South Shetland Islands, Antarctic Peninsula) and a combination of hydro-oceanographic characteristics (bathymetry, sea ice and glacier melting, seasonal entrance of water masses, turbidity, vertical fluxes) create conditions favoring organic carbon deposition on the seafloor and microbial activities. We sampled surface sediments from 15 sites across Admiralty Bay (100–502 m total depth) and the adjacent North Bransfield Basin (693–1147 m), and used the amplicon 454-sequencing of 16S rRNA gene tags to compare the bacterial composition, diversity, and microbial community structure across environmental parameters (sediment grain size, pigments and organic nutrients) between the two areas. Marine sediments had a high abundance of heterotrophic Gammaproteobacteria (92.4% and 83.8% inside and outside the bay, respectively), followed by Alphaproteobacteria (2.5 and 5.5%), Firmicutes (1.5 and 1.6%), Bacteroidetes (1.1 and 1.7%), Deltaproteobacteria (0.8 and 2.5%) and Actinobacteria (0.7 and 1.3%). Differences in alpha-diversity and bacterial community structure were found between the two areas, reflecting the physical and chemical differences in the sediments, and the organic matter input.
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Affiliation(s)
- Diego C Franco
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo São Paulo, Brazil
| | - Camila N Signori
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo São Paulo, Brazil
| | - Rubens T D Duarte
- Centro de Ciências Biológicas, Universidade Federal de Santa Catarina Florianópolis, Brazil
| | - Cristina R Nakayama
- Departamento de Ciências Ambientais, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo Diadema, Brazil
| | - Lúcia S Campos
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro Rio de Janeiro, Brazil
| | - Vivian H Pellizari
- Departamento de Oceanografia Biológica, Instituto Oceanográfico, Universidade de São Paulo São Paulo, Brazil
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24
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Dugat-Bony E, Garnier L, Denonfoux J, Ferreira S, Sarthou AS, Bonnarme P, Irlinger F. Highlighting the microbial diversity of 12 French cheese varieties. Int J Food Microbiol 2016; 238:265-273. [DOI: 10.1016/j.ijfoodmicro.2016.09.026] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 09/05/2016] [Accepted: 09/26/2016] [Indexed: 02/08/2023]
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25
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Okyay TO, Nguyen HN, Castro SL, Rodrigues DF. CO 2 sequestration by ureolytic microbial consortia through microbially-induced calcite precipitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 572:671-680. [PMID: 27524723 DOI: 10.1016/j.scitotenv.2016.06.199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/25/2016] [Accepted: 06/25/2016] [Indexed: 06/06/2023]
Abstract
Urea is an abundant nitrogen-containing compound found in urine of mammals and widely used in fertilizers. This compound is part of the nitrogen biogeochemical cycle and is easily biodegraded by ureolytic microorganisms that have the urease enzyme. Previous studies, with ureolytic isolates, have shown that some ureolytic microorganisms are able to sequester CO2 through a process called microbially-induced calcium carbonate precipitation. The present study investigates 15 ureolytic consortia obtained from the "Pamukkale travertines" and the "Cave Without A Name" using different growth media to identify the possible bacterial genera responsible for CO2 sequestration through the microbially-induced calcite precipitation (MICP). The community structure and diversity were determined by deep-sequencing. The results showed that all consortia presented varying CO2 sequestration capabilities and MICP rates. The CO2 sequestration varied between 0 and 86.4%, and it depended largely on the community structure, as well as on pH. Consortia with predominance of Comamonas, Plesiomonas and Oxalobacter presented reduced CO2 sequestration. On the other hand, consortia dominated by Sporosarcina, Sphingobacterium, Stenotrophomonas, Acinetobacter, and Elizabethkingia showed higher rates of CO2 uptake in the serum bottle headspace.
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Affiliation(s)
- Tugba O Okyay
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77204-4003, USA
| | - Hang N Nguyen
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77204-4003, USA
| | - Sarah L Castro
- NASA Johnson Space Center Microbiology Laboratory, Houston, TX 77058, USA
| | - Debora F Rodrigues
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77204-4003, USA.
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26
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Lee CS, Kim M, Lee C, Yu Z, Lee J. The Microbiota of Recreational Freshwaters and the Implications for Environmental and Public Health. Front Microbiol 2016; 7:1826. [PMID: 27909431 PMCID: PMC5112438 DOI: 10.3389/fmicb.2016.01826] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/31/2016] [Indexed: 12/03/2022] Open
Abstract
The microbial communities in recreational freshwaters play important roles in both environmental and public health perspectives. In this study, the bacterial community structure and its associations with freshwater environments were investigated by analyzing the summertime microbiomes of three beach waters in Ohio (East Fork, Delaware, and Madison lakes) together with environmental and microbial water quality parameters. From the swimming season of 2009, 21 water samples were collected from the three freshwater beaches. From the samples, 110,000 quality-checked bacterial 16S rRNA gene sequences were obtained and analyzed, resulting in an observation of 4500 bacterial operational taxonomic units (OTUs). The most abundant bacteria were Mycobacterium and Arthrobacter of the Actinobacteria (33.2%), Exiguobacterium and Paenisporosarcina of the Firmicutes (23.4%), Planktothrix and Synechococcus of the Cyanobacteria (20.8%), and Methylocystis and Polynucleobacter of the Proteobacteria (16.3%). Considerable spatial and temporal variations were observed in the bacterial community of Actinobacteria, Cyanobacteria, and Firmicutes, where the bacterial community structure was greatly influenced by hydrological and weather conditions. The most influential factors were (1) water inflow for Bacteroidia and Clostridia, (2) turbidity for Gammaproteobacteria, (3) precipitation for Bacilli, and (4) temperature and pH for Cyanobacteria. One noticeable microbial interaction in the bacterial community was a significant negative relationship between Cyanobacteria and Bacilli (P < 0.05). Concerning beach water quality, the level of the genetic markers for cyanobacterial toxin (mcyA) was linked to the abundance of Cyanobacteria. In addition, unique distributions of the genera Enterococcus, Staphylococcus, Streptococcus, Bacteroides, Clostridium, Finegoldia, Burkholderia, and Klebsiella, together with a high density of fecal indicator Escherichia coli, were markedly observed in the sample from Madison Lake on July 13, suggesting a distinctly different source of bacterial loading into the lake, possibly fecal contamination. In conclusion, deep sequencing-based microbial community analysis can provide detailed profiles of bacterial communities and information on potential public health risks at freshwater beaches.
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Affiliation(s)
- Chang Soo Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State UniversityColumbus, OH, USA
| | - Minseok Kim
- Department of Animal Sciences, The Ohio State UniversityColumbus, OH, USA
| | - Cheonghoon Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State UniversityColumbus, OH, USA
| | - Zhongtang Yu
- Department of Animal Sciences, The Ohio State UniversityColumbus, OH, USA
| | - Jiyoung Lee
- Division of Environmental Health Sciences, College of Public Health, The Ohio State UniversityColumbus, OH, USA
- Department of Food Science and Technology, The Ohio State UniversityColumbus, OH, USA
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Gawor J, Grzesiak J, Sasin-Kurowska J, Borsuk P, Gromadka R, Górniak D, Świątecki A, Aleksandrzak-Piekarczyk T, Zdanowski MK. Evidence of adaptation, niche separation and microevolution within the genus Polaromonas on Arctic and Antarctic glacial surfaces. Extremophiles 2016; 20:403-13. [PMID: 27097637 PMCID: PMC4921121 DOI: 10.1007/s00792-016-0831-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/05/2016] [Indexed: 10/26/2022]
Abstract
Polaromonas is one of the most abundant genera found on glacier surfaces, yet its ecology remains poorly described. Investigations made to date point towards a uniform distribution of Polaromonas phylotypes across the globe. We compared 43 Polaromonas isolates obtained from surfaces of Arctic and Antarctic glaciers to address this issue. 16S rRNA gene sequences, intergenic transcribed spacers (ITS) and metabolic fingerprinting showed great differences between hemispheres but also between neighboring glaciers. Phylogenetic distance between Arctic and Antarctic isolates indicated separate species. The Arctic group clustered similarly, when constructing dendrograms based on 16S rRNA gene and ITS sequences, as well as metabolic traits. The Antarctic strains, although almost identical considering 16S rRNA genes, diverged into 2 groups based on the ITS sequences and metabolic traits, suggesting recent niche separation. Certain phenotypic traits pointed towards cell adaptation to specific conditions on a particular glacier, like varying pH levels. Collected data suggest, that seeding of glacial surfaces with Polaromonas cells transported by various means, is of greater efficiency on local than global scales. Selection mechanisms present of glacial surfaces reduce the deposited Polaromonas diversity, causing subsequent adaptation to prevailing environmental conditions. Furthermore, interactions with other supraglacial microbiota, like algae cells may drive postselectional niche separation and microevolution within the Polaromonas genus.
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Affiliation(s)
- Jan Gawor
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland.
| | - Joanna Sasin-Kurowska
- Institute of Genetics and Biotechnology, Faculty of Biology, Warsaw University, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Piotr Borsuk
- Institute of Genetics and Biotechnology, Faculty of Biology, Warsaw University, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Robert Gromadka
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Dorota Górniak
- Department of Microbiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury, Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Aleksander Świątecki
- Department of Microbiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury, Oczapowskiego 1A, 10-719, Olsztyn, Poland
| | - Tamara Aleksandrzak-Piekarczyk
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
| | - Marek K Zdanowski
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106, Warsaw, Poland
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Abd-Elnaby HM, Abou-Elela GM, Ghozlan HA, Hussein H, Sabry SA. Characterization and bioremediation potential of marine Psychrobacter species. THE EGYPTIAN JOURNAL OF AQUATIC RESEARCH 2016; 42:193-203. [DOI: 10.1016/j.ejar.2016.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Zeng YX, Yu Y, Liu Y, Li HR. Psychrobacter glaciei sp. nov., isolated from the ice core of an Arctic glacier. Int J Syst Evol Microbiol 2016; 66:1792-1798. [DOI: 10.1099/ijsem.0.000939] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yin-Xin Zeng
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, PRChina
| | - Yong Yu
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, PRChina
| | - Yang Liu
- Central Laboratory of Fujian Academy of Agricultural Sciences, Fujian 350003, PRChina
| | - Hui-Rong Li
- Key Laboratory for Polar Science of State Oceanic Administration, Polar Research Institute of China, Shanghai 200136, PRChina
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Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau. Extremophiles 2016; 20:337-49. [DOI: 10.1007/s00792-016-0825-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/11/2016] [Indexed: 10/22/2022]
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A cold-adapted, solvent and salt tolerant esterase from marine bacterium Psychrobacter pacificensis. Int J Biol Macromol 2015; 81:180-7. [DOI: 10.1016/j.ijbiomac.2015.07.045] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 11/20/2022]
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Chong CW, Pearce DA, Convey P. Emerging spatial patterns in Antarctic prokaryotes. Front Microbiol 2015; 6:1058. [PMID: 26483777 PMCID: PMC4588704 DOI: 10.3389/fmicb.2015.01058] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 09/14/2015] [Indexed: 11/13/2022] Open
Abstract
Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate. Based on our synthesis, it is clear that spatial patterns of Antarctic prokaryotes can be unique at local scales, while the limited evidence available to date supports the group exhibiting overall regional biogeographical patterns similar to the eukaryotes. We further consider the applicability of the concept of “functional redundancy” for the Antarctic microbial community and highlight the requirements for proper consideration of their important and distinctive roles in Antarctic terrestrial ecosystems.
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Affiliation(s)
- Chun-Wie Chong
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur Malaysia ; National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia
| | - David A Pearce
- National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia ; Faculty of Health and Life Sciences, University of Northumbria, Newcastle upon Tyne UK ; University Centre in Svalbard, Longyearbyen Norway ; British Antarctic Survey, Cambridge UK
| | - Peter Convey
- National Antarctic Research Center, University of Malaya, Kuala Lumpur Malaysia ; British Antarctic Survey, Cambridge UK
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Puja G, Jyoti V. Culturable bacterial diversity and hydrolytic enzymes from drass, a cold desert in India. ACTA ACUST UNITED AC 2015. [DOI: 10.5897/ajmr2015.7424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Structural Investigation of the Oligosaccharide Portion Isolated from the Lipooligosaccharide of the Permafrost Psychrophile Psychrobacter arcticus 273-4. Mar Drugs 2015. [PMID: 26204948 PMCID: PMC4515632 DOI: 10.3390/md13074539] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Psychrophilic microorganisms have successfully colonized all permanently cold environments from the deep sea to mountain and polar regions. The ability of an organism to survive and grow in cryoenviroments depends on a number of adaptive strategies aimed at maintaining vital cellular functions at subzero temperatures, which include the structural modifications of the membrane. To understand the role of the membrane in the adaptation, it is necessary to characterize the cell-wall components, such as the lipopolysaccharides, that represent the major constituent of the outer membrane. The aim of this study was to investigate the structure of the carbohydrate backbone of the lipooligosaccharide (LOS) isolated from the cold-adapted Psychrobacter arcticus 273-4. The strain, isolated from a 20,000-to-30,000-year-old continuously frozen permafrost in Siberia, was cultivated at 4 °C. The LOS was isolated from dry cells and analyzed by means of chemical methods. In particular, it was degraded either by mild acid hydrolysis or by hydrazinolysis and investigated in detail by 1H and 13C NMR spectroscopy and by ESI FT-ICR mass spectrometry. The oligosaccharide was characterized by the substitution of the heptose residue, usually linked to Kdo in the inner core, with a glucose, and for the unusual presence of N-acetylmuramic acid.
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Growth-dependent catalase localization in Exiguobacterium oxidotolerans T-2-2T reflected by catalase activity of cells. PLoS One 2013; 8:e76862. [PMID: 24204687 PMCID: PMC3800074 DOI: 10.1371/journal.pone.0076862] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 08/28/2013] [Indexed: 12/19/2022] Open
Abstract
A psychrotolerant and H2O2-resistant bacterium, Exiguobacterium oxidotolerans T-2-2T, exhibits extraordinary H2O2 resistance and produces catalase not only intracellularly but also extracellularly. The intracellular and extracellular catalases exhibited the same enzymatic characteristics, that is, they exhibited the temperature-dependent activity characteristic of a cold-adapted enzyme, their heat stabilities were similar to those of mesophilic enzymes and very high catalytic intensity. In addition, catalase gene analysis indicated that the bacterium possessed the sole clade 1 catalase gene corresponding to intracellular catalase. Hence, intracellular catalase is secreted into the extracellular space. In addition to intracellular and extracellular catalases, the inner circumference of the cells showed the localization of catalase in the mid-stationary growth phase, which was observed by immunoelectron microscopy using an antibody against the intracellular catalase of the strain. The cells demonstrated higher catalase activity in the mid-stationary growth phase than in the exponential growth phase. The catalase localized in the inner circumference can be dissociated by treatment with Tween 60. Thus, the localized catalase is not tightly bound to the inner circumference of the cells and may play a role in the oxidative defense of the cells under low metabolic state.
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Chong CW, Goh YS, Convey P, Pearce D, Tan IKP. Spatial pattern in Antarctica: what can we learn from Antarctic bacterial isolates? Extremophiles 2013; 17:733-45. [PMID: 23812890 DOI: 10.1007/s00792-013-0555-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/13/2013] [Indexed: 11/30/2022]
Abstract
A range of small- to moderate-scale studies of patterns in bacterial biodiversity have been conducted in Antarctica over the last two decades, most suggesting strong correlations between the described bacterial communities and elements of local environmental heterogeneity. However, very few of these studies have advanced interpretations in terms of spatially associated patterns, despite increasing evidence of patterns in bacterial biogeography globally. This is likely to be a consequence of restricted sampling coverage, with most studies to date focusing only on a few localities within a specific Antarctic region. Clearly, there is now a need for synthesis over a much larger spatial to consolidate the available data. In this study, we collated Antarctic bacterial culture identities based on the 16S rRNA gene information available in the literature and the GenBank database (n > 2,000 sequences). In contrast to some recent evidence for a distinct Antarctic microbiome, our phylogenetic comparisons show that a majority (~75 %) of Antarctic bacterial isolates were highly similar (≥99 % sequence similarity) to those retrieved from tropical and temperate regions, suggesting widespread distribution of eurythermal mesophiles in Antarctic environments. However, across different Antarctic regions, the dominant bacterial genera exhibit some spatially distinct diversity patterns analogous to those recently proposed for Antarctic terrestrial macroorganisms. Taken together, our results highlight the threat of cross-regional homogenisation in Antarctic biodiversity, and the imperative to include microbiota within the framework of biosecurity measures for Antarctica.
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Affiliation(s)
- Chun Wie Chong
- Department of Life Sciences, International Medical University, Kuala Lumpur, Malaysia.
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Diversity of bacteria in surface ice of Austre Lovénbreen glacier, Svalbard. Arch Microbiol 2013; 195:313-22. [DOI: 10.1007/s00203-013-0880-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 01/04/2013] [Accepted: 02/21/2013] [Indexed: 12/24/2022]
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Azevedo JSN, Correia A, Henriques I. Molecular analysis of the diversity of genus Psychrobacter present within a temperate estuary. FEMS Microbiol Ecol 2013; 84:451-60. [PMID: 23330979 DOI: 10.1111/1574-6941.12075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 01/04/2013] [Accepted: 01/10/2013] [Indexed: 11/27/2022] Open
Abstract
Many members of the genus Psychrobacter are endemic in extremely cold and saline environments and the genus has been described as only marginally successful in warmer habitats. In a previous study the Psychrobacter genus was, unexpectedly, the most frequently isolated bacterial genus from the sea-surface microlayer (SML) and the underlying water (UW) of a temperate estuary (Ria de Aveiro, Portugal). Here we analysed the diversity in Psychrobacter populations inhabiting this estuary. Samples were collected at three dates and three locations from sea-SML and UW. Isolated Psychrobacter strains were well-adapted to temperatures and salt concentrations above the ones described as optimal for most members of this genus. Hydrocarbon-degrading potential was not confirmed for these strains. We developed and optimized a reliable and specific denaturing gradient gel electrophoresis (DGGE)-based method for the analysis of Psychrobacter populations in aquatic systems. DGGE profiles inferred that Psychrobacter populations were very stable in the estuary, a strong indication for the presence of well-adapted phylotypes. The analysis of genus-specific clone libraries revealed a surprisingly high diversity among Psychrobacter in Ria de Aveiro. Results indicated that novel species were probably cultivated. Significant differences between sea-SML and UW Psychrobacter communities were revealed. Observed diversity trends may be related to environmental factors such as salinity and/or anthropogenic pressures such as contamination with hydrocarbons.
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Li A, Chu Y, Wang X, Ren L, Yu J, Liu X, Yan J, Zhang L, Wu S, Li S. A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:3. [PMID: 23320936 PMCID: PMC3618299 DOI: 10.1186/1754-6834-6-3] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 01/11/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND A solid-state anaerobic digestion method is used to produce biogas from various solid wastes in China but the efficiency of methane production requires constant improvement. The diversity and abundance of relevant microorganisms play important roles in methanogenesis of biomass. The next-generation high-throughput pyrosequencing platform (Roche/454 GS FLX Titanium) provides a powerful tool for the discovery of novel microbes within the biogas-generating microbial communities. RESULTS To improve the power of our metagenomic analysis, we first evaluated five different protocols for extracting total DNA from biogas-producing mesophilic solid-state fermentation materials and then chose two high-quality protocols for a full-scale analysis. The characterization of both sequencing reads and assembled contigs revealed that the most prevalent microbes of the fermentation materials are derived from Clostridiales (Firmicutes), which contribute to degrading both protein and cellulose. Other important bacterial species for decomposing fat and carbohydrate are Bacilli, Gammaproteobacteria, and Bacteroidetes (belonging to Firmicutes, Proteobacteria, and Bacteroidetes, respectively). The dominant bacterial species are from six genera: Clostridium, Aminobacterium, Psychrobacter, Anaerococcus, Syntrophomonas, and Bacteroides. Among them, abundant Psychrobacter species, which produce low temperature-adaptive lipases, and Anaerococcus species, which have weak fermentation capabilities, were identified for the first time in biogas fermentation. Archaea, represented by genera Methanosarcina, Methanosaeta and Methanoculleus of Euryarchaeota, constitute only a small fraction of the entire microbial community. The most abundant archaeal species include Methanosarcina barkeri fusaro, Methanoculleus marisnigri JR1, and Methanosaeta theromphila, and all are involved in both acetotrophic and hydrogenotrophic methanogenesis. CONCLUSIONS The identification of new bacterial genera and species involved in biogas production provides insights into novel designs of solid-state fermentation under mesophilic or low-temperature conditions.
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Affiliation(s)
- An Li
- Institute of Nuclear and New Energy Technology, Tsinghua University, Tsinghua Garden, Haidian District, 100084, Beijing, China
| | - Ya’nan Chu
- The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1-7 Beichen West Road, Chaoyang District, 100101, Beijing, China
| | - Xumin Wang
- The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1-7 Beichen West Road, Chaoyang District, 100101, Beijing, China
| | - Lufeng Ren
- The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1-7 Beichen West Road, Chaoyang District, 100101, Beijing, China
| | - Jun Yu
- The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1-7 Beichen West Road, Chaoyang District, 100101, Beijing, China
| | - Xiaoling Liu
- Institute of Nuclear and New Energy Technology, Tsinghua University, Tsinghua Garden, Haidian District, 100084, Beijing, China
| | - Jianbin Yan
- Institute of Nuclear and New Energy Technology, Tsinghua University, Tsinghua Garden, Haidian District, 100084, Beijing, China
| | - Lei Zhang
- Institute of Nuclear and New Energy Technology, Tsinghua University, Tsinghua Garden, Haidian District, 100084, Beijing, China
| | - Shuangxiu Wu
- The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1-7 Beichen West Road, Chaoyang District, 100101, Beijing, China
| | - Shizhong Li
- Institute of Nuclear and New Energy Technology, Tsinghua University, Tsinghua Garden, Haidian District, 100084, Beijing, China
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Rodrigues DF, Jaisi DP, Elimelech M. Toxicity of functionalized single-walled carbon nanotubes on soil microbial communities: implications for nutrient cycling in soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:625-633. [PMID: 23205469 DOI: 10.1021/es304002q] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Culture-dependent and -independent methods were employed to determine the impact of carboxyl-functionalized single-walled carbon nanotubes (SWNTs) on fungal and bacterial soil microbial communities. Soil samples were exposed to 0 (control), 250, and 500 μg of SWNTs per gram of soil. Aliquots of soil were sampled for up to 14 days for culture-dependent analyses, namely, plate count agar and bacterial community level physiological profiles, and culture-independent analyses, namely, quantitative real-time polymerase chain reaction (qPCR), mutliplex-terminal restriction fragment length polymorphism (M-TRFLP), and clone libraries. Results from culture-independent and -dependent methods show that the bacterial soil community is transiently affected by the presence of SWNTs. The major impact of SWNTs on bacterial community was observed after 3 days of exposure, but the bacterial community completely recovered after 14 days. However, no recovery of the fungal community was observed for the duration of the experiment. Physiological and DNA microbial community analyses suggest that fungi and bacteria involved in carbon and phosphorus biogeochemical cycles can be adversely affected by the presence of SWNTs. This study suggests that high concentrations of SWNTs can have widely varying effects on microbial communities and biogeochemical cycling of nutrients in soils.
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Affiliation(s)
- Debora F Rodrigues
- Department of Civil and Environmental Engineering, University of Houston, Houston, Texas 77204-5003, United States.
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Kuhn E. Toward understanding life under subzero conditions: the significance of exploring psychrophilic "cold-shock" proteins. ASTROBIOLOGY 2012; 12:1078-86. [PMID: 23082745 DOI: 10.1089/ast.2012.0858] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Understanding the behavior of proteins under freezing conditions is vital for detecting and locating extraterrestrial life in cold environments, such as those found on Mars and the icy moons of Jupiter and Saturn. This review highlights the importance of studying psychrophilic "cold-shock" proteins, a topic that has yet to be explored. A strategy for analyzing the psychrophilic RNA helicase protein CsdA (Psyc_1082) from Psychrobacter arcticus 273-4 as a key protein for life under freezing temperatures is proposed. The experimental model presented here was developed based on previous data from investigations of Escherichia coli, P. arcticus 273-4, and RNA helicases. P. arcticus 273-4 is considered a model for life in freezing environments. It is capable of growing in temperatures as cold as -10°C by using physiological strategies to survive not only in freezing temperatures but also under low-water-activity and limited-nutrient-availability conditions. The analyses of its genome, transcriptome, and proteome revealed specific adaptations that allow it to inhabit freezing environments by adopting a slow metabolic strategy rather than a cellular dormancy state. During growth at subzero temperatures, P. arcticus 273-4 genes related to energy metabolism and carbon substrate incorporation are downregulated, and genes for maintenance of membranes, cell walls, and nucleic acid motion are upregulated. At -6°C, P. arcticus 273-4 does not upregulate the expression of either RNA or protein chaperones; however, it upregulates the expression of its cold-shock induced DEAD-box RNA helicase protein A (CsdA - Psyc_1082). CsdA - Psyc_1082 was investigated as a key helper protein for sustaining life in subzero conditions. Proving CsdA - Psyc_1082 to be functional as a key protein for life under freezing temperatures may extend the known minimum growth temperature of a mesophilic cell and provide key information about the mechanisms that underlie cold-induced biological systems in icy worlds.
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Affiliation(s)
- Emanuele Kuhn
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada 89512, USA.
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For quite a few chromosomes more: the origin of eukaryotes…. J Mol Biol 2012; 423:135-42. [PMID: 22796299 DOI: 10.1016/j.jmb.2012.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 07/01/2012] [Accepted: 07/03/2012] [Indexed: 11/21/2022]
Abstract
The evolution of eukaryotes addresses an enigmatic question: what are the evolutionary advantages of having a nucleus? The nucleus is traditionally thought to act as protection for DNA, but eukaryotes are more fragile than bacteria. The compartmentalization of the eukaryotic cell might stem from invaginations of the plasma membrane, and I argue that this autogenous origin of the nucleus constituted a selective innovation caused by cellular constraints due to a large genome. The protoeukaryotic nucleus appears to be a physical and chemical solution to the problem of large amounts of DNA in the form of many linear chromosomes. The selective advantages of having a nuclear envelope are to house a large genome in a stabilized structure and to decouple gene translation from transcription. Supporting the karyogenic model, this new hypothesis opens an original perspective to help in understanding the very ancient origin of eukaryotes.
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Rebollar EA, Avitia M, Eguiarte LE, González-González A, Mora L, Bonilla-Rosso G, Souza V. Water-sediment niche differentiation in ancient marine lineages of Exiguobacterium endemic to the Cuatro Cienegas Basin. Environ Microbiol 2012; 14:2323-33. [PMID: 22639906 DOI: 10.1111/j.1462-2920.2012.02784.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The evolutionary history and ecological differentiation of the genus Exiguobacterium was characterized within natural communities from the Cuatro Cienegas Basin, Mexico. Exiguobacterium comprises both halophilic and alkaliphilic bacteria that are abundant among the aquatic systems of the Cuatro Cienegas Basin. We obtained complete sequences of the 16srRNA gene and partial sequences of four housekeeping genes (citC, rpoB, recA and hsp70) in 183 Exiguobacterium isolates retrieved from distinct aquatic systems. We defined three main phylogroups that are closely related to marine and thermophilic species of the genus. These phylogroups were neither specific to a given aquatic system nor to a particular salinity. Phylogenetic reconstruction indicated the presence of several small clusters within the phylogroups. These clusters consisted of isolates predominantly retrieved from sediment or water. Unifrac and AdaptML analyses confirmed this observation, pointing towards a clear pattern of differentiation linked to either sediment or water habitats. Our results are in line with the concept that niche differentiation is one of the main factors shaping prokaryotic populations and leading to evolutionary divergence.
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Affiliation(s)
- Eria A Rebollar
- Laboratorio de Evolución Molecular y Experimental, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Lasek R, Dziewit L, Bartosik D. Plasmid pP62BP1 isolated from an Arctic Psychrobacter sp. strain carries two highly homologous type II restriction-modification systems and a putative organic sulfate metabolism operon. Extremophiles 2012; 16:363-76. [PMID: 22392282 PMCID: PMC3346939 DOI: 10.1007/s00792-012-0435-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 02/21/2012] [Indexed: 11/28/2022]
Abstract
The complete nucleotide sequence of plasmid pP62BP1 (34,467 bp), isolated from Arctic Psychrobacter sp. DAB_AL62B, was determined and annotated. The conserved plasmid backbone is composed of several genetic modules, including a replication system (REP) with similarities to the REP region of the iteron-containing plasmid pPS10 of Pseudomonas syringae. The additional genetic load of pP62BP1 includes two highly related type II restriction-modification systems and a set of genes (slfRCHSL) encoding enzymes engaged in the metabolism of organic sulfates, plus a putative transcriptional regulator (SlfR) of the AraC family. The pP62BP1 slf locus has a compact and unique structure. It is predicted that the enzymes SlfC, SlfH, SlfS and SlfL carry out a chain of reactions leading to the transformation of alkyl sulfates into acyl-CoA, with dodecyl sulfate (SDS) as a possible starting substrate. Comparative analysis of the nucleotide sequences of pP62BP1 and other Psychrobacter spp. plasmids revealed their structural diversity. However, the presence of a few highly conserved DNA segments in pP62BP1, plasmid 1 of P. cryohalolentis K5 and pRWF-101 of Psychrobacter sp. PRwf-1 is indicative of recombinational shuffling of genetic information, and is evidence of lateral gene transfer in the Arctic environment.
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Affiliation(s)
- Robert Lasek
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
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Characterization of catalase from psychrotolerant Psychrobacter piscatorii T-3 exhibiting high catalase activity. Int J Mol Sci 2012; 13:1733-1746. [PMID: 22408420 PMCID: PMC3291989 DOI: 10.3390/ijms13021733] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 01/16/2012] [Accepted: 01/30/2012] [Indexed: 12/30/2022] Open
Abstract
A psychrotolerant bacterium, strain T-3 (identified as Psychrobacter piscatorii), that exhibited an extraordinarily high catalase activity was isolated from the drain pool of a plant that uses H2O2 as a bleaching agent. Its cell extract exhibited a catalase activity (19,700 U·mg protein−1) that was higher than that of Micrococcus luteus used for industrial catalase production. Catalase was approximately 10% of the total proteins in the cell extract of the strain. The catalase (PktA) was purified homogeneously by only two purification steps, anion exchange and hydrophobic chromatographies. The purified catalase exhibited higher catalytic efficiency and higher sensitivity of activity at high temperatures than M. luteus catalase. The deduced amino acid sequence showed the highest homology with catalase of Psycrobacter cryohalolentis, a psychrotolelant bacterium obtained from Siberian permafrost. These findings suggest that the characteristics of the PktA molecule reflected the taxonomic relationship of the isolate as well as the environmental conditions (low temperatures and high concentrations of H2O2) under which the bacterium survives. Strain T-3 efficiently produces a catalase (PktA) at a higher rate than Exiguobacterium oxidotolerans, which produces a very strong activity of catalase (EktA) at a moderate rate, in order to adapt to high concentration of H2O2.
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Spatial and temporal analysis of estuarine bacterioneuston and bacterioplankton using culture-dependent and culture-independent methodologies. Antonie van Leeuwenhoek 2012; 101:819-35. [DOI: 10.1007/s10482-012-9697-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 01/03/2012] [Indexed: 10/14/2022]
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Bruce T, de Castro A, Kruger R, Thompson CC, Thompson FL. Microbial Diversity of Brazilian Biomes. ADVANCES IN MICROBIAL ECOLOGY 2012. [DOI: 10.1007/978-1-4614-2182-5_13] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Darcy JL, Lynch RC, King AJ, Robeson MS, Schmidt SK. Global distribution of Polaromonas phylotypes--evidence for a highly successful dispersal capacity. PLoS One 2011; 6:e23742. [PMID: 21897856 PMCID: PMC3163589 DOI: 10.1371/journal.pone.0023742] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/25/2011] [Indexed: 11/18/2022] Open
Abstract
Bacteria from the genus Polaromonas are dominant phylotypes in clone libraries and culture collections from polar and high-elevation environments. Although Polaromonas has been found on six continents, we do not know if the same phylotypes exist in all locations or if they exhibit genetic isolation by distance patterns. To examine their biogeographic distribution, we analyzed all available, long-read 16S rRNA gene sequences of Polaromonas phylotypes from glacial and periglacial environments across the globe. Using genetic isolation by geographic distance analyses, including Mantel tests and Mantel correlograms, we found that Polaromonas phylotypes are globally distributed showing weak isolation by distance patterns at global scales. More focused analyses using discrete, equally sampled distances classes, revealed that only two distance classes (out of 12 total) showed significant spatial structuring. Overall, our analyses show that most Polaromonas phylotypes are truly globally distributed, but that some, as yet unknown, environmental variable may be selecting for unique phylotypes at a minority of our global sites. Analyses of aerobiological and genomic data suggest that Polaromonas phylotypes are globally distributed as dormant cells through high-elevation air currents; Polaromonas phylotypes are common in air and snow samples from high altitudes, and a glacial-ice metagenome and the two sequenced Polaromonas genomes contain the gene hipA, suggesting that Polaromonas can form dormant cells.
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Affiliation(s)
- John L. Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Ryan C. Lynch
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Andrew J. King
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Michael S. Robeson
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
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Microbes in high arctic snow and implications for the cold biosphere. Appl Environ Microbiol 2011; 77:3234-43. [PMID: 21460114 DOI: 10.1128/aem.02611-10] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We applied molecular, microscopic, and culture techniques to characterize the microbial communities in snow and air at remote sites in the Canadian High Arctic (Ward Hunt Island, Ellesmere Island, and Cornwallis Island, latitudes 74 to 83(o)N). Members of the Bacteria and Eukarya were prevalent in the snow, and their small subunit (SSU) rRNA gene signatures indicated strong local aerial transport within the region over the preceding 8 months of winter snowpack accumulation. Many of the operational taxonomic units (OTUs) were similar to previously reported SSU rRNA gene sequences from the Arctic Ocean, suggesting the importance of local aerial transport processes for marine microbiota. More than 47% of the cyanobacterial OTUs in the snow have been previously found in microbial mats in the region, indicating that this group was also substantially derived from local sources. Viable cyanobacteria isolated from the snow indicated free exchange between the snow and adjacent mat communities. Other sequences were most similar to those found outside the Canadian Arctic but were from snow, lake and sea ice, glaciers and permafrost, alpine regions, Antarctica, and other regions of the Arctic, supporting the concept of global distribution of microbial ecotypes throughout the cold biosphere.
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