Microbes and Environments
Online ISSN : 1347-4405
Print ISSN : 1342-6311
ISSN-L : 1342-6311
Volume 29 , Issue 1
Showing 1-18 articles out of 18 articles from the selected issue
Research Highlight
Minireview
  • Kazuo Isobe, Nobuhito Ohte
    Type: Minireview
    2014 Volume 29 Issue 1 Pages 4-16
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: March 13, 2014
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    Nitrogen (N) cycles have been directly linked to the functional stability of ecosystems because N is an essential element for life. Furthermore, the supply of N to organisms regulates primary productivity in many natural ecosystems. Microbial communities have been shown to significantly contribute to N cycles because many N-cycling processes are microbially mediated. Only particular groups of microbes were implicated in N-cycling processes, such as nitrogen fixation, nitrification, and denitrification, until a few decades ago. However, recent advances in high-throughput sequencing technologies and sophisticated isolation techniques have enabled microbiologists to discover that N-cycling microbes are unexpectedly diverse in their functions and phylogenies. Therefore, elucidating the link between biogeochemical N-cycling processes and microbial community dynamics can provide a more mechanistic understanding of N cycles than the direct observation of N dynamics. In this review, we summarized recent findings that characterized the microbes governing novel N-cycling processes. We also discussed the ecological role of N-cycling microbial community dynamics, which is essential for advancing our understanding of the functional stability of ecosystems.
Regular Papers
  • Dong Han Choi, Jae Hoon noH, Jung-Hyun Lee
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 17-22
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: December 28, 2013
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    Synechococcus are distributed throughout the world’s oceans and are composed of diverse genetic lineages. However, as they are much less abundant than Prochlorococcus in oligotrophic open oceans, their in-depth genetic diversity cannot be investigated using commonly used primers targeting both Prochlorococcus and Synechococcus. Thus, in this study, we designed a primer specific to the 16S–23S rRNA internal transcribed spacer (ITS) of the Synechococcus subcluster 5.1. Using the primer, we could selectively amplify Synechococcus sequences in oligotrophic seawater samples. Further, we showed that a barcoded amplicon pyrosequencing method could be applicable to investigate Synechococcus diversity using sequences retrieved in GenBank and obtained from environmental samples. Allowing sequence analyses of a large number of samples, this high-throughput method would be useful to study global biodiversity and biogeographic patterns of Synechococcus in marine environments.
  • Joanna C. Koenig, Kathrin D. Groissmeier, Mike J. Manefield
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 23-30
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: January 17, 2014
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    The aim of this research was to evaluate the effects of four chlorinated aliphatic hydrocarbons (CAHs), perchloroethene (PCE), carbon tetrachloride (CT), chloroform (CF) and 1,2-dichloroethane (1,2-DCA), on the growth of eight anaerobic bacteria: four fermentative species (Escherichia coli, Klebsiella sp., Clostridium sp. and Paenibacillus sp.) and four respiring species (Pseudomonas aeruginosa, Geobacter sulfurreducens, Shewanella oneidensis and Desulfovibrio vulgaris). Effective concentrations of solvents which inhibited growth rates by 50% (EC50) were determined. The octanol-water partition coefficient or log Po/w of a CAH proved a generally satisfactory measure of its toxicity. Most species tolerated approximately 3-fold and 10-fold higher concentrations of the two relatively more polar CAHs CF and 1,2-DCA, respectively, than the two relatively less polar compounds PCE and CT. EC50 values correlated well with growth rates observed in solvent-free cultures, with fast-growing organisms displaying higher tolerance levels. Overall, fermentative bacteria were more tolerant to CAHs than respiring species, with iron- and sulfate-reducing bacteria in particular appearing highly sensitive to CAHs. These data extend the current understanding of the impact of CAHs on a range of anaerobic bacteria, which will benefit the field of bioremediation.
  • Kentaro Kakoi, Masatoshi Yamaura, Toshihito Kamiharai, Daiki Tamari, M ...
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 31-37
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: December 28, 2013
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    Frankia is a nitrogen (N)-fixing multicellular actinomycete which establishes root-nodule symbiosis with actinorhizal plants. Several aspects of Frankia N fixation and symbiosis are distinct, but genes involved in the specific features are largely unknown because of the lack of an efficient mutant screening method. In this study, we isolated mutants of Frankia sp. strain CcI3 using hyphae fragments mutagenized by chemical mutagens. Firstly, we isolated uracil auxotrophs as gain-of-function mutants resistant to 5-fluoroorotic acid (5-FOA). We obtained seven 5-FOA resistant mutants, all of which required uracil for growth. Five strains carried a frame shift mutation in orotidine-5′-phosphate decarboxylase gene and two carried an amino acid substitution in the orotate phosphoribosyltransferase gene. Secondly, we isolated mutants showing loss-of-function phenotypes. Mutagenized hyphae were fragmented by ultrasound and allowed to multiply at their tips. Hyphae were fragmented again and short fragments were enriched by filtration through 5 μm pores filters. Next-generation and Sanger sequencing revealed that colonies formed from the short hyphae fragments consisted of cells with an identical genotype. From the mutagenized colony population, we isolated three pigmentation mutants and a mutant with reduced N-fixation activity. These results indicate that our procedure is useful for the isolation of loss-of-function mutants using hyphae of Frankia.
  • Yong Guo, Reiko Fujimura, Yoshinori Sato, Wataru Suda, Seok-won Kim, K ...
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 38-49
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: January 24, 2014
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    The 2000 eruption of Mount Oyama on the island of Miyake (Miyake-jima) created a unique opportunity to study the early ecosystem development on newly exposed terrestrial substrates. In this study, bacterial and fungal communities on 9- and 11-year-old volcanic deposits at poorly to fully vegetation-recovered sites in Miyake-jima, Japan, were characterized by conventional culture-based methods and pyrosequencing of 16S rRNA and 18S rRNA genes. Despite the differences in the vegetation cover, the upper volcanic deposit layer samples displayed low among-site variation for chemical properties (pH, total organic carbon, and total nitrogen) and microbial population densities (total direct count and culturable count). Statistical analyses of pyrosequencing data revealed that the microbial communities of volcanic deposit samples were phylogenetically diverse, in spite of very low-carbon environmental conditions, and their diversity was comparable to that in the lower soil layer (buried soil) samples. Comparing with the microbial communities in buried soil, the volcanic deposit communities were characterized by the presence of Betaproteobacteria and Gammaproteobacteria as the main bacterial class, Deinococcus- Thermus as the minor bacterial phyla, and Ascomycota as the major fungal phyla. Multivariate analysis revealed that several bacterial families and fungal classes correlated positively or negatively with plant species.
  • Seishi Ikeda, Kazuhiro Sasaki, Takashi Okubo, Akifumu Yamashita, Kimih ...
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 50-59
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: January 24, 2014
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    Reduced fertilizer usage is one of the objectives of field management in the pursuit of sustainable agriculture. Here, we report on shifts of bacterial communities in paddy rice ecosystems with low (LN), standard (SN), and high (HN) levels of N fertilizer application (0, 30, and 300 kg N ha−1, respectively). The LN field had received no N fertilizer for 5 years prior to the experiment. The LN and HN plants showed a 50% decrease and a 60% increase in biomass compared with the SN plant biomass, respectively. Analyses of 16S rRNA genes suggested shifts of bacterial communities between the LN and SN root microbiomes, which were statistically confirmed by metagenome analyses. The relative abundances of Burkholderia, Bradyrhizobium and Methylosinus were significantly increased in root microbiome of the LN field relative to the SN field. Conversely, the abundance of methanogenic archaea was reduced in the LN field relative to the SN field. The functional genes for methane oxidation (pmo and mmo) and plant association (acdS and iaaMH) were significantly abundant in the LN root microbiome. Quantitative PCR of pmoA/mcrA genes and a 13C methane experiment provided evidence of more active methane oxidation in the rice roots of the LN field. In addition, functional genes for the metabolism of N, S, Fe, and aromatic compounds were more abundant in the LN root microbiome. These results suggest that low-N-fertilizer management is an important factor in shaping the microbial community structure containing key microbes for plant associations and biogeochemical processes in paddy rice ecosystems.
  • Keiichiro Nayuki, Baodong Chen, Ryo Ohtomo, Yukari Kuga
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 60-66
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: February 06, 2014
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    Arbuscular mycorrhizal (AM) fungi function as extended roots and take an active part in plant acquisition of nutrients and also soil pollutants, such as heavy metals. The objective of this study was to establish a method to observe the localization of cadmium (Cd) Kα at subcellular levels using X-ray fluorescence (XRF) imaging with a synchrotron irradiation microbeam in resin-embedded sections of mycorrhizas. To evaluate the methodology, distributions of Cd in high-pressure-frozen Lotus japonicusRhizophagus irregularis mycorrhizal roots were compared between two treatments; Cd was exposed either to the roots or to the extraradical hyphae. Results showed that, in the latter treatment, Cd was restricted to fungal structures, whereas in the former, Cd was detected in cell walls of the two organisms. Plunge-frozen extraradical mycelium of Gigaspora margarita exposed to Cd showed high signals of Cd in the cell walls and vacuoles, and low in the cytoplasm. With selective staining and elemental mapping by electron-dispersive X-ray spectrometry (EDS), a positive correlation between distributions of Cd and P was revealed in the vacuole, which suggested polyP as a counter ion of Cd. These results indicated that there was no Cd relocation in rapidly frozen resin-embedded materials, therefore supporting the usefulness of this methodology.
  • Nadine Gordon-Bradley, Despoina S. Lymperopoulou, Henry Neal Williams
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 67-73
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: February 19, 2014
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    The phylogenetic composition of the epiphytic bacterial community of an invasive aquatic plant (Hydrilla verticillata) and a native species (Vallisneria americana [eelgrass]) of the Wakulla Spring (Florida) was investigated, along with the water column bacterial composition, using clone libraries of the 16S rRNA genes. The bacterial clones from three clone libraries were classified into 182 operational taxonomic units (OTUs), most of which were affiliated with bacterial divisions commonly found in freshwater ecosystems. Based on the identified classes, the bacterial communities on eelgrass and Hydrilla were distinct, such that Planctomycetes, Cyanobacteria, Bacilli and Actinobacteria were found on eelgrass and in the water column but not on Hydrilla. On the other hand, Deltaproteobacteria and Verrucomicrobiae were found on Hydrilla and in the water column but not on eelgrass. Further distinctions observed were that Armatimonadia and Deinococci were found only on Hydrilla while Gemmatimonadetes was found only on eelgrass. Our results indicated differences between the epiphytic bacterial community on the two plants and the water column at the species level, but an even representation of the most abundant phylogenetic taxa (classes) in all three libraries was revealed. Statistical comparison of the retrieved sequences confirmed that the three libraries did not differ significantly at the community level (LIBSHUFF, p <0.05).
  • Jun Murase, Yuriko Takenouchi, Kazufumi Iwasaki, Makoto Kimura
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 74-81
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: February 07, 2014
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    Irrigated rice field soil is subjected to frequent changes in oxygen status due to the water regime by agricultural management. In this study, the community response of microeukaryotes in rice field soil to the oxygen status was explored in a microcosm experiment under defined conditions. Water-saturated soil was incubated under a two-level factorial design of oxygen and organic enrichment with plant residue. The eukaryotic microbial community composition, which was either present or potentially active in the soils, was analyzed using denaturing gradient gel electrophoresis (DGGE) targeting the 18S rRNA gene or reverse-transcribed 18S rRNA. Oxygen availability was a primary factor shaping the microeukaryotic community in both DNA- and RNA-based analyses, revealing a shift within a week of incubation. Plant residue also affected the microeukaryotic community, which was more notable in the active community showing rRNA expression with time. Sequences of amplicons in DGGE bands indicated that protozoa (ciliates, flagellates, and amoebae) were the most prominent microeukaryotes in water-saturated rice field soil both in DNA- and RNA-based analyses. The use of a modified primer for soil protozoa suggested the functional importance of Heterolobosea amoeba in rice field soil, particularly in anoxic soil with organic enrichment.
  • Nobuyasu Yamaguchi, Jonguk Park, Makiko Kodama, Tomoaki Ichijo, Takash ...
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 82-88
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: February 19, 2014
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    Bacterial abundance and community compositions have been examined in aeolian dust in order to clarify their possible impacts on public health and ecosystems. The influence of transcontinentally transported bacterial cells on microbial communities in the outdoor environments of downwind areas should be determined because the rapid influx of a large amount of bacterial cells can disturb indigenous microbial ecosystems. In the present study, we analyzed bacteria in air samples (approximately 100 m3 d−1) that were collected on both Asian dust days and non-Asian dust days over 2 years (between November 2010 and July 2012). Changes in bacterial abundance and community composition were investigated based on their 16S rRNA gene amount and sequence diversity. Seasonal monitoring revealed that airborne bacterial abundance was more than 10-fold higher on severe dust days, while moderate dust events did not affect airborne bacterial abundance. A comparison of bacterial community compositions revealed that bacteria in Asian dust did not immediately disturb the airborne microbial community in areas 3,000–5,000 km downwind of dust source regions, even when a large amount of bacterial cells were transported by the atmospheric event. However, microbes in aeolian dust may have a greater impact on indigenous microbial communities in downwind areas near the dust source. Continuous temporal and spatial analyses from dust source regions to downwind regions (e.g., from the Gobi desert to China, Korea, Japan, and North America) will assist in estimating the impact of atmospherically transported bacteria on indigenous microbial ecosystems in downwind areas.
  • Masao Sakai, Akifumi Hosoda, Kenjiro Ogura, Makoto Ikenaga
    Type: Regular Papers
    2014 Volume 29 Issue 1 Pages 89-95
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: March 13, 2014
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    An agar-degrading bacterium was isolated from soil collected in a vegetable cropping field. The growth of this isolate was enhanced by supplying culture supernatants of bacteria belonging to the order Rhizobiales. Phylogenetic analysis based on 16S rRNA gene sequences indicated the novel bacterium, strain KA5–BT, belonged to the genus Steroidobacter in Gammaproteobacteria, but differed from its closest relative, Steroidobacter denitrificans FST, at the species level with 96.5% similarity. Strain KA5–BT was strictly aerobic, Gram-negative, non-motile, non-spore forming, and had a straight to slightly curved rod shape. Cytochrome oxidase and catalase activities were positive. The strain grew on media containing culture supernatants in a temperature range of 15–37°C and between pH 4.5 and 9.0, with optimal growth occurring at 30°C and pH 6.0–8.0. No growth occurred at 10 or 42°C or at NaCl concentrations more than 3% (w/v). The main cellular fatty acids were iso–C15:0, C16:1ω7c, and iso–C17:1ω9c. The main quinone was ubiquinone-8 and DNA G+C content was 62.9 mol%. In contrast, strain FST was motile, did not grow on the agar plate, and its dominant cellular fatty acids were C15:0 and C17:1ω8c. Based on its phylogenetic and phenotypic properties, strain KA5–BT (JCM 18477T = KCTC 32107T) represents a novel species in genus Steroidobacter, for which the name Steroidobacter agariperforans sp. nov. is proposed.
Short Communications
  • Hiroe Hayashi, Yasurou Kurusu
    Type: Short Communication
    2014 Volume 29 Issue 1 Pages 96-99
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: January 17, 2014
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    We have identified and analyzed two DNA regions responsible for stable maintenance of a plasmid in the genus Sphingomonas and Escherichia coli. A 37 bp fragment, upstream of the repA gene, is required for stable maintenance of the low-copy-number small plasmid pYAN-2 (4,687 bp) from Sphingobium yanoikuyae. It does not encode any significant protein sequence and has one direct repeat for possible secondary structures. Moreover, a 70 bp fragment, upstream of the above sequence, completely stabilized the unstable pSC101 plasmid in E. coli.
  • Yuki Sato-Takabe, Koji Hamasaki, Koji Suzuki
    Type: Short Communication
    2014 Volume 29 Issue 1 Pages 100-103
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: February 04, 2014
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    This paper describes the photosynthetic response of a Roseobacter strain of marine aerobic anoxygenic phototrophic bacteria to an organic substrate limitation. In batch cultures, higher values of the spheroidenone/bacteriochlorophyll a ratio were observed under substrate-deficient conditions. Interestingly, the maximum photochemical quantum efficiencies of the photosystem under substrate-deficient conditions using blue or green excitation were significantly higher than those under substrate-replete conditions. These results indicate that spheroidenone, which can absorb green light, may play an important role in their photosynthesis as a light-harvesting antenna pigment, and the photosynthetic competence of the Roseobacter strain can increase in an organic substrate-deficient environment.
  • Kaori Ono, Rie Oka, Masanori Toyofuku, Ayane Sakaguchi, Masakaze Hamad ...
    Type: Short Communication
    2014 Volume 29 Issue 1 Pages 104-106
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: February 19, 2014
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    Pseudomonas aeruginosa responds to environmental changes and regulates its life cycle from planktonic to biofilm modes of growth. The control of cell attachment to surfaces is one of the critical processes that determine this transition. Environmental signals are typically relayed to the cytoplasm by second messenger systems. We here demonstrated that the second messenger, cAMP, regulated the attachment of cells. Our results suggest cAMP inhibited the transition from reversible to irreversible attachment. Further analyses revealed that cell surface hydrophobicity, one of the key factors in cell attachment, was altered by cAMP.
  • Jing Li, Guangshan Wei, Ningxin Wang, Zheng Gao
    Type: Short Communication
    2014 Volume 29 Issue 1 Pages 107-110
    Published: 2014
    Released: April 02, 2014
    [Advance publication] Released: March 13, 2014
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    We investigated the diversity and community composition of denitrifying bacteria in surface water from the Yellow River estuary. Our results indicated that the diversity of the denitrifying community in freshwater based on the nirK gene was higher than that in seawater. Furthermore, phylogenetic analysis suggested that the bacteria community could be distributed into eight clusters (Clusters I to VIII). Redundancy analysis (RDA) revealed that community compositions were related to multiple environment factors, such as salinity and nitrate concentration. The results of the present study have provided a novel insight into the denitrifying community in water columns in estuaries.
Errata
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