Distribution of putative denitrifying methane oxidizing bacteria in sediment of a freshwater lake, Lake Biwa

2012 ◽  
Vol 35 (4) ◽  
pp. 233-238 ◽  
Author(s):  
Hisaya Kojima ◽  
Masazumi Tsutsumi ◽  
Kanako Ishikawa ◽  
Tomoya Iwata ◽  
Marc Mußmann ◽  
...  
Keyword(s):  
Lake Biwa ◽  
Freshwater Lake ◽  
Methane Oxidizing Bacteria

Contribution of large bacteria to bacterial biomass in a deep freshwater lake (Lake Biwa, Japan)

2020 ◽  
Vol 85 ◽  
pp. 131-139
Author(s):  
S Shen ◽  
Y Shimizu
Keyword(s):  
Cell Volume ◽  
Bacterial Cell ◽  
Lake Biwa ◽  
Bacterial Biomass ◽  
Spatial Variations ◽  
Freshwater Lake ◽  
Heterotrophic Nanoflagellates ◽  
Bacterial Productivity ◽  
Transmission Electron ◽  
Seasonal And Spatial Variations

Despite the importance of bacterial cell volume in microbial ecology in aquatic environments, literature regarding the effects of seasonal and spatial variations on bacterial cell volume remains scarce. We used transmission electron microscopy to examine seasonal and spatial variations in bacterial cell size for 18 mo in 2 layers (epilimnion 0.5 m and hypolimnion 60 m) of Lake Biwa, Japan, a large and deep freshwater lake. During the stratified period, we found that the bacterial cell volume in the hypolimnion ranged from 0.017 to 0.12 µm3 (median), whereas that in the epilimnion was less variable (0.016 to 0.033 µm3, median) and much lower than that in the hypolimnion. Additionally, in the hypolimnion, cell volume during the stratified period was greater than that during the mixing period (up to 5.7-fold). These differences in cell volume resulted in comparable bacterial biomass in the hypolimnion and epilimnion, despite the fact that there was lower bacterial abundance in the hypolimnion than in the epilimnion. We also found that the biomass of larger bacteria, which are not likely to be grazed by heterotrophic nanoflagellates, increased in the hypolimnion during the stratified period. Our data suggest that estimation of carbon flux (e.g. bacterial productivity) needs to be interpreted cautiously when cell volume is used as a constant parametric value. In deep freshwater lakes, a difference in cell volume with seasonal and spatial variation may largely affect estimations.

scholarly journals Draft Genome Sequences of Tersicoccus phoenicis DSM 30849T, Isolated from a Cleanroom for Spacecraft Assembly, and Tersicoccus sp. Strain Bi-70, Isolated from a Freshwater Lake

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Yu Nakajima ◽  
Susumu Yoshizawa ◽  
Keiji Nakamura ◽  
Yoshitoshi Ogura ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
Lake Biwa ◽  
Draft Genome ◽  
Freshwater Lake ◽  
Genome Sequences ◽  
Content Type ◽  
Spacecraft Assembly

ABSTRACT Here, we report the draft genome sequences of Tersicoccus phoenicis DSM 30849T, isolated from a spacecraft assembly cleanroom at the National Aeronautics and Space Administration (NASA), and Tersicoccus sp. strain Bi-70, isolated from Lake Biwa, the largest lake in Japan. These genome sequences facilitate our understanding of the adaptation of these closely related strains to different habitats.

scholarly journals nifH Sequences and Nitrogen Fixation in Type I and Type II Methanotrophs

2001 ◽  
Vol 67 (9) ◽  
pp. 4009-4016 ◽  
Author(s):  
Ann J. Auman ◽  
Catherine C. Speake ◽  
Mary E. Lidstrom
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogenase Activity ◽  
Freshwater Lake ◽  
Type I ◽  
Type Ii ◽  
Nitrogen Fixing ◽  
Protein Sequence Analysis ◽  
High Identity ◽  
Rice Roots ◽  
Methane Oxidizing Bacteria

ABSTRACT Some methane-oxidizing bacteria (methanotrophs) are known to be capable of expressing nitrogenase and utilizing N2 as a nitrogen source. However, no sequences are available fornif genes in these strains, and the known nitrogen-fixing methanotrophs are confined mainly to a few genera. The purpose of this work was to assess the nitrogen-fixing capabilities of a variety of methanotroph strains. nifH gene fragments from four type I methanotrophs and seven type II methanotrophs were PCR amplified and sequenced. Nitrogenase activity was confirmed in selected type I and type II strains by acetylene reduction. Activities ranged from 0.4 to 3.3 nmol/min/mg of protein. Sequence analysis shows that thenifH sequences from the type I and type II strains cluster with nifH sequences from other gamma proteobacteria and alpha proteobacteria, respectively. The translatednifH sequences from three Methylomonas strains show high identity (95 to 99%) to several published translated environmental nifH sequences PCR amplified from rice roots and a freshwater lake. The translated nifHsequences from the type II strains show high identity (94 to 99%) to published translated nifH sequences from a variety of environments, including rice roots, a freshwater lake, an oligotrophic ocean, and forest soil. These results provide evidence for nitrogen fixation in a broad range of methanotrophs and suggest that nitrogen-fixing methanotrophs may be widespread and important in the nitrogen cycling of many environments.

scholarly journals Genome-resolved viral and cellular metagenomes revealed potential key virus-host interactions in a deep freshwater lake

2019 ◽  
Author(s):  
Yusuke Okazaki ◽  
Yosuke Nishimura ◽  
Takashi Yoshida ◽  
Hiroyuki Ogata ◽  
Shin-ichi Nakano
Keyword(s):  
Surface Waters ◽  
Lake Biwa ◽  
Freshwater Lake ◽  
Read Coverage ◽  
Freshwater Systems ◽  
Viral Genomes ◽  
Viral Propagation ◽  
Host Interactions ◽  
Vertical Partitioning ◽  
Assimilatory Sulfate Reduction

SummaryMetagenomics has dramatically expanded the known virosphere, but freshwater viral diversity and their ecological interaction with hosts remain poorly understood. Here, we conducted a metagenomic exploration of planktonic dsDNA prokaryotic viruses by sequencing both virion (<0.22 μm) and cellular (0.22–5.0 μm) fractions collected spatiotemporally from a deep freshwater lake (Lake Biwa, Japan). This simultaneously reconstructed 183 complete (i.e., circular) viral genomes and 57 bacterioplankton metagenome-assembled genomes. Analysis of metagenomic read coverage revealed vertical partitioning of the viral community analogous to the vertically stratified bacterioplankton community. The hypolimnetic community was generally stable during stratification, but occasionally shifted abruptly, presumably due to lysogenic induction. Genes involved in assimilatory sulfate reduction were encoded in 20 (10.9%) viral genomes, including those of dominant viruses, and may aid viral propagation in sulfur-limited freshwater systems. Hosts were predicted for 40 (21.9%) viral genomes, encompassing 10 phyla (or classes of Proteobacteria) including ubiquitous freshwater bacterioplankton lineages (e.g., Ca. Fonsibacter and Ca. Nitrosoarchaeum). Comparison with viral genomes derived from published metagenomes revealed viral phylogeographic connectivity in geographically isolated habitats. Notably, analogous to their hosts, actinobacterial viruses were among the most diverse, ubiquitous, and abundant viral groups in freshwater systems, with potential high lytic activity in surface waters.

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