Freshwater Lake In Japan Research Articles

Draft Genome Sequence of Thermolongibacillus altinsuensis Strain B1-1, a Novel Hydrogenogenic CO Oxidizer Isolated from Sediment from Lake Biwa in Japan.

A facultative anaerobic, thermophilic, hydrogenogenic CO-oxidizing bacterial strain, B1-1, was isolated from a sediment sample from Lake Biwa, a freshwater lake in Japan. B1-1, which is a novel strain of Thermolongibacillus altinsuensis, is capable of hydrogenogenic CO oxidation. Here, we report the draft genome sequence of B1-1 (2.92 Mbp, with a GC content of 41.3%).

Whole-Genome Sequence of Sediminibacterium sp. Strain TEGAF015, Isolated from a Shallow Eutrophic Freshwater Lake in Japan.

The genus Sediminibacterium comprises bacteria representing the ubiquitous taxa of freshwater bacterioplankton. Here, we report the whole-genome sequence of Sediminibacterium sp. strain TEGAF015, isolated from a shallow eutrophic freshwater lake in Japan.

Temporal dynamics of Campylobacter and Arcobacter in a freshwater lake that receives fecal inputs from migratory geese

Migratory geese could influence the microbiological water quality; however, their impacts on pathogen dynamics remain largely unknown. In this study, we analyzed the population dynamics of Campylobacter and Arcobacter group bacteria (AGB) in a freshwater lake in Japan over two years. The bacteria were quantified by using both culture-dependent and -independent methods. The potential sources of these bacteria were examined by a high-throughput flaA sequencing approach. Campylobacter was abundantly detected both by culture-dependent and -independent methods in the lake, especially when migratory geese were present in the lake. High-throughput flaA sequencing suggests that geese were the likely source of Campylobacter in the lake. The viable population of Campylobacter exceeds the concentrations that can potentially cause 10−4 infections per person per year when water is used to grow fresh vegetables. The occurrence of AGB, on the other hand, was not directly related to the population of migratory geese. AGB were not detected in geese fecal samples. Diverse AGB flaA genotypes occurred in the lake over multiple seasons. Our results suggest that AGB likely comprise a part of the indigenous microbial population of the lake and grow in response to high nutrient, warm temperature, and low dissolved oxygen concentrations in the lake. Geese therefore can indirectly impact the AGB population by providing nutrients to cause eutrophication and lower the dissolved oxygen concentration. Since geese travel long-distance and disperse their fecal microbiota and nutrients to wide areas, they may have significant impacts on water quality and public health.

Seasonal Seismicity in the Lake Biwa Region of Central Japan Moderately Modulated by Lake Water Storage Changes

AbstractSeasonal seismicity in Japan has been observed and attributed to variations induced by hydrological loading, as well as atmospheric and pore‐fluid pressure. We examine the seasonal variations of crustal (<15 km depth) and low magnitude (M < 4.5) earthquakes in central Japan near the Biwako‐Seigan Fault Zone (BSFZ), and analyze their correlation with the annual hydrological cycle of nearby Lake Biwa, the largest freshwater lake in Japan. The 2002–2018 lake water storage is estimated using water‐level gauge and satellite altimetry data. Regional surface mass loading from soil moisture and snow predicted by the Global Land Data Assimilation System is used to augment the lake mass variation. We compute the stress and stressing‐rate changes induced by the surface mass loading from lake storage, snow, and soil moisture at seismogenic depth (10 km) along the BSFZ using a finite element model incorporating a 3D Earth structure. The results show that seasonal surface mass loading generates 1–5 kPa peak‐to‐peak Coulomb stress change and 2.5–15 kPa/year stressing‐rate variations on the fault segments along the BSFZ. Two of the four fault segments present significant correlation between local seismicity rate and loading‐derived stress and/or stressing rate changes. Among the hydrological load components, lake water, snow, and soil moisture exhibit different annual phases, and the lake water storage dominates the total annual stress changes. Our analysis indicates that seasonal surface hydrological loads, especially lake water variations, modulate the seismicity rate along the BSFZ in central Japan.

Detection of planktonic coenzyme factor 430 in a freshwater lake: small-scale analysis for probing archaeal methanogenesis

We present the first data describing molecular evidence of planktonic coenzyme factor 430 (hereafter referred to as F430), a key signature of methanogenic archaea, obtained from a water column sample in a freshwater lake in Japan. We report concentrations of native F430 ranging from 6.8–35 × 102 femto mol g-wet−1 and 8.5–86 × 102 femto mol g-wet−1 in the water column and core-top sediment, respectively. Among these profiles, the epimer F430 of the deactivated chemical formula was very low overall in both planktonic and benthic environments. Small subunit (SSU) rRNA gene sequencing revealed that the planktonic microbial community was clearly different from that of the benthic sediment. Planktonic cyanobacteria (e.g., Microcystis) were predominant in the water column, whereas a wide variety of bacteria and archaea, including methanogens (e.g., Methanobacterium, Methanoregula, Methanothrix, Methanosarcina, and Methanocella), were observed in the core-top sediment. These results suggest that the planktonic cyanobacterial community may be rapidly degraded at the water–sediment interface driven by activated benthic microbial heterotrophic processes.Graphic abstract

Trace metal geochemical and Zn stable isotope data as tracers for anthropogenic metal contributions in a sediment core from Lake Biwa, Japan

The catchment of Lake Biwa, the largest freshwater lake in Japan, has experienced rapid urbanization and industrialization in the second half of the 20th century; yet little is known about the historical trend of metal pollution. We analyzed the elemental concentrations and zinc stable isotope ratios (δ66Zn) in a sediment core from the Northern basin of the lake. The goals were 1) to reconstruct the historical trend of trace metals in the lake and 2) to understand whether the range of Zn concentrations was derived from natural or anthropogenic sources. The first increase in Cu and Zn concentrations from the late 1910s until approximately 1940 could be due to human-induced higher contributions from the surrounding mafic igneous rocks. A second increase in the Zn concentrations accompanied by a slight decrease in the δ66Zn values from the late 1950s coincided with the period of the industrialization and urbanization. The δ66Zn values fell in a binary mixing process between a lithogenic (∼+0.28‰) and an anthropogenic endmember (∼+0.14‰). Although industrial effluents were strictly regulated by law from the late 1960s, constant Zn concentrations throughout the 1980s indicated contributions from domestic wastewaters and diffusive sources such as runoff from paddy fields, roads, and industrial areas. Zinc, Ni, and Co were still enriched in recent surface sediment compared to the pre-industrial times. The metal fractions obtained by the BCR sequential extraction procedure showed that Pb was mainly hosted in the reducible fraction, and Cu and Zn were mainly hosted in the residual fraction. The increasing trace metal concentrations in the acid-labile and reducible fractions towards the surface indicate these fractions were the primary host for anthropogenic trace metals. We conclude it is unlikely that the natural condition of the lake sediment will be recovered owing to the continuing urbanization around Lake Biwa.

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

BackgroundFreshwater ecosystems are inhabited by members of cosmopolitan bacterioplankton lineages despite the disconnected nature of these habitats. The lineages are delineated based on > 97% 16S rRNA gene sequence similarity, but their intra-lineage microdiversity and phylogeography, which are key to understanding the eco-evolutional processes behind their ubiquity, remain unresolved. Here, we applied long-read amplicon sequencing targeting nearly full-length 16S rRNA genes and the adjacent ribosomal internal transcribed spacer sequences to reveal the intra-lineage diversities of pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe.ResultsOur single nucleotide-resolved analysis, which was validated using shotgun metagenomic sequencing, uncovered 7–101 amplicon sequence variants for each of the 11 predominant bacterial lineages and demonstrated sympatric, allopatric, and temporal microdiversities that could not be resolved through conventional approaches. Clusters of samples with similar intra-lineage population compositions were identified, which consistently supported genetic isolation between Japan and Europe. At a regional scale (up to hundreds of kilometers), dispersal between lakes was unlikely to be a limiting factor, and environmental factors or genetic drift were potential determinants of population composition. The extent of microdiversification varied among lineages, suggesting that highly diversified lineages (e.g., Iluma-A2 and acI-A1) achieve their ubiquity by containing a consortium of genotypes specific to each habitat, while less diversified lineages (e.g., CL500-11) may be ubiquitous due to a small number of widespread genotypes. The lowest extent of intra-lineage diversification was observed among the dominant hypolimnion-specific lineage (CL500-11), suggesting that their dispersal among lakes is not limited despite the hypolimnion being a more isolated habitat than the epilimnion.ConclusionsOur novel approach complemented the limited resolution of short-read amplicon sequencing and limited sensitivity of the metagenome assembly-based approach, and highlighted the complex ecological processes underlying the ubiquity of freshwater bacterioplankton lineages. To fully exploit the performance of the method, its relatively low read throughput is the major bottleneck to be overcome in the future.CdoWEXw9NgzJzSXXN2MHFrVideo abstract.

Aquipluma nitroreducens gen. nov. sp. nov., a novel facultatively anaerobic bacterium isolated from a freshwater lake.

A novel facultatively anaerobic, nitrate-reducing bacterium, designated MeG22T, was isolated from a freshwater lake in Japan. Cells of the strain were straight rods (0.8×2.5-10 µm), motile, and Gram-stain-negative. For growth, the optimum NaCl concentration was 0 % and the optimum temperature was 30 °C. Under anoxic conditions, strain MeG22T reduced nitrate to nitrite. Major cellular fatty acids were C15 : 1 ω6c (13.6 %), C17 : 0 (11.9 %), anteiso-C15 : 0 (10.6 %) and iso-C15 : 0 (10.6 %). The major respiratory quinone was menaquinone-7. The genome sequence of strain MeG22T consists of 5 712 279 bp with a G+C content of 40.3 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Prolixibacteraceae within the phylum Bacteroidetes. The closest relative of strain MeG22T was Sunxiuqinia faeciviva strain JAM-BA0302T with a 16S rRNA gene sequence similarity of 90.9 %. On the basis of phylogenetic and phenotypic characterization, Aquipluma nitroreducens, gen. nov., sp. nov., belonging to the family Prolixibacteraceae is proposed with the type strain MeG22T (=NBRC 112896T=DSM 106262T).

A protocol for the analysis of aquatic biodiversity by multiple β diversities

Species assemblage can be fairly unstable in aquatic ecosystems because of strong environmental constraints. Measuring β diversity is one of the most useful tools for assessing community dynamics and differentiations among communities. Whereas many β diversity measurements have been proposed for these issues, we present here a unifying framework based on the properties of Hill number, q, to unravel the complex changes occurring in dynamic communities. Using ideal numerical examples of an aquatic community, the sensitivity of β diversity with q = 0 ∼ 2 was examined. Whereas β diversity for q = 0 has a higher sensitivity to rare species drift (rapid exchanges or migration of many rare species) than do others, β diversity for q = 2 adequately responds to the variation or changes of dominant species. A scatterplot based on these two β diversity measures is proposed for the detailed examination of aquatic community dynamics. We show that the scatterplot is able to describe the monthly dynamics of dominant and rare species in the phytoplankton assemblage of a freshwater lake in Japan.

Environmental DNA reveals nonmigratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters

AbstractIn Lake Biwa, the largest freshwater lake in Japan, the lacustrine shrimp Palaemon paucidens has been reported to undertake seasonal migrations, living in deep waters from autumn to winter ...

NUMERICAL ASSESSMENT OF THE IMPACT OF STRONG WIND ON THERMAL STRATIFICATION IN LAKE BIWA, JAPAN

Water temperature near the surface of a lake increases with increasing air temperature, whichresults in stratification. The strength of stratification substantially influences the transport of dissolved oxygenfrom the surface to the bottom water of a lake. In recent years, the decrease in dissolved oxygen at the bottom ofthe northern part of the Lake Biwa, the largest freshwater lake in Japan, has been observed. The main cause ofthis is considered to be the change in stratification, which depends on weather and climate conditions. In thepresent study, numerical simulations were carried out to investigate the effect of strong wind on the structure ofstratification in Lake Biwa. The baseline simulation was conducted using actual meteorological data, andexperimental simulations were conducted using meteorological data with modified wind speed and direction.The numerical experiments showed that if the magnitude of the wind is strong enough, the stratificationcollapses and the wind can enhance the vertical mixing in the bottom layer even in the summer season withstrong thermal stratification. In a stratified season, when the strong wind blows predominantly in one direction,the rate of the vertical mixing changes by the wind direction. Moreover, as the duration of the strong windextends, vertical mixing easily occurs.

Evaluation of Thermal Stratification and Flow Field Reproduced by a Three-Dimensional Hydrodynamic Model in Lake Biwa, Japan

Water temperature near the surface of a lake increases with increasing air temperature, which results in stratification. The strength of stratification substantially influences the transport of water parcels from the surface to the bottom of a lake. In recent years, the stratification in Lake Biwa—the largest freshwater lake in Japan—has been stronger. However, it is difficult to reproduce the stratification well in the simulations. In the present study, we built a hydrodynamic model for the purpose of analyzing the structure of the stratification in detail. Using the model, we evaluated the reproducibility of the seasonal and annual changes of vertical water distribution and flow field in Lake Biwa from 2007 to 2011. The hydrodynamic model results show that the vertical water distribution approximately agrees with the field observations based on the statistical analysis. The seasonal change of thermal stratification is reasonably reproduced by the hydrodynamic model simulations. In the simulation, there are mainly two circulation flows at the surface layer of the lake. The first flows anticlockwise and the second flows clockwise in the northern part of Lake Biwa. In order to compensate for the surface water flow, the water under the thermocline sometimes flows in the opposite direction under each circulation flow.

Acidocella aquatica sp. nov., a novel acidophilic heterotrophic bacterium isolated from a freshwater lake.

A novel acidophilic heterotrophic bacterium, strain Ok2GT, was isolated from a freshwater lake in Japan. Cells of the isolate were Gram-stain-negative and non-motile rods (0.6-0.8×1.0-2.8 µm). Growth was observed at 4-35 °C with an optimum growth temperature of 28 °C. The pH range for growth was 3.0-6.2 with an optimum pH of 4.5. The strain utilized fructose, glucose, sucrose, mannitol, sorbitol, ethanol, benzyl alcohol, pyruvate, yeast extract and tryptone as carbon and energy sources for aerobic growth. DNA G+C content was 62.6 mol%. The major cellular fatty acid and the isoprenoid quinone were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and Q-10, respectively. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain Ok2GT belongs to the genus Acidocella but is distinct from existing species with sequence similarities lower than 97 %. On the basis of these results, strain Ok2GT (=NBRC 112502T=DSM 104037T) is proposed as the type strain of a novel species, Acidocellaaquatica sp. nov.

Sulfurirhabdus autotrophica gen. nov., sp. nov., isolated from a freshwater lake.

A novel sulfur-oxidizing bacterium, designated strain BiS0T, was isolated from a sediment sample collected from a freshwater lake in Japan. The cells were rod-shaped, 1.4-4.6 × 0.4-0.7 μm and Gram-stain-negative. The G+C content of the genomic DNA was around 44 mol%. The isolate possessed summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C10 : 0 3-OH as major cellular fatty acids. Strain BiS0T grew by carbon dioxide fixation and oxidation of inorganic sulfur compounds with oxygen as the electron acceptor. Growth was observed over a temperature range of 0-32 °C (optimum, 15-22 °C), an NaCl concentration range of 0-546.4 mM (optimum 0-66.7 mM) and a pH range of 5.2-8.1 (optimum 6.1-6.3). Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain BiS0T belongs to the family Sulfuricellaceae in the class Betaproteobacteria. The closest cultured relatives were Sulfuricella denitrificans skB26T and Sulfuricella sp. T08, with 16S rRNA gene sequence similarities of 96.3 %. On the basis of the data obtained in this study, strain BiS0T represents a novel species of a novel genus, for which the name Sulfurirhabdus autotrophica gen. nov., sp. nov. is proposed. The type strain is BiS0T ( = NBRC 110941T = DSM 100309T).

Draft Genome Sequence of a Sulfur-Oxidizing Autotroph, Sulfuricella sp. Strain T08, Isolated from a Freshwater Lake.

Sulfuricella sp. strain T08 is a sulfur-oxidizing autotroph newly isolated from a freshwater lake in Japan. Strain T08 is the second isolate of the genus Sulfuricella. Here, we report the annotated draft genome sequence of the isolate.

Sulfuriferula multivorans gen. nov., sp. nov., isolated from a freshwater lake, reclassification of ‘Thiobacillus plumbophilus’ as Sulfuriferula plumbophilus sp. nov., and description of Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.

A sulfur-oxidizing bacterium, strain TTN(T), was isolated from a Thioploca sample obtained from a freshwater lake in Japan. The isolate shared 97.1% 16S rRNA gene sequence similarity with an obligately aerobic chemolithoautotroph, 'Thiobacillus plumbophilus' Gro7(T). Cells were rods, motile, and Gram-stain-negative. The G+C content of the genomic DNA was approximately 66 mol%. Strain TTN(T) grew over a temperature range of 8-32 °C (optimum 22-25 °C), an NaCl concentration range of 0-133.3 mM (optimum 0-3.3 mM) and a pH range of 5.3-8.6 (optimum pH 6.4-7.0). Strain TTN(T) was facultatively anaerobic and could utilize nitrate as an electron acceptor. The isolate oxidized tetrathionate, thiosulfate and elemental sulfur as the sole energy sources for autotrophic growth, and could also grow heterotrophically on a number of organic substrates. Based on its phylogenetic and phenotypic properties, strain TTN(T) represents a novel species of a novel genus, for which the name Sulfuriferula multivorans gen. nov., sp. nov. is proposed. The type strain is TTN(T) ( =NBRC 110683(T) =DSM 29343(T)). Along with this, the reclassification of 'Thiobacillus plumbophilus' as Sulfuriferula plumbophilus sp. nov. (type strain Gro7(T) =NBRC 107929(T) =DSM 6690(T)) is proposed. Based on the data obtained in this study, we describe the designations Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.

Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence.

Large sulfur-oxidizing bacteria, which accumulate a high concentration of nitrate, are important constituents of aquatic sediment ecosystems. No representative of this group has been isolated in pure culture, and only fragmented draft genome sequences are available for these microorganisms. In this study, we successfully reconstituted the genome of Thioploca ingrica from metagenomic sequences, thereby generating the first complete genome sequence from this group. The Thioploca samples for the metagenomic analysis were obtained from a freshwater lake in Japan. A PCR-free paired-end library was constructed from the DNA extracted from the samples and was sequenced on the Illumina MiSeq platform. By closing gaps within and between the scaffolds, we obtained a circular chromosome and a plasmid-like element. The reconstituted chromosome was 4.8 Mbp in length with a 41.2% GC content. A sulfur oxidation pathway identical to that suggested for the closest relatives of Thioploca was deduced from the reconstituted genome. A full set of genes required for respiratory nitrate reduction to dinitrogen gas was also identified. We further performed a proteomic analysis of the Thioploca sample and detected many enzymes/proteins involved in sulfur oxidation, nitrate respiration and inorganic carbon fixation as major components of the protein extracts from the sample, suggesting that these metabolic activities are strongly associated with the physiology of T. ingrica in lake sediment.

Mizugakiibacter sediminis gen. nov., sp. nov., isolated from a freshwater lake.

A novel, moderately thermophilic, bacterial strain (skMP5(T)) was isolated from sediment of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-stain-negative. Growth was observed at temperatures ranging from 25 to 52 °C, with optimum growth observed at 48-50 °C. The pH range for growth was pH 5.0-8.2, with optimum growth at pH 6.0-7.0. The G+C content of genomic DNA was 72 mol%. The major components in the fatty acid profile were iso-C17 : 0 and iso-C17 : 1ω9c. The predominant isoprenoid quinone of the strain was ubiquinone Q-8. The strain was facultatively anaerobic, and reduced nitrate to nitrite under anoxic conditions. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was a member of the family Xanthomonadaceae within the class Gammaproteobacteria, showing highest sequence similarity with Tahibacter aquaticus RaM5-2 (93.6 %) and Metallibacterium scheffleri DKE6(T) (93.3 %). On the basis of phylogenetic and phenotypic properties, strain skMP5(T) represents a novel species of a new genus, Mizugakiibacter sediminis gen. nov., sp. nov. The type strain of the type species is skMP5(T) ( = DSM 27098(T) = NBRC 109608(T)).

Proposal of Effusibacillus lacus gen. nov., sp. nov., and reclassification of Alicyclobacillus pohliae as Effusibacillus pohliae comb. nov. and Alicyclobacillus consociatus as Effusibacillus consociatus comb. nov.

A novel thermophilic, facultatively anaerobic bacterium, strain skLN1(T), was isolated from the sediment of a freshwater lake in Japan. Cells of strain skLN1(T) were rod-shaped and Gram-stain-variable. A KOH lysis test suggested that the cell wall of the isolate has a Gram-positive structure. For aerobic growth, the optimum pH was pH 7.25-7.50 and the optimum temperature was 50-52 °C. The G+C content of the genomic DNA was 50.8 mol%. Nitrate was reduced to nitrite. Alicyclic fatty acids were not detected, and branched-chain fatty acids were major components in the cellular fatty acid profile. MK-7 was the predominant respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolated strain was related most closely to Alicyclobacillus consociatus CCUG 53762(T) (95% similarity). This analysis also showed that the monophyly of the genus Alicyclobacillus had been lost. On the basis of phylogenetic and phenotypic characterization, Effusibacillus lacus gen. nov., sp. nov. is proposed. The type strain of Effusibacillus lacus is skLN1(T) ( = NBRC 109614(T) = DSM 27172(T)). It is also proposed that Alicyclobacillus pohliae and Alicyclobacillus consociatus should be reclassified to the genus Effusibacillus as Effusibacillus pohliae comb. nov. and Effusibacillus consociatus comb. nov., respectively.

Sulfurisoma sediminicola gen. nov., sp. nov., a facultative autotroph isolated from a freshwater lake

A novel facultatively autotrophic bacterium, strain BSN1T was isolated from sediment of a freshwater lake in Japan. The cells were rod-shaped, motile and Gram-stain-negative. As sole energy sources for autotrophic growth, the strain oxidized thiosulfate, elemental sulfur and hydrogen. Strain BSN1T was a facultative anaerobe utilizing nitrate as an electron acceptor. Growth was observed at temperatures lower than 34 °C, and the optimum growth was observed at 30-32 °C. The range of pH for growth was pH 6.8-8.8, and the optimum pH was pH 7.8-8.1. The optimum growth of the isolate occurred at concentrations of NaCl less than 50 mM. The G+C content of genomic DNA was 67 mol%. The major component in the fatty acid profile of strain BSN1T grown on fumarate was summed feature 3 (C16:1ω7c and/or iso-C15:0 2-OH). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was a member of the class Betaproteobacteria, and it showed the highest sequence similarity with Georgfuchsia toluolica G5G6T (96.2%). Phylogenetic analyses were also performed on genes involved in sulfur oxidation. On the basis of its phylogenetic and phenotypic properties, strain BSN1T (=DSM 26916T=NBRC 109412T) is proposed as the type strain of a novel species of a novel genus, Sulfurisoma sediminicola gen. nov., sp. nov.