Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland

Viruses are the most abundant and ubiquitous biological entities in various ecosystems, yet few investigations of viral communities in wetlands have been performed. To address this data gap, water samples from 6 wetlands were randomly collected across northeast China; viruses in the water were concentrated by sequential tangential flow filtration, and viral communities were assessed through randomly amplified polymorphic DNA-PCR (RAPD-PCR) with 4 decamer oligonucleotide primers. Principal coordinate analysis and hierarchical clustering analysis of the DNA fingerprints showed that viral community compositions differed among the water samples: communities in the 2 coastal wetlands were more similar to each other than to those in the 4 freshwater wetlands. The Shannon-Weaver index (H) and evenness index (E) of the RAPD-PCR fingerprint also differed among the 6 wetlands. Mantel test revealed that the changes in viral communities in wetland water were most closely related to the water NH4+-N and inorganic C content, followed by total K, P, C and NO3--N. DNA sequence analysis of the excised bands revealed that viruses accounted for ~40% of all sequences. Among the hit viral homologs, the majority belonged to the Microviridae. Moreover, variance partitioning analysis showed that the viral community contributed 24.58% while environmental factors explained 30.56% of the bacterial community variation, indicating that the bacterial community composition was strongly affected by both viral community and water variables. This work provides an initial outline of the viral communities from different types of wetlands in northeast China and improves our understanding of the viral diversity in these ecosystems.

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

Aquatic Microbial Ecology ◽

10.3354/ame01949 ◽

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.

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Faculty Opinions recommendation of High diversity of the viral community from an Antarctic lake.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1168159.630295 ◽

2009 ◽

Author(s):

Jose Valpuesta

Keyword(s):

Antarctic Lake ◽

Viral Community ◽

High Diversity

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The Eastern Scheldt Project

Water Science & Technology ◽

10.2166/wst.1984.0044 ◽

1984 ◽

Vol 16 (1-2) ◽

pp. 51-77 ◽

Cited By ~ 34

Author(s):

M Knoester ◽

J Visser ◽

B A Bannink ◽

C J Colijn ◽

W P A Broeders

Keyword(s):

Local Government ◽

Adverse Effects ◽

Policy Analysis ◽

Storm Surge ◽

Freshwater Lake ◽

Tidal Basin ◽

Decisionmaking Process ◽

Analysis Methods ◽

Civil Engineers

In the planning of the Delta-works, carried out in the Southwestern Netherlands, the Eastern Scheldt was the largest and therefore last tidal basin to be fully closed mainly to protect the area from floods. Increased recognition for the natural value of estuaries and a strong lobby from nature conservationists and shellfish producers led to a reconsideration of original plans, confirmed by a series of governmental decisions. Per consequence execution of the present plans will result in a storm-surge barrier at the entrance of the tidal basin together with two partitioning dams, separating the (reduced) tidal Eastern Scheldt from a new freshwater lake. Attention is paid to the present values in the Eastern Scheldt and briefly to changes involved by the project. The decisionmaking process is described and discussed: In the course of the project the majority of decisions taken were prepared by teams of ecologists, civil engineers, hydrologists and financial experts using policy-analysis methods. For guidance of developments in the influenced area the local government accepted a policy plan, in which human uses are regulated. Operations of the barrier are designed such that safety from flooding is guaranteed, while adverse effects for the tidal ecosystems are minimized.

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Studies of turbulence in the surface layer over water (Lough Neagh). Part II. Production and dissipation of velocity and temperature fluctuations

Quarterly Journal of the Royal Meteorological Society ◽

10.1002/qj.49709841712 ◽

1972 ◽

Vol 98 (417) ◽

pp. 642-657 ◽

Cited By ~ 34

Author(s):

J. R. Garratt

Keyword(s):

Surface Layer ◽

Temperature Fluctuations ◽

Lough Neagh

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Pelorhabdus rhamnosifermentans gen. nov., sp. nov.,a strictly anaerobic rhamnose degrader from freshwater lake sediment

Systematic and Applied Microbiology ◽

10.1016/j.syapm.2021.126225 ◽

2021 ◽

pp. 126225

Author(s):

Fabian Gräßle ◽

Caroline Plugge ◽

Paolo Franchini ◽

Bernhard Schink ◽

David Schleheck ◽

...

Keyword(s):

Lake Sediment ◽

Freshwater Lake ◽

Strictly Anaerobic

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Fecal Viral Community Responses to High-Fat Diet in Mice

mSphere ◽

10.1128/msphere.00833-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 2

Author(s):

Anjelique Schulfer ◽

Tasha M. Santiago-Rodriguez ◽

Melissa Ly ◽

Joshua M. Borin ◽

Jessica Chopyk ◽

...

Keyword(s):

Bacterial Communities ◽

High Fat Diet ◽

Alpha Diversity ◽

Diet Shift ◽

Significant Shift ◽

Diet Change ◽

Gi Tract ◽

High Fat ◽

Viral Community ◽

Viral Communities

ABSTRACT Alterations in diet can have significant impact on the host, with high-fat diet (HFD) leading to obesity, diabetes, and inflammation of the gut. Although membership and abundances in gut bacterial communities are strongly influenced by diet, substantially less is known about how viral communities respond to dietary changes. Examining fecal contents of mice as the mice were transitioned from normal chow to HFD, we found significant changes in the relative abundances and the diversity in the gut of bacteria and their viruses. Alpha diversity of the bacterial community was significantly diminished in response to the diet change but did not change significantly in the viral community. However, the diet shift significantly impacted the beta diversity in both the bacterial and viral communities. There was a significant shift away from the relatively abundant Siphoviridae accompanied by increases in bacteriophages from the Microviridae family. The proportion of identified bacteriophage structural genes significantly decreased after the transition to HFD, with a conserved loss of integrase genes in all four experimental groups. In total, this study provides evidence for substantial changes in the intestinal virome disproportionate to bacterial changes, and with alterations in putative viral lifestyles related to chromosomal integration as a result of shift to HFD. IMPORTANCE Prior studies have shown that high-fat diet (HFD) can have profound effects on the gastrointestinal (GI) tract microbiome and also demonstrate that bacteria in the GI tract can affect metabolism and lean/obese phenotypes. We investigated whether the composition of viral communities that also inhabit the GI tract are affected by shifts from normal to HFD. We found significant and reproducible shifts in the content of GI tract viromes after the transition to HFD. The differences observed in virome community membership and their associated gene content suggest that these altered viral communities are populated by viruses that are more virulent toward their host bacteria. Because HFD also are associated with significant shifts in GI tract bacterial communities, we believe that the shifts in the viral community may serve to drive the changes that occur in associated bacterial communities.

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