scholarly journals Communities of T4-like bacteriophages associated with bacteria in Lake Baikal: diversity and biogeography

PeerJ ◽  
2022 ◽  
Vol 10 ◽  
pp. e12748
Author(s):  
Sergey Anatoljevich Potapov ◽  
Irina Vasilievna Tikhonova ◽  
Andrey Yurjevich Krasnopeev ◽  
Maria Yurjevna Suslova ◽  
Natalia Albertovna Zhuchenko ◽  
...  
Keyword(s):  
Lake Baikal ◽  
Water Samples ◽  
Lake Biwa ◽  
Amino Acid Level ◽  
Amplicon Sequencing ◽  
Lake Ecosystem ◽  
The Pacific ◽  
Close Relationship ◽  
T4 Bacteriophage ◽  
Marine Viruses

Lake Baikal phage communities are important for lake ecosystem functioning. Here we describe the diversity of T4-bacteriophage associated with the bacterial fraction of filtered water samples collected from the pelagic zone, coastal zone and shallow bays. Although the study of the diversity of phages for the g23 gene has been carried out at Lake Baikal for more than ten years, shallow bays that comprise a significant part of the lake’s area have been neglected, and this gene has not previously been studied in the bacterial fraction. Phage communities were probed using amplicon sequencing methods targeting the gene of major capsid protein (g23) and compared phylogenetically across sample locations and with sequences previously retrieved from non-bacterial fractions (<0.2 um) and biofilms (non-fractionated). In this study, we examined six water samples, in which 24 to 74 viral OTUs were obtained. The sequences from shallow bays largely differed from those in the pelagic and coastal samples and formed individual subcluster in the UPGMA tree that was obtained from the comparison of phylogenetic distances of g23 sequence sets from various ecosystems, reflecting differences in viral communities depending on the productivity of various sites of Lake Baikal. According to the RefSeq database, from 58.3 to 73% of sequences of each sample had cultivated closest relatives belonging to cyanophages. In this study, for phylogenetic analysis, we chose the closest relatives not only from the RefSeq and GenBank NR databases but also from two marine and one freshwater viromes: eutrophic Osaka Bay (Japan), oligotrophic area of the Pacific Ocean (Station ALOHA) and mesotrophic and ancient Lake Biwa (Japan), which allowed us to more fully compare the diversity of marine and freshwater phages. The identity with marine sequences at the amino acid level ranged from 35 to 80%, and with the sequences from the viral fraction and bacterial one from Lake Biwa—from 35.3 to 98% and from 33.9 to 89.1%, respectively. Therefore, the sequences from marine viromes had a greater difference than those from freshwater viromes, which may indicate a close relationship between freshwater viruses and differences from marine viruses.

scholarly journals Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics

2021 ◽  
Vol 9 (4) ◽  
pp. 760
Author(s):  
Tatyana V. Butina ◽  
Yurij S. Bukin ◽  
Ivan S. Petrushin ◽  
Alexey E. Tupikin ◽  
Marsel R. Kabilov ◽  
...  
Keyword(s):  
Lake Baikal ◽  
Biological Diversity ◽  
Anthropogenic Impacts ◽  
Lake Ecosystem ◽  
Published Data ◽  
Full Diversity ◽  
True Diversity ◽  
Viral Communities ◽  
Diversity Studies ◽  
Insight Into

Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake’s viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still unknown. The new metaviromic data will be useful for future studies of viral composition, distribution, and the dynamics associated with global climatic and anthropogenic impacts on this ecosystem.

scholarly journals Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing

2020 ◽  
Author(s):  
Kimothy L Smith ◽  
Howard A Shuman ◽  
Douglas Findeisen
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Water Samples ◽  
Ad Hoc ◽  
Microbial Community Composition ◽  
Amplicon Sequencing ◽  
The Other ◽  
Water Usage ◽  
16S Rrna Amplicon Sequencing ◽  
Oxford Nanopore

AbstractWe conducted two studies of water samples from buildings with normal occupancy and water usage compared to water from buildings that were unoccupied with little or no water usage due to the COVID-19 shutdown. Study 1 had 52 water samples obtained ad hoc from buildings in four metropolitan locations in different states in the US and a range of building types. Study 2 had 36 water samples obtained from two buildings in one metropolitan location with matched water sample types. One of the buildings had been continuously occupied, and the other substantially vacant for approximately 3 months. All water samples were analyzed using 16S rRNA amplicon sequencing with a MinION from Oxford Nanopore Technologies. More than 127 genera of bacteria were identified, including genera with members that are known to include more than 50 putative frank and opportunistic pathogens. While specific results varied among sample locations, 16S rRNA amplicon abundance and the diversity of bacteria were higher in water samples from unoccupied buildings than normally occupied buildings as was the abundance of sequenced amplicons of genera known to include pathogenic bacterial members. In both studies Legionella amplicon abundance was relatively small compared to the abundance of the other bacteria in the samples. Indeed, when present, the relative abundance of Legionella amplicons was lower in samples from unoccupied buildings. Legionella did not predominate in any of the water samples and were found, on average, in 9.6% of samples in Study 1 and 8.3% of samples in Study 2.SynopsisComparison of microbial community composition in the plumbing of occupied and unoccupied buildings during the COVID-19 pandemic shutdown.

scholarly journals Construction and Validation of Lake Biwa Basin Simulation Model with Integration of Three Components of Land, Lake Flow, and Lake Ecosystem

2011 ◽  
Vol 34 (9) ◽  
pp. 125-141 ◽  
Author(s):  
Yuichi SATO ◽  
Eiji KOMATSU ◽  
Hideaki NAGARE ◽  
Hiroshi UEHARA ◽  
Takashi YUASA ◽  
...  
Keyword(s):  
Simulation Model ◽  
Lake Biwa ◽  
Lake Ecosystem ◽  
Three Components

Limitations of the A-IM Method for Fecal Coliform Enumeration in the Pacific Oyster (Crassostrea gigas)

1987 ◽  
Vol 70 (3) ◽  
pp. 535-537
Author(s):  
Charles A Kaysner ◽  
Stephen D Weagant
Keyword(s):  
Escherichia Coli ◽  
Positive Reaction ◽  
Crassostrea Gigas ◽  
Water Samples ◽  
Fecal Coliform ◽  
Pacific Oyster ◽  
Food Products ◽  
Fecal Coliforms ◽  
Pacific Oysters ◽  
The Pacific

Abstract Use of the A-IM method, which was originally devised for testing water samples, has recently been extended for enumeration of fecal coliforms and Escherichia coli in shellfish and other food products. Results of our study indicate that while this method is reliable for analysis of growing waters, the use of the A-IM method for testing Pacific oysters may be less reliable because bacteria not belonging to the coliform group but which are sometimes present in these animals also give a positive reaction.

Characterization of Marine Temperate Phage-Host Systems Isolated from Mamala Bay, Oahu, Hawaii

1998 ◽  
Vol 64 (2) ◽  
pp. 535-542 ◽  
Author(s):  
Sunny C. Jiang ◽  
Christina A. Kellogg ◽  
John H. Paul
Keyword(s):  
Water Samples ◽  
Blot Hybridization ◽  
Temperate Phage ◽  
Dot Blot ◽  
Dot Blot Hybridization ◽  
Double Stranded Dna ◽  
The Family ◽  
Marine Viruses

ABSTRACT To understand the ecological and genetic role of viruses in the marine environment, it is critical to know the infectivity of viruses and the types of interactions that occur between marine viruses and their hosts. We isolated four marine phages from turbid plaques by using four indigenous bacterial hosts obtained from concentrated water samples from Mamala Bay, Oahu, Hawaii. Two of the rod-shaped bacterial hosts were identified as Sphingomonas paucimobilis andFlavobacterium sp. All of the phage isolates were tailed phages and contained double-stranded DNA. Two of the phage isolates had morphologies typical of the family Siphoviridae, while the other two belonged to the families Myoviridae andPodoviridae. The head diameters of these viruses ranged from 47 to 70.7 nm, and the tail lengths ranged from 12 to 146 nm. The burst sizes ranged from 7.8 to 240 phage/bacterial cell, and the genome sizes, as determined by restriction digestion, ranged from 36 to 112 kb. The members of the Siphoviridae, T-φHSIC, and T-φD0, and the member of the Myoviridae, T-φD1B, were found to form lysogenic associations with their bacterial hosts, which were isolated from the same water samples. Hybridization of phage T-φHSIC probe with lysogenic host genomic DNA was observed in dot blot hybridization experiments, indicating that prophage T-φHSIC was integrated within the host genome. These phage-host systems are available for use in studies of marine lysogeny and transduction.

Human Adenovirus Diversity in Water Samples Using a Next-Generation Amplicon Sequencing Approach

2015 ◽  
Vol 7 (2) ◽  
pp. 112-121 ◽  
Author(s):  
Leslie Ogorzaly ◽  
Cécile Walczak ◽  
Mélissa Galloux ◽  
Stéphanie Etienne ◽  
Benoît Gassilloud ◽  
...  
Keyword(s):  
Water Samples ◽  
Human Adenovirus ◽  
Amplicon Sequencing ◽  
Next Generation

scholarly journals Relationships between the occurrence of Giardia and Cryptosporidium and physicochemical properties of marine waters of the Pacific Coast of Mexico

2010 ◽  
Vol 8 (4) ◽  
pp. 797-802 ◽  
Author(s):  
Dalia Magana-Ordorica ◽  
Kristina Mena ◽  
Jose B. Valdez-Torres ◽  
Marcela Soto-Beltran ◽  
Josefina Leon-Felix ◽  
...  
Keyword(s):  
Water Samples ◽  
Physicochemical Parameters ◽  
Pacific Coast ◽  
Microbial Quality ◽  
Recreational Water ◽  
Regression Analyses ◽  
Recreational Waters ◽  
Untreated Sewage ◽  
The Pacific

Untreated sewage has adversely affected the quality of marine recreational waters worldwide. Exposure to marine recreational water with poor microbial quality may pose a threat to bathers. The objectives of this study were to assess the effect of physicochemical parameters on Cryptosporidium and Giardia presence in marine recreational water of Sinaloa, Mexico, by Logistic Regression Analyses. Thirty-two 10-litre water samples were collected from two tourist beaches, Altata and Mazatlan, between November 2006 and May 2007. Water samples were processed by the EPA 1623 method and pH, temperature, salinity and turbidity were also determined. Cryptosporidium and Giardia were present in 71 and 57% of the samples collected from Altata, respectively. In Mazatlan, Cryptosporidium and Giardia were found in 83 and 72% of the samples, respectively. The overall concentration of Cryptosporidium ranged from 150 to 2,050 oocysts/10 L with an average of 581 oocysts/10 L and Giardia ranged from 10 to 300 cysts/10 L with an average of 73 cysts/10 L. The occurrence of both parasites increased in water with decreasing temperatures and increasing turbidity of the water.

scholarly journals A Brief Review on the Researches of Cultural Relationship Between Indigenous Bai Yue in Southeast of China and Pacific Austronesian

2021 ◽  
pp. 209-219
Author(s):  
Chunming Wu
Keyword(s):  
Twentieth Century ◽  
Southeast Asia ◽  
Indigenous Peoples ◽  
South China ◽  
Pacific Islands ◽  
Southeast Coast ◽  
The Pacific ◽  
Close Relationship ◽  
History Of ◽  
The Relationship

AbstractAncient “Bai Yue” (百越) and “Austronesian” are indigenous peoples with very close relationship, distributing from south China, Southeast Asia, and the Pacific Islands. The relationship between Bai Yue and Proto-Austronesian has long been studied in both Chinese and Euro-American academies. During most of the twentieth century, Chinese historians and archaeologists mainly discussed the origins of Malay ethnics as one branch of Austronesian within the academic framework of the ethno-history of Bai Yue centering on the southeast coast of China, while western academic peers mainly based on the linguistic investigation of modern Austronesian and carried out multi-disciplines’ research on the origin of Proto-Austronesian.

scholarly journals The impact of bacterial diversity on resistance to biocides in oilfields

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gabriela Feix Pereira ◽  
Harry Luiz Pilz-Junior ◽  
Gertrudes Corção
Keyword(s):  
Water Samples ◽  
Produced Water ◽  
Functional Characterization ◽  
Amplicon Sequencing ◽  
Oil Field ◽  
Oil Fields ◽  
Sulfate Reducing ◽  
16S Rrna Amplicon Sequencing ◽  
Dimethyl Benzyl ◽  
The Impact

AbstractExtreme conditions and the availability of determinate substrates in oil fields promote the growth of a specific microbiome. Sulfate-reducing bacteria (SRB) and acid-producing bacteria (APB) are usually found in these places and can harm important processes due to increases in corrosion rates, biofouling and reservoir biosouring. Biocides such as glutaraldehyde, dibromo-nitrilopropionamide (DBNPA), tetrakis (hydroxymethyl) phosphonium sulfate (THPS) and alkyl dimethyl benzyl ammonium chloride (ADBAC) are commonly used in oil fields to mitigate uncontrolled microbial growth. The aim of this work was to evaluate the differences among microbiome compositions and their resistance to standard biocides in four different Brazilian produced water samples, two from a Southeast Brazil offshore oil field and two from different Northeast Brazil onshore oil fields. Microbiome evaluations were carried out through 16S rRNA amplicon sequencing. To evaluate the biocidal resistance, the Minimum Inhibitory Concentration (MIC) of the standard biocides were analyzed using enriched consortia of SRB and APB from the produced water samples. The data showed important differences in terms of taxonomy but similar functional characterization, indicating the high diversity of the microbiomes. The APB and SRB consortia demonstrated varying resistance levels against the biocides. These results will help to customize biocidal treatments in oil fields.

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