scholarly journals Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0257862
Author(s):  
Kaoru Matsumoto ◽  
Tomoko Sakami ◽  
Tsuyoshi Watanabe ◽  
Yukiko Taniuchi ◽  
Akira Kuwata ◽  
...  
Keyword(s):  
Phytoplankton Bloom ◽  
Taxonomic Composition ◽  
Future Research ◽  
Prokaryotic Community ◽  
Spring Phytoplankton Bloom ◽  
Community Function ◽  
Bloom Period ◽  
Fundamental Information ◽  
Marine Microbial Communities ◽  
Functional Profiles

The taxonomic compositions of marine prokaryotic communities are known to follow seasonal cycles, but functional metagenomic insights into this seasonality is still limited. We analyzed a total of 22 metagenomes collected at 11 time points over a 14-month period from two sites in Sendai Bay, Japan to obtain seasonal snapshots of predicted functional profiles of the non-cyanobacterial prokaryotic community. Along with taxonomic composition, functional gene composition varied seasonally and was related to chlorophyll a concentration, water temperature, and salinity. Spring phytoplankton bloom stimulated increased abundances of putative genes that encode enzymes in amino acid metabolism pathways. Several groups of functional genes, including those related to signal transduction and cellular communication, increased in abundance during the mid- to post-bloom period, which seemed to be associated with a particle-attached lifestyle. Alternatively, genes in carbon metabolism pathways were generally more abundant in the low chlorophyll a period than the bloom period. These results indicate that changes in trophic condition associated with seasonal phytoplankton succession altered the community function of prokaryotes. Our findings on seasonal changes of predicted function provide fundamental information for future research on the mechanisms that shape marine microbial communities.

scholarly journals A newly observed physical cause of the onset of the subsurface spring phytoplankton bloom in the southwestern East Sea/Sea of Japan

2014 ◽  
Vol 11 (5) ◽  
pp. 1319-1329 ◽  
Author(s):  
Y.-T. Son ◽  
K.-I. Chang ◽  
S.-T. Yoon ◽  
T. Rho ◽  
J. H. Kwak ◽  
...  
Keyword(s):  
Sea Of Japan ◽  
Mixed Layer ◽  
Spring Bloom ◽  
Phytoplankton Bloom ◽  
Mixed Layer Depth ◽  
East Sea ◽  
Ulleung Basin ◽  
Intermediate Water ◽  
Spring Phytoplankton Bloom ◽  
Bloom Period

Abstract. An ocean buoy, UBIM (Ulleung Basin Integrated Mooring), deployed during the spring transition from February to May 2010 reveals for the first time highly resolved temporal variation of biochemical properties of the upper layer of the Ulleung Basin in the southwestern East Sea/Sea of Japan. The time-series measurement captured the onset of subsurface spring bloom at 30 m, and collocated temperature and current data gives an insight into a mechanism that triggers the onset of the spring bloom not documented so far. Low-frequency modulation of the mixed layer depth ranging from 10 m to 53 m during the entire mooring period is mainly determined by shoaling and deepening of isothermal depths depending on the placement of UBIM on the cold or warm side of the frontal jet. The occurrence of the spring bloom at 30 m is concomitant with the appearance of colder East Sea Intermediate Water at buoy UBIM, which results in subsurface cooling and shoaling of isotherms to the shallower depth levels during the bloom period than those that occurred during the pre-bloom period. Isolines of temperature-based NO3 are also shown to be uplifted during the bloom period. It is suggested that the springtime spreading of the East Sea Intermediate Water is one of the important factors that triggers the subsurface spring bloom below the mixed layer.

scholarly journals Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the Northern North Atlantic

2019 ◽  
Vol 366 (13) ◽  
Author(s):  
Ciara Willis ◽  
Dhwani Desai ◽  
Julie LaRoche
Keyword(s):  
Community Composition ◽  
Phytoplankton Bloom ◽  
Variable Region ◽  
Marine Microbes ◽  
Taxonomic Assignment ◽  
Spring Phytoplankton Bloom ◽  
Variable Regions ◽  
Region Selection ◽  
Marine Microbial Communities ◽  
Rna Genes

ABSTRACT Marine microbes play essential roles in global energy and nutrient cycles. A primary method of determining their diversity and distribution is through sequencing of 16S ribosomal RNA genes from environmental samples. However, the perceived community composition may vary significantly based on differences in methodology, including choice of 16S variable region(s). This study investigated the influence of 16S variable region selection (V4-V5 or V6-V8) on perceived community composition and diversity for bacteria, Archaea and chloroplasts by tag-Illumina sequencing. We used 24 samples from the photic zone of the Scotian Shelf, northwest Atlantic, collected during a spring phytoplankton bloom. Taxonomic assignment and community composition varied greatly depending on the choice of variable regions while observed patterns of beta diversity were reproducible between variable regions. V4-V5 was considered the preferred variable region for future studies based on its superior recognition of Archaea, which has received little attention in bloom dynamics. The V6-V8 region captured more of the bacterial diversity, including the abundant SAR11 clades and, to a lesser extent, that of chloroplasts. However, the magnitude of difference between variable regions for bacteria and chloroplast was less than for Archaea.

scholarly journals On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shan Sun ◽  
Xiangzhu Zhu ◽  
Xiang Huang ◽  
Harvey J. Murff ◽  
Reid M. Ness ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Rectal Swab ◽  
Taxonomic Composition ◽  
Mucosal Tissue ◽  
Tissue Samples ◽  
Health And Disease ◽  
Inflammatory Drugs ◽  
Metagenome Sequencing ◽  
Functional Profiles

AbstractThe gut microbiota plays an important role in human health and disease. Stool, rectal swab and rectal mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. In this study, we report differences in stool, rectal swab and rectal mucosal tissue microbial communities with shotgun metagenome sequencing of 1397 stool, swab and mucosal tissue samples from 240 participants. The taxonomic composition of stool and swab samples was distinct, but less different to each other than mucosal tissue samples. Functional profile differences between stool and swab samples are smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or rectal swab gave broadly significantly correlated results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for determination of how inference can change for taxa and pathways depending on the choice of where to sample within the human gut.

Gametogenesis and the reproductive cycle in the deep-sea anemone Paracalliactis stephensoni (Cnidaria: Actiniaria)

1990 ◽  
Vol 70 (1) ◽  
pp. 163-172 ◽  
Author(s):  
Michel Praet-Van
Keyword(s):  
Organic Matter ◽  
Shallow Water ◽  
Deep Sea ◽  
Phytoplankton Bloom ◽  
Sea Anemone ◽  
Bay Of Biscay ◽  
Sea Anemones ◽  
Spring Phytoplankton Bloom ◽  
Sea Floor ◽  
Ultrastructural Investigation

This ultrastructural investigation of gametogenesis in a deep-sea anemone of the Bay of Biscay trawled around 2000 m depth, contributes to the knowledge of biology and strategy of reproduction of deep-sea benthos.This sea anemone is dioecious. The sperm appears very similar to those of shallow water sea anemones of the genus, Calliactis. The ultrastructural investigation of oogenesis allows the characteristics of the stages of previtellogenesis and vitellogenesis to be defined. The latter begins with a period of lipogenesis correlated with the formation of a trophonema. Mature oocytes measure up to 180 (im in diameter. Study of spermatogenesis and oogenesis reveals that spawning occurs in April/May. In males, the main area of testicular cysts, full of sperm, reaches maximal development from March to May and, in females, the percentage of mature oocytes decreases from 33% in April to 1% in May.Spawning may be induced by the advent in the deep-sea of the products of the spring phytoplankton bloom. This period of spawning, during the increased deposition of organic matter to the deep-sea floor, may be an advantageous strategy for early development of Paracalliactis.

scholarly journals Seasonal changes in the D  /  H ratio of fatty acids of pelagic microorganisms in the coastal North Sea

2016 ◽  
Vol 13 (19) ◽  
pp. 5527-5539 ◽  
Author(s):  
Sandra Mariam Heinzelmann ◽  
Nicole Jane Bale ◽  
Laura Villanueva ◽  
Danielle Sinke-Schoen ◽  
Catharina Johanna Maria Philippart ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Isotopic Composition ◽  
North Sea ◽  
Phytoplankton Bloom ◽  
Isotopic Fractionation ◽  
Spring Phytoplankton Bloom ◽  
Fractionation Factor ◽  
Culture Studies ◽  
Hydrogen Isotopic Composition

Abstract. Culture studies of microorganisms have shown that the hydrogen isotopic composition of fatty acids depends on their metabolism, but there are only few environmental studies available to confirm this observation. Here we studied the seasonal variability of the deuterium-to-hydrogen (D / H) ratio of fatty acids in the coastal Dutch North Sea and compared this with the diversity of the phyto- and bacterioplankton. Over the year, the stable hydrogen isotopic fractionation factor ε between fatty acids and water (εlipid/water) ranged between −172 and −237 ‰, the algal-derived polyunsaturated fatty acid nC20:5 generally being the most D-depleted (−177 to −235 ‰) and nC18:0 the least D-depleted fatty acid (−172 to −210 ‰). The in general highly D-depleted nC20:5 is in agreement with culture studies, which indicates that photoautotrophic microorganisms produce fatty acids which are significantly depleted in D relative to water. The εlipid/water of all fatty acids showed a transient shift towards increased fractionation during the spring phytoplankton bloom, indicated by increasing chlorophyll a concentrations and relative abundance of the nC20:5 polyunsaturated fatty acids, suggesting increased contributions of photoautotrophy. Time periods with decreased fractionation (less negative εlipid/water values) can potentially be explained by an increased contribution of heterotrophy to the fatty acid pool. Our results show that the hydrogen isotopic composition of fatty acids is a promising tool to assess the community metabolism of coastal plankton potentially in combination with the isotopic analysis of more specific biomarker lipids.

scholarly journals Iron stable isotopes track pelagic iron cycling during a subtropical phytoplankton bloom

2014 ◽  
Vol 112 (1) ◽  
pp. E15-E20 ◽  
Author(s):  
Michael J. Ellwood ◽  
David A. Hutchins ◽  
Maeve C. Lohan ◽  
Angela Milne ◽  
Philipp Nasemann ◽  
...  
Keyword(s):  
Stable Isotopes ◽  
Mixed Layer ◽  
Phytoplankton Bloom ◽  
Iron Bioavailability ◽  
Global Ocean ◽  
Minor Role ◽  
Surface Mixed Layer ◽  
Spring Phytoplankton Bloom ◽  
Dissolved Iron ◽  
Particulate Iron

The supply and bioavailability of dissolved iron sets the magnitude of surface productivity for ∼40% of the global ocean. The redox state, organic complexation, and phase (dissolved versus particulate) of iron are key determinants of iron bioavailability in the marine realm, although the mechanisms facilitating exchange between iron species (inorganic and organic) and phases are poorly constrained. Here we use the isotope fingerprint of dissolved and particulate iron to reveal distinct isotopic signatures for biological uptake of iron during a GEOTRACES process study focused on a temperate spring phytoplankton bloom in subtropical waters. At the onset of the bloom, dissolved iron within the mixed layer was isotopically light relative to particulate iron. The isotopically light dissolved iron pool likely results from the reduction of particulate iron via photochemical and (to a lesser extent) biologically mediated reduction processes. As the bloom develops, dissolved iron within the surface mixed layer becomes isotopically heavy, reflecting the dominance of biological processing of iron as it is removed from solution, while scavenging appears to play a minor role. As stable isotopes have shown for major elements like nitrogen, iron isotopes offer a new window into our understanding of the biogeochemical cycling of iron, thereby allowing us to disentangle a suite of concurrent biotic and abiotic transformations of this key biolimiting element.

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