Zooming on dynamics of marine microbial communities in the phycosphere of Akashiwo sanguinea (Dinophyta) blooms.
Ontology highlight
ABSTRACT:
SUBMITTER: Kang J
PROVIDER: S-EPMC7839783 | biostudies-literature | 2020 Oct
REPOSITORIES: biostudies-literature
Publications
Zooming on dynamics of marine microbial communities in the phycosphere of Akashiwo sanguinea (Dinophyta) blooms.
Kang Junsu J Park Joon Sang JS Jung Seung Won SW Kim Hyun-Jung HJ Joo Hyoung Min HM Kang Donhyug D Seo Hyojeong H Kim Sunju S Jang Min-Chul MC Lee Kyun-Woo KW Jin Oh Seok S Lee Sukchan S Lee Taek-Kyun TK
Molecular ecology 20201114 1
Characterizing ecological relationships between viruses, bacteria and phytoplankton in the ocean is critical to understanding the ecosystem; however, these relationships are infrequently investigated together. To understand the dynamics of microbial communities and environmental factors in harmful algal blooms (HABs), we examined the environmental factors and microbial communities during Akashiwo sanguinea HABs in the Jangmok coastal waters of South Korea by metagenomics. Specific bacterial spec ...[more]
Similar Datasets
Project description:We investigated the dynamics of the bacterial composition and metabolic function within Akashiwo sanguinea bloom using a 100-L indoor microcosm and metagenomic next-generation sequencing. We found that the bacterial community was classified into three groups at 54% similarity. Group I was associated with "during the A. sanguinea bloom stage" and mainly consisted of Alphaproteobacteria, Flavobacteriia and Gammaproteobacteria. Meanwhile, groups II and III were associated with the "late bloom/decline stage to post-bloom stage" with decreased Flavobacteriia and Gammaproteobacteria in these stages. Upon the termination of the A. sanguinea bloom, the concentrations of inorganic nutrients (particularly PO43-, NH4+ and dissolved organic carbon) increased rapidly and then decreased. From the network analysis, we found that the A. sanguinea node is associated with certain bacteria. After the bloom, the specific increases in NH4+ and PO43- nodes are associated with other bacterial taxa. The changes in the functional groups of the bacterial community from chemoheterotrophy to nitrogen association metabolisms were consistent with the environmental impacts during and after A. sanguinea bloom. Consequently, certain bacterial communities and the environments dynamically changed during and after harmful algal blooms and a rapid turnover within the bacterial community and their function can respond to ecological interactions.
| S-EPMC7997919 | biostudies-literature
Project description:The fungal community living with the laboratory-cultured Akashiwo sanguinea
| PRJNA892755 | ENA
Project description:Phytoplankton blooms are a worldwide problem and can greatly affect ecological processes in aquatic systems, but its impacts on the functional potential of microbial communities are limited. In this study, a high-throughput microarray-based technology (GeoChip) was used to profile the functional potential of free-living microbes from the Xiamen Sea Area in response to a 2011 Akashiwo sanguinea bloom. The bloom altered the overall community functional structure. Genes that were significantly (p < 0.05) increased during the bloom included carbon degradation genes and genes involved in nitrogen (N) and/or phosphorus (P) limitation stress. Such significantly changed genes were well explained by chosen environmental factors (COD, nitrite-N, nitrate-N, dissolved inorganic phosphorus, chlorophyll-a and algal density). Overall results suggested that this bloom might enhance the microbial converting of nitrate to N2 and ammonia nitrogen, decrease P removal from seawater, activate the glyoxylate cycle, and reduce infection activity of bacteriophage. This study presents new information on the relationship of algae to other microbes in aquatic systems, and provides new insights into our understanding of ecological impacts of phytoplankton blooms.
| S-EPMC5050414 | biostudies-literature
Project description:Surfaces of marine macrophytes are inhabited by diverse microbial communities. Most studies focusing on epiphytic communities of macrophytes did not take into account temporal changes or applied low sampling frequency approaches. The seasonal dynamics of epiphytic microbial communities was determined in a meadow of Cymodocea nodosa invaded by Caulerpa cylindracea and in a monospecific settlement of C. cylindracea at monthly intervals. For comparison the ambient prokaryotic picoplankton community was also characterized. At the OTU level, the microbial community composition differed between the ambient water and the epiphytic communities exhibiting host-specificity. Also, successional changes were observed connected to the macrophyte growth cycle. Taxonomic analysis, however, showed similar high rank taxa (phyla and classes) in the ambient water and the epiphytic communities, with the exception of Desulfobacterota, which were only found on C. cylindracea. Cyanobacteria showed seasonal changes while other high rank taxa were present throughout the year. In months of high Cyanobacteria presence the majority of cyanobacterial sequences were classified as Pleurocapsa. Phylogenetic groups present throughout the year (e.g., Saprospiraceae, Rhodobacteraceae, members without known relatives within Gammaproteobacteria, Desulfatitalea, and members without known relatives within Desulfocapsaceae) constituted most of the sequences, while less abundant taxa showed seasonal patterns connected to the macrophyte growth cycle. Taken together, epiphytic microbial communities of the seagrass C. nodosa and the macroalga C. cylindracea appear to be host-specific and contain taxa that undergo successional changes.
| S-EPMC8482799 | biostudies-literature
Project description:Given the ecological significance of microorganisms in algal blooming events, it is critical to understand the mechanisms regarding their distribution under different conditions. We tested the hypothesis that microbial community succession is strongly associated with algal bloom stages, and that the assembly mechanisms are cocontrolled by deterministic and stochastic processes. Community structures and underlying ecological processes of microbial populations (attached and free-living bacteria) at three algal bloom stages (pre-, during, and postbloom) over a complete dinoflagellate Scrippsiella trochoidea bloom were investigated. Both attached and free-living taxa had a strong response to the bloom event, and the latter was more sensitive than the former. The contribution of environmental parameters to microbial variability was 40.2%. Interaction analysis showed that complex positive or negative correlation networks exist in phycosphere microbes. These relationships were the potential drivers of mutualist and competitive interactions that impacted bacterial succession. Null model analysis showed that the attached bacterial community primarily exhibited deterministic processes at pre- and during-bloom stages, while dispersal-related processes contributed to a greater extent at the postbloom stage. In the free-living bacterial community, homogeneous selection and dispersal limitation dominated in the initial phase, which gave way to more deterministic processes at the two later stages. Relative contribution analyses further demonstrated that the community turnover of attached bacteria was mainly driven by environmental selection, while stochastic factors had partial effects on the assembly of free-living bacteria. Taken together, these data demonstrated that a robust link exists between bacterioplankton community structure and bloom progression, and phycosphere microbial succession trajectories are cogoverned by both deterministic and random processes.IMPORTANCE Disentangling the mechanisms shaping bacterioplankton communities during a marine ecological event is a core concern for ecologists. Harmful algal bloom (HAB) is a typical ecological disaster, and its formation is significantly influenced by alga-bacterium interactions. Microbial community shifts during the HAB process are relatively well known. However, the assembly processes of microbial communities in an HAB are not fully understood, especially the relative influences of deterministic and stochastic processes. We therefore analyzed the relative contributions of deterministic and stochastic processes during an HAB event. Both free-living and attached bacterial groups had a dramatic response to the HAB, and the relative importance of determinism versus stochasticity varied between the two bacterial groups at various bloom stages. Environmental factors and biotic interactions were the main drivers impacting the microbial shift process. Our results strengthen the understanding of the ecological mechanisms controlling microbial community patterns during the HAB process.
| S-EPMC6643250 | biostudies-literature
Project description:Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to thirteen of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual ORF, and distributed along each ~40-160kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having ≤~75% genomic identity. In addition, the array correctly identified target cells added to a background of environmental DNA, with a limit of detection of ~0.1% of the community, corresponding to ~10^3 cells/ml in these samples. Signal correlated to cell concentration with an R2 of 1.0 across six orders of magnitude. In addition the array could track a related strain (at 86% genomic identity to that targeted) with a linearity of R2=0.9999 and a limit of detection of ~1% of the community. Closely related genotypes were distinguishable by differing hybridization patterns across each probe set. This array’s multiple-probe, “genome-proxy” approach and consequent ability to track both target genotypes and their close relatives is important for the array’s environmental application given the recent discoveries of considerable intra-population diversity within marine microbial communities. Keywords: target addition experiment, proof-of-concept for GPL6012
2007-10-31 | GSE9384 | GEO
Project description:Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a âgenome proxyâ microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to thirteen of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual ORF, and distributed along each ~40-160kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having â¤~75% genomic identity. In addition, the array correctly identified target cells added to a background of environmental DNA, with a limit of detection of ~0.1% of the community, corresponding to ~10^3 cells/ml in these samples. Signal correlated to cell concentration with an R2 of 1.0 across six orders of magnitude. In addition the array could track a related strain (at 86% genomic identity to that targeted) with a linearity of R2=0.9999 and a limit of detection of ~1% of the community. Closely related genotypes were distinguishable by differing hybridization patterns across each probe set. This arrayâs multiple-probe, âgenome-proxyâ approach and consequent ability to track both target genotypes and their close relatives is important for the arrayâs environmental application given the recent discoveries of considerable intra-population diversity within marine microbial communities. Keywords: target addition experiment, proof-of-concept for GPL6012 ***Overall Array design*** The prototype microarray targeted thirteen BAC or fosmid genome fragments (20-160kb) from both bacteria and archaea, recovered from a variety of marine habitats, as well as the cyanobacterium Prochlorococcus MED4. These clones were originally sequenced because of the presence of taxonomic marker or specific functional genes. This array consisted of sets of 70-bp oligonucleotides targeting each genome or genome fragment (Fig. 1), dispersed along the target sequences with no more than one probe per gene, and excluding rRNA genes as targets. The probes were selected solely based on theoretical thermodynamic properties and GC content (~40%); that is, probe selection did not focus on specific genes or regions, but simply produced the âoptimalâ probes for each genome proxy based on the probesâ predicted hybridization properties. rRNA genes were excluded, because this probe design approach, which avoids sequence alignments and considerations of RNA secondary structure, would be unlikely to result in useful rRNA probes. Furthermore, rRNA probes of traditional design could not be included on the array because their appropriate hybridization conditions would be very different from those of this arrayâs probes. ***Microarray probe design*** Microarray 70-mer probes were designed using the program ArrayOligoSelector (Zhu et al., 2003) with the following settings: target %GC = 40%, 1 probe/gene, with the ORFs for each genome fragment as both the input and the database file. The output candidate 70mers were then sorted based on their %GC and those closest to 40% were chosen. In the case of more than the target number of probes having 40%GC, the subset with the lowest free energy of hybridization were selected as probes. Generally, 20 probes were selected per organism. Prochlorococcus MED4 was represented by 60 probes total, 20 each for three different 80kb âgenome-proxyâ regions: 0-80kb, 1.29-1.37Mbp, and 1.58 to 1.66Mbp. Using the same method, a set (n=20) of positive control probes were designed to the genome of the halophillic archaeon Halobacterium salinarum NRC-1. Negative control probes (n=28) were designed to a set of 49 random 1000-base sequences (Stothard, 2000). ***Microarray construction and hybridization*** Oligonucleotides were synthesized (Illumina, San Diego, California), suspended in 3XSSC to a concentration of 40pmol/μl, and spotted on homemade poly-L-lysine-coated glass slides using a QArray 2 microarraying robot (Genetix, Hampshire, England). Six replicates of each probe were spotted. ***Microarray data analysis*** Hybridized arrays were scanned using an Axon Instruments 4000B scanner (Foster City, CA) and the data was normalized and filtered using perl scripts written for the purpose, by the following steps. (1) Signal intensities for each spot were calculated by subtracting the local background (mean F532 â median B532, as calculated by GenePix Pro 5.1 software, Axon Instruments). (2) The median value across replicates was calculated for each probe. (3) For each probe set, the number of probes greater than twice the mean negative control signal was calculated, before further processing. (4) Filter I: Arrays with less than half their positive control probes exceeding twice the mean negative control signal were considered poor quality, low dynamic range, arrays and were excluded from further analysis. (5) Each probe signal was corrected for non-specific binding by subtracting the mean negative control spot signal. (6) The data was then normalized for array-to-array variations in brightness by dividing each probe signal by the mean positive control signal. This positive control signal was the mean signal across the Halobacterium salinarum probes in each hybridization, with identical amounts of H. salinarum DNA having been added to each reaction prior to amplification and labeling. (7) Filter II: In order for a genotype to be considered âpresentâ, at least 45% of its probes had to exceed twice the mean negative control signal. (8) Finally, each genotype signal was calculated as either the MEAN or TUKEY BIWEIGHT across its probe set. ***Experimental Design*** The array was hybridized to laboratory mixtures of cloned environmental genomic DNA targeted by the array, in varying ratios. The use of multiple probes to target many genes from each organism helped to normalize probe-to-probe heterogeneity, by averaging across all probes in a set (as described below). The evenness of probe response across each genotypeâs set was also used to evaluate the relatedness of hybridizing DNA. To more precisely define the arrayâs phylogenetic range and specificity, it was tested against DNA from Prochlorococcus MED4 and related strains, spanning the known range of Prochlorococcus phylogenetic diversity. To test the effects of hybridization stringency on the specificity and signal of the MED4 probes, Prochlorococcus strains were hybridized at a range of conditions. To test whether the specificity results for Prochlorococcus were comparable for other targeted clades, two genome fragments recovered from closely related phylotypes within the SAR86 clade of the gamma-proteobacteria were represented on the array, and were tested for specificity. To understand the equivalence of probe sets targeting different regions of the same organismâs genome, we targeted three 80kb âgenome proxyâ regions of the Prochlorococcus MED4 genome. One of the regions fell in a genomic âislandâ where inter-strain variability is concentrated (âISL5â in Coleman et al., 2006). To test the array in a complex environmental context, we collected coastal seawater (lacking detectable Prochlorococcus cells by flow cytometry) and added Prochlorococcus cells from strains MED4, MIT9515, MIT9312 and MIT9313 over a range of concentrations from ~101 â 106 cells/ml (Fig. 3). The seawater was then filtered and the DNA extracted, amplified, labeled, and hybridized to the array.
2010-05-25 | E-GEOD-9384 | biostudies-arrayexpress
Project description:Jellyfish blooms occur in many estuarine and coastal regions and may be increasing in their magnitude and extent worldwide. Voracious jellyfish predation impacts food webs by converting large quantities of carbon (C), fixed by primary producers and consumed by secondary producers, into gelatinous biomass, which restricts C transfer to higher trophic levels because jellyfish are not readily consumed by other predators. In addition, jellyfish release colloidal and dissolved organic matter (jelly-DOM), and could further influence the functioning of coastal systems by altering microbial nutrient and DOM pathways, yet the links between jellyfish and bacterioplankton metabolism and community structure are unknown. Here we report that jellyfish released substantial quantities of extremely labile C-rich DOM, relative to nitrogen (25.6 ± 31.6 C:1N), which was quickly metabolized by bacterioplankton at uptake rates two to six times that of bulk DOM pools. When jelly-DOM was consumed it was shunted toward bacterial respiration rather than production, significantly reducing bacterial growth efficiencies by 10% to 15%. Jelly-DOM also favored the rapid growth and dominance of specific bacterial phylogenetic groups (primarily γ-proteobacteria) that were rare in ambient waters, implying that jelly-DOM was channeled through a small component of the in situ microbial assemblage and thus induced large changes in community composition. Our findings suggest major shifts in microbial structure and function associated with jellyfish blooms, and a large detour of C toward bacterial CO(2) production and away from higher trophic levels. These results further suggest fundamental transformations in the biogeochemical functioning and biological structure of food webs associated with jellyfish blooms.
| S-EPMC3121804 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2014-12-21 | GSE64376 | GEO
Project description:Most marine bacteria produce exopolysaccharides (EPS), and bacterial EPS represent an important source of dissolved organic carbon in marine ecosystems. It was proposed that bacterial EPS rich in uronic acid is resistant to mineralization by microbes and thus has a long residence time in global oceans. To confirm this hypothesis, bacterial EPS rich in galacturonic acid was isolated from Alteromonas sp. JL2810. The EPS was used to amend natural seawater to investigate the bioavailability of this EPS by native populations, in the presence and absence of ammonium and phosphate amendment. The data indicated that the bacterial EPS could not be completely consumed during the cultivation period and that the bioavailability of EPS was not only determined by its intrinsic properties, but was also determined by other factors such as the availability of inorganic nutrients. During the experiment, the humic-like component of fluorescent dissolved organic matter (FDOM) was freshly produced. Bacterial community structure analysis indicated that the class Flavobacteria of the phylum Bacteroidetes was the major contributor for the utilization of EPS. This report is the first to indicate that Flavobacteria are a major contributor to bacterial EPS degradation. The fraction of EPS that could not be completely utilized and the FDOM (e.g., humic acid-like substances) produced de novo may be refractory and may contribute to the carbon storage in the oceans.
| S-EPMC4646686 | biostudies-literature