Dataset Information

Stable Associations Masked by Temporal Variability in the Marine Copepod Microbiome.

ABSTRACT: Copepod-bacteria interactions include permanent and transient epi- and endobiotic associations that may play roles in copepod health, transfer of elements in the food web, and biogeochemical cycling. Microbiomes of three temperate copepod species (Acartia longiremis, Centropages hamatus, and Calanus finmarchicus) from the Gulf of Maine were investigated during the early summer season using high throughput amplicon sequencing. The most prominent stable component of the microbiome included several taxa within Gammaproteobacteria, with Pseudoalteromonas spp. especially abundant across copepod species. These Gammaproteobacteria appear to be promoted by the copepod association, likely benefitting from nutrient enriched microenvironments on copepods, and forming a more important part of the copepod-associated community than Vibrio spp. during the cold-water season in this temperate system. Taxon-specific associations included an elevated relative abundance of Piscirickettsiaceae and Colwelliaceae on Calanus, and Marinomonas sp. in Centropages. The communities in full and voided gut copepods had distinct characteristics, thus the presence of a food-associated microbiome was evident, including higher abundance of Rhodobacteraceae and chloroplast sequences in the transient communities. The observed variability was partially explained by collection date that may be linked to factors such as variable time since molting, gender differences, and changes in food availability and type over the study period. While some taxon-specific and stable associations were identified, temporal changes in environmental conditions, including food type, appear to be key in controlling the composition of bacterial communities associated with copepods in this temperate coastal system during the early summer.

SUBMITTER: Moisander PH

PROVIDER: S-EPMC4579122 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Stable Associations Masked by Temporal Variability in the Marine Copepod Microbiome.

Moisander Pia H PH Sexton Andrew D AD Daley Meaghan C MC

PloS one 20150922 9

Copepod-bacteria interactions include permanent and transient epi- and endobiotic associations that may play roles in copepod health, transfer of elements in the food web, and biogeochemical cycling. Microbiomes of three temperate copepod species (Acartia longiremis, Centropages hamatus, and Calanus finmarchicus) from the Gulf of Maine were investigated during the early summer season using high throughput amplicon sequencing. The most prominent stable component of the microbiome included several ...[more]

PMID: 26393930

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Project description:A primary goal of modern cheese manufacturing is consistent product quality. One aspect of product quality that remains poorly understood is the variability of microbial subpopulations due to temporal or facility changes within cheese production environments. Therefore, our aim was to quantify this variability by measuring day-day and facility-facility changes in the cheese facility microbiome. In-process product (i.e., milk and cheese) and food-contact surfaces were sampled over the course of three production days at three cheese manufacturing facilities. Microbial communities were characterized using 16S rRNA metabarcoding and by plating on selective growth media. Each facility produced near-identical Cheddar cheese recipes on near-identical processing equipment during the time of sampling. Each facility also used a common pool of Lactococcus starter cultures which were rotated daily as groups of 4-5 strains and selected independently at each facility. Diversity analysis revealed significant facility-facility and day-day differences at each sample location. Facility differences were greatest on the food contact surfaces (i.e., draining-matting conveyor belts), explaining between 25 and 41% of the variance. Conversely, daily differences within each facility explained a greater proportion of the variance in the milk (20% vs. 12%) and cheese (29% vs. 20%). Further investigation into the sources of these differences revealed the involvement of several industrially relevant bacteria, including lactobacilli, which play a central role in flavor and texture development during Cheddar cheese ripening. Additionally, Streptococcus was found to contribute notably to differences observed in milk samples, whereas Acinetobacter, Streptococcus, Lactococcus, Exiguobacterium, and Enterobacteriaceae contributed notably to differences on the food contact surfaces. Facility differences in the cheese were overwhelmingly attributed to the rotation of Lactococcus starter cultures, thus highlighting circumstances where daily microbial shifts could be misinterpreted and emphasizing the importance of repeated sampling over time. The outcomes of this work highlight the complexity of the cheese facility microbiome and demonstrate daily and facility-facility microbial variations which might impact cheese product quality.

Project description:Human performance shows substantial endogenous variability over time, and this variability is a robust marker of individual differences. Of growing interest to psychologists is the realisation that variability is not fully random, but often exhibits temporal dependencies. However, their measurement and interpretation come with several controversies. Furthermore, their potential benefit for studying individual differences in healthy and clinical populations remains unclear. Here, we gather new and archival datasets featuring 11 sensorimotor and cognitive tasks across 526 participants, to examine individual differences in temporal structures. We first investigate intra-individual repeatability of the most common measures of temporal structures - to test their potential for capturing stable individual differences. Secondly, we examine inter-individual differences in these measures using: (1) task performance assessed from the same data, (2) meta-cognitive ratings of on-taskness from thought probes occasionally presented throughout the task, and (3) self-assessed attention-deficit related traits. Across all datasets, autocorrelation at lag 1 and Power Spectra Density slope showed high intra-individual repeatability across sessions and correlated with task performance. The Detrended Fluctuation Analysis slope showed the same pattern, but less reliably. The long-term component (d) of the ARFIMA(1,d,1) model showed poor repeatability and no correlation to performance. Overall, these measures failed to show external validity when correlated with either mean subjective attentional state or self-assessed traits between participants. Thus, some measures of serial dependencies may be stable individual traits, but their usefulness in capturing individual differences in other constructs typically associated with variability in performance seems limited. We conclude with comprehensive recommendations for researchers.Supplementary informationThe online version contains supplementary material available at 10.1007/s42113-022-00162-1.

Dataset Information

Stable Associations Masked by Temporal Variability in the Marine Copepod Microbiome.

Publications

Stable Associations Masked by Temporal Variability in the Marine Copepod Microbiome.

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