Microbial metatranscriptomes from the thermally stratified Gulf of Aqaba/Eilat during summer

Miller, Dan; Pfreundt, Ulrike; Elifantz, Hila; Hess, Wolfgang R.; Berman‐Frank, Ilana

doi:10.1016/j.margen.2016.12.001

Cited by 6 publications

(6 citation statements)

References 22 publications

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“…However, our results show that archaea were always present and abundant throughout the water column during the winter but were almost absent in the UP region during the stratification. Similar observation was made using metatranscriptomes from the stratified water column in the Gulf of Aqaba/Eilat [ 30 ]. In the same way as the Planctomycetes or Chloroflexi that only appeared below the DCM (Fig.…”

Section: Resultssupporting

confidence: 73%

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

et al. 2018

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BackgroundThe photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two more samples during the winter when the photic water column was mixed. We were able to recover 94 new metagenome-assembled genomes (MAGs) from these metagenomes and examine the distribution of key marine microbes within the photic zone using metagenomic recruitment.ResultsOur results showed significant differences in the microbial composition of different layers within the stratified photic water column. The majority of microorganisms were confined to discreet horizontal layers of no more than 30 m (stenobathic). Only a few such as members of the SAR11 clade appeared at all depths (eurybathic). During the winter mixing period, only some groups of bloomers such as Pseudomonas were favored. Although most microbes appeared in both seasons, some groups like the SAR116 clade and some Bacteroidetes and Verrucomicrobia seemed to disappear during the mixing period. Furthermore, we found that some microbes previously considered seasonal (e.g., Archaea or Actinobacteria) were living in deeper layers within the photic zone during the stratification period. A strong depth-related specialization was detected, not only at the taxonomic level but also at the functional level, even within the different clades, for the manipulation and uptake of specific polysaccharides. Rhodopsin sequences (green or blue) also showed narrow depth distributions that correlated with the taxonomy of the microbe in which they were found but not with depth.ConclusionsAlthough limited to a single location in the Mediterranean, this study has profound implications for our understanding of how marine microbial communities vary with depth within the photic zone when stratified. Our results highlight the importance of collecting samples at different depths in the water column when comparing seasonal variations and have important ramifications for global marine studies that most often take samples from only one single depth. Furthermore, our perspective and approaches (metagenomic assembly and recruitment) are broadly applicable to other metagenomic studies.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0513-5) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 73%

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

et al. 2018

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“…Salinity remained stable at 40.7 PSU from the surface to 500 m. The concentrations of inorganic nutrients ranged from 1.7−2.2 µmol l −1 NO 3 + N O 2 (hereafter total inorganic nitrogen, TIN ), 0.99− 1.08 µmol l −1 Si(OH) 4 , and 0.1−0.12 µmol l −1 PO 4 . N utrient concentrations were higher than typical summer values, when surface concentrations decline to 0.05 µmol l −1 TIN, 0.8 µmol l −1 Si(OH) 4 , and < 0.01− 0.02 µmol l −1 PO 4 (Mackey et al 2007, Lazar et al 2008, Meeder et al 2012, Miller et al 2017, emphasizing the seasonal variability in nutrient availability. The measured winter concentrations were nonetheless comparable to low dissolved inorganic nutrient concentrations measured from the upper surface layers in other oligotrophic locations (Karl et al 1993, Dore et al 1996.…”

Section: Defining Environmental Conditionsmentioning

confidence: 94%

Winter mixing impacts gene expression in marine microbial populations in the Gulf of Aqaba

Miller¹,

Pfreundt²,

Hou³

et al. 2017

Aquat. Microb. Ecol.

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In aquatic systems, changes in temperature and irradiance fundamentally characterize the water column and regulate microbial population structure and function. In systems with stable thermal stratification, the warm surface mixed layer is typically nutrient impoverished, limiting biological production. In periods of destratification, convective mixing of the water column exposes the microorganisms inhabiting these mixed systems to rapid variations in light availability and spectra. We explored the impact of winter deep-mixing (500 m deep mixed layer) on microbial communities from the surface (2.5 m) and the aphotic waters (440 m) in the Gulf of Aqaba by examining changes in both population composition and function via DNA and RNA sequencing. The greatest fraction of 16S sequences was assigned to Euryarchaeota, while metatranscriptomes were dominated by Synechococcus transcripts. Community composition was highly similar at both depths, yet transcription profiles differed. Phototrophic organisms found at the photic surface overexpressed genes related to catabolism and energy metabolism, while genes affiliated with biosynthesis were overexpressed at the aphotic depth. Similar transcriptional trends were observed in the non-photoautotrophs SAR11, Euryarchaeota, and Thaumarchaeota, with niche partitioning based on differential utilization of nitrogen and phosphorus occurring between the 2 archaeal groups. We did not detect upregulated expression of cyanobacterial genes indicative of mixotrophy or glycogen metabolism in the aphotic zone, suggesting they survive the aphotic period by utilizing photosynthates produced in the photic zone. Indications for a mixotrophic lifestyle were observed for prasinophytes, with genes related to phagocytosis overexpressed at the aphotic depth compared with the surface.

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“…For the RNA sample, 200 liter of seawater was collected and immediately filtered in a shaded area onboard through a 0.22 μm polyethersulfone filter that was suspended with RNAlater and kept on dry ice until storage at −80 °C. RNA extraction was performed according to the phenolic PGTX (Miller et al, ). Metatranscriptome was sequenced using Illumina Hiseq‐4000 (150 bp, paired‐end read) (Macrogen, Republic of Korea).…”

Section: Methodsmentioning

confidence: 99%

Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes

López‐Pérez

Haro-Moreno

Torre

et al. 2018

Environmental Microbiology

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Summary Marine Group I (MGI) Thaumarchaeota are some of the most abundant microorganisms in the deep ocean and responsible for much of the ammonia oxidation occurring in this environment. In this work, we present 35 sequences assembled from metagenomic samples of the first uncultivated Caudovirales viruses associated with Thaumarchaeota, which we designated marthavirus. Most of the sequences were obtained from cellular metagenomes confirming that they represent an important tool to study environmental viral communities due to cells retrieved while undergoing viral lysis. Metagenomic recruitment showed that this viral population is formed by very divergent entities with high intrapopulation homogeneity. However, metatranscriptomic analyses revealed the same differential expression profile with the capsid as major transcript, indicative of viruses during the lytic cycle. The cobalamine biosynthesis gene cobS, an auxiliary metabolic gene, was also highly expressed during the infection. These analyses expand our understanding of the global diversity of archaeal viruses.

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Microbial metatranscriptomes from the thermally stratified Gulf of Aqaba/Eilat during summer

Cited by 6 publications

References 22 publications

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

Winter mixing impacts gene expression in marine microbial populations in the Gulf of Aqaba

Novel Caudovirales associated with Marine Group I Thaumarchaeota assembled from metagenomes

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