Microbiomes of the Arctic carnivorous sponges <i>Chondrocladia grandis</i> and <i>Cladorhiza oxeata</i> suggest a specific, but differential involvement of bacterial associates

Verhoeven, Joost T. P.; Dufour, Suzanne C.

doi:10.1139/as-2017-0015

Cited by 12 publications

(18 citation statements)

References 34 publications

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“…However, a much lower number of bacterial phyla (22 phyla, including candidate ones) were revealed compared to our results with at least 33 bacterial phyla from one sponge species. Similarly, using single primer set based approach for regions V1V2 and V6V8, core microbiome stability of sponges was demonstrated with the geographical and temporal variations 29,30 , but only with 11 phyla and six phyla, respectively. When combining two 16S rRNA gene regions of V3 and V6, Asbestopluma hypogea -associated microbiome was assigned to 20 bacterial and two archaeal phyla (45 classes in total) 31 that is still with significantly smaller microbial coverage than the findings in the current study (minimum 33 phyla and 88 classes) (Tables 1 and 2).…”

Section: Discussionmentioning

confidence: 93%

Uncovering the hidden marine sponge microbiome by applying a multi-primer approach

Yang

Franco

Zhang

2019

Sci Rep

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Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.

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Section: Discussionmentioning

confidence: 93%

Uncovering the hidden marine sponge microbiome by applying a multi-primer approach

Yang

Franco

Zhang

2019

Sci Rep

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“…Data were combined with those obtained from the 3-month fallow site studied previously (Verhoeven et al, 2016). Illumina reads were processed using the in-house SPONS-2 (Streamlined Processor Of Next-gen Sequences, version 2) pipeline with settings as previously described (Verhoeven and Dufour, 2017), with minor modifications. Briefly, the operational taxonomic unit (OTU) creation process using SWARM (Mahé et al, 2015) was modified to be more lenient [maximum differences between amplicons ( d ) increased from 1 to 3] to prevent an observed overestimation of found OTUs.…”

Section: Methodsmentioning

confidence: 99%

Temporal Bacterial Surveillance of Salmon Aquaculture Sites Indicates a Long Lasting Benthic Impact With Minimal Recovery

et al. 2018

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Coastal aquaculture has experienced substantial growth in the last few decades and associated impacts on natural environments are of increasing importance. Understanding both the effects of aquaculture on marine ecosystems and the processes of recovery during fallowing periods is crucial for the development of a more environmentally sustainable industry. Because bacteria are sensitive to environmental change, surveying fluctuations in bacterial communities is a promising tool for monitoring the status of benthic environments. Here, we used 16S rRNA gene high-throughput sequencing to characterize bacterial communities in flocculent matter samples collected over a period of 3 years and at various distances from cages (0–200 meters) at production and fallow (3–35 months) salmon aquaculture sites in southern Newfoundland to evaluate the environmental impact of aquaculture on predominantly hard-bottom substrates. Bacterial composition analysis revealed four clusters, three of which (defined as “recently disturbed,” “intermediate impact,” and “high impact”) differed markedly from a fourth “low impact” cluster that contained far-field samples collected >500 m from cages. Samples within the high impact group were most often collected directly under cages, whereas those in the intermediate impact group were mainly sampled from 20 to 40 m from cages. Large scale phylum shifts (increases of Bacteroidetes, Firmicutes, Spirochaetes, and decreases in Proteobacteria and Epsilonbacteraeota) and a decline in bacterial diversity were observed in the high impact cluster, indicating significant ecological change. Samples from sites of different fallow duration were found in the high impact cluster, indicating a lack of recovery, even after 35 months of fallowing. Finally, we identified 28 genera as bacterial biomarkers, specific to one or more clusters, including genera associated with organically enriched environments and previously reported in the context of aquaculture impacts. Tracking the relative abundance of biomarkers in relation to different lengths of fallowing in the three more impacted clusters showed that these markers remained significantly above low impact cluster levels at all times, further pointing toward incomplete recovery. Our results suggest that coastal aquaculture on hard-bottom substrates is prone to long lasting impacts on bacterial communities, especially below cages, and that effects can be accurately tracked using bacterial community profiles or specific biomarkers.

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“…Sequence data were processed using the in-house developed SPONS-2 pipeline, as described in Verhoeven and Dufour (2017), with a few modifications. In short, sequences were trimmed to remove both low-quality bases using Trimmomatic version 0.38 (20-base sliding window with a minimum average quality of 15 per base) and short reads (<100 bases) (Bolger et al, 2014).…”

Section: S Rrna Gene Sequencing and Processingmentioning

confidence: 99%

Bacterial Communities in Tissues and Surficial Mucus of the Cold-Water Coral Paragorgia arborea

2018

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Coral bacterial associates can play important functional roles for the holobiont, such as nitrogen cycling, nutrient processing, and supporting immunity. While bacteria found within the microbiome of corals may benefit the host, they can also be linked to pathogenesis. In the deep-sea, cold-water corals, like their warm shallowwater counterparts, host bacterial communities, but have received little attention due to logistical constraints in sampling. In particular, bacteria associated with surficial mucus of cold-water corals have not yet been investigated. Here, tissue and mucus samples of Paragorgia arborea were collected from three submarine canyons along the continental slope of the Gulf of Maine. Bacterial DNA was extracted from tissue and mucus samples and sequencing of the V6-V8 hypervariable region of the 16S rRNA gene was performed using Illumina MiSeq. The bacterial communities associated with P. arborea compartments (tissue and mucus) and sampling locations (canyon) differed significantly in composition. Proteobacteria, Tenericutes, and Spirochaetes were the dominant phyla across the majority of coral tissue samples, with Gammaproteobacteria and Alphaproteobacteria identified as the largest Proteobacteria contributors across all samples. Operational taxonomic units (OTUs) belonging to the taxa Spirochaeta, Mycoplasma, Flavobacteriaceae, Terasakiellaceae, Campylobacterales, and Rickettsiales were identified as biomarkers (bacterial taxa significantly more abundant in a specific coral microhabitat) of P. arborea tissues, while Paracoccus was a biomarker of P. arborea mucus. Many of the recovered biomarker taxa may be involved in nitrogen cycling. Representatives from several bacterial families (Vibrionaceae, Campylobacteraceae, Rhodobacteraceae, Flavobacteriaceae, and Burkholderiaceae) previously reported in diseased scleractinians, were present in P. arborea as rare bacterial taxa. Characterizing the bacterial associates present in visibly healthy coral colonies provides a benchmark of dominant and rare bacterial groups present in the cold-water coral holobiont. This is the first characterization of bacterial groups associated with P. arborea, examining both tissue-and mucus-specific communities.

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Microbiomes of the Arctic carnivorous sponges Chondrocladia grandis and Cladorhiza oxeata suggest a specific, but differential involvement of bacterial associates

Cited by 12 publications

References 34 publications

Uncovering the hidden marine sponge microbiome by applying a multi-primer approach

Uncovering the hidden marine sponge microbiome by applying a multi-primer approach

Temporal Bacterial Surveillance of Salmon Aquaculture Sites Indicates a Long Lasting Benthic Impact With Minimal Recovery

Bacterial Communities in Tissues and Surficial Mucus of the Cold-Water Coral Paragorgia arborea

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