Data_Sheet_1_Metagenomic Analysis Shows the Presence of Bacteria Related to Free-Living Forms of Sulfur-Oxidizing Chemolithoautotrophic Symbionts in the Rhizosphere of the Seagrass Zostera marina.PDF

<p>Seagrasses play an important role as ecosystem engineers; they provide shelter to many animals and improve water quality by filtering out nutrients and by controlling pathogens. Moreover, their rhizosphere promotes a myriad of microbial interactions and processes, which are dominated by microorganisms involved in the sulfur cycle. This study provides a detailed insight into the metabolic sulfur pathways in the rhizobiome of the seagrass Zostera marina, a dominant seagrass species across the temperate northern hemisphere. Shotgun metagenomic sequencing revealed the relative dominance of Gamma- and Deltaproteobacteria, and comparative analysis of sulfur genes identified a higher abundance of genes related to sulfur oxidation than sulfate reduction. We retrieved four high-quality draft genomes that are closely related to the gill symbiont of the clam Solemya velum, which suggests the presence of putative free-living forms of symbiotic bacteria. These are potentially highly versatile chemolithoautotrophic bacteria, able to alternate their metabolism between parallel pathways of sulfide oxidation (via sqr and fcc), nitrate reduction (denitrification or DNRA) and carbon fixation (via CBB or TCA cycle), depending on the environmental availability of sulfide. Our results support the hypothesis that seagrass meadows might function as a source of symbionts for invertebrates that inhabit within or around seagrass meadows. While providing ideal conditions for the proliferation of these free-living forms of symbionts, seagrasses would benefit from their genetic versatility, which contributes to sulfide detoxification and ammonium production, the seagrasses' preferred nitrogen source.</p

Whole-genome GBDP phylogeny (based on the nucleotide data).

<p>Bootstrap values over 60% are shown at each node. An assignment to genomic species was based on the distance threshold equivalent to 70% dDDH (dDDH ≥ 70% indicates same genomic species) and dDDH < 70% (indicates distinct genomic species). Genomic species groups are marked by numbers whereas genomic subspecies groups are denoted by letters. The orange box indicates the outlying <i>Thioalkalivibrio</i> strains, contesting the monophyly of the genus.</p

Characteristics of 16S rRNA, single housekeeping and concatenated housekeeping genes (MLSA).

<p>Characteristics of 16S rRNA, single housekeeping and concatenated housekeeping genes (MLSA).</p

Dendrogram constructed from the ANI_b analysis.

<p><i>De novo</i> species clusters obtained without consideration of type strains. Clusters are indicated by dots (green: ANI > 96% (strains belong to the same genomic species); yellow: 94% < ANI < 96% (strains might belong to the same genomic species); red: ANI < 94% (strains do not belong to the same genomic species). The genomic species groups are marked by numbers. The orange box indicates the outlying <i>Thioalkalivibrio</i> strains, contesting the monophyly of the genus.</p

Whole-genome GDBP phylogeny (based on the amino acid data).

<p>Bootstrap values over 60% were shown at each node. The orange box indicates the outlying <i>Thioalkalivibrio</i> strains, contesting the monophyly of the genus.</p

Genomic diversity within the haloalkaliphilic genus <i>Thioalkalivibrio</i> - Fig 1

<p><b>Phylogenetic tree constructed from 16S rRNA gene sequence analysis (A) and from MLSA (B).</b> Bootstrap values over 60% were shown at each node. The orange box indicates the outlying <i>Thioalkalivibrio</i> strains, contesting the monophyly of the genus.</p

Identification of key factors in Accelerated Low Water Corrosion through experimental simulation of tidal conditions: influence of stimulated indigenous microbiota

<div><p>Biotic and abiotic factors favoring Accelerated Low Water Corrosion (ALWC) on harbor steel structures remain unclear warranting their study under controlled experimental tidal conditions. Initial stimulation of marine microbial consortia by a pulse of organic matter resulted in localized corrosion and the highest corrosion rates (up to 12-times higher than non-stimulated conditions) in the low water zone, persisting after nine months exposure to natural seawater. Correlations between corrosion severity and the abundance and composition of metabolically active sulfate-reducing bacteria (SRB) indicated the importance and persistence of specific bacterial populations in accelerated corrosion. One phylotype related to the electrogenic SRB <i>Desulfopila corrodens</i> appeared as the major causative agent of the accelerated corrosion. The similarity of bacterial populations related to sulfur and iron cycles, mineral and tuberculation with those identified in ALWC support the relevance of experimental simulation of tidal conditions in the management of steel corrosion exposed to harbor environments.</p></div

DataSheet_3_Sponges on shifting reefs: holobionts show similar molecular and physiological responses to coral versus macroalgal food.pdf

IntroductionMany coral reefs witness an ongoing coral-to-algae phase shift. Corals and algae release large quantities of (in)organic nutrients daily, of which a large part is utilized by sponges. In turn, sponges are important cyclers of precious resources to other inhabitants on reefs residing in oligotrophic waters. Here, we investigated whether sponge holobionts (i.e., host and prokaryotic symbionts) adapt their physiology to food released by coral- versus macroalgae.MethodsThereto, two sponge species, Plakortis angulospiculatus and Halisarca caerulea (high and low microbial abundance, respectively), were continuously exposed for 12 days to coral and macroalgal exudates in running seawater aquaria. Transcript expression of host and prokaryotic symbionts, changes in prokaryotic community composition, and holobiont physiological responses (i.e., respiratory demand, fluxes of carbon and nitrogen) were investigated after coral- versus macroalgae dominated treatments and compared to a seawater only control treatment.ResultsIn both sponge holobionts differential transcript expression between the coral and macroalgae treatments was very low (DiscussionAfter 12 days of exposure sponges appear to opportunistically feed on different food sources without having to adjust their metabolic pathways or associated prokaryotic communities. This suggests that sponges could be well-adapted to predicted changes in food source availability due to coral-to-algal phase shifts on many coral reefs.</p

DataSheet_2_Sponges on shifting reefs: holobionts show similar molecular and physiological responses to coral versus macroalgal food.xlsx

IntroductionMany coral reefs witness an ongoing coral-to-algae phase shift. Corals and algae release large quantities of (in)organic nutrients daily, of which a large part is utilized by sponges. In turn, sponges are important cyclers of precious resources to other inhabitants on reefs residing in oligotrophic waters. Here, we investigated whether sponge holobionts (i.e., host and prokaryotic symbionts) adapt their physiology to food released by coral- versus macroalgae.MethodsThereto, two sponge species, Plakortis angulospiculatus and Halisarca caerulea (high and low microbial abundance, respectively), were continuously exposed for 12 days to coral and macroalgal exudates in running seawater aquaria. Transcript expression of host and prokaryotic symbionts, changes in prokaryotic community composition, and holobiont physiological responses (i.e., respiratory demand, fluxes of carbon and nitrogen) were investigated after coral- versus macroalgae dominated treatments and compared to a seawater only control treatment.ResultsIn both sponge holobionts differential transcript expression between the coral and macroalgae treatments was very low (DiscussionAfter 12 days of exposure sponges appear to opportunistically feed on different food sources without having to adjust their metabolic pathways or associated prokaryotic communities. This suggests that sponges could be well-adapted to predicted changes in food source availability due to coral-to-algal phase shifts on many coral reefs.</p

DataSheet_1_Sponges on shifting reefs: holobionts show similar molecular and physiological responses to coral versus macroalgal food.xlsx

IntroductionMany coral reefs witness an ongoing coral-to-algae phase shift. Corals and algae release large quantities of (in)organic nutrients daily, of which a large part is utilized by sponges. In turn, sponges are important cyclers of precious resources to other inhabitants on reefs residing in oligotrophic waters. Here, we investigated whether sponge holobionts (i.e., host and prokaryotic symbionts) adapt their physiology to food released by coral- versus macroalgae.MethodsThereto, two sponge species, Plakortis angulospiculatus and Halisarca caerulea (high and low microbial abundance, respectively), were continuously exposed for 12 days to coral and macroalgal exudates in running seawater aquaria. Transcript expression of host and prokaryotic symbionts, changes in prokaryotic community composition, and holobiont physiological responses (i.e., respiratory demand, fluxes of carbon and nitrogen) were investigated after coral- versus macroalgae dominated treatments and compared to a seawater only control treatment.ResultsIn both sponge holobionts differential transcript expression between the coral and macroalgae treatments was very low (DiscussionAfter 12 days of exposure sponges appear to opportunistically feed on different food sources without having to adjust their metabolic pathways or associated prokaryotic communities. This suggests that sponges could be well-adapted to predicted changes in food source availability due to coral-to-algal phase shifts on many coral reefs.</p