Metal resistance genes enrichment in marine biofilm communities selected by biocide-containing surfaces in temperate and tropical coastal environments.

Microorganisms able to form biofilms in marine ecosystems are selected depending on immersed surfaces and environmental conditions. Cell attachment directly on toxic surfaces like antifouling coatings suggests a selection of tolerant (or resistant) organisms with characteristics conferring adaptive advantages. We investigated if environment would drive metal resistance gene abundance in biofilms on artificial surfaces. Biofilms were sampled from three surfaces (a PVC reference and two antifouling coatings) deployed in three coastal waters with dissimilar characteristics: The Mediterranean Sea (Toulon) and Atlantic (Lorient) and Indian (Reunion) Oceans. The two coatings differed in metals composition, either Cu thiocyanate and Zn pyrithione (A3) or Cu2O (Hy). Metal resistance genes (MRG) specific to copper (cusA, copA, cueO) or other metals (czcA and pbrT) were monitored with qPCR in parallel to the microbial community using 16S rRNA gene metabarcoding. A lower α-diversity on A3 or Hy than on PVC was observed independent on the site. Weighted Unifrac suggested segregation of communities primarily by surface, with lower site effect. Metacoder log2 fold change ratio and LeFSe discrimination suggested Marinobacter to be specific of Hy and Altererythrobacter, Erythrobacter and Sphingorhabdus of A3. Likewise, the relative abundance of MRG (MRG/bacterial 16S rRNA) varied between surfaces and sites. A3 presented the greatest relative abundances for cusA, cueO and czcA. The latter could only be amplified from A3 communities, except at Toulon. Hy surface presented the highest relative abundance for copA, specifically at Lorient. These relative abundances were correlated with LeFSe discriminant taxa. Dasania correlated positively with all MRG except cueO. Marinobacter found in greater abundance in Hy biofilm communities correlated with the highest abundances of copA and Roseovarius with czcA. These results prove the selection of specific communities with abilities to tolerate metallic biocides forming biofilms over antifouling surfaces, and the secondary but significant influence of local environmental factors.

Shear Stress as a Major Driver of Marine Biofilm Communities in the NW Mediterranean Sea.

While marine biofilms depend on environmental conditions and substrate, little is known about the influence of hydrodynamic forces. We tested different immersion modes (dynamic, cyclic and static) in Toulon Bay (north-western Mediterranean Sea; NWMS). The static mode was also compared between Toulon and Banyuls Bays. In addition, different artificial surfaces designed to hamper cell attachment (self-polishing coating: SPC; and fouling-release coating: FRC) were compared to inert plastic. Prokaryotic community composition was affected by immersion mode, surface characteristics and site. Rhodobacteriaceae and Flavobacteriaceae dominated the biofilm community structure, with distinct genera according to surface type or immersion mode. Cell density increased with time, greatly limited by hydrodynamic forces, and supposed to delay biofilm maturation. After 1 year, a significant impact of shear stress on the taxonomic structure of the prokaryotic community developed on each surface type was observed. When surfaces contained no biocides, roughness and wettability shaped prokaryotic community structure, which was not enhanced by shear stress. Conversely, the biocidal effect of SPC surfaces, already major in static immersion mode, was amplified by the 15 knots speed. The biofilm community on SPC was 60% dissimilar to the biofilm on the other surfaces and was distinctly colonized by Sphingomonadaceae ((Alter)Erythrobacter). At Banyuls, prokaryotic community structures were more similar between the four surfaces tested than at Toulon, due possibly to a masking effect of environmental constraints, especially hydrodynamic, which was greater than in Toulon. Finally, predicted functions such as cell adhesion confirmed some of the hypotheses drawn regarding biofilm formation over the artificial surfaces tested here.

Ammonia oxidisers in a non-nitrifying Brazilian savanna soil.

Low nitrification rates in Brazilian savanna (Cerrado) soils have puzzled researchers for decades. Potential mechanisms include biological inhibitors, low pH, low microbial abundance and low soil moisture content, which hinders microbial activity, including ammonia oxidation. Two approaches were used to evaluate these potential mechanisms: (i) manipulation of soil moisture and pH in microcosms containing Cerrado soil and (ii) assessment of nitrification inhibition in slurries containing mixtures of Cerrado soil and an actively nitrifying agricultural soil. Despite high ammonium concentration in Cerrado soil microcosms, little NO3- accumulation was observed with increasing moisture or pH, but in some Cerrado soil slurries, ammonia-oxidising archaea (AOA) amoA transcripts were detected after 14 days. In mixed soil slurries, the final NO3- concentration reflected the initial proportions of agricultural and Cerrado soils in the mixture, providing no evidence of nitrification inhibitors in Cerrado soil. AOA community denaturing gradient gel electrophoresis profiles were similar in the mixed and nitrifying soils. These results suggest that nitrification in Cerrado soils is not constrained by water availability, ammonium availability, low pH or biological inhibitors, and alternative potential explanations for low nitrification levels are discussed.

Soil Acidobacterial 16S rRNA Gene Sequences Reveal Subgroup Level Differences between Savanna-Like Cerrado and Atlantic Forest Brazilian Biomes.

16S rRNA sequences from the phylum Acidobacteria have been commonly reported from soil microbial communities, including those from the Brazilian Savanna (Cerrado) and the Atlantic Forest biomes, two biomes that present contrasting characteristics of soil and vegetation. Using 16S rRNA sequences, the present work aimed to study acidobacterial diversity and distribution in soils of Cerrado savanna and two Atlantic forest sites. PCA and phylogenetic reconstruction showed that the acidobacterial communities found in "Mata de galeria" forest soil samples from the Cerrado biome have a tendency to separate from the other Cerrado vegetation microbial communities in the direction of those found in the Atlantic Forest, which is correlated with a high abundance of Acidobacteria subgroup 2 (GP2). Environmental conditions seem to promote a negative correlation between GP2 and subgroup 1 (GP1) abundance. Also GP2 is negatively correlated to pH, but positively correlated to high Al(3+) concentrations. The Cerrado soil showed the lowest Acidobacteria richness and diversity indexes of OTUs at the species and subgroups levels when compared to Atlantic Forest soils. These results suggest specificity of acidobacterial subgroups to soils of different biomes and are a starting point to understand their ecological roles, a topic that needs to be further explored.