Microbial communities in the deep-sea sediments of the South São Paulo Plateau, Southwestern Atlantic Ocean

Microbial communities play a key role in the ocean, acting as primary producers, nutrient recyclers, and energy providers. The São Paulo Plateau is a region located on the southeastern coast of Brazil within economic importance, due to its oil and gas reservoirs. With this focus, this study examined the diversity and composition of microbial communities in marine sediments located at three oceanographic stations in the southern region of São Paulo Plateau using the HOV Shinkai 6500 in 2013. The 16S rRNA gene was sequenced using the universal primers (515F and 926R) by the Illumina Miseq platform. The taxonomic compositions of samples recovered from SP3 station were markedly distinct from those obtained from SP1 and SP2. Although all three stations exhibited a high abundance of Gammaproteobacteria (> 15%), this taxon dominated more than 90% of composition of the A and C sediment layers at SP3. The highest abundance of the archaeal class Nitrososphaeria was presented at SP1, mainly at layer C (~ 21%), being absent at SP3 station. The prediction of chemoheterotrophy and fermentation as important microbial functions was supported by the data. Additionally, other metabolic pathways related to the cycles of nitrogen, carbon and sulfur were also predicted. The core microbiome analysis comprised only two ASVs. Our study contributes to a better understanding of microbial communities in an economically important little-explored region. This is the third microbiological survey in plateau sediments and the first focused on the southern region.


Introduction
Deep-sea environments compose the largest habitat on Earth and are a major carbon sink on the planet (Burdige 2007;Corinaldesi 2015;Bienhold et al. 2016).Even though they present harsh environmental conditions, such as low temperatures (− 1 to 4 °C), high hydrostatic pressure, absence of solar radiation, and low supply of organic matter, these environments harbor microbial assemblages with high genetic and metabolic diversity (Corinaldesi 2015;Bienhold et al. 2016).
Microbes play a vital role in deep-sea environments, driving a wide range of processes, including those related to biogeochemical cycles, organic matter remineralization, and primary production by chemosynthetic organisms (Azam and Malfatti 2007).In these environments, most of the total microbial cell biomass appears to be composed of bacteria, although it may change towards anoxic subsurfaces, where archaea can dominate (Biddle et al. 2006;Corinaldesi 2015)..A lot of effort has been made in the past years to characterize and identify these deep-sea microbes, with most information coming from biodiversity hotspots, such as hydrothermal vents or cold seeps (Jørgensen and Boetius 2007;Corinaldesi 2015).However, the knowledge of the microbial communities present in "soft bottoms" are still very limited, even this habitat representing about 90% of the seabed (Corinaldesi 2015), with even less research conducted in the South Atlantic Ocean (Schauer et al. 2010;Giongo et al. 2016;Jiang et al. 2018;Queiroz et al. 2020).
Recently, an asphalt seep ecosystem was discovered in the northern region of São Paulo Plateau (Santos Basin, Southwestern Atlantic Ocean) at the depth of 2,700 m (Fujikura et al. 2017).Asphalt seeps are cold seeps where an escape of hydrocarbons occurs (Suess 2014;Medina-Silva et al. 2018).Other types of cold infiltration have already been described on the Brazilian margin (Miller et al. 2015;Giongo et al. 2016) and often have associated chemosynthetic communities (Giongo et al. 2016).However, the asphalt seeps found in the north region of the plateau had no evidence of an active chemosynthetic-based community due to a state of heavy biodegradation of the asphalt (Fujikura et al. 2017).Areas in the northern region of the Plateau covered with manganese oxide crusts and nodules have also been observed (Aguiar et al. 2014;Fujikura et al. 2017;Jiang et al. 2018).
Even though cold seeps, oxide crusts, or nodules have not yet been observed in the southern region of the São Paulo Plateau, this region is still poorly explored and may present important habitats for microbial assemblages.Previous research carried out in this region has already demonstrated the great taxonomic diversity of microbial communities in areas of asphalt exudation, with a high abundance of the Proteobacteria, Firmicutes, and Actinobacteria phyla.(Jiang et al. 2018;Queiroz et al. 2020).
To have a broader view of the microbial communities in the São Paulo Plateau, the main goal of this study was to assess the bacterial and archaeal diversity, taxonomic composition, predicted functions, and community structure in the deep-sea sediments of the southern region using high throughput 16S rRNA gene sequencing.Our study contributes to a better understanding of the benthic microbial communities of an economically important area such as the São Paulo Plateau; it is the third microbiology survey in sediments across the plateau and the first focused on the southern region.The samples were collected during a Japanese-Brazilian joint cruise (Kitazato et al. 2017) under the scope of the Quest for Limits of Life (QUELLE) Project, an around-the-world voyage of the Shinkai 6500 to unveil extreme habitats in different ocean basins.

Study area and sampling strategy
The São Paulo Plateau, located in the Santos Basin, is anomalously higher than the adjacent areas of the southeastern Brazilian margin.With great regional importance and a width of 120 to 250 km, the São Paulo plateau is relatively flat, with the main irregularities caused by the presence of salt diapirs and outcrops of igneous rocks.The region is also characterized by the presence of muddy sediments with bioclastic fragments (Kumar and Gambôa 1979;Almeida and Kowsmann 2015;Jiang et al. 2018).
Sediment sampling was carried out aboard the R/V Yokosuka as part of the QUELLE2013 project, under the Iatá-piúna subproject.The sampling expedition occurred in May 2013 using the research submersible SHINKAI 6500.The samples were collected at an average depth of 3,120 m with the aid of their mechanical arms and acrylic core samplers (30 cm length, 10 cm diameter).Sediment core samples were collected at three oceanographic stations (SP1, SP2, and SP3) (Fig. 1) located in the southern portion of the São Paulo Plateau (22°50'S-23°00'S and 39°10'W-38°30'W).The cores were extruded and subsampled from the water-sediment interface in 0-1 cm (A), 1-4 cm (B), and 4-7 cm (C) (Supplementary Table 1), and stored in Whirl-pack bags at − 80 °C.

DNA extraction, PCR, and sequencing
Each sample was homogenized and divided into two to generate a duplicate.DNA was extracted from 10 g of sediment using the commercial PowerMax Soil Isolation kit (Qiagen, Germany), following the manufacturer's protocol.The DNA from the duplicates was joined and concentrated using a Speed Vacuum (Eppendorf).DNA integrity was verified by electrophoresis in 1% (v/v) agarose gel, and concentration was assessed using the Qubit dsDNA HS assay kit (Thermo Fisher Scientific, Waltham, MA, USA).DNA quality was checked with NanoDrop ND1000 (Thermo Scientific, USA).A control sample was used throughout the procedure to ensure the efficiency and purity of the DNA extraction kit.The V4-V5 hypervariable region of the 16S rRNA gene was amplified with the universal primers (Bacteria and Archaea) 515F (5'-GTG YCA GCMGCC GCG GTAA-3') and 926R (5'-CCG YCA ATTYMTTT RAG TTT-3') (Quince et al. 2011;Parada et al. 2016).The initial PCR reaction consisted of a denaturation step at 95 °C for 3 min, followed by 35 cycles with 95 °C for 30 s, annealing at 57 °C for 30 s, extension at 72 °C for 30 s, and final extension at 72 °C for 5 min.Library preparation and sequencing were performed by Mr DNA/Molecular Research (Shallowater, TX, USA), using Illumina Miseq platform (2 × 250 bp system)..All sequenced data have been deposited in the National Center for Biotechnology Information Sequence Read Archives (SRA) under BioProject ID PRJNA701432.

Data analysis
Using the QIIME2 program (Quantitative Insights into Microbial Ecology -version 2019.4)(Bolyen et al. 2019), the sequences were demultiplexed; quality control and clustering were performed using DADA2 software (Callahan et al. 2016).Forward and reverse raw sequences were trimmed, filtered, denoised to exclude poor quality reads (below Phred score 30), and the chimera were removed.The taxonomy was assigned to reads as Amplicon Sequences Variant (ASVs) through a classify-learn plugin (Pedregosa et al. 2011) and SILVA database v.138 (Klindworth et al. 2013).The ASV table was normalized by a rarefaction method at a sampling depth of 37,248 sequences.
Core microbiome analysis within and across substrates was carried out using the Vegan (v.2.5.7)package.Prediction of metabolisms and ecological processes based on the 16S rRNA gene was performed using the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database 1.2.3 (Louca et al. 2016).

Profile of microbial communities
The 16S rRNA gene sequencing of the 9 samples resulted in a total of 4,360 ASVs, of which 3,773 belong to Bacteria and only 582 to Archaea.The samples from SP1 had the highest average number of ASV (1,287, SD ± 234), followed by SP2 which had an average of 545 ASVs per samples (SD ± 312), and SP3, which presented the lowest mean of ASV of 101 per samples (SD ± 36.7).The highest mean values of Chao1 and Shannon were also observed in SP1 (1,295 SD ± 245.3 and 6.53, SD ± 0.22, respectively), while SP3 presented the lowest mean values for these indexes (101, SD ± 36.7 and 2.7, SD ± 1.1, respectively).Alpha diversity indices are described in detail in Supplementary Table 2.No significant differences (p < 0.05) in alpha diversity indices among sediment layers or collection stations were detected.
The analysis of the non-metric multidimensional scale (Bray Curtis) does not reveal a clear distinction among the layers or among the collection stations, however, it is possible to observe a greater separation of the samples belonging to SP3 in relation to the others samples (Fig. 2).According to the PERMANOVA analysis, 39% of the variability of the microbial community was explained by the collection station and 25% of the variability was explained by the sediment layers.However, in both situations, the values obtained were not significantly different (p = 1), and the station x layers interaction was responsible for 35% of the variability (p = 1).(Supplementary Table 3).

Microbial taxonomic diversity in marine sediments
The composition of microbial communities varied between stations sampled and between different layers.The Bacteria domain was the most abundant in all analyzed samples, representing 89% of the groups identified in this study, while the Archaea domain represented only 11%.The Gammaproteobacteria class was dominant at SP2 and SP3, comprising 28% and 68% of the respective compositions.At SP1, a group of rare taxonomic classes (< 0.02% of abundance) showed predominance.The Nitrososphaeria and Nanoarchaeia were the only two archaeal classes that showed a presence bigger than 0.02% at the samples, with both being absent at SP3 station.
Besides the rare groups that exhibited similar distribution (between 24 and 28%) across the three sediment layers, other taxa that contributed significantly for the SP1 composition were Nitrososphaeria, Gammaproteobacteria, and Alphaproteobacteria.The Nitrososphaeria was present in high abundance across the sediment layers (> 13%), with particularly high presence levels in layer C (21.7%), which is the deepest layer.Gammaproteobacteria exhibited high presence in layer B (26%), while also being present at significant levels in the other sediment layers, comprising 15.7% of layer A and 9.6% of layer C. In contrast, the Alphaproteobacteria were primarily found in layer C (16%), comprising 8.6% and 9% of the layers A and B, respectively.Nanoarchaeia was identified in all samples of SP1, with relative abundances equal to 3%, 3%, and 6% for A, B and C layers, respectively.
At SP2, the abundance of both Gammaproteobacteria and Alphaproteobacteria was higher in layer B (38.8% and 27.5%, respectively) compared to layer A (15% and 12.6%).The Bacteroidia class also had a significant presence in layer B at SP2, accounting for 12% of the composition, however, its contribution was relatively minor (less than 4%) in the other sediment layers.Nitrososphaeria showed a high abundance in layers A (10%) and C (12%), but significantly lower presence in layer B (1.7%).Nanoarchaeia exhibited a comparable pattern, with higher abundance in layers A (2.8%) and C (2.7%) and lower abundance in layer B (0.1%).
The layers A and C in SP3 presented quite similar taxonomic composition, with predominance of the Gammaproteobacteria class representing 92% and 90% of the composition in the respective sediment layers.At layer B, Gammaproteobacteria represented 22% of the identified classes.Cyanobacteria, Bacteroidia, and Actinobacteria were also abundant classes in layer B, with relative abundance of 25%, 18%, and 12.7%, respectively.Interestingly, the Archaea domain was not detected in layers A and C at this station, while in layer B, only Methanobacteria were identified, representing 0.3% of the total composition and exclusively found in this sample (Fig. 3).

Core microbiome
The central core microbiome was composed of only two ASVs, both belonging to the Burkholderiaceae family, part of the Gammaproteobacteria class (Supplementary Table 4).When considering the three stations (SP1, SP2 and SP3) independently, regardless of the analyzed sediment layer, we observed that SP1 had the highest number of exclusive ASVs (151), followed by SP2 with 12 exclusive ASVs and SP3 with only 10.Only one ASV Bacteroidia class () was shared between stations SP1 and SP3.Between SP2 and SP3, we found six ASVs shared exclusively between their samples.They belonged to the classes Gammaproteobacteria, Actinobacteria, and Bacilli.Stations SP1 and SP2 shared 14 ASVs, 10 belonging to the Nitrososphaeria classand the others to the Alphaproteobacteria, Methylomirabilia, BD2-11 terrestrial group, and Gammaproteobacteria.
Analyzing the samples by the sediment layers, we observed that layer A presented only three exclusive ASVs, belonging to the Alphaproteobacteria, Anaerolineae and Acidimicrobiia classes.The layer B presented four unique ASVs that were Bacteroidia, Alphaproteobacteria, Gammaproteobacteria, and PAUC43f marine benthic group classes..The layers C samples also showed only four unique ASVs, which belong to the classes Gammaproteobacteria, Actinobacteria and Bacilli.No shared ASVs were found among A and C layers samples, nor between C and B layers.However, A and B layers shared three ASVs, which belong to the Actinobacteria and Gammaproteobacteria classes.

Predicted functions
To predict the potential functions by the microbial communities in the three stations of the south São Paulo Plateau, we analyzed the 4,360 ASVs detected using the cultured representatives of the FAPROTAX database (Louca et al. 2016).The predicted metabolisms included methanogenesis, methylotrophy (including methanotrophy), chemoheterotrophy, fermentation, functions related to the nitrogen cycle and hydrocarbon degradation, photoautotrophy, and oxidation of sulfur, thiosulfate, manganese, and hydrogen (Fig. 4).Chemoheterotrophy and fermentation were predicted in almost all samples, with a lower proportion at station SP1 and both absent in layer C of this station.
At the SP1 station, metabolisms related to the nitrogen cycle were highlighted, with aerobic oxidation of ammonia, aerobic oxidation of nitrite, and nitrification in all layers and nitrate respiration, nitrate reduction, nitrogen respiration especially in layer B. Nitrogen-related processes were also highlighted.significant in station SP2, especially in layer A and C. In station SP3, nitrate respiration, nitrate reduction and nitrogen respiration stood out especially in layer A.
Processes associated with the sulfur cycle have also been predicted, including the oxidation of hydrogen (in layer C at SP2 and layer B at SP3), and the oxidation of thiosulfate and sulfur compounds (with high abundance observed only in layer A at SP2).Metabolisms related to the photoautotrophy process, such as oxygenic photoautotrophy, photoautotrophy, photoheterotrophy, phototrophy, were predicted in high abundance exclusively in layer B of SP3.Methanogenesis was predicted only for samples from layer C of SP1 and layer B of SP3.The main type of methanogenesis predicted in layer C at SP1 was related to the reduction of methyl compounds, while for the layer B in SP3 samples it was mostly related to the reduction of carbon dioxide and hydrogen The oxidation of methanol was predicted only in layer C of SP3.Methylotrophy and methanotrophy were predicted in layer B of SP3, with methylotrophs also being predicted in the deeper layer (C) of SP1 and SP3.
Aromatic compound degradation is a process that was predicted in almost all samples, being absent only in layer A of SP3 station, while the degradation of hydrocarbons seems to be absent at SP1 and mostly abundant in SP3.The specific degradation of aromatic hydrocarbons was predicted in high abundance only in layer B of SP2.Less abundant processes, such as ureolysis (only at layer A of SP1 and layer B in SP3) and manganese oxidation (high abundance but only in layer B of SP3) also were predicted in the samples.

Description of the microbial communities of the South Plateau of São Paulo
The southeastern margin of Brazil is responsible for a large part of the country's oil production (Mariano and La Rovere 2007;Cordes et al. 2016).This area is relatively well studied with respect to oceanographic patterns (Bernardino et al. 2016), however, the microbial communities in this region are still poorly studied, especially in potential seepage areas.The investigation and discovery of asphalt infiltrations in the northern region of São Paulo Plateau (Fujikura et al. 2017) were significantly important Fig. 3 Relative abundance of Bacteria and Archaea (> 0.02%) in each sample.Each box represents a station, and each color represents a class where the bar size of the respective color is the abundance of respective taxa.Rare groups (< 0.02%) are presented in Figure S1 for the description and understanding of this habitat, especially for the study of microbial communities.In the southern region of São Paulo Plateau, although there are still no records of asphalt exudations, it is a geologically active area, with numerous geological faults associated with diapirism (Fujikura et al. 2017).In this study, we provide the first insights into the characterization (diversity, composition, structure and predicted metabolisms) of microbial communities that inhabit the sediments of the southern region of the Planalto de São Paulo.
A high diversity of prokaryotes was recovered, covering more than 4,000 ASVs and 40 phyla, with a predominance of Bacteria over Archaea.The most abundant phyla were Proteobacteria and Crenarchaeota.The high abundance of these groups in surface marine sediments has already been reported in several previous studies (Hongxiang et al. 2008;Li et al. 2009;Schauer et al. 2010;Zinger et al. 2011;Petro et al. 2017;Hoshino et al. 2020;Franco et al. 2021).Nitrososphaeria, representative of the phylum Crenarchaeota and one of the most abundant classes in this study, is one of the most widely distributed classes of Archaea globally, especially in underground marine sediments (Kubo et al. 2012;Petro et al. 2017;Hoshino et al. 2020).The two bacterial classes with more abundance in this study representing the Proteobacteria phylum were Gamma-and Alphaproteobacteria.Both taxa, but mainly Gamma-can be commonly found dominating deep-sea sediments (Xie et al 2005;Hongxiang et al 2008;Danovaro et al 2010;Queiroz et al 2020).As in our study, Queiroz et al., investigating the microbial communities of the North Plateau that were under the influence of asphalt exudations, found Alpha and Gammaproteobacteria as the most abundant classes of the phylum Proteobacteria.Other representative phyla in this study, such as Bacteroidota, Actinobacteria, Chloroflexi, Firmicutes and Acidobacteriota are also commonly cited in microbial communities from deepwater environments (Schauer et al. 2010;Petro et al. 2017;Hoshino et al. 2020;Franco et al. 2021).
Interestingly, cyanobacteria were found in all samples, but in low abundance, while in layer B of station SP3 this group was found in high proportions.This group was long thought to be restricted to areas exposed or occasionally exposed to sunlight (Philippot et al. 2010).Today it is known that Cyanobacteria are very versatile microorganisms (Whitton and Potts 2012), and with the ability to generate energy independent of sunlight (Stal 2012).Several works have already reported the presence of cyanobacteria in deep subsurface samples (Thiel et al. 1990;Tang et al. 2014;Lindh et al. 2017), especially as discussed in detail by Hubalek et al. (2016).The presence of cyanobacteria at depth may also be related to the pelagicbenthic integration, in which there may be deposition of phytodetrital aggregates from the surface to regions of great depth (Pfannkuche and Lochte 1993).There are also reports that cyanobacteria in deep marine sediments survive by hydrogenotrophy in the absence of light (Puente-Sánchez et al. 2018).In the present study, due to the high abundance of this group in the SP3 station, these microorganisms are probably indigenous to the collected station.

Core microbiome analysis
The ASVs that composed the core microbiome were assigned to Burkholderiaceae, a metabolically diverse family that occupies several niches (Chen et al. 2017;Okrasińska et al. 2021).Compared to a previous study conducted in the  2020), the relative abundance of bacterial taxa in sediments showed some differences.The most representative phylum was Proteobacteria for both plateau regions (north and south), however, the second most representative phylum of the northern region was Actinobacteria (20.8%), which in this study represents only 5.3% of the samples.At the class level, this difference could also be observed.When analyzing Proteobacteria, the most representative class in the southern region was Gammaproteobacteria, whereas in the northern region it was Alphaproteobacteria.Also, the Deltaproteobacteria class found in the northern region did not appear in the south.This contrast in abundance could be the result of the different methodologies and sequencing processes used or different environmental drivers of the two regions of the plateau (north and south).

Prediction of metabolic potential
Microorganisms play a fundamental role in biogeochemical cycles acting as the main or exclusive actors of these processes in the ocean (Gilbert and Neufeld 2014).Two different pathways of the nitrogen cycle appeared as predicted functions in the South São Paulo Plateau: ammonia oxidation, which is a rate-limiting step of nitrification (Nicol and Schleper 2006), and the reduction of nitrate and nitrogen respiration, which are part of the denitrification process.The ammonia oxidation is likely related to the presence of the class Nitrosophaeria.Crenarchaeota are an abundant component of oceanic microbiota (Karner et al. 2001;Wuchter et al. 2003;Hallam et al. 2006).Wang et al (2005) also found Crenarchaeota as the predominant archaeal group in deep sediments of the west Pacific.The role of Crenarchaeota in the nitrogen and carbon cycles has already been discussed (Wuchter et al. 2003(Wuchter et al. , 2006;;Nicol and Schleper 2006;Francis et al. 2005Francis et al. , 2007) ) indicating this group as active nitrifiers and possible important constituents of these biogeochemical cycles in marine environments.
Other predicted metabolisms, such as thiosulfate and sulfur compound oxidation, are related with sulfur and carbon cycles, appearing in high proportions, but only in a few samples.The sulfur cycle in marine sediments is primarily driven by the sulfate reduction (Wasmund et al. 2017) with the thiosulfate oxidation acting as an intermediate (Jørgensen 1990), and some thiosulfate oxidation pathways playing a key role in deep-sea cold-seep environments (Zhang et al. 2020).It is suggested that up to 29% of remineralization of organic matter in the seafloor is facilitated by sulfatereducing microbes (Bowles et al. 2014), with the process of remineralization being a central part of the marine carbon cycle (Arnosti 2014).The sulfur oxidation in the samples is likely related to the presence of some strains of Gammaproteobacteria and Alphaproteobacteria.These are the only two classes found in the samples which is known to possess the rdsr enzyme capable of realizing these metabolic pathway (Anantharaman et al 2018).The thiosulfate oxidation is probably related to the presence of some Alphaproteobacteria strains that have already been described acting as thiosulfate-oxidizing in marine sediments (Teske et al 2000).Besides sulfate-reducing related with remineralization, the natural production and oxidation of methane (methanogenesis and methanotrophy) and its derivatives (methylotrophs) also appear in the samples.These predicted functions indicate the important role of the microbial communities in the south São Paulo plateau for the maintenance of the biogeochemical cycles of sulfur, carbon, and especially nitrogen.
An important and common characteristic of the São Paulo Plateau's area is the presence of outcrops of mudstones covered by a thin layer of black manganese oxide (Fujikura et al. 2017;Jiang et al. 2018), described in the northern region just in non-asphalt areas (Fujikura et al. 2017;Queiroz et al. 2020).It has already been described that the ability of oxidation of soluble manganese by manganese-oxidizing organisms, including prokaryotes, results in the accumulation of black or brown manganese oxides deposits (Nealson 2006).We predicted the metabolism related to the oxidation of manganese in the microbial communities from the south São Paulo Plateau in only one sample at station SP3.However, we also found other metabolisms that could be related to the possible influence of asphalt seeps in the microbial communities from this station, such as hydrocarbon degradation, methanotrophy and methylotrophy.
Although it has not been detected through Shinkai images in the southern region of the plateau, these hydrocarbon exudations can be an important microbial environment in the region, considering the geological characteristics of the area and the recent discovery of asphalt seeps in the northern region (Jiang et al. 2018;Queiroz et al. 2020).Cold seep ecosystems are often related to chemosynthetic life (Schubotz et al. 2011a, b), and have high levels of endemism, sharing a core community (Ruff et al. 2015).Schubotz et al (2011a, b a,b) studied solidified deposits of asphalts associated with salt diapirism from the southern Gulf of Mexico, indicating the occurrence of microbial hydrocarbon degradation in the asphalt deposits..The use of hydrocarbon as source of carbon and energy is widespread across classes of metabolically versatile Bacteria (Prince et al 2010;Gutierrez and Kleindienst 2020), however, some bacteria are specialized in the degradation of hydrocarbons, which the majority genera are part of the Gammaproteobacteria class (Gutierrez 2018;Gutierrez and Kleindienst 2020).The degradation of hydrocarbons, aromatic compounds and methylotrophy was predicted in the south region of the plateau, mainly at the SP3 station.
The methanotrophy is a metabolic pathway that involves the consumption of methane, which can occur in either an aerobic or anaerobic environment (Tavormina et al 2008;Knittel and Boetius 2009;Ruff 2020).Aerobic methanotrophic bacteria are commonly found present in the oxic sediment layer of hydrocarbon seeps (Tavormina et al 2008;Ruff 2020), while anaerobic methanotrophic archaea (ANME) typically occur coupled with sulfate-reducing bacteria (Knittel and Boetius 2009;Ruff 2020).Methanotrophs have been predicted exclusively in layer B of SP3 station, since this station, with exception of Methanobacteria, is absent from archaea, the process could be related with some members of Gammaproteobacteria and Alphaproteobactia classes.The Methanobacteria affiliated with Euryarchaeota is one of the clades most involved in syntrophic interactions related to methanogenic oil degradation (Pannekens et al. 2019).Besides that, Shlimon et al (2020) analyzed the microbial diversity of asphalt seeps in the Kurdistan Region of Iraq (KRI) and observed a high prevalence of several phyla, including members of the order Burkholderiales, which comprise two members of the core microbiome of this study.
Although no statistical differences were detected between the alpha diversity indices related to the stations, it is possible to observe some differences in the archaeal composition and predicted functions of SP3 versus the other stations.

Conclusion
This study is the first report of microbial (archaea and bacteria) communities in sediments of the South São Paulo Plateau.The observed pattern of deep-sea microbial composition is comparable to previous studies in other ocean basins, mainly in the northern plateau, with some differences related to the relative abundance of each taxon.The bacterial class Gammaproteobacteria, with the Burkholderiaceae family being part of the core microbiome, and the archaeal group Crenarchaeota were the most predominant taxa identified in our study.Also, no significant differences were detected in alpha diversity indices between sediment layers or geographic locations.The predicted functions indicate a role of the microbial communities in the biogeochemical cycles, mainly nitrogen along with carbon and sulfur.

Fig. 1
Fig. 1 Sampling map comprising the three oceanographic stations (SP1, SP2, and SP3) in the South São Paulo Plateau area at Southwestern Atlantic Ocean and the distance between the sampling location and the Brazilian coastal area

Fig. 2
Fig.2Non-metric multidimensional scaling (nMDS) based on Bray-Curtis distance.The colors represent the stations: red for SP1, green for SP2, and blue for SP3.The geometric figures represent the sediment layers: circle for A (0-1 cm), triangle for B (1-4 cm), and square for C (4-7 cm)

Fig. 4
Fig. 4 Predictions on the potential metabolisms and ecological processes harbored by the microbial communities at the sediment of the South São Paulo Plateau.The size of circles represents the relative abundance of each function and the color indicates the sample