Biology subjects

Bergo, N. M.

Publications and source records attributed to Bergo, N. M..

5 recordsLinked to original sources

bioRxiv2025

Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean

BackgroundThe pelagic environment may present a mosaic of biogeographical domains that regional oceanographic processes can influence. Here, a coastal-to-open ocean microbiome investigation was conducted on 64 water samples from the Santos Basin (SB), South Atlantic Ocean. Using metagenomics and machine learning approaches, we assessed the diversity and distribution of pelagic microbes, identified key bacterial and archaeal taxa, and inferred their ecosystem functions. ResultsUnsupervised machine learning revealed a clear spatial and vertical (light availability) distribution pattern across SB, with some indicator taxa previously observed in other marine waters. Supervised learning further revealed that environmental variables, notably phosphate, salinity, and nitrate, which are key markers of local upwelling and the La Plata River plume, are primary drivers of microbial community structure. Furthermore, we recovered 307 metagenome-assembled genomes with 45% of Archaea and 42% of Bacteria possible new taxa. In terms of functionality, the SB dataset revealed a pelagic ecosystem resembling typical marine (e.g., Atlantic Ocean) waters, with photoautotrophs and nitrogen fixers in the photic zone and different autotrophic pathways in the aphotic environment. Surprisingly, the SB dataset revealed genes for CO bio-oxidation and algal dimethylsulfoniopropionate (DMSP) degradation at all depths. Furthermore, we observed potential non- cyanobacterial diazotrophs in dark water. ConclusionsOur results revealed that the SB represents a unique ecosystem with local oceanographic processes shaping the distribution of diverse and uncharacterized microbiomes. Additionally, these findings highlight the importance of mixotrophic microbes in SB biogeochemical cycles. This massive investigation of the SB pelagic microbiome provided knowledge-based data for understanding local ecosystem health, services, and dynamics, which are essential for future sustainable ocean management.

microbiology↗

bioRxiv2025

A Machine Learning Approach Elucidates Spatial Patterns of Environmental Properties Driving Microbial Composition Over Santos Basin, South Atlantic

Microbial communities in marine ecosystems play a pivotal role in global biogeochemical cycles, with particular relevance in ecologically and industrially significant regions such as the Santos Basin (SB), Brazils largest marine sedimentary basin and a hub for oil and gas exploration. Yet, our capacity of predicting the microbial community structure and function remains limited for marine ecosystems. This study investigated the structure of microbial communities across different depths in the SB, using amplicon sequencing data and quantitative cell counts obtained via flow cytometry. Using a hybrid machine learning framework combining Self-Organizing Maps and Random Forest, we identified five distinct microbial assemblages (named microbial associations) in the SB predicted with 86% accuracy. These associations were primarily driven by temperature, water density, salinity, and nutrients such as phosphate and nitrate. Our findings showed a clear stratification of microbial communities across pelagic zones, with temperature as the main factor driving the structure in epipelagic and mesopelagic layers, while salinity and density exerted greater influence in the deeper bathypelagic communities. Temporal and spatial variations, particularly between 2019 and 2021, in regions influenced by the Cabo Frio upwelling and Rio de la Plata plume, further highlighted the impact of regional and local oceanographic processes on community dynamics. The associations from deeper waters harbored more diverse microbial assemblages, and shallow waters, on the other hand, possess higher absolute abundance of microbial cells, suggesting niche specialization across depths. This study underscores the importance of environmental gradients as well as local oceanographic processes in shaping microbial diversity, providing valuable insights into the ecological dynamics of the SB, which are essential for understanding the potential impacts of human activities, such as oil and gas exploration and production, on these critical marine ecosystems.

microbiology↗

bioRxiv2022

Spatial Patterns of Microbial Diversity, Composition and Community Structure in Fe-Mn Deposits and Associated Sediments in the Atlantic and Pacific Oceans

Mining of deep-sea Fe-Mn deposits will remove crusts and nodules in large areas from the seafloor. The growth of a few millimeters of these minerals by Fe and Mn oxides precipitation takes millions of years, and yet little is known about their microbiome. Besides being key elements of the biogeochemical cycles and essential links of food and energy to deep-sea trophic webs, microbes have been identified to affect manganese oxide formation. Hence, polymetallic crusts and nodules may present unique habitats that deserve better understanding. In this study, we determined the composition and diversity of Bacteria and Archaea in deep-sea Fe-Mn crusts, nodules, and associated sediments from two oceanic elevations in the Atlantic Ocean, the Tropic Seamount in the northeast and the Rio Grande Rise (RGR) in the southwest. Sequencing of the 16S rRNA gene was performed using the Illumina MiSeq platform and statistical analyses using environmental data were performed in R. Additionally, we included public domain environmental DNA data of Fe-Mn crusts, nodules, and associated sediments from Clarion-Clipperton Zone and Takuyo-Daigo Seamount in the Pacific Ocean to compare microbial diversity in Fe-Mn deposits from different ocean basins. Our results indicated that Atlantic seamounts harbor an unusual and unknown Fe-Mn deposit microbiome with lower diversity and richness compared to deposits from Pacific areas. Crusts and nodules from Atlantic seamounts revealed the presence of unique taxa (Alteromonadales, Nitrospira, and Magnetospiraceae) and a higher relative abundance of sequences related to potential metal-cycling bacteria, such as Betaproteobacteriales and Pseudomonadales. The microbial beta-diversity from Atlantic seamounts was clearly grouped into microhabitats according to crusts, nodules, and sediments geochemical composition. Furthermore, community structure analysis using principal coordinate analysis also showed that the microbial communities of all seamounts were significantly divided into ocean basins and sampling areas. Despite the time scale of million years for these deposits to grow, a combination of environmental settings (temperature, salinity, depth, substrate geochemistry, nutrient, and organic matter availability) played a significant role in shaping the crusts and nodules microbiome, which was distinct between the Atlantic and Pacific Fe-Mn deposits. Our results suggest that the microbial community inhabiting Fe-Mn deposits participate in biogeochemical reactions indispensable to deep-sea ecosystems, which implies that understanding the microbial community is of utmost importance for any baseline environmental study in areas of potential deep-sea mining. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/485154v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1214ccorg.highwire.dtl.DTLVardef@1139796org.highwire.dtl.DTLVardef@144f967org.highwire.dtl.DTLVardef@151f069_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAtlantic deposits showed lower diversity and richness compared to Pacific deposits C_LIO_LIFe-Mn crusts and nodules are a potential specific ecological niche C_LIO_LIAtlantic Fe-Mn deposits harbor an unusual and unknown microbiome C_LIO_LITemperature, salinity, depth, and substrate geochemistry at Atlantic Fe-Mn deposits may drive community composition C_LI

microbiology↗

bioRxiv2021

Abundance and Microbial Diversity from Surface to Deep Water Layers Over the Rio Grande Rise, South Atlantic

Marine microbes control the flux of matter and energy essential for life in the oceans. Until now, the distribution and diversity of planktonic microorganisms above Fe-Mn crusts has received relatively little attention. Future mining\dredging of these minerals is predicted to affect microbial diversity and functioning in the deep sea. Here, we studied the ecology of planktonic microbes among pelagic environments of an Fe-Mn deposit region, at Rio Grande Rise, Southwestern Atlantic Ocean. We investigated microbial community composition using high-throughput sequencing of 16S rRNA genes and their abundance estimated by flow cytometry. Our results showed that the majority of picoplanktonic was found in epi- and mesopelagic waters, corresponding to the Tropical Water and South Atlantic Central Water. Bacterial and archaeal groups related to phototrophy, heterotrophy and chemosynthesis, such as Synechococcales, Sar11 (Proteobacteria) and Nitrosopumilales (Thaumarchaeota) were the main representatives of the pelagic microbial community. Additionally, we detected abundant assemblages involved in biodegradation of marine organic matter and iron oxidation at deep waters, i.e., Pseudoalteromonas and Alteromonas. No differences were observed in microbial community alpha diversity. However, we detected differences in community structure between water masses, suggesting that changes in an environmental setting (i.e. nutrient availability or circulation) play a significant role in structuring the pelagic zones, also affecting the meso- and bathypelagic microbiome. HighlightsO_LIRio Grande Rise pelagic microbiome C_LIO_LIPicoplankton carbon biomass partitioning through pelagic zones C_LIO_LIUnique SAR11 Clade I oligotype in the shallowest Tropical Water C_LIO_LIHigher number of shared oligotypes between deepest water masses C_LIO_LINitrogen, carbon and sulfur may be important contributors for the pelagic microbiome C_LI

microbiology↗

bioRxiv2020

Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean

Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial community based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. We observed differences of microbial structure according to the sampling location and depth, suggesting an influence of water circulation and availability of particulate organic matter. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Nitrosopumilus within Thaumarchaeota group were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i. e. Ca. Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.

microbiology↗