Biology subjects

Paula, F. S.

Publications and source records attributed to Paula, F. S..

5 recordsLinked to original sources

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↗

bioRxiv2021

Development of chemosynthetic microbial communities in organic falls deployed in the deep Southwest Atlantic Ocean

The assembly and successional processes of microbial communities inhabiting deep-sea whale and wood falls are highly complex and vastly unknown, as a myriad of factors may affect the development of a chemosynthetic-based ecosystem on these organic islands. The chemoautotrophy supported by organic substrates is the basis of long-lasting ecosystems, considered biodiversity hotspots in the oligotrophic deep sea. Understanding how these microbial communities develop and the factors affecting them could shed light on processes related to the maintenance of biodiversity in this environment. We performed a whale- and wood-fall experiment in the southwest Atlantic on the Brazilian continental margin and investigated biofilm-forming bacterial and archaeal communities colonising these substrates, deployed at 1500 and 3300 m depth. The composition of the prokaryotic communities shared some similarities with previously reported organic falls in the north Pacific and the Mediterranean Sea, mainly regarding sulphur oxidising chemolithotrophic taxa from the phyla Campylobacterota and Proteobacteria. Communities were found to be highly different between the organic substrates, as whale fall associated biofilms presented a higher dominance of sulphur oxidising chemolithotrophs. We also observed a significant difference between the two sites, with the whale associated communities at the 1500 isobath presenting a faster establishment of the chemosynthetic taxa.

microbiology↗

bioRxiv2020

Seasonal dynamics of methane cycling microbial communities in Amazonian floodplain sediments.

The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and provide a significant contribution to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here we provide the first report of the in situ seasonal dynamics of CH4 cycling microbial communities in Amazonian floodplains. We asked how abiotic factors may affect both overall and CH4 cycling microbial communities and further investigated their responses to seasonal changes. We collected sediment samples during wet and dry seasons from three different types of floodplain forests, along with upland forest soil samples, from the Eastern Amazon, Brazil. We used high-resolution sequencing of archaeal and bacterial 16S rRNA genes combined with real-time PCR to quantify Archaea and Bacteria, as well as key functional genes indicative of the methanogenic (methyl coenzyme-M reductase - mcrA) and methanotrophic (particulate methane monooxygenase - pmoA) metabolisms. Methanogens were found to be present in high abundance in floodplain sediments and they seem to resist to dramatic seasonal environmental changes. Methanotrophs known to use different pathways to oxidise CH4 were detected, including anaerobic archaeal and bacterial taxa, indicating that a wide metabolic diversity may be harboured in this highly variable environment. The floodplain environmental variability, which is affected by the river origin, drives not only the sediment chemistry, but also the composition of the microbial communities. The results presented may contribute to the understanding of the current state of CH4 cycling in this region.

microbiology↗

bioRxiv2019

Organic soil amendment with Spent Mushroom Substrate results in fungal colonisation, alters bacterial-fungal co-occurrence patterns and improves plant productivity.

In agricultural systems based on organic fertilisers, the activity of prokaryotes and fungi is essential for degradation of complex substrates and release of nutrients for plant uptake. Understanding the dynamics of microbial communities in these systems is, therefore, desirable for designing successful management strategies aiming to optimise nutrient availability and to improve plant productivity. Of particular interest is how the microbial inoculum provided by an organic substrate persists in the soil and interacts with soil and plant microbiomes, as these processes may affect the long-term benefits of organic amendments. We aimed to investigate how these dynamics occurred in soil treated with stabilised spent mushroom substrate (SMS), a soil amendment rich in nutrients and complex organic matter. We carried out a 14 weeks soil trial to assess the plant growth promoting properties of the SMS and to monitor the successional processes of the resulting SMS-soil communities compared to a mineral amended control. Bacterial and fungal communities were analysed by high-throughput sequencing at both DNA and RNA (cDNA) levels. Using a combination of computational tools, including SourceTracker and Network analysis, we assessed the persistence of SMS-derived taxa in soil, and the changes in co-occurrence patterns and microbial community structure over time. Prokaryotic and fungal communities presented remarkably distinct trajectories following SMS treatment. The soil prokaryotic communities displayed higher levels of resilience to the changes introduced by SMS treatment and rapidly tended toward a soil-like profile, with low persistence of SMS-derived prokaryotes. In contrast, the SMS fungal community had greater success in soil colonisation during the time monitored. SMS treatment promoted an increase in the participation of fungi in the highly connected fraction of the active community, including fungal taxa of SMS origin. We observed the presence of highly connected microbial guilds, composed by fungal and bacterial taxa with reported capabilities of complex organic matter degradation. Many of these taxa were also significantly correlated with the organic matter content and plant yield, suggesting that these highly connected taxa may play key roles not only in the community structure, but also in the plant-soil system under organic fertilisation.

microbiology↗

bioRxiv2019

The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation in Methanosarcina mazei.

Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeon Methanosarcina mazei. Pi-starved M. mazei cells increased transcript abundance of the PHO-regulated alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starved M. mazei cells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a >5.7-fold increase in ppk1 gene transcripts. Ppk1 expression in M. mazei thus appears not to be under classical PHO regulon control.

microbiology↗