Andressa M. Venturini has a bachelor’s and licentiate’s degrees in biological science from the Luiz de Queiroz College of Agriculture (ESALQ/USP). Venturini received her doctorate degree in science in 2019 from the Center for Nuclear Energy in Agriculture of the University of São Paulo (CENA/USP) in Brazil, having previously received a master’s degree in science from the same institution in 2014. In 2021, her thesis received the USP Outstanding Thesis Award - 10th Edition in the area of Environmental Sustainability. She also spent a period abroad at the Netherlands Institute of Ecology (NIOO-KNAW) and, during her Ph.D., at the University of Oregon (UO). Venturini has previously worked at the Paulista University (UNIP) and as a postdoc at CENA/USP. She has experience in Soil Microbial Ecology, Molecular Biology, and Bioinformatics. Her research is focused on the microbial communities of tropical soils, their role in biogeochemical cycles, and how they are being impacted by land-use and climate change. During the 2021-22 academic year, Venturini was a Fung Global Fellow Postdoctoral Research Associate at Princeton University.
Honors & Awards
USP Outstanding Thesis Award - 10th Edition - Area of Environmental Sustainability, University of São Paulo (USP - Brazil) (2021)
2nd Best Poster (co-author) - 1st Amazon Meeting, Brazilian Society of Biochemistry and Molecular Biology (SBBq - Brazil) (2019)
Best Poster - 1st Amazon Meeting, Brazilian Society of Biochemistry and Molecular Biology (SBBq - Brazil) (2019)
Best Scientific Abstract - VI Scientific Symposium of CENA Graduate Students, Graduate Students’ Association (APG-CENA/USP - Brazil) (2013)
Second Best Biological Photograph - X SerBio, Methodist University of Piracicaba (UNIMEP - Brazil) (2011)
Honorable Mention - 56º Brazilian Congress of Genetics, Brazilian Society of Genetics (SBG - Brazil) (2010)
Scientific Merit and Best Biomedical Theme, State University of Campinas (UNICAMP - Brazil) (2010)
Third Best Poster - I Brazilian School of Bioinformatics, Brazilian Society of Computation (SBC - Brazil) (2008)
Kabir Peay, Postdoctoral Faculty Sponsor
Metagenome-Assembled Genomes from Amazonian Soil Microbial Consortia
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
2022; 11 (11): e0080422
Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.
View details for DOI 10.1128/mra.00804-22
View details for Web of Science ID 000878201400001
View details for PubMedID 36301097
View details for PubMedCentralID PMC9670897
Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon
2022; 212: 113139
Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.
View details for DOI 10.1016/j.envres.2022.113139
View details for Web of Science ID 000793114600009
View details for PubMedID 35337832
Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments.
2022; 10 (9)
Although floodplains are recognized as important sources of methane (CH4) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH4 emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functional potential and life strategies of these organisms living under seasonal flooding is still missing. Here, we described the first metagenome-assembled genome (MAG) of a Methylocystis sp. recovered from Amazonian floodplains sediments, and we explored its functional potential and ecological traits through phylogenomic, functional annotation, and pan-genomic approaches. Both phylogenomics and pan-genomics identified the closest placement of the bin.170_fp as Methylocystis parvus. As expected for Type II methanotrophs, the Core cluster from the pan-genome comprised genes for CH4 oxidation and formaldehyde assimilation through the serine pathway. Furthermore, the complete set of genes related to nitrogen fixation is also present in the Core. Interestingly, the MAG singleton cluster revealed the presence of unique genes related to nitrogen metabolism and cell motility. The study sheds light on the genomic characteristics of a dominant, but as yet unexplored methanotroph from the Amazonian floodplains. By exploring the genomic potential related to resource utilization and motility capability, we expanded our knowledge on the niche breadth of these dominant methanotrophs in the Amazonian floodplains.
View details for DOI 10.3390/microorganisms10091747
View details for PubMedID 36144349
View details for PubMedCentralID PMC9506196
Molecular evidence for stimulation of methane oxidation in Amazonian floodplains by ammonia-oxidizing communities
FRONTIERS IN MICROBIOLOGY
2022; 13: 913453
Ammonia oxidation is the rate-limiting first step of nitrification and a key process in the nitrogen cycle that results in the formation of nitrite (NO2 -), which can be further oxidized to nitrate (NO3 -). In the Amazonian floodplains, soils are subjected to extended seasons of flooding during the rainy season, in which they can become anoxic and produce a significant amount of methane (CH4). Various microorganisms in this anoxic environment can couple the reduction of different ions, such as NO2 - and NO3 -, with the oxidation of CH4 for energy production and effectively link the carbon and nitrogen cycle. Here, we addressed the composition of ammonium (NH4 +) and NO3 --and NO2 --dependent CH4-oxidizing microbial communities in an Amazonian floodplain. In addition, we analyzed the influence of environmental and geochemical factors on these microbial communities. Soil samples were collected from different layers of forest and agroforest land-use systems during the flood and non-flood seasons in the floodplain of the Tocantins River, and next-generation sequencing of archaeal and bacterial 16S rRNA amplicons was performed, coupled with chemical characterization of the soils. We found that ammonia-oxidizing archaea (AOA) were more abundant than ammonia-oxidizing bacteria (AOB) during both flood and non-flood seasons. Nitrogen-dependent anaerobic methane oxidizers (N-DAMO) from both the archaeal and bacterial domains were also found in both seasons, with higher abundance in the flood season. The different seasons, land uses, and depths analyzed had a significant influence on the soil chemical factors and also affected the abundance and composition of AOA, AOB, and N-DAMO. During the flood season, there was a significant correlation between ammonia oxidizers and N-DAMO, indicating the possible role of these oxidizers in providing oxidized nitrogen species for methanotrophy under anaerobic conditions, which is essential for nitrogen removal in these soils.
View details for DOI 10.3389/fmicb.2022.913453
View details for Web of Science ID 000840765400001
View details for PubMedID 35979497
View details for PubMedCentralID PMC9376453
Metagenomes from Eastern Brazilian Amazonian Floodplains in the Wet and Dry Seasons
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
2022; 11 (8): e0043222
Here, we report the metagenomes from two Amazonian floodplain sediments in eastern Brazil. Tropical wetlands are well known for their role in the global carbon cycle. Microbial information on this diversified and dynamic landscape will provide further insights into its significance in regional and global biogeochemical cycles.
View details for DOI 10.1128/mra.00432-22
View details for Web of Science ID 000827875700001
View details for PubMedID 35852316
View details for PubMedCentralID PMC9387299
Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils.
2022; 8 (7)
Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.
View details for DOI 10.1099/mgen.0.000853
View details for PubMedID 35894927
View details for PubMedCentralID PMC9455692
Responses of Low-Cost Input Combinations on the Microbial Structure of the Maize Rhizosphere for Greenhouse Gas Mitigation and Plant Biomass Production
FRONTIERS IN PLANT SCIENCE
2021; 12: 683658
The microbial composition of the rhizosphere and greenhouse gas (GHG) emissions under the most common input combinations in maize (Zea mays L.) cultivated in Brazil have not been characterized yet. In this study, we evaluated the influence of maize stover coverage (S), urea-topdressing fertilization (F), and the microbial inoculant Azospirillum brasilense (I) on soil GHG emissions and rhizosphere microbial communities during maize development. We conducted a greenhouse experiment and measured methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) fluxes from soil cultivated with maize plants under factorial combinations of the inputs and a control treatment (F, I, S, FI, FS, IS, FIS, and control). Plant biomass was evaluated, and rhizosphere soil samples were collected at V5 and V15 stages and DNA was extracted. The abundance of functional genes (mcrA, pmoA, nifH, and nosZ) was determined by quantitative PCR (qPCR) and the structure of the microbial community was assessed through 16S rRNA amplicon sequencing. Our results corroborate with previous studies which used fewer input combinations and revealed different responses for the following three inputs: F increased N2O emissions around 1 week after application; I tended to reduce CH4 and CO2 emissions, acting as a plant growth stimulator through phytohormones; S showed an increment for CO2 emissions by increasing carbon-use efficiency. IS and FIS treatments presented significant gains in biomass that could be related to Actinobacteria (19.0%) and Bacilli (10.0%) in IS, and Bacilli (9.7%) in FIS, which are the microbial taxa commonly associated with lignocellulose degradation. Comparing all factors, the IS (inoculant + maize stover) treatment was considered the best option for plant biomass production and GHG mitigation since FIS provides small gains toward the management effort of F application.
View details for DOI 10.3389/fpls.2021.683658
View details for Web of Science ID 000673424600001
View details for PubMedID 34276734
View details for PubMedCentralID PMC8278312
Not just a methane source: Amazonian floodplain sediments harbour a high diversity of methanotrophs with different metabolic capabilities
2021; 30 (11): 2560-2572
The Amazonian floodplain forests are dynamic ecosystems of great importance for the regional hydrological and biogeochemical cycles and function as a significant CH4 source contributing to the global carbon balance. Unique geochemical factors may drive the microbial community composition and, consequently, affect CH4 emissions across floodplain areas. Here, we report the in situ composition of CH4 cycling microbial communities in Amazonian floodplain sediments. We considered how abiotic factors may affect the microbial community composition and, more specifically, CH4 cycling groups. 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 presence of methanogenic (mcrA) and methanotrophic (pmoA) microorganisms. Methanogens were found to be present in high abundance in floodplain sediments, and they seem to resist the dramatic environmental changes between flooded and nonflooded conditions. 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. These environmental changes seem also to affect the pools of methanotrophs occupying distinct niches. Understanding these shifts in the methanotrophic communities could improve our comprehension of the CH4 emissions in the region.
View details for DOI 10.1111/mec.15912
View details for Web of Science ID 000639752200001
View details for PubMedID 33817881
Combined use of vinasse and nitrogen as fertilizers affects nitrification, ammonification and denitrification by prokaryotes
Frontiers in Soil Science
View details for DOI 10.3389/fsoil.2021.746745
Belowground changes to community structure alter methane-cycling dynamics in Amazonia
2020; 145: 106131
Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6 ± 9482.3 μg CH4 m-2 d-1), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8 ± 120.5 μg CH4 m-2 d-1), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2 ± 35.7 μg CH4 m-2 d-1), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.
View details for DOI 10.1016/j.envint.2020.106131
View details for Web of Science ID 000580632000047
View details for PubMedID 32979812
Metagenome assembled-genomes reveal similar functional profiles ofCPR/Patescibacteria phyla in soils
ENVIRONMENTAL MICROBIOLOGY REPORTS
2020; 12 (6): 651-655
Soil microbiome is one of the most heterogeneous biological systems. State-of-the-art molecular approaches such as those based on single-amplified genomes (SAGs) and metagenome assembled-genomes (MAGs) are now improving our capacity for disentailing soil microbial-mediated processes. Here, we analysed publicly available datasets of soil microbial genomes and MAG's reconstructed from the Amazon's tropical soil (primary forest and pasture) and active layer of permafrost, aiming to evaluate their genome size. Our results suggest that the Candidate Phyla Radiation (CPR)/Patescibacteria phyla have genomes with an average size fourfold smaller than the mean identified in the RefSoil database, which lacks any representative of this phylum. Also, by analysing the potential metabolism of 888 soil microbial genomes, we show that CPR/Patescibacteria representatives share similar functional profiles, but different from other microbial phyla and are frequently neglected in the soil microbial surveys. Finally, we argue that the use of MAGs may be a better choice over SAGs to expand the soil microbial databases, like RefSoil.
View details for DOI 10.1111/1758-2229.12880
View details for Web of Science ID 000566448000001
View details for PubMedID 32815317
Robust DNA protocols for tropical soils
2020; 6 (5): e03830
Studies in the Amazon are being intensified to evaluate the alterations in the microbial communities of soils and sediments in the face of increasing deforestation and land-use changes in the region. However, since these environments present highly heterogeneous physicochemical properties, including contaminants that hinder nucleic acids isolation and downstream techniques, the development of best molecular practices is crucial. This work aimed to optimize standard protocols for DNA extraction and gene quantification by quantitative real-time PCR (qPCR) based on natural and anthropogenic soils and sediments (primary forest, pasture, Amazonian Dark Earth, and várzea, a seasonally flooded area) of the Eastern Amazon. Our modified extraction protocol increased the fluorometric DNA concentration by 48%, reaching twice the original amount for most of the pasture and várzea samples, and the 260/280 purity ratio by 15% to values between 1.8 to 2.0, considered ideal for DNA. The addition of bovine serum albumin in the qPCR reaction improved the quantification of the 16S rRNA genes of Archaea and Bacteria and its precision among technical replicates, as well as allowed their detection in previously non-amplifiable samples. It is concluded that the changes made in the protocols improved the parameters of the DNA samples and their amplification, thus increasing the reliability of microbial communities' analysis and its ecological interpretations.
View details for DOI 10.1016/j.heliyon.2020.e03830
View details for Web of Science ID 000537749900015
View details for PubMedID 32426533
View details for PubMedCentralID PMC7226647
Aulas práticas de laboratório como método de ensino de genética molecular
Revista De Graduação USP
2018; 3 (2)
View details for DOI 10.11606/issn.2525-376X.v3i2p81-85
Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon
FRONTIERS IN MICROBIOLOGY
2015; 6: 1443
Members of the phylum Acidobacteria are among the most abundant soil bacteria on Earth, but little is known about their response to environmental changes. We asked how the relative abundance and biogeographic patterning of this phylum and its subgroups responded to forest-to-pasture conversion in soils of the western Brazilian Amazon. Pyrosequencing of 16S rRNA genes was employed to assess the abundance and composition of the Acidobacteria community across 54 soil samples taken using a spatially nested sampling scheme at the landscape level. Numerically, Acidobacteria represented 20% of the total bacterial community in forest soils and 11% in pasture soils. Overall, 15 different Acidobacteria subgroups of the current 26 subgroups were detected, with Acidobacteria subgroups 1, 3, 5, and 6 accounting together for 87% of the total Acidobacteria community in forest soils and 75% in pasture soils. Concomitant with changes in soil chemistry after forest-to-pasture conversion-particularly an increase in properties linked to soil acidity and nutrient availability-we observed an increase in the relative abundances of Acidobacteria subgroups 4, 10, 17, and 18, and a decrease in the relative abundances of other Acidobacteria subgroups in pasture relative to forest soils. The composition of the total Acidobacteria community as well as the most abundant Acidobacteria subgroups (1, 3, 5, and 6) was significantly more similar in composition across space in pasture soils than in forest soils. These results suggest that preponderant responses of Acidobacteria subgroups, especially subgroups 1, 3, 4, 5, and 6, to forest-to-pasture conversion effects in soils could be used to define management-indicators of agricultural practices in the Amazon Basin. These acidobacterial responses are at least in part through alterations on acidity- and nutrient-related properties of the Amazon soils.
View details for DOI 10.3389/fmicb.2015.01443
View details for Web of Science ID 000366996600002
View details for PubMedID 26733981
View details for PubMedCentralID PMC4686610
- Métodos de detecção de organismos geneticamente modificados Fundamentos técnicos e sistema nacional de biossegurança em biotecnologia 2015