MIP5121 | Microbial Ecology

Course coordinator: Prof. Rubens T. D. Duarte

Offered: Every first semester

Course type: Elective course

Programs: Agronomy, Biological Sciences, and Environmental and Sanitary Engineering

Schedule: Monday – 15:10-18:00

Throughout the course, students explore topics including culture-dependent and culture-independent methods, environmental factors affecting microorganisms, biogeochemical cycles, interactions between microorganisms and other organisms, microbial population and community dynamics, and diversity indices.

The course also addresses applications of microbial ecology in environmental assessment, wastewater treatment, waste management, and bioremediation.

Practical Activities

The course combines theoretical content with laboratory activities, allowing students to explore different approaches to the study of environmental microbial communities.

Practical activities include:

• Preparation and monitoring of Winogradsky columns;

• Viable cell counting;

• Selection and cultivation of microbial isolates;

• Assessment of spore-forming, cellulolytic, and phosphate-solubilizing microorganisms;

• Assessment of photosynthetic microorganisms;

• Soil respiration assays;

• Studies of xenobiotic biodegradation.

Microbial Ecology and Biotechnology

The course also highlights the potential of microorganisms in environmental biotechnology, relating microbial ecology to the understanding of elemental cycles, waste and wastewater treatment, and bioremediation processes.

The course integrates theoretical knowledge, experimentation, and discussion of current topics, contributing to the education of students interested in environmental microbiology, microbial ecology, biotechnology, and environmental conservation.

30 years of history, innovation, and transformation!

For three decades, the Graduate Program in Biotechnology and Biosciences at UFSC has been training researchers, driving scientific discoveries, and contributing to the advancement of biotechnology in Brazil and around the world.

This marks 30 years of dedication to science, the training of qualified human resources, and the generation of knowledge that impacts society. It is a journey built by faculty members, staff, students, alumni, and partners who have been—and continue to be—part of this story.

We invite the entire academic community, alumni, and friends of PPGBTC to celebrate this very special milestone with us!

August 5, 2026 — 2:00 PM

CCB Auditorium – UFSC

Bioinformatics and Metagenomic Data Analysis – 3 credits

Graduate Program in Biotechnology and Biosciences – 2026.2

Prof. Dr. Rubens Tadeu Delgado Duarte (Course Coordinator)

Dr. Lívia Budziarek Eslabão (Invited Postdoctoral Researcher)

During the 2026.2 semester, the Graduate Program in Biotechnology and Biosciences at UFSC is offering the course Bioinformatics II: Metagenomic Data Analysis, focused on the analysis and interpretation of data generated by high-throughput sequencing technologies. The course covers strategies for the structural and functional analysis of genomes and metagenomes, integration of omics datasets, and applications in systems biology, culminating in the development of a biological data analysis project.

📅 Enrollment
• Regular graduate students: July 16–20
• Students from other UFSC graduate programs: starting July 22
• Non-degree (special enrollment) students: July 29–31

Info: Programa de Pós-Graduação em Biotecnologia e Biociências

From July 8 to 10, the Laboratory of Molecular Ecology and Extremophiles (LEMEx) hosted a training course on Nanopore sequencing using the MinION platform, taught by Dr. Fernando Lucas Melo, a researcher at Embrapa.

Throughout the three-day course, participants gained both theoretical and practical knowledge of third-generation sequencing technology, covering topics ranging from sample and library preparation to instrument operation, data analysis, and applications in various fields of scientific research.

The Board of the Center for Biological Sciences of the Federal University of Santa Catarina (CCB/UFSC) warmly invites the academic community and the people of Santa Catarina to attend the Solemn Parliamentary Session celebrating the 50th Anniversary of the Center for Biological Sciences, promoted by the Legislative Assembly of Santa Catarina (ALESC).

The event honors the history and achievements of CCB/UFSC, nationally recognized for its excellence in teaching, research, extension, innovation, and its significant scientific contributions in the fields of biodiversity, environmental conservation, biotechnology, and biomedical sciences.

Over the past five decades, the Center for Biological Sciences has established itself as one of Brazil’s leading institutions for scientific research and knowledge production, educating thousands of professionals and contributing substantially to the scientific, technological, and sustainable development of Santa Catarina and Brazil.

During the ceremony, tributes will be paid to the Center for Biological Sciences, its former directors, academic departments, undergraduate programs, and graduate programs that have played a significant role in shaping the history of both CCB and UFSC.

Your presence will be a great honor as we celebrate science, public higher education, and the remarkable legacy of the Center for Biological Sciences at UFSC.

📍 Solemn Parliamentary Session – 50th Anniversary of CCB/UFSC
📅 June 18, 2026 (Thursday)
🕖 7:00 p.m.
📌 Antonieta de Barros Auditorium – Legislative Assembly of Santa Catarina (ALESC)
Palácio Barriga Verde – 310 Dr. Jorge Luz Fontes Street, Florianópolis, Santa Catarina, Brazil
📺 Live broadcast: TVAL and the AssembleiaSC YouTube Channel

The X-Meeting, organized by the Brazilian Association for Bioinformatics and Computational Biology (AB3C), is the leading Brazilian scientific conference dedicated to bioinformatics. The 2026 edition was held in Garibaldi (“Vale dos Vinhedos”), Rio Grande do Sul, from June 9 to 12.

The conference brings together researchers, scientists, students, and professionals in bioinformatics and related fields to share cutting-edge research and discuss technological advances in computational biology. The program includes lectures by national and international experts, scientific presentations, poster sessions, workshops, and specialized online short courses held before the event. This edition focused on Artificial Intelligence (AI) applied to the biological sciences, generative models, deep learning, and precision bioinformatics.

Our laboratory member and undergraduate Biological Sciences student, Ediane M. Rubas, presented the study entitled “WEB-BASED TOOL FOR THE ANALYSIS AND VISUALIZATION OF DATA PROCESSED IN MOTHUR.” The study addresses a recurring bottleneck in microbial ecology: the large volume of data generated by sequencing, whose processing and interpretation require programming skills that are not always available to all researchers. The proposed solution is an interactive application developed in R using the Shiny package, which organizes the main stages of data analysis for data processed through the mothur pipeline into independent modules. The tool will be distributed via shinyapps.io, requiring no installation or configuration by the user, with its source code openly available in a public GitHub repository.

For LEMEx, participation in the event brings new perspectives and reinforces the laboratory’s commitment to making microbiome data analysis more accessible to researchers from different backgrounds.

The 33rd Brazilian Congress of Microbiology (CBM), one of the most important scientific events in the field of microbiology in Brazil, was held from October 25 to 28, 2025, in Aracaju, Sergipe. Organized biennially, the congress brought together members of the scientific community, undergraduate and graduate students, representatives from government and civil society, companies in the microbiology sector, and the general public.

With the central theme “Microbiology in the Context of Climate Change and Artificial Intelligence,” the event fostered discussions on two of today’s most pressing global challenges. Owing to its remarkable biodiversity, Brazil plays a strategic role in understanding and mitigating the causes and impacts of climate change. In addition, the congress highlighted the growing applications of artificial intelligence in microbiology, emphasizing its potential to advance basic and applied research, education, and the development of innovative solutions.

The 33rd CBM provided an important platform for knowledge exchange, scientific collaboration, and the continued advancement of microbiology in Brazil.

During the event, our Ph.D. student, Camila Kinasz, presented the abstract entitled “Metagenomic Reconstruction of Microbial Genomes from Volcanic Tephra Entrapped in Collins Glacier, Antarctica.” The study highlighted the application of metagenomic approaches to investigate microbial diversity and reconstruct microbial genomes from volcanic tephra trapped within Antarctic glacial ice, contributing to a better understanding of microbial adaptation and evolution in extreme environments.

During the congress, several outstanding lectures were presented, particularly in the field of environmental microbiology. Among them, we highlight “Life in the Dark: Exploring Extremophiles in Terrestrial and Marine Subsurface Environments in Brazil as New Models for Evolution and Astrobiology,” delivered by Prof. Dr. Amanda Bendia (USP). We also congratulate Ana Carolina de Araújo Butarelli, from Prof. Vivian Helena Pellizari’s research group, whose presentation, “Unveiling the Role of Archaea in the Rare Biosphere: Potential Keystone Taxa in Ecosystem Dynamics in Lençóis Maranhenses National Park,” received the Environmental Microbiology Award.

In addition to attending the congress, we took the opportunity to explore Aracaju, the capital of the state of Sergipe. Founded in 1855 with a distinctive urban plan, Aracaju is known for its harmonious blend of modernity and rich cultural heritage. Bordered by the Atlantic Ocean and the Sergipe, Poxim, and Vaza Barris rivers, the city offers remarkable natural attractions, including the iconic Atalaia Waterfront and its urban parks, as well as historic landmarks such as Santo Antônio Hill and the traditional central markets. Together, these attractions create a vibrant and welcoming destination that combines history, leisure, and regional cuisine.

Brazilian scientist Mariangela Hungria, a researcher at Embrapa Soybean and a full member and board member of the Brazilian Academy of Sciences, has been awarded the World Food Prize, recognized as the “Nobel Prize” of agriculture. The announcement was made on Tuesday (13) at the headquarters of the World Food Prize Foundation in the United States. Awarded annually, the prize recognizes individuals who contribute to improving the quality and availability of food worldwide.

In its announcement, the foundation highlighted that Mariangela’s discoveries helped Brazil become a global agricultural powerhouse. With more than 40 years dedicated to research, Mariangela is recognized for developing innovative technologies in soil microbiology.

“Replacing the use of chemical products with biological products in agriculture has been the fight of my life. I am very proud to contribute to food production while also reducing environmental impact. The goal was to increase productivity with the lowest possible use of chemical products, and we achieved this with more biological products,” Mariangela said in a statement about the award.

For her, the award also represents recognition for science conducted in Brazil and encouragement for other women researchers. “I cannot believe that I am now receiving the World Food Prize. Many people questioned my abilities throughout my career, but I believed in what I was doing and persevered. The role of women in agriculture, from farming to science, deserves greater recognition. I hope my achievement inspires others to pursue their passions in science.”

Inspired by Johanna Döbereiner, internationally recognized for her contributions to agriculture, Mariangela was one of the early advocates of biological nitrogen fixation, a process in which crops form mutually beneficial associations with soil bacteria that provide nitrogen, an essential nutrient for plant growth.

Throughout her career, she has developed dozens of biological treatments, reducing the need for synthetic fertilizers and increasing agricultural productivity. Her technologies are estimated to have been used on more than 40 million hectares in Brazil, saving farmers up to US$25 billion per year in input costs and preventing more than 230 million tons of CO₂-equivalent emissions annually.

According to Embrapa, where she has worked since 1982, Mariangela’s research has focused on increasing food production and quality by partially or completely replacing chemical fertilizers with microorganisms possessing properties such as biological nitrogen fixation, phytohormone synthesis, and the solubilization of phosphate and potassium-bearing rocks.

In addition to her research on soybeans, Mariangela has also coordinated studies that led to technologies for other crops, including beans, corn, and wheat. In 2020, she was ranked among the 100,000 most influential scientists in the world by Stanford University in the United States.

Mariangela holds a degree in Agronomic Engineering from Esalq/USP, a master’s degree in Soil Science and Plant Nutrition from Esalq/USP, a PhD in Soil Science from UFRRJ, and completed postdoctoral research at three universities: Cornell University, the University of California, Davis, and the University of Seville. She began her career in 1982 at Embrapa Agrobiology in Seropédica, Rio de Janeiro. Since 1991, she has worked at Embrapa Soybean in Londrina, Paraná. She is also a professor at the State University of Londrina (UEL) and the Federal University of Technology – Paraná (UTFPR).

Scientist is the first Brazilian woman to receive the award, which has previously honored three other Brazilians

This is the third time the World Food Prize has been awarded to Brazilians and the first time to a Brazilian woman. In 2006, agronomists Edson Lobato and Alysson Paulinelli shared the prize with A. Colin McClung of the United States for their work in developing agriculture in Brazil’s Cerrado region. In 2011, two former presidents, Luiz Inácio Lula da Silva of Brazil and John Kufuor of Ghana, were selected for their efforts to combat hunger while serving as heads of government.

The prize was established by Norman E. Borlaug, winner of the 1970 Nobel Peace Prize for his work in agriculture and widely considered the “father” of the Green Revolution. The award was created in 1986 with sponsorship from General Foods Corporation. As part of the recognition, Mariangela will receive US$500,000 and a sculpture designed by artist and designer Saul Bass. The award ceremony will take place on October 23 in Des Moines, Iowa, United States.

Present at the announcement, Iowa Governor Kim Reynolds highlighted Mariangela’s example for other women. “As a pioneering scientist and mother, Dr. Hungria also serves as an inspiring example for women researchers seeking to embody both roles. Her discoveries have helped Brazil become a global breadbasket,” she said.

“Dr. Hungria was selected for her extraordinary scientific achievements in biological fixation, which have transformed the sustainability of agriculture in South America,” said Gebisa Ejeta, chair of the committee responsible for selecting the award recipients. “Her brilliant scientific work and committed vision for advancing sustainable agricultural production have earned her global recognition, both at home and abroad.”
Source: https://www.abc.org.br/2025/05/14/mariangela-hungria-nobel-da-agricultura/

The Federal University of Santa Catarina (UFSC) Central Library hosted the exhibition “Cultures and Microcosms: From the Laboratory to the Classroom – A Petri Dish Exhibition” from September 18 to 27, 2024, in the Main Hall Exhibition Gallery. The exhibition was organized by the Laboratory of Molecular Ecology and Extremophiles (LEMEx) at UFSC.

LEMEx, coordinated by Prof. Dr. Rubens Tadeu Delgado Duarte, is located in the Center for Biological Sciences (CCB/UFSC), Building E, 7th floor, Room 711. The laboratory conducts research in microbial ecology, biotechnology, and astrobiology, with a particular focus on microorganisms that inhabit extreme environments. Its research integrates molecular markers with bioinformatics analyses of omics data, including genomics, metagenomics, and metatranscriptomics.

In addition to advanced molecular approaches, LEMEx employs both classical and modern microbial cultivation techniques to isolate and characterize extremophilic microorganisms. Many microorganisms can be cultivated under laboratory conditions using culture media that provide water and essential nutrients, including energy sources (typically sugars) and elements required for biosynthesis and metabolism, particularly nitrogen, sulfur, and phosphorus.

Solid culture media enable the growth and isolation of individual microbial colonies on their surface. Each colony typically originates from a single colony-forming unit (CFU), usually a single bacterial cell, and is therefore assumed to represent a single strain and species.

These solid media are prepared by adding 1–2% agar, a mixture of agarose and agaropectin derived from algae. After sterilization by autoclaving, the medium is cooled and poured into Petri dishes, where it solidifies. The resulting gel matrix provides water and nutrients that support microbial growth after inoculation onto the agar surface.

The exhibition highlighted the scientific and educational value of microbial cultures, demonstrating how Petri dishes serve not only as essential research tools but also as effective resources for science communication and teaching.

Organized by: UFSC University Library (BU/UFSC) Exhibitions.

UFSC Research Investigates How Antarctic Bacteria May Help Us Understand Climate Change

Alanna and Professor Rubens studying material collected in Antarctica.

Thousands of microorganisms inhabit our planet, most of them still unknown to science. These microscopic life forms may also provide answers to one of today’s greatest global challenges: climate change. A series of research projects at the Federal University of Santa Catarina (UFSC), coordinated by Prof. Dr. Rubens Tadeu Delgado Duarte from the Department of Microbiology, Immunology and Parasitology, investigates how Antarctic bacteria can improve our understanding of climate change while also revealing new opportunities for biotechnology.

One of these studies was conducted by undergraduate researcher Alanna Maylle Cararo Luiz as part of her final-year research project and was recently presented at the Brazilian Society for Microbiology meeting. The study, Growth Strategies of Microorganisms from Antarctic Glacier Forefield Soils in Terms of r/K Selection, is based on samples collected during a 2017 Antarctic expedition as part of the Microsfera Project – Microbial Life in the Antarctic Cryosphere: Climate Change and Bioprospecting.

The research is carried out at the Laboratory of Molecular Ecology and Extremophiles (LEMEx). Molecular ecology combines molecular techniques with ecological studies to investigate living organisms, while extremophiles are organisms capable of surviving under extreme environmental conditions, such as those found on the coldest continent on Earth. At LEMEx, researchers use molecular approaches to characterize Antarctic bacteria and uncover previously unknown biological properties and functions.

“There are thousands—indeed tens of thousands—of bacterial species in just a single gram of soil,” explains Prof. Duarte. “A teaspoon of soil contains millions of microbial individuals waiting to be studied.”

Antarctica is central to these investigations because of its importance in understanding climate change. As glaciers retreat, rising sea levels and cascading ecological changes affect biodiversity worldwide. The researchers aim to determine whether specific bacterial communities can indicate the rate of environmental change. “We want to use these bacteria as biological thermometers that can help us monitor climate change,” says Duarte.

While larger organisms, such as penguins, are commonly used as indicators of environmental change, their responses occur over relatively long timescales because they depend on reproduction and population dynamics. Bacteria, in contrast, respond much more rapidly to environmental disturbances, making them potentially more sensitive indicators of ecosystem change.

Collins and Baranowski Glaciers

The UFSC studies focus on soil and ice samples collected from two Antarctic glaciers: Collins Glacier and Baranowski Glacier. These glaciers exhibit markedly different retreat rates. According to Prof. Duarte, Baranowski Glacier retreated in only 43 years by approximately the same distance that Collins Glacier required more than one thousand years to retreat.

As glaciers recede, newly exposed soils become available for microbial colonization. This process creates a natural space-time gradient that allows researchers to collect samples immediately adjacent to the glacier, where the soil has only recently been exposed, as well as from locations that have remained ice-free for 20, 30, or 40 years.

“This gradient allows us to understand how bacterial communities change over time,” Duarte explains.

Comparing both glaciers also enables scientists to identify microorganisms associated with different glacier retreat rates. Bacteria characteristic of rapidly retreating glaciers may serve as biological indicators of accelerated climate change.

Ecological Succession in Antarctic Soils

Alanna’s research investigates how glacier retreat influences ecological succession by examining bacterial communities isolated from the 2017 expedition samples.

To illustrate ecological succession, Prof. Duarte compares glacier retreat to forest recovery after a wildfire. Following a fire, grasses colonize first, followed by shrubs and eventually trees, while animal communities gradually return. Antarctic glacier retreat follows a similar ecological sequence, although involving microorganisms rather than plants.

Once glacier ice melts, newly exposed soil comes into contact with atmospheric oxygen. Certain bacterial species colonize the soil first, followed by progressively more diverse microbial communities.

“The populations change over time,” Duarte explains. “This happens after virtually any environmental disturbance.”

The succession reflects natural selection according to resource availability and the growth strategies of different microorganisms.

Some Antarctic bacteria grow rapidly, forming visible colonies within approximately 48 hours, whereas others require much longer incubation periods. Recently exposed soils tend to be dominated by fast-growing bacteria, while older soils exhibit greater microbial diversity. These patterns also differ between Collins and Baranowski glaciers.

Researchers collected soil samples at distances of 0, 50, 100, 200, 300, and 400 meters from both glaciers. Viable bacterial cells were quantified, and colonies were monitored daily and classified according to whether they became visible before or after 48 hours of incubation.

Ecological theory predicts that fast-growing organisms dominate the earliest stages of succession and are gradually replaced by slower-growing species. Therefore, detecting fast-growing bacteria far from the glacier could indicate recent glacier retreat and accelerated ice loss. Comparing these observations between the two glaciers, together with regional climate records, may provide a novel biological tool for monitoring climate change in polar environments.

Although studies such as these generally require genetic sequencing of selected bacterial isolates, the high costs of sequencing and limited research funding often restrict this stage of the investigation.

Microbial Diversity and Biotechnological Applications

The Antarctic samples collected by UFSC also support research into the biotechnological potential of extremophilic microorganisms. In addition to Alanna’s project, at least seven other studies at LEMEx currently utilize these samples.

One important adaptation of cold-loving microorganisms is the production of antifreeze proteins, which interfere with ice crystal formation and recrystallization, protecting cells from freezing damage.

According to Prof. Duarte, these proteins have promising applications in biotechnology. One potential use is improving the stability of DNA- and viral vector-based vaccines during freezing and storage, including technologies similar to those developed for COVID-19 vaccines.

A related project led by Ph.D. candidate Joana Camila Lopes focuses on characterizing these antifreeze proteins and exploring their potential technological applications. Although still in its early stages, the research may also contribute to agricultural innovations, such as improving crop resistance to frost.

All of these studies rely on soil and ice samples collected during scientific expeditions conducted through the Brazilian Antarctic Program (PROANTAR), with LEMEx’s most recent expedition taking place in 2017. The preserved samples remain stored at the laboratory and continue to support research projects ranging from undergraduate studies to doctoral research, while also serving as a valuable resource for future scientific investigations.

Material coletado na Antártida – 2021

Material coletado na Antártida – 2021